Psyllid ID: psy2029

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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
MVQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEVLE
Secondary Structure (PSIPRED)
ccccccEEEEccccccHHHHHHHHHcccccccccccEEEcccccHHHHHHHHHHHHHHHHHHHHHcHHHHccccccEEEEEEccccHHHHHHHHHHHHHHHcccEEEEEccHHHHHHHHHHHHHHHHHHccEEEEEcc
Secondary Structure Prediction (SSPRO)
ccccccEEEEcccccHHHHHHHHHHHHHHHHHcccEEEEEcccccHHHHHHHHHHHcHHHHcHHHHHHHcccccccEEEEcccccHHHHHHHHHHHHHHHHHcccEEEEHHHHHHHHHHHHHHHHHHHHcccEEEEcc
Coil and Loop (DISEMBL)
mvqnkncvlsiptsggktLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIqnkncvlsiptsggktLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEVLE
Flexible Loop (DISEMBL)
mvqnkncvlsiptsggktlVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEVLE
Low Complexity Region (SEG)
MVQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEVLE
Disordered region (IsUnstruct)
******CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV**
Disordered Region (DISOPRED)
MVQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEVL*
Disordered Region (DISEMBL)
MVQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEVLE
Disordered Region (DISPRO)
***NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEVL*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MVQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEVLE
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]
Q2VPA6	1069	Helicase POLQ-like OS=Mus	yes	N/A	0.456	0.058	0.492	3e-11
Q8TDG4	1101	Helicase POLQ-like OS=Hom	yes	N/A	0.456	0.057	0.460	2e-09
O75417	2590	DNA polymerase theta OS=H	no	N/A	0.565	0.030	0.389	1e-08
Q5JGV6	1125	Putative ski2-type helica	yes	N/A	0.398	0.048	0.381	2e-05
Q58524	1195	Putative ski2-type helica	yes	N/A	0.434	0.050	0.369	4e-05
O73946	720	Putative ski2-type helica	yes	N/A	0.384	0.073	0.358	0.0001
Q97AI2	674	Putative ski2-type helica	yes	N/A	0.398	0.081	0.428	0.0002

>sp|Q2VPA6|HELQ_MOUSE Helicase POLQ-like OS=Mus musculus GN=Helq PE=2 SV=2

 Score = 67.0 bits (162), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 31/63 (49%), Positives = 45/63 (71%)

Query: 3   QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF 62
           + KN + S+PTSGGKTLV EIL+++EL  +QK  + ILPY+++V EK  SL+    E  F
Sbjct: 310 ERKNLIYSLPTSGGKTLVAEILMLQELLCRQKDVLMILPYVAIVQEKISSLSSFGIELGF 369

Query: 63  YLE 65
           ++E
Sbjct: 370 FVE 372

DNA-dependent ATPase and 5' to 3' DNA helicase.
Mus musculus (taxid: 10090)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 2

>sp|Q8TDG4|HELQ_HUMAN Helicase POLQ-like OS=Homo sapiens GN=HELQ PE=1 SV=2

 Score = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 29/63 (46%), Positives = 43/63 (68%)

Query: 3   QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF 62
           + KN + S+PTSGGKTLV EIL+++EL   +K  + ILPY+++V EK   L+    E  F
Sbjct: 351 ERKNLIYSLPTSGGKTLVAEILMLQELLCCRKDVLMILPYVAIVQEKISGLSSFGIELGF 410

Query: 63  YLE 65
           ++E
Sbjct: 411 FVE 413

DNA-dependent ATPase and 5' to 3' DNA helicase.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|O75417|DPOLQ_HUMAN DNA polymerase theta OS=Homo sapiens GN=POLQ PE=1 SV=2

 Score = 58.2 bits (139), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 37/95 (38%), Positives = 53/95 (55%), Gaps = 17/95 (17%)

Query: 46  VHEKYQSLAKAAEEFKFYLEGKCL---EMIQNKNCVLSIPTSGGKTLVGEILIMKELKIK 102
           V EKY S         F  + +CL   ++++ KN V S PTS GKTLV E+LI+K +   
Sbjct: 80  VLEKYHSFGVKK---MFEWQAECLLLGQVLEGKNLVYSAPTSAGKTLVAELLILKRVLEM 136

Query: 103 QKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEVL 137
           +K A+FILP++S+  EK           K+YL+ L
Sbjct: 137 RKKALFILPFVSVAKEK-----------KYYLQSL 160

Has a DNA polymerase activity on nicked double-stranded DNA and on a singly primed DNA template. The enzyme activity is resistant to aphidicolin, and inhibited by dideoxynucleotides. Exhibites a single-stranded DNA-dependent ATPase activity. Could be involved in the repair of interstrand cross-links.

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 7

>sp|Q5JGV6|HELS_PYRKO Putative ski2-type helicase OS=Pyrococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) GN=TK1332 PE=3 SV=1

 Score = 47.8 bits (112), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 21/55 (38%), Positives = 38/55 (69%)

Query: 71  MIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK 125
           +++ KN VL+IPT+ GKTLV EI+++ +L  +   A++++P  +L  EKY+   +
Sbjct: 36  VLEGKNLVLAIPTASGKTLVSEIVMVNKLLSEGGKAVYLVPLKALAEEKYREFKE 90

Pyrococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (taxid: 69014)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|Q58524|HELS_METJA Putative ski2-type helicase OS=Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) GN=MJ1124 PE=3 SV=1

 Score = 47.0 bits (110), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/65 (36%), Positives = 37/65 (56%), Gaps = 5/65 (7%)

Query: 1  MVQNKNCVLSIPTSGGKTLVGEILIMKEL-----KIKQKSAIFILPYISLVHEKYQSLAK 55
          + +NKN ++SIPT+ GKTL+GE+ ++  L         K  IFI+P  +L  EKY+    
Sbjct: 29 LDKNKNFLISIPTASGKTLIGEMALINHLLDGNKNPTNKKGIFIVPLKALASEKYEEFKS 88

Query: 56 AAEEF 60
            E +
Sbjct: 89 KYERY 93

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (taxid: 243232)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|O73946|HELS_PYRFU Putative ski2-type helicase OS=Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) GN=PF0677 PE=1 SV=1

 Score = 45.4 bits (106), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/53 (35%), Positives = 35/53 (66%)

Query: 71  MIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSL 123
           +++ KN ++SIPT+ GKTL+ EI ++  +  +   A++I+P  +L  EK+Q  
Sbjct: 36  ILEGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPLKALAEEKFQEF 88

Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (taxid: 186497)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|Q97AI2|HELS_THEVO Putative ski2-type helicase OS=Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1) GN=TV0828 PE=3 SV=1

 Score = 44.7 bits (104), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/56 (42%), Positives = 36/56 (64%), Gaps = 1/56 (1%)

Query: 3  QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE 58
          + KN ++S+PT+ GKTL+    I +  K K KS I+I+P  SL  EKY+ L++  E
Sbjct: 36 KGKNIMVSVPTAAGKTLIAYSAIYETFKKKLKS-IYIVPLRSLAMEKYEELSRLRE 90

Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1) (taxid: 273116)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

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
198437907	1014	PREDICTED: similar to DNA helicase HEL30	0.536	0.072	0.480	7e-12
449662379	886	PREDICTED: helicase POLQ-like [Hydra mag	0.456	0.071	0.555	8e-12
443734649	820	hypothetical protein CAPTEDRAFT_161173 [	0.739	0.124	0.405	1e-11
256074218	923	DNA polymerase theta [Schistosoma manson	0.652	0.097	0.439	2e-11
350645162	923	DNA polymerase theta, putative [Schistos	0.652	0.097	0.439	3e-11
47210458	969	unnamed protein product [Tetraodon nigro	0.485	0.069	0.573	4e-11
348532301	993	PREDICTED: helicase POLQ [Oreochromis ni	0.456	0.063	0.571	5e-11
193659627	825	PREDICTED: helicase POLQ-like isoform 1	0.768	0.128	0.378	7e-11
410904054	1016	PREDICTED: helicase POLQ-like [Takifugu	0.485	0.065	0.544	2e-10
432953220	932	PREDICTED: helicase POLQ-like, partial [	0.456	0.067	0.523	2e-10

>gi|198437907|ref|XP_002120889.1| PREDICTED: similar to DNA helicase HEL308 [Ciona intestinalis]

 Score = 75.5 bits (184), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 37/77 (48%), Positives = 54/77 (70%), Gaps = 3/77 (3%)

Query: 62  FYLEGKCLEMI---QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHE 118
           +  + KCL +    + +N + S+PTSGGKTLV EILI +EL  K+K A+F+LP++++V E
Sbjct: 257 YDWQHKCLTLDGVKEGRNLIYSLPTSGGKTLVAEILIFRELLCKKKDAVFVLPFVAIVQE 316

Query: 119 KYQSLAKAAEEFKFYLE 135
           K QSLA+ A E  F +E
Sbjct: 317 KIQSLAQFAVELGFLVE 333

Source: Ciona intestinalis

Species: Ciona intestinalis

Genus: Ciona

Family: Cionidae

Order: Enterogona

Class: Ascidiacea

Phylum: Chordata

Superkingdom: Eukaryota

>gi|449662379|ref|XP_002160420.2| PREDICTED: helicase POLQ-like [Hydra magnipapillata]

 Score = 75.1 bits (183), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 35/63 (55%), Positives = 50/63 (79%)

Query: 3   QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF 62
           + KN + S+PTSGGKTLV E+LIMKE+  ++K+AIF+LPY+S+V EK + L+  A EF F
Sbjct: 175 KRKNLIYSLPTSGGKTLVAELLIMKEILKQKKNAIFVLPYVSIVQEKVRELSPFAVEFNF 234

Query: 63  YLE 65
           ++E
Sbjct: 235 HVE 237

Source: Hydra magnipapillata

Species: Hydra magnipapillata

Genus: Hydra

Family: Hydridae

Order: Hydroida

Class: Hydrozoa

Phylum: Cnidaria

Superkingdom: Eukaryota

>gi|443734649|gb|ELU18559.1| hypothetical protein CAPTEDRAFT_161173 [Capitella teleta]

 Score = 74.7 bits (182), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 43/106 (40%), Positives = 66/106 (62%), Gaps = 4/106 (3%)

Query: 34  KSAIFILPYISL---VHEKYQSLAKAAEEFKFYLEGKCL-EMIQNKNCVLSIPTSGGKTL 89
           K++ F+ P+  L   V E ++SL    E + +  E  CL E+ Q KN + S+PTSGGKTL
Sbjct: 15  KASDFVQPFGGLPVKVLELFESLRGIKELYDWQKECLCLPEVRQGKNLIYSLPTSGGKTL 74

Query: 90  VGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLE 135
           V E+LI ++L I++  AI ILP++++V EK + +   A E  F +E
Sbjct: 75  VAEVLIFRQLLIRKLDAILILPFVAIVQEKVRIIGAFASELDFVVE 120

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|256074218|ref|XP_002573423.1| DNA polymerase theta [Schistosoma mansoni]

 Score = 73.6 bits (179), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 40/91 (43%), Positives = 56/91 (61%), Gaps = 1/91 (1%)

Query: 46  VHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQK 104
           V E +  L    + + + +E   L  + N  N V S+PTSGGKTLV EIL++KEL I  K
Sbjct: 26  VKELFHELRGVTKLYDWQVECLNLTAVANGSNLVYSLPTSGGKTLVAEILMLKELLIYNK 85

Query: 105 SAIFILPYISLVHEKYQSLAKAAEEFKFYLE 135
           S +FILP++S+V EK +SL     E  F++E
Sbjct: 86  SVLFILPFVSIVQEKVRSLTPMGLELGFWVE 116

Source: Schistosoma mansoni

Species: Schistosoma mansoni

Genus: Schistosoma

Family: Schistosomatidae

Order: Strigeidida

Class: Trematoda

Phylum: Platyhelminthes

Superkingdom: Eukaryota

>gi|350645162|emb|CCD60104.1| DNA polymerase theta, putative [Schistosoma mansoni]

 Score = 73.6 bits (179), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 40/91 (43%), Positives = 56/91 (61%), Gaps = 1/91 (1%)

Query: 46  VHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQK 104
           V E +  L    + + + +E   L  + N  N V S+PTSGGKTLV EIL++KEL I  K
Sbjct: 26  VKELFHELRGVTKLYDWQVECLNLTAVANGSNLVYSLPTSGGKTLVAEILMLKELLIYNK 85

Query: 105 SAIFILPYISLVHEKYQSLAKAAEEFKFYLE 135
           S +FILP++S+V EK +SL     E  F++E
Sbjct: 86  SVLFILPFVSIVQEKVRSLTPMGLELGFWVE 116

Source: Schistosoma mansoni

Species: Schistosoma mansoni

Genus: Schistosoma

Family: Schistosomatidae

Order: Strigeidida

Class: Trematoda

Phylum: Platyhelminthes

Superkingdom: Eukaryota

>gi|47210458|emb|CAF94327.1| unnamed protein product [Tetraodon nigroviridis]

 Score = 73.2 bits (178), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 39/68 (57%), Positives = 48/68 (70%), Gaps = 1/68 (1%)

Query: 69  LEMIQ-NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA 127
           LE IQ  KN + S+PTSGGKTLV EILI++EL  ++K  +FILPYISLV EK + LA   
Sbjct: 227 LECIQARKNLIYSLPTSGGKTLVAEILILRELLCRRKDCLFILPYISLVQEKVRGLASFG 286

Query: 128 EEFKFYLE 135
            E  F +E
Sbjct: 287 LELDFMVE 294

Source: Tetraodon nigroviridis

Species: Tetraodon nigroviridis

Genus: Tetraodon

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|348532301|ref|XP_003453645.1| PREDICTED: helicase POLQ [Oreochromis niloticus]

 Score = 72.4 bits (176), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 36/63 (57%), Positives = 45/63 (71%)

Query: 3   QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF 62
           Q KN + S+PTSGGKTLV EILI++EL  ++K  +FILPYISLV EK + LA    E  F
Sbjct: 260 QRKNLIYSLPTSGGKTLVAEILILRELLCRRKDCLFILPYISLVQEKVRGLASFGLELDF 319

Query: 63  YLE 65
            +E
Sbjct: 320 MVE 322

Source: Oreochromis niloticus

Species: Oreochromis niloticus

Genus: Oreochromis

Family: Cichlidae

Order: Perciformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|193659627|ref|XP_001943294.1| PREDICTED: helicase POLQ-like isoform 1 [Acyrthosiphon pisum] gi|328698000|ref|XP_003240510.1| PREDICTED: helicase POLQ-like isoform 2 [Acyrthosiphon pisum]

 Score = 72.0 bits (175), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 42/111 (37%), Positives = 69/111 (62%), Gaps = 5/111 (4%)

Query: 27  KELKIKQKSAIFILPY-ISLVHEKYQSLAKAAEEFKFYLEGKCLEMI-QNKNCVLSIPTS 84
           K L +   S  F LP+ +  + +K++ + +    + + +E   L+ I + KN + ++PTS
Sbjct: 27  KRLHVDGDSDFFGLPHKVKHLFKKHKGITQL---YDWQIECLNLDAIKRRKNLIYALPTS 83

Query: 85  GGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLE 135
           GGKTLV EIL++KEL + +++ IFILPY++LV EK QSL       +F +E
Sbjct: 84  GGKTLVAEILMLKELIVYERNVIFILPYVALVQEKVQSLCPFGLNLEFNVE 134

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|410904054|ref|XP_003965508.1| PREDICTED: helicase POLQ-like [Takifugu rubripes]

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 37/68 (54%), Positives = 48/68 (70%), Gaps = 1/68 (1%)

Query: 69  LEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA 127
           LE +Q  KN + S+PTSGGKTLV EILI++EL  ++K  +FILPYI+LV EK + LA   
Sbjct: 274 LECVQERKNLIYSLPTSGGKTLVAEILILRELLCRRKDCLFILPYITLVQEKVRGLASFG 333

Query: 128 EEFKFYLE 135
            E  F +E
Sbjct: 334 LELDFMVE 341

Source: Takifugu rubripes

Species: Takifugu rubripes

Genus: Takifugu

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|432953220|ref|XP_004085307.1| PREDICTED: helicase POLQ-like, partial [Oryzias latipes]

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 33/63 (52%), Positives = 44/63 (69%)

Query: 3   QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF 62
           Q +N + S+PTSGGKTLV EILI++EL  ++K  + +LPYISLV EK + LA    E  F
Sbjct: 223 QRRNLIYSLPTSGGKTLVAEILILRELLCRRKDCLLVLPYISLVQEKVRGLASLGLELDF 282

Query: 63  YLE 65
            +E
Sbjct: 283 LVE 285

Source: Oryzias latipes

Species: Oryzias latipes

Genus: Oryzias

Family: Adrianichthyidae

Order: Beloniformes

Class: Actinopterygii

Phylum: Chordata

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
UNIPROTKB|J9P160	1072	HELQ "Uncharacterized protein"	0.811	0.104	0.346	6.1e-11
UNIPROTKB|E2RST3	1106	HELQ "Uncharacterized protein"	0.811	0.101	0.346	6.4e-11
MGI|MGI:2176740	1069	Helq "helicase, POLQ-like" [Mu	0.826	0.106	0.352	1.1e-11
WB|WBGene00021905	923	helq-1 [Caenorhabditis elegans	0.615	0.092	0.358	2.4e-11
UNIPROTKB|Q8TDG4	1101	HELQ "Helicase POLQ-like" [Hom	0.811	0.101	0.346	1.7e-10
ZFIN|ZDB-GENE-060503-421	1010	helq "helicase, POLQ-like" [Da	0.666	0.091	0.434	6.2e-12
UNIPROTKB|E9PSY5	805	Helq "Protein Helq" [Rattus no	0.826	0.141	0.352	7.5e-12
UNIPROTKB|E9PT19	879	Helq "Protein Helq" [Rattus no	0.826	0.129	0.352	8.5e-12
UNIPROTKB|F1RVE2	1103	HELQ "Uncharacterized protein"	0.826	0.103	0.360	1.9e-11
FB|FBgn0002899	1051	mus301 "mutagen-sensitive 301"	0.826	0.108	0.322	1.8e-11

UNIPROTKB|J9P160 HELQ "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 165 (63.1 bits), Expect = 6.1e-11, P = 6.1e-11
 Identities = 43/124 (34%), Positives = 72/124 (58%)

Query:    22 EILIMKELKIKQK----SAIFILPYISL---VHEKYQSLAKAAEEFKFYLEGKCLEM--I 72
             E L+ +E+ + +K    S+  + P+ SL   V + Y    K  E+  +  +  CL +  +
Sbjct:   264 ETLLSEEINVAKKAIESSSDDLGPFYSLPTKVRDLYVQF-KGIEKL-YEWQHTCLTLNSV 321

Query:    73 QN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFK 131
             Q  KN + S+PTSGGKTLV EIL+++EL  +++  + ILPY+++V EK   L+    E  
Sbjct:   322 QERKNLIYSLPTSGGKTLVAEILMLQELLCRRRDVLMILPYVAIVQEKISGLSSFGIELG 381

Query:   132 FYLE 135
             F++E
Sbjct:   382 FFVE 385

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|E2RST3 HELQ "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 165 (63.1 bits), Expect = 6.4e-11, P = 6.4e-11
 Identities = 43/124 (34%), Positives = 72/124 (58%)

Query:    22 EILIMKELKIKQK----SAIFILPYISL---VHEKYQSLAKAAEEFKFYLEGKCLEM--I 72
             E L+ +E+ + +K    S+  + P+ SL   V + Y    K  E+  +  +  CL +  +
Sbjct:   298 ETLLSEEINVAKKAIESSSDDLGPFYSLPTKVRDLYVQF-KGIEKL-YEWQHTCLTLNSV 355

Query:    73 QN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFK 131
             Q  KN + S+PTSGGKTLV EIL+++EL  +++  + ILPY+++V EK   L+    E  
Sbjct:   356 QERKNLIYSLPTSGGKTLVAEILMLQELLCRRRDVLMILPYVAIVQEKISGLSSFGIELG 415

Query:   132 FYLE 135
             F++E
Sbjct:   416 FFVE 419

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

MGI|MGI:2176740 Helq "helicase, POLQ-like" [Mus musculus (taxid:10090)]

 Score = 172 (65.6 bits), Expect = 1.1e-11, P = 1.1e-11
 Identities = 43/122 (35%), Positives = 70/122 (57%)

Query:    22 EILIMKELKIKQKS----AIFILPYISL---VHEKYQSLAKAAEEFKFYLEGKCLEMIQN 74
             E L+ +E+ + +K+    +  + P+ SL   V + Y  L    + + +      L  +Q 
Sbjct:   251 EALLSEEISVAKKAIESPSDDLGPFYSLPSKVRDLYVQLKGIKKLYDWQHTCLTLRSVQE 310

Query:    75 -KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFY 133
              KN + S+PTSGGKTLV EIL+++EL  +QK  + ILPY+++V EK  SL+    E  F+
Sbjct:   311 RKNLIYSLPTSGGKTLVAEILMLQELLCRQKDVLMILPYVAIVQEKISSLSSFGIELGFF 370

Query:   134 LE 135
             +E
Sbjct:   371 VE 372

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006200 "ATP catabolic process" evidence=ISO

GO:0006259 "DNA metabolic process" evidence=ISO

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

GO:0016787 "hydrolase activity" evidence=IEA

GO:0017116 "single-stranded DNA-dependent ATP-dependent DNA helicase activity" evidence=ISO

GO:0017117 "single-stranded DNA-dependent ATP-dependent DNA helicase complex" evidence=ISO

WB|WBGene00021905 helq-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 168 (64.2 bits), Expect = 2.4e-11, P = 2.4e-11
 Identities = 33/92 (35%), Positives = 59/92 (64%)

Query:    48 EKYQSLAKAAEEFKFY-LEGKCLE---MIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQ 103
             E Y+ + K     KFY  + +CL    ++  +NC+LS+PT  GKTL+ E+L+++E  +++
Sbjct:   157 EMYRKIKKLD---KFYDWQQECLSDKRLLDGENCILSLPTGAGKTLIAEVLMLREAIVRK 213

Query:   104 KSAIFILPYISLVHEKYQSLAKAAEEFKFYLE 135
             ++AI +LPY+++V EK  +LA   + F   +E
Sbjct:   214 RNAILVLPYVAIVQEKISALAPFEDAFGINIE 245

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

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

GO:0000712 "resolution of meiotic recombination intermediates" evidence=IGI

GO:0051117 "ATPase binding" evidence=IPI

GO:0017116 "single-stranded DNA-dependent ATP-dependent DNA helicase activity" evidence=IDA

UNIPROTKB|Q8TDG4 HELQ "Helicase POLQ-like" [Homo sapiens (taxid:9606)]

 Score = 161 (61.7 bits), Expect = 1.7e-10, P = 1.7e-10
 Identities = 43/124 (34%), Positives = 71/124 (57%)

Query:    22 EILIMKELKIKQK----SAIFILPYISL---VHEKYQSLAKAAEEFKFYLEGKCLEM--I 72
             + L+ +E+ + +K    S+  + P+ SL   V + Y    K  E+  +  +  CL +  +
Sbjct:   292 DTLLSEEINVAKKTVESSSNDLGPFYSLPSKVRDLYAQF-KGIEKL-YEWQHTCLTLNSV 349

Query:    73 QN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFK 131
             Q  KN + S+PTSGGKTLV EIL+++EL   +K  + ILPY+++V EK   L+    E  
Sbjct:   350 QERKNLIYSLPTSGGKTLVAEILMLQELLCCRKDVLMILPYVAIVQEKISGLSSFGIELG 409

Query:   132 FYLE 135
             F++E
Sbjct:   410 FFVE 413

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

ZFIN|ZDB-GENE-060503-421 helq "helicase, POLQ-like" [Danio rerio (taxid:7955)]

 Score = 174 (66.3 bits), Expect = 6.2e-12, P = 6.2e-12
 Identities = 43/99 (43%), Positives = 58/99 (58%)

Query:     3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF 62
             Q +N + S+PTSGGKTLV EILI KEL  ++K A+ ILPYISLV EK + L+    E  F
Sbjct:   272 QRRNLIYSLPTSGGKTLVAEILIFKELLCRKKDALLILPYISLVQEKVRGLSSFGIELDF 331

Query:    63 YLE------GKCLEMIQ-NKNCVLSIPTSGGKTLVGEIL 94
              +E      GK   + + NKN +       G +LV  ++
Sbjct:   332 LVEEYAGSKGKFPPVKRRNKNSLYITTIEKGHSLVNSLI 370

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

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

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|E9PSY5 Helq "Protein Helq" [Rattus norvegicus (taxid:10116)]

 Score = 172 (65.6 bits), Expect = 7.5e-12, P = 7.5e-12
 Identities = 43/122 (35%), Positives = 69/122 (56%)

Query:    22 EILIMKELKIKQKS----AIFILPYISL---VHEKYQSLAKAAEEFKFYLEGKCLEMIQN 74
             E L+ +E+ + +K+    +  + P+ SL   V + Y  L      + +      L  +Q 
Sbjct:   247 ETLLSEEISVARKAIESPSDDLGPFYSLPSKVRDLYAQLKGIKRLYDWQHTCLTLSSVQE 306

Query:    75 -KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFY 133
              KN + S+PTSGGKTLV EIL+++EL  +QK  + ILPY+++V EK  SL+    E  F+
Sbjct:   307 RKNLIYSLPTSGGKTLVAEILMLQELLCRQKDVLLILPYVAIVQEKISSLSSFGIELGFF 366

Query:   134 LE 135
             +E
Sbjct:   367 VE 368

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

UNIPROTKB|E9PT19 Helq "Protein Helq" [Rattus norvegicus (taxid:10116)]

 Score = 172 (65.6 bits), Expect = 8.5e-12, P = 8.5e-12
 Identities = 43/122 (35%), Positives = 69/122 (56%)

Query:    22 EILIMKELKIKQKS----AIFILPYISL---VHEKYQSLAKAAEEFKFYLEGKCLEMIQN 74
             E L+ +E+ + +K+    +  + P+ SL   V + Y  L      + +      L  +Q 
Sbjct:   247 ETLLSEEISVARKAIESPSDDLGPFYSLPSKVRDLYAQLKGIKRLYDWQHTCLTLSSVQE 306

Query:    75 -KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFY 133
              KN + S+PTSGGKTLV EIL+++EL  +QK  + ILPY+++V EK  SL+    E  F+
Sbjct:   307 RKNLIYSLPTSGGKTLVAEILMLQELLCRQKDVLLILPYVAIVQEKISSLSSFGIELGFF 366

Query:   134 LE 135
             +E
Sbjct:   367 VE 368

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

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

UNIPROTKB|F1RVE2 HELQ "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 170 (64.9 bits), Expect = 1.9e-11, P = 1.9e-11
 Identities = 44/122 (36%), Positives = 71/122 (58%)

Query:    22 EILIMKELKIKQK----SAIFILPYISLVHEKYQSLAKAAEEFKFY-LEGKCLEM--IQN 74
             E L+ +E+ + +K    S+  + P+ SL  +     A+     K Y  +  CL +  +Q 
Sbjct:   294 ETLLSEEINVAKKTIASSSDDLGPFYSLPSKVRDLYAQFRGIEKLYEWQHTCLTLKSVQE 353

Query:    75 -KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFY 133
              KN + S+PTSGGKTLV EIL+++EL  ++K A+ ILPY+++V EK   L+    E  F+
Sbjct:   354 RKNLIYSLPTSGGKTLVAEILMLQELLCRRKDALMILPYVAIVQEKIAGLSSFGIELGFF 413

Query:   134 LE 135
             +E
Sbjct:   414 VE 415

GO:0005730 "nucleolus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

FB|FBgn0002899 mus301 "mutagen-sensitive 301" [Drosophila melanogaster (taxid:7227)]

 Score = 170 (64.9 bits), Expect = 1.8e-11, P = 1.8e-11
 Identities = 40/124 (32%), Positives = 72/124 (58%)

Query:     3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF 62
             Q KN + ++PTSGGKTLV EIL+++EL  ++++ +FILPY+S+V EK  +++  A +  F
Sbjct:   279 QRKNLIYALPTSGGKTLVAEILMLRELLCRERNVLFILPYVSIVQEKVSAMSPFAIDLDF 338

Query:    63 YLE------GKCLEMIQNKNCVLSIPT-SGGKTLVGEILIMKELKIKQKSAIFILPYISL 115
              +E      GKC    + K   L I +   G  L+  ++   +++   +  + ++  + L
Sbjct:   339 IVEEYTAGKGKCPPQPRRKRRSLFIASIEKGAVLMDSLI---DVQRPHEIGLVVVDELHL 395

Query:   116 VHEK 119
             + EK
Sbjct:   396 IGEK 399

GO:0007294 "germarium-derived oocyte fate determination" evidence=IGI;IMP

GO:0008298 "intracellular mRNA localization" evidence=IMP;TAS

GO:0048477 "oogenesis" evidence=IGI;TAS

GO:0009949 "polarity specification of anterior/posterior axis" evidence=IMP

GO:0030717 "karyosome formation" evidence=IMP

GO:0009951 "polarity specification of dorsal/ventral axis" evidence=IMP

GO:0006417 "regulation of translation" evidence=TAS

GO:0030532 "small nuclear ribonucleoprotein complex" evidence=ISS

GO:0005682 "U5 snRNP" evidence=ISS

GO:0004386 "helicase activity" evidence=ISS

GO:0009994 "oocyte differentiation" evidence=NAS

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0016321 "female meiosis chromosome segregation" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	138
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	3e-09
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	3e-09
PRK00254	720	PRK00254, PRK00254, ski2-like helicase; Provisiona	2e-07
PRK00254	720	PRK00254, PRK00254, ski2-like helicase; Provisiona	3e-07
PRK01172	674	PRK01172, PRK01172, ski2-like helicase; Provisiona	3e-07
PRK01172	674	PRK01172, PRK01172, ski2-like helicase; Provisiona	3e-07
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	5e-06
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	1e-05
PRK02362	737	PRK02362, PRK02362, ski2-like helicase; Provisiona	1e-04
PRK02362	737	PRK02362, PRK02362, ski2-like helicase; Provisiona	1e-04
COG1111	542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	0.004

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

 Score = 53.5 bits (129), Expect = 3e-09
 Identities = 17/55 (30%), Positives = 31/55 (56%)

Query: 4   NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE 58
           ++N ++S PT  GKTL+  + I+  L       ++I+P  +L  EKY+  ++  E
Sbjct: 47  DENVLISAPTGSGKTLIALLAILSTLLEGGGKVVYIVPLKALAEEKYEEFSRLEE 101

Length = 766

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

 Score = 53.5 bits (129), Expect = 3e-09
 Identities = 17/55 (30%), Positives = 31/55 (56%)

Query: 74  NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE 128
           ++N ++S PT  GKTL+  + I+  L       ++I+P  +L  EKY+  ++  E
Sbjct: 47  DENVLISAPTGSGKTLIALLAILSTLLEGGGKVVYIVPLKALAEEKYEEFSRLEE 101

Length = 766

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

 Score = 48.7 bits (116), Expect = 2e-07
 Identities = 24/64 (37%), Positives = 41/64 (64%), Gaps = 7/64 (10%)

Query: 70  EMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEE 129
            +++ KN VL+IPT+ GKTLV EI+++ +L  +   A++++P  +L  EKY+       E
Sbjct: 35  GVLEGKNLVLAIPTASGKTLVAEIVMVNKLLREGGKAVYLVPLKALAEEKYR-------E 87

Query: 130 FKFY 133
           FK +
Sbjct: 88  FKDW 91

Length = 720

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

 Score = 47.5 bits (113), Expect = 3e-07
 Identities = 24/63 (38%), Positives = 41/63 (65%), Gaps = 7/63 (11%)

Query: 1  MVQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEF 60
          +++ KN VL+IPT+ GKTLV EI+++ +L  +   A++++P  +L  EKY+       EF
Sbjct: 36 VLEGKNLVLAIPTASGKTLVAEIVMVNKLLREGGKAVYLVPLKALAEEKYR-------EF 88

Query: 61 KFY 63
          K +
Sbjct: 89 KDW 91

Length = 720

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

 Score = 47.6 bits (113), Expect = 3e-07
 Identities = 20/53 (37%), Positives = 33/53 (62%), Gaps = 1/53 (1%)

Query: 3  QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK 55
          + +N ++S+PT+ GKTL+    I +      KS I+I+P  SL  EKY+ L++
Sbjct: 36 KGENVIVSVPTAAGKTLIAYSAIYETFLAGLKS-IYIVPLRSLAMEKYEELSR 87

Length = 674

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

 Score = 47.6 bits (113), Expect = 3e-07
 Identities = 20/53 (37%), Positives = 33/53 (62%), Gaps = 1/53 (1%)

Query: 73  QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK 125
           + +N ++S+PT+ GKTL+    I +      KS I+I+P  SL  EKY+ L++
Sbjct: 36  KGENVIVSVPTAAGKTLIAYSAIYETFLAGLKS-IYIVPLRSLAMEKYEELSR 87

Length = 674

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

 Score = 43.0 bits (102), Expect = 5e-06
 Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 2/58 (3%)

Query: 70  EMIQNKNCVLSIPTSGGKTLVGEILIMKEL--KIKQKSAIFILPYISLVHEKYQSLAK 125
            ++  K+ ++  PT  GKTL   + I++ L  K     A+ + P   L  + Y+ L K
Sbjct: 10  AILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQIYEELKK 67

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|215832 pfam00270, DEAD, DEAD/DEAH box helicase

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 2/55 (3%)

Query: 3  QNKNCVLSIPTSGGKTLVGEILIMKEL--KIKQKSAIFILPYISLVHEKYQSLAK 55
            K+ ++  PT  GKTL   + I++ L  K     A+ + P   L  + Y+ L K
Sbjct: 13 SGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQIYEELKK 67

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|235032 PRK02362, PRK02362, ski2-like helicase; Provisional

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 22/66 (33%), Positives = 38/66 (57%), Gaps = 10/66 (15%)

Query: 68  CLEM--IQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK 125
            +E   +  KN + +IPT+ GKTL+ E+ ++K +    K A++I+P  +L  EK+     
Sbjct: 31  AVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIARGGK-ALYIVPLRALASEKF----- 84

Query: 126 AAEEFK 131
             EEF+
Sbjct: 85  --EEFE 88

Length = 737

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 21/59 (35%), Positives = 35/59 (59%), Gaps = 8/59 (13%)

Query: 3  QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFK 61
            KN + +IPT+ GKTL+ E+ ++K +    K A++I+P  +L  EK+       EEF+
Sbjct: 38 DGKNLLAAIPTASGKTLIAELAMLKAIARGGK-ALYIVPLRALASEKF-------EEFE 88

Length = 737

>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication, recombination, and repair]

 Score = 35.8 bits (83), Expect = 0.004
 Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 4/71 (5%)

Query: 57  AEEFKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLV 116
              ++  +  K L     KN ++ +PT  GKT +  ++I   L+      +F+ P   LV
Sbjct: 16  PRLYQLNIAAKALF----KNTLVVLPTGLGKTFIAAMVIANRLRWFGGKVLFLAPTKPLV 71

Query: 117 HEKYQSLAKAA 127
            +  +   K  
Sbjct: 72  LQHAEFCRKVT 82

Length = 542

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	138
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.6
COG1204	766	Superfamily II helicase [General function predicti	99.59
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.59
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.58
KOG0952|consensus	1230		99.58
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.57
PRK02362	737	ski2-like helicase; Provisional	99.56
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.55
PRK00254	720	ski2-like helicase; Provisional	99.55
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.55
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.54
COG1204	766	Superfamily II helicase [General function predicti	99.53
KOG0330|consensus	476		99.53
COG1205	851	Distinct helicase family with a unique C-terminal	99.53
PTZ00110	545	helicase; Provisional	99.52
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.51
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.51
PTZ00424	401	helicase 45; Provisional	99.49
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.49
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.48
PRK01172	674	ski2-like helicase; Provisional	99.46
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.44
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.43
KOG0952|consensus	1230		99.4
COG1202	830	Superfamily II helicase, archaea-specific [General	99.38
KOG0348|consensus	708		99.37
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.37
KOG0350|consensus	620		99.37
KOG0345|consensus	567		99.35
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.35
KOG0338|consensus	691		99.35
PRK13767	876	ATP-dependent helicase; Provisional	99.34
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.33
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.33
KOG0331|consensus	519		99.32
KOG0340|consensus	442		99.31
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.3
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.3
PRK13767	876	ATP-dependent helicase; Provisional	99.29
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.29
PTZ00110	545	helicase; Provisional	99.29
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.29
PRK02362	737	ski2-like helicase; Provisional	99.29
PRK00254	720	ski2-like helicase; Provisional	99.28
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.28
PRK09401	1176	reverse gyrase; Reviewed	99.27
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.27
KOG0330|consensus	476		99.26
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.25
COG1205	851	Distinct helicase family with a unique C-terminal	99.25
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.25
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.24
PTZ00424	401	helicase 45; Provisional	99.23
KOG0951|consensus	1674		99.23
KOG0348|consensus	708		99.23
KOG0354|consensus	746		99.22
KOG0350|consensus	620		99.22
KOG0343|consensus	758		99.22
KOG0346|consensus	569		99.21
KOG0342|consensus	543		99.21
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.2
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.2
KOG0344|consensus	593		99.2
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.19
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.19
KOG0343|consensus	758		99.19
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.18
KOG0331|consensus	519		99.18
KOG0346|consensus	569		99.17
PRK01172	674	ski2-like helicase; Provisional	99.17
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.16
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.15
KOG0335|consensus	482		99.15
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.15
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.15
PRK14701	1638	reverse gyrase; Provisional	99.14
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.13
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.12
KOG0347|consensus	731		99.11
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.11
KOG0345|consensus	567		99.07
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.07
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.07
PRK10689	1147	transcription-repair coupling factor; Provisional	99.06
KOG0333|consensus	673		99.06
KOG0948|consensus	1041		99.06
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.05
PRK09401	1176	reverse gyrase; Reviewed	99.04
KOG0334|consensus	997		99.03
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.02
KOG0950|consensus	1008		99.0
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.0
KOG0342|consensus	543		99.0
COG1202	830	Superfamily II helicase, archaea-specific [General	98.99
PHA02558	501	uvsW UvsW helicase; Provisional	98.99
KOG0335|consensus	482		98.99
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	98.99
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	98.99
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	98.98
KOG0344|consensus	593		98.94
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	98.93
KOG0947|consensus	1248		98.92
KOG0354|consensus	746		98.91
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	98.91
KOG0337|consensus	529		98.91
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	98.9
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	98.9
PRK14701	1638	reverse gyrase; Provisional	98.9
KOG0951|consensus	1674		98.88
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	98.88
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	98.87
PRK13766	773	Hef nuclease; Provisional	98.87
KOG0947|consensus	1248		98.87
PRK09200	790	preprotein translocase subunit SecA; Reviewed	98.86
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	98.85
PHA02558	501	uvsW UvsW helicase; Provisional	98.84
KOG0340|consensus	442		98.83
PRK10689	1147	transcription-repair coupling factor; Provisional	98.83
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	98.83
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	98.81
KOG0326|consensus	459		98.81
KOG0948|consensus	1041		98.79
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	98.78
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.78
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	98.77
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	98.76
KOG0338|consensus	691		98.76
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	98.75
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	98.75
KOG0328|consensus	400		98.74
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.74
KOG4284|consensus	980		98.73
PRK13766	773	Hef nuclease; Provisional	98.73
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	98.72
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	98.71
KOG0334|consensus	997		98.7
KOG0341|consensus	610		98.7
PRK05580	679	primosome assembly protein PriA; Validated	98.66
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	98.66
PRK05580	679	primosome assembly protein PriA; Validated	98.64
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	98.64
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	98.64
KOG0327|consensus	397		98.62
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	98.61
TIGR00595	505	priA primosomal protein N'. All proteins in this f	98.61
KOG0347|consensus	731		98.6
KOG0339|consensus	731		98.59
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	98.59
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	98.56
smart00487	201	DEXDc DEAD-like helicases superfamily.	98.55
KOG0949|consensus	1330		98.55
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.55
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	98.54
KOG0329|consensus	387		98.54
KOG0337|consensus	529		98.54
KOG0352|consensus	641		98.53
KOG0339|consensus	731		98.51
KOG0950|consensus	1008		98.5
PRK09694	878	helicase Cas3; Provisional	98.5
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.48
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	98.48
smart00487	201	DEXDc DEAD-like helicases superfamily.	98.46
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	98.46
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	98.46
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	98.46
PRK09694	878	helicase Cas3; Provisional	98.46
KOG0332|consensus	477		98.44
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	98.43
PRK09200	790	preprotein translocase subunit SecA; Reviewed	98.41
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	98.4
KOG0336|consensus	629		98.4
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	98.39
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	98.39
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.39
KOG0351|consensus	941		98.38
TIGR00595	505	priA primosomal protein N'. All proteins in this f	98.38
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.37
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	98.33
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.33
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	98.32
PHA02653	675	RNA helicase NPH-II; Provisional	98.3
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	98.29
PHA02653	675	RNA helicase NPH-II; Provisional	98.29
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	98.29
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	98.29
KOG0341|consensus	610		98.28
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	98.27
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	98.26
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	98.25
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	98.24
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	98.22
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	98.21
PRK12904	830	preprotein translocase subunit SecA; Reviewed	98.2
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	98.19
KOG0336|consensus	629		98.18
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	98.17
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	98.14
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	98.13
PF13245	76	AAA_19: Part of AAA domain	98.12
PRK13107	908	preprotein translocase subunit SecA; Reviewed	98.11
KOG0352|consensus	641		98.11
KOG0333|consensus	673		98.09
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.09
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	98.09
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	98.09
KOG0328|consensus	400		98.08
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	98.05
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	98.01
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	98.0
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	97.98
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	97.96
KOG0332|consensus	477		97.94
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	97.93
KOG0353|consensus	695		97.93
KOG0353|consensus	695		97.93
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	97.91
PRK12326	764	preprotein translocase subunit SecA; Reviewed	97.9
KOG0949|consensus	1330		97.87
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	97.87
COG4096	875	HsdR Type I site-specific restriction-modification	97.83
PRK04328	249	hypothetical protein; Provisional	97.82
COG1198	730	PriA Primosomal protein N' (replication factor Y)	97.81
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	97.8
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	97.79
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.79
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	97.79
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	97.75
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	97.73
KOG0327|consensus	397		97.71
PRK12904	830	preprotein translocase subunit SecA; Reviewed	97.71
PRK13107	908	preprotein translocase subunit SecA; Reviewed	97.7
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	97.69
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	97.64
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.61
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	97.61
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	97.6
KOG0326|consensus	459		97.59
PF13245	76	AAA_19: Part of AAA domain	97.56
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	97.56
KOG0351|consensus	941		97.56
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	97.55
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	97.52
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.51
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	97.51
PRK06835	329	DNA replication protein DnaC; Validated	97.48
cd01394	218	radB RadB. The archaeal protein radB shares simila	97.47
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	97.44
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	97.42
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.42
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	97.41
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	97.41
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	97.39
PRK15483	986	type III restriction-modification system StyLTI en	97.39
CHL00122	870	secA preprotein translocase subunit SecA; Validate	97.38
PRK08181	269	transposase; Validated	97.36
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.34
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.34
PRK08116	268	hypothetical protein; Validated	97.3
KOG4284|consensus	980		97.29
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.29
PRK12326	764	preprotein translocase subunit SecA; Reviewed	97.29
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.29
PRK09302	509	circadian clock protein KaiC; Reviewed	97.28
COG4096	875	HsdR Type I site-specific restriction-modification	97.28
KOG0329|consensus	387		97.28
PRK08533	230	flagellar accessory protein FlaH; Reviewed	97.26
TIGR00665	434	DnaB replicative DNA helicase. This model describe	97.2
PRK06921	266	hypothetical protein; Provisional	97.19
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	97.19
PRK06067	234	flagellar accessory protein FlaH; Validated	97.18
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	97.17
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.15
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	97.14
PRK09354	349	recA recombinase A; Provisional	97.1
PRK09302	509	circadian clock protein KaiC; Reviewed	97.08
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.07
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	97.07
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	97.06
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	97.05
PRK05973	237	replicative DNA helicase; Provisional	97.05
PRK06526	254	transposase; Provisional	97.05
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	97.04
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	97.04
PRK04301	317	radA DNA repair and recombination protein RadA; Va	97.01
PRK12377	248	putative replication protein; Provisional	97.01
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.0
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	96.99
PRK08760	476	replicative DNA helicase; Provisional	96.98
PRK10867	433	signal recognition particle protein; Provisional	96.95
TIGR02236	310	recomb_radA DNA repair and recombination protein R	96.9
PRK14873	665	primosome assembly protein PriA; Provisional	96.9
PRK05748	448	replicative DNA helicase; Provisional	96.86
PRK15483	986	type III restriction-modification system StyLTI en	96.85
PRK11823	446	DNA repair protein RadA; Provisional	96.84
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	96.83
COG1198	730	PriA Primosomal protein N' (replication factor Y)	96.82
PRK10536	262	hypothetical protein; Provisional	96.82
PRK09183	259	transposase/IS protein; Provisional	96.8
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.8
PHA02542	473	41 41 helicase; Provisional	96.78
TIGR00376	637	DNA helicase, putative. The gene product may repre	96.72
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	96.72
PF12846	304	AAA_10: AAA-like domain	96.71
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	96.71
KOG1802|consensus	935		96.68
smart00382	148	AAA ATPases associated with a variety of cellular	96.67
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	96.66
TIGR00959	428	ffh signal recognition particle protein. This mode	96.64
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	96.62
PRK08727	233	hypothetical protein; Validated	96.59
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.57
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.54
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	96.54
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	96.51
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.51
PTZ00035	337	Rad51 protein; Provisional	96.47
PRK07773	886	replicative DNA helicase; Validated	96.46
PRK08506	472	replicative DNA helicase; Provisional	96.46
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	96.46
TIGR00376	637	DNA helicase, putative. The gene product may repre	96.46
PRK05636	505	replicative DNA helicase; Provisional	96.44
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	96.42
PRK07952	244	DNA replication protein DnaC; Validated	96.4
COG4889	1518	Predicted helicase [General function prediction on	96.39
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	96.38
CHL00122	870	secA preprotein translocase subunit SecA; Validate	96.38
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	96.37
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	96.37
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	96.36
PRK08939	306	primosomal protein DnaI; Reviewed	96.36
PRK13851	344	type IV secretion system protein VirB11; Provision	96.36
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	96.35
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	96.35
PRK05595	444	replicative DNA helicase; Provisional	96.33
PRK07004	460	replicative DNA helicase; Provisional	96.33
PRK08084	235	DNA replication initiation factor; Provisional	96.32
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	96.3
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	96.26
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	96.26
cd00983	325	recA RecA is a bacterial enzyme which has roles in	96.25
PRK09165	497	replicative DNA helicase; Provisional	96.25
PRK05642	234	DNA replication initiation factor; Validated	96.23
PRK04914	956	ATP-dependent helicase HepA; Validated	96.22
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	96.2
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	96.18
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	96.18
PRK14873	665	primosome assembly protein PriA; Provisional	96.17
PRK09519	790	recA DNA recombination protein RecA; Reviewed	96.1
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	96.08
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	96.03
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	96.02
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.02
PLN02199	303	shikimate kinase	96.01
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.0
KOG0745|consensus	564		95.97
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	95.97
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	95.96
PRK13833	323	conjugal transfer protein TrbB; Provisional	95.93
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	95.92
COG2256	436	MGS1 ATPase related to the helicase subunit of the	95.92
PRK06893	229	DNA replication initiation factor; Validated	95.91
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	95.87
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	95.87
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	95.86
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	95.81
COG3587	985	Restriction endonuclease [Defense mechanisms]	95.8
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	95.8
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	95.78
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	95.74
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	95.72
PRK14974	336	cell division protein FtsY; Provisional	95.72
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	95.7
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	95.69
PRK08903	227	DnaA regulatory inactivator Hda; Validated	95.69
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	95.65
TIGR03744	893	traC_PFL_4706 conjugative transfer ATPase, PFL_470	95.65
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	95.64
PRK06321	472	replicative DNA helicase; Provisional	95.62
PRK04296	190	thymidine kinase; Provisional	95.6
KOG1803|consensus	649		95.59
PF13555	62	AAA_29: P-loop containing region of AAA domain	95.57
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	95.57
PRK13764	602	ATPase; Provisional	95.55
PRK14087	450	dnaA chromosomal replication initiation protein; P	95.53
TIGR03754	643	conj_TOL_TraD conjugative coupling factor TraD, TO	95.52
PRK10436	462	hypothetical protein; Provisional	95.5
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	95.5
PRK14729	300	miaA tRNA delta(2)-isopentenylpyrophosphate transf	95.48
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	95.47
TIGR02759	566	TraD_Ftype type IV conjugative transfer system cou	95.46
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	95.43
PRK11054	684	helD DNA helicase IV; Provisional	95.39
KOG4150|consensus	1034		95.36
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	95.36
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	95.35
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	95.34
cd03115	173	SRP The signal recognition particle (SRP) mediates	95.33
PHA02535	581	P terminase ATPase subunit; Provisional	95.32
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	95.31
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	95.31
KOG0953|consensus	700		95.31
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	95.29
PRK08006	471	replicative DNA helicase; Provisional	95.24
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	95.23
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	95.2
COG0610	962	Type I site-specific restriction-modification syst	95.19
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	95.19
KOG1131|consensus	755		95.16
KOG1802|consensus	935		95.15
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	95.14
PRK00131	175	aroK shikimate kinase; Reviewed	95.11
PRK12422	445	chromosomal replication initiation protein; Provis	95.09
PRK06749	428	replicative DNA helicase; Provisional	95.08
PRK10536	262	hypothetical protein; Provisional	95.08
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	95.05
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	95.0
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	94.99
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	94.95
KOG0953|consensus	700		94.93
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	94.89
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	94.87
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	94.87
PRK00149	450	dnaA chromosomal replication initiation protein; R	94.86
PRK11054	684	helD DNA helicase IV; Provisional	94.85
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	94.83
TIGR02746	797	TraC-F-type type-IV secretion system protein TraC.	94.79
KOG1123|consensus	776		94.78
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	94.77
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	94.76
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	94.76
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	94.76
COG3451	796	VirB4 Type IV secretory pathway, VirB4 components	94.71
COG3587	985	Restriction endonuclease [Defense mechanisms]	94.7
PLN02165	334	adenylate isopentenyltransferase	94.69
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	94.68
KOG0390|consensus	776		94.68
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	94.66
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	94.65
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	94.65
TIGR00064	272	ftsY signal recognition particle-docking protein F	94.64
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	94.58
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	94.57
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	94.55
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	94.55
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	94.55
PF12846	304	AAA_10: AAA-like domain	94.54
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	94.54
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	94.53
PF00004	132	AAA: ATPase family associated with various cellula	94.51
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	94.51
PRK10416	318	signal recognition particle-docking protein FtsY;	94.48
PRK14088	440	dnaA chromosomal replication initiation protein; P	94.46
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	94.45
PRK13700	732	conjugal transfer protein TraD; Provisional	94.45
COG0593	408	DnaA ATPase involved in DNA replication initiation	94.44
CHL00181	287	cbbX CbbX; Provisional	94.43
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	94.42
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	94.4
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	94.38
PRK13850	670	type IV secretion system protein VirD4; Provisiona	94.38
PRK00300	205	gmk guanylate kinase; Provisional	94.37
TIGR02533	486	type_II_gspE general secretory pathway protein E.	94.34
PRK13897	606	type IV secretion system component VirD4; Provisio	94.28
PRK13891	852	conjugal transfer protein TrbE; Provisional	94.28
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	94.26
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	94.25
KOG2028|consensus	554		94.21
COG1484	254	DnaC DNA replication protein [DNA replication, rec	94.15
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	94.15
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	94.14
PHA00729	226	NTP-binding motif containing protein	94.14
PHA02244	383	ATPase-like protein	94.11
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	94.09
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	94.08
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	94.07
KOG1803|consensus	649		94.05
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	94.04
PRK13873	811	conjugal transfer ATPase TrbE; Provisional	94.04
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	94.04
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	93.99
PRK14086	617	dnaA chromosomal replication initiation protein; P	93.99
PF01745	233	IPT: Isopentenyl transferase; InterPro: IPR002648	93.98
PRK00091	307	miaA tRNA delta(2)-isopentenylpyrophosphate transf	93.94
) 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	93.94
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	93.94
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	93.92
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	93.92
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	93.91
PF13173	128	AAA_14: AAA domain	93.88
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	93.88
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	93.75
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	93.71
PF09439	181	SRPRB: Signal recognition particle receptor beta s	93.7
COG3973	747	Superfamily I DNA and RNA helicases [General funct	93.68
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	93.67
PHA03333	752	putative ATPase subunit of terminase; Provisional	93.67
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	93.67
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	93.62
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	93.61
PRK13897	606	type IV secretion system component VirD4; Provisio	93.6

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.60  E-value=4.6e-15  Score=113.77  Aligned_cols=92  Identities=16%  Similarity=0.091  Sum_probs=81.4

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh---------CCCeEEEEccchh
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI---------KQKSAIFILPYIS  114 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~---------~~~~~~~i~P~~~  114 (138)
                      |.....+.+.+.++..+.++|.+++|.+.+ +|+++.+|||+|||+++++++++.+..         .+.++++++|+++
T Consensus        15 l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~lil~Ptre   94 (423)
T PRK04837         15 LHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALIMAPTRE   94 (423)
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEEEECCcHH
Confidence            456778888888899999999999998888 999999999999999999999998864         1357999999999


Q ss_pred             HHHHHHHHHHHHhhhcCceeee
Q psy2029         115 LVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus       115 l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      |+.|+++.+..+....|+++..
T Consensus        95 La~Qi~~~~~~l~~~~~~~v~~  116 (423)
T PRK04837         95 LAVQIHADAEPLAQATGLKLGL  116 (423)
T ss_pred             HHHHHHHHHHHHhccCCceEEE
Confidence            9999999999999888887654

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.59  E-value=5.2e-15  Score=119.89  Aligned_cols=81  Identities=23%  Similarity=0.402  Sum_probs=70.2

Q ss_pred             HHhhhhhhhhHHH-hhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCcee
Q psy2029          57 AEEFKFYLEGKCL-EMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYL  134 (138)
Q Consensus        57 ~~~~~~~~Q~~~~-~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v  134 (138)
                      +....++.|..+. +...+ +|+++++|||+|||++|++++++++.+.+.|++||+|++||++|++++|+ .++.+|++|
T Consensus        28 ~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~~~k~vYivPlkALa~Ek~~~~~-~~~~~GirV  106 (766)
T COG1204          28 GIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGGGKVVYIVPLKALAEEKYEEFS-RLEELGIRV  106 (766)
T ss_pred             ChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhcCCcEEEEeChHHHHHHHHHHhh-hHHhcCCEE
Confidence            4445667777676 55555 99999999999999999999999999878899999999999999999999 778899999


Q ss_pred             eecC
Q psy2029         135 EVLE  138 (138)
Q Consensus       135 ~~~~  138 (138)
                      .+++
T Consensus       107 ~~~T  110 (766)
T COG1204         107 GIST  110 (766)
T ss_pred             EEec
Confidence            8753

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

Probab=99.59  E-value=5.3e-15  Score=120.07  Aligned_cols=93  Identities=13%  Similarity=0.199  Sum_probs=81.9

Q ss_pred             hhHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHHHHHHH
Q psy2029          44 SLVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        44 aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~~q~~~  121 (138)
                      .|..+..+.+.+.++..++++|.++++.+.+ +|+++.+|||+|||+++.+++++.+.. .+.+++|++|++||++|+.+
T Consensus        20 ~l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~~~~~aL~l~PtraLa~q~~~   99 (742)
T TIGR03817        20 WAHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADDPRATALYLAPTKALAADQLR   99 (742)
T ss_pred             cCCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhCCCcEEEEEcChHHHHHHHHH
Confidence            4667778888888888999999999999888 999999999999999999999999875 45799999999999999999


Q ss_pred             HHHHHhhhcCceeeec
Q psy2029         122 SLAKAAEEFKFYLEVL  137 (138)
Q Consensus       122 ~~~~~~~~~~~~v~~~  137 (138)
                      .++++. ..++++..|
T Consensus       100 ~l~~l~-~~~i~v~~~  114 (742)
T TIGR03817       100 AVRELT-LRGVRPATY  114 (742)
T ss_pred             HHHHhc-cCCeEEEEE
Confidence            999986 446666555

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.

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.58  E-value=6.5e-15  Score=114.48  Aligned_cols=93  Identities=17%  Similarity=0.148  Sum_probs=81.9

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC---------CCeEEEEccchh
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK---------QKSAIFILPYIS  114 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~---------~~~~~~i~P~~~  114 (138)
                      |.....+.+.+.++..++++|.++++.+.+ +|+++.+|||+|||+++.+++++.+...         ..+++|++|+++
T Consensus        94 l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~aLil~Ptre  173 (475)
T PRK01297         94 LAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTRE  173 (475)
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceEEEEeCcHH
Confidence            556777888888888999999999998888 9999999999999999999999988752         358999999999


Q ss_pred             HHHHHHHHHHHHhhhcCceeeec
Q psy2029         115 LVHEKYQSLAKAAEEFKFYLEVL  137 (138)
Q Consensus       115 l~~q~~~~~~~~~~~~~~~v~~~  137 (138)
                      |+.|+++.++++....++.+..+
T Consensus       174 La~Q~~~~~~~l~~~~~~~v~~~  196 (475)
T PRK01297        174 LVVQIAKDAAALTKYTGLNVMTF  196 (475)
T ss_pred             HHHHHHHHHHHhhccCCCEEEEE
Confidence            99999999999988887776543

>KOG0952|consensus

Probab=99.58  E-value=5.5e-15  Score=120.06  Aligned_cols=82  Identities=20%  Similarity=0.317  Sum_probs=74.4

Q ss_pred             HHhhhhhhhhHHHhhhhc--cceEEEeecCCCchHhHHHHHHHHHHh---------CCCeEEEEccchhHHHHHHHHHHH
Q psy2029          57 AEEFKFYLEGKCLEMIQN--KNCVLSIPTSGGKTLVGEILIMKELKI---------KQKSAIFILPYISLVHEKYQSLAK  125 (138)
Q Consensus        57 ~~~~~~~~Q~~~~~~~~~--~~~ii~~ptg~GKt~~~~~~~l~~~~~---------~~~~~~~i~P~~~l~~q~~~~~~~  125 (138)
                      ++..+..+|..+.|...+  .|+++|+|||+|||.+|++.+++.+.+         ..-|++||+|++|||.|+++.|.+
T Consensus       107 ~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~~~~k  186 (1230)
T KOG0952|consen  107 SFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDKFSK  186 (1230)
T ss_pred             cHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHHHHhh
Confidence            355688899999987765  999999999999999999999999985         345999999999999999999999


Q ss_pred             HhhhcCceeeecC
Q psy2029         126 AAEEFKFYLEVLE  138 (138)
Q Consensus       126 ~~~~~~~~v~~~~  138 (138)
                      -+.++|++|.||+
T Consensus       187 kl~~~gi~v~ELT  199 (1230)
T KOG0952|consen  187 KLAPLGISVRELT  199 (1230)
T ss_pred             hcccccceEEEec
Confidence            9999999999985

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.57  E-value=1.1e-14  Score=115.34  Aligned_cols=92  Identities=16%  Similarity=0.129  Sum_probs=81.6

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC---------CCeEEEEccchh
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK---------QKSAIFILPYIS  114 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~---------~~~~~~i~P~~~  114 (138)
                      |...+.+.+.+.++..++++|.+++|.+.+ +|+++.+|||+|||+++++++++.+...         ..++||++|+++
T Consensus        16 l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raLIl~PTre   95 (572)
T PRK04537         16 LHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAPTRE   95 (572)
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEEEEeCcHH
Confidence            456778888888899999999999998888 9999999999999999999999988641         368999999999


Q ss_pred             HHHHHHHHHHHHhhhcCceeee
Q psy2029         115 LVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus       115 l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      |+.|+++.+.+++...++++..
T Consensus        96 La~Qi~~~~~~l~~~~~i~v~~  117 (572)
T PRK04537         96 LAIQIHKDAVKFGADLGLRFAL  117 (572)
T ss_pred             HHHHHHHHHHHHhccCCceEEE
Confidence            9999999999999888877653

>PRK02362 ski2-like helicase; Provisional

Probab=99.56  E-value=9.2e-15  Score=118.86  Aligned_cols=91  Identities=24%  Similarity=0.424  Sum_probs=76.6

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhh-hhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEM-IQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQS  122 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~-~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~  122 (138)
                      |.....+.+.+.+...++++|.++++. +.+ +|+++++|||+|||+++++++++.+. .+.+++|++|+++|+.|++++
T Consensus         8 lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~-~~~kal~i~P~raLa~q~~~~   86 (737)
T PRK02362          8 LPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIA-RGGKALYIVPLRALASEKFEE   86 (737)
T ss_pred             CCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHh-cCCcEEEEeChHHHHHHHHHH
Confidence            445666777777788899999999975 555 99999999999999999999999886 478999999999999999999


Q ss_pred             HHHHhhhcCceeeec
Q psy2029         123 LAKAAEEFKFYLEVL  137 (138)
Q Consensus       123 ~~~~~~~~~~~v~~~  137 (138)
                      |+++ .+.|++|..+
T Consensus        87 ~~~~-~~~g~~v~~~  100 (737)
T PRK02362         87 FERF-EELGVRVGIS  100 (737)
T ss_pred             HHHh-hcCCCEEEEE
Confidence            9975 3457776543

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.55  E-value=2.4e-14  Score=110.81  Aligned_cols=90  Identities=12%  Similarity=0.147  Sum_probs=79.0

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC--------CCeEEEEccchhH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK--------QKSAIFILPYISL  115 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~--------~~~~~~i~P~~~l  115 (138)
                      |...+.+.+.+.++..++++|.++++.+.+ +|+++.+|||+|||+++.+++++.+...        ..++++++|+++|
T Consensus         8 l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil~PtreL   87 (456)
T PRK10590          8 LSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTREL   87 (456)
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEEeCcHHH
Confidence            456778888888899999999999998888 9999999999999999999999988642        2379999999999


Q ss_pred             HHHHHHHHHHHhhhcCcee
Q psy2029         116 VHEKYQSLAKAAEEFKFYL  134 (138)
Q Consensus       116 ~~q~~~~~~~~~~~~~~~v  134 (138)
                      +.|+.+.+++++...++.+
T Consensus        88 a~Qi~~~~~~~~~~~~~~~  106 (456)
T PRK10590         88 AAQIGENVRDYSKYLNIRS  106 (456)
T ss_pred             HHHHHHHHHHHhccCCCEE
Confidence            9999999999987766654

>PRK00254 ski2-like helicase; Provisional

Probab=99.55  E-value=1.9e-14  Score=116.73  Aligned_cols=92  Identities=27%  Similarity=0.430  Sum_probs=78.9

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhh-hhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEM-IQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQS  122 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~-~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~  122 (138)
                      +.+...+.+.+.+...++++|.++++. ..+ +|+++++|||+|||+++++++++.+...+.+++|++|+++|++|++++
T Consensus         8 l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~~~~~l~l~P~~aLa~q~~~~   87 (720)
T PRK00254          8 VDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLREGGKAVYLVPLKALAEEKYRE   87 (720)
T ss_pred             CCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhcCCeEEEEeChHHHHHHHHHH
Confidence            345667777888888899999999964 555 999999999999999999999998887778999999999999999999


Q ss_pred             HHHHhhhcCceeeec
Q psy2029         123 LAKAAEEFKFYLEVL  137 (138)
Q Consensus       123 ~~~~~~~~~~~v~~~  137 (138)
                      |.++ ...|++|..+
T Consensus        88 ~~~~-~~~g~~v~~~  101 (720)
T PRK00254         88 FKDW-EKLGLRVAMT  101 (720)
T ss_pred             HHHH-hhcCCEEEEE
Confidence            9985 4567777543

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

Probab=99.55  E-value=2.6e-14  Score=112.18  Aligned_cols=90  Identities=17%  Similarity=0.146  Sum_probs=78.1

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh---------CCCeEEEEccchh
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI---------KQKSAIFILPYIS  114 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~---------~~~~~~~i~P~~~  114 (138)
                      |.....+.+.+.++..++++|.++++.+.. +|+++.+|||+|||++++++++..+..         .+.+++|++|+++
T Consensus       128 l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~~~aLIL~PTre  207 (518)
T PLN00206        128 LPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRE  207 (518)
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCCceEEEEeCCHH
Confidence            556777888888888999999999998888 999999999999999999999987753         3468999999999


Q ss_pred             HHHHHHHHHHHHhhhcCcee
Q psy2029         115 LVHEKYQSLAKAAEEFKFYL  134 (138)
Q Consensus       115 l~~q~~~~~~~~~~~~~~~v  134 (138)
                      |+.|..+.++.+....++++
T Consensus       208 La~Qi~~~~~~l~~~~~~~~  227 (518)
T PLN00206        208 LCVQVEDQAKVLGKGLPFKT  227 (518)
T ss_pred             HHHHHHHHHHHHhCCCCceE
Confidence            99999999998887766554

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.54  E-value=2.9e-14  Score=109.62  Aligned_cols=93  Identities=13%  Similarity=0.115  Sum_probs=81.4

Q ss_pred             hhHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh------CCCeEEEEccchhHH
Q psy2029          44 SLVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI------KQKSAIFILPYISLV  116 (138)
Q Consensus        44 aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~------~~~~~~~i~P~~~l~  116 (138)
                      .|..+..+.+.+.++..++++|.++++.+.+ +++++.+|||+|||+++++++++.+..      ...+++|++|+++|+
T Consensus         7 ~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~Pt~eLa   86 (434)
T PRK11192          7 ELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELA   86 (434)
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEECCcHHHH
Confidence            3456778888888888999999999988888 999999999999999999999998864      135899999999999


Q ss_pred             HHHHHHHHHHhhhcCceeee
Q psy2029         117 HEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus       117 ~q~~~~~~~~~~~~~~~v~~  136 (138)
                      .|.++.++.+....++++..
T Consensus        87 ~Q~~~~~~~l~~~~~~~v~~  106 (434)
T PRK11192         87 MQVADQARELAKHTHLDIAT  106 (434)
T ss_pred             HHHHHHHHHHHccCCcEEEE
Confidence            99999999998888777654

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.53  E-value=1.6e-14  Score=117.06  Aligned_cols=54  Identities=30%  Similarity=0.588  Sum_probs=50.5

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK   55 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~   55 (138)
                      .+|+|+++|+|||||||++|++++++++.+.+++++|++|+++|+.|+++++.+
T Consensus        45 ~~~~N~li~aPTgsGKTlIA~lai~~~l~~~~~k~vYivPlkALa~Ek~~~~~~   98 (766)
T COG1204          45 LSDENVLISAPTGSGKTLIALLAILSTLLEGGGKVVYIVPLKALAEEKYEEFSR   98 (766)
T ss_pred             cCCCcEEEEcCCCCchHHHHHHHHHHHHHhcCCcEEEEeChHHHHHHHHHHhhh
Confidence            457899999999999999999999999988778999999999999999999993

>KOG0330|consensus

Probab=99.53  E-value=4.5e-14  Score=104.89  Aligned_cols=93  Identities=13%  Similarity=0.119  Sum_probs=84.1

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC--CCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~--~~~~~~i~P~~~l~~q~~~  121 (138)
                      +.++..+.+++.++..+.++|.+++|.+.. ++++..+-||+|||..+.+|+++++...  ...+++++|+|+|+.|+.+
T Consensus        68 v~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVLtPtRELA~QI~e  147 (476)
T KOG0330|consen   68 VHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVLTPTRELAQQIAE  147 (476)
T ss_pred             cCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCCCceEEEecCcHHHHHHHHH
Confidence            345778888888899999999999999988 9999999999999999999999999973  3689999999999999999


Q ss_pred             HHHHHhhhcCceeeec
Q psy2029         122 SLAKAAEEFKFYLEVL  137 (138)
Q Consensus       122 ~~~~~~~~~~~~v~~~  137 (138)
                      .|+.++...|++|..+
T Consensus       148 ~fe~Lg~~iglr~~~l  163 (476)
T KOG0330|consen  148 QFEALGSGIGLRVAVL  163 (476)
T ss_pred             HHHHhccccCeEEEEE
Confidence            9999999999987653

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

Probab=99.53  E-value=5.6e-14  Score=115.19  Aligned_cols=89  Identities=20%  Similarity=0.256  Sum_probs=80.3

Q ss_pred             HHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHHHHHHHHHHHHh
Q psy2029          50 YQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAA  127 (138)
Q Consensus        50 ~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~~q~~~~~~~~~  127 (138)
                      ...+.+.+...++++|.++...+++ +|+++++|||||||.++++|+++++.. ...+++|+.||+||+++|.+.|+++.
T Consensus        60 ~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a~AL~lYPtnALa~DQ~~rl~~~~  139 (851)
T COG1205          60 KSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTNALANDQAERLRELI  139 (851)
T ss_pred             HHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcCccEEEEechhhhHhhHHHHHHHHH
Confidence            6677777777799999999999998 999999999999999999999999987 45689999999999999999999999


Q ss_pred             hhcC--ceeeecC
Q psy2029         128 EEFK--FYLEVLE  138 (138)
Q Consensus       128 ~~~~--~~v~~~~  138 (138)
                      ..++  +.+..||
T Consensus       140 ~~~~~~v~~~~y~  152 (851)
T COG1205         140 SDLPGKVTFGRYT  152 (851)
T ss_pred             HhCCCcceeeeec
Confidence            9997  7777665

>PTZ00110 helicase; Provisional

Probab=99.52  E-value=5.2e-14  Score=111.08  Aligned_cols=90  Identities=13%  Similarity=0.059  Sum_probs=78.6

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC-------CCeEEEEccchhHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK-------QKSAIFILPYISLV  116 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~-------~~~~~~i~P~~~l~  116 (138)
                      |.+.+.+.+.+.++..++++|.+++|.+.. +++++.+|||+|||++++++++..+...       ++.+++++|+++|+
T Consensus       137 l~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp~~LIL~PTreLa  216 (545)
T PTZ00110        137 FPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTRELA  216 (545)
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCcEEEEECChHHHH
Confidence            456677888888888999999999998888 9999999999999999999999887642       45799999999999


Q ss_pred             HHHHHHHHHHhhhcCcee
Q psy2029         117 HEKYQSLAKAAEEFKFYL  134 (138)
Q Consensus       117 ~q~~~~~~~~~~~~~~~v  134 (138)
                      .|+.+.++++....++++
T Consensus       217 ~Qi~~~~~~~~~~~~i~~  234 (545)
T PTZ00110        217 EQIREQCNKFGASSKIRN  234 (545)
T ss_pred             HHHHHHHHHHhcccCccE
Confidence            999999999987766654

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

Probab=99.51  E-value=6.1e-14  Score=113.43  Aligned_cols=111  Identities=17%  Similarity=0.255  Sum_probs=81.6

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhhcC-------CeEEEEcchhhhHHHHHHHHHHHHHhhhhhhhhHHH----
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKIKQ-------KSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCL----   69 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~-------~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~----   69 (138)
                      |.+|+|+++.||||||||++|.+|++..+.+.+       -.++|+.|++||.+++.+++..++...+.+++...+    
T Consensus        34 i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkALn~Di~~rL~~~~~~~G~~v~vRhGDT~~  113 (814)
T COG1201          34 IHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKALNNDIRRRLEEPLRELGIEVAVRHGDTPQ  113 (814)
T ss_pred             HhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHHHHHHHHHHHHHHHHcCCccceecCCCCh
Confidence            468999999999999999999999999887752       378999999999999999999999888888765555    


Q ss_pred             ----hhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHH
Q psy2029          70 ----EMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLV  116 (138)
Q Consensus        70 ----~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~  116 (138)
                          .+..+ .++++++|    -|+..++.- ..+.+  .+-+.++|.=-.+|+
T Consensus       114 ~er~r~~~~PPdILiTTP----EsL~lll~~-~~~r~~l~~vr~VIVDEiHel~  162 (814)
T COG1201         114 SEKQKMLKNPPHILITTP----ESLAILLNS-PKFRELLRDVRYVIVDEIHALA  162 (814)
T ss_pred             HHhhhccCCCCcEEEeCh----hHHHHHhcC-HHHHHHhcCCcEEEeehhhhhh
Confidence                23344 78899999    344433222 11111  234555555555554

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.51  E-value=8.7e-14  Score=107.78  Aligned_cols=91  Identities=16%  Similarity=0.187  Sum_probs=78.2

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC--CCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~--~~~~~~i~P~~~l~~q~~~  121 (138)
                      |.....+.+.+.++..++++|.++++.+.+ +++++.+|||+|||+++.+++++.+...  ..++++++|+++|+.|+++
T Consensus        11 l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~PtreLa~Q~~~   90 (460)
T PRK11776         11 LPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRELADQVAK   90 (460)
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCHHHHHHHHH
Confidence            456777888888888999999999998888 9999999999999999999999988652  3579999999999999999


Q ss_pred             HHHHHhhhc-Cceee
Q psy2029         122 SLAKAAEEF-KFYLE  135 (138)
Q Consensus       122 ~~~~~~~~~-~~~v~  135 (138)
                      +++.++... ++++.
T Consensus        91 ~~~~~~~~~~~~~v~  105 (460)
T PRK11776         91 EIRRLARFIPNIKVL  105 (460)
T ss_pred             HHHHHHhhCCCcEEE
Confidence            999887654 45543

>PTZ00424 helicase 45; Provisional

Probab=99.49  E-value=1.4e-13  Score=104.69  Aligned_cols=90  Identities=12%  Similarity=0.105  Sum_probs=78.0

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~  121 (138)
                      |.+...+.+.+.++..+.++|.++++.+.+ ++.++.+|||+|||+++.+++++.+..  .+.+++|++|+++|+.|..+
T Consensus        35 l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~Pt~~L~~Q~~~  114 (401)
T PTZ00424         35 LNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTRELAQQIQK  114 (401)
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECCCHHHHHHHHH
Confidence            556778888888888899999999988888 999999999999999999999987754  35689999999999999999


Q ss_pred             HHHHHhhhcCcee
Q psy2029         122 SLAKAAEEFKFYL  134 (138)
Q Consensus       122 ~~~~~~~~~~~~v  134 (138)
                      .+..++...++.+
T Consensus       115 ~~~~~~~~~~~~~  127 (401)
T PTZ00424        115 VVLALGDYLKVRC  127 (401)
T ss_pred             HHHHHhhhcCceE
Confidence            9998876655543

>cd00268 DEADc DEAD-box helicases

Probab=99.49  E-value=2.2e-13  Score=94.60  Aligned_cols=91  Identities=15%  Similarity=0.141  Sum_probs=78.1

Q ss_pred             HHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC----CCeEEEEccchhHHHHHH
Q psy2029          46 VHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK----QKSAIFILPYISLVHEKY  120 (138)
Q Consensus        46 ~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~----~~~~~~i~P~~~l~~q~~  120 (138)
                      ...+.+.+.+.+...++++|.++.+.+.+ +++++.+|||+|||+++.+++++.+...    +.+++|++|+++|+.|..
T Consensus         7 ~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~L~~q~~   86 (203)
T cd00268           7 SPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQIA   86 (203)
T ss_pred             CHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHHHHHHHH
Confidence            35667788877777899999999988777 9999999999999999999999888763    468999999999999999


Q ss_pred             HHHHHHhhhcCceeee
Q psy2029         121 QSLAKAAEEFKFYLEV  136 (138)
Q Consensus       121 ~~~~~~~~~~~~~v~~  136 (138)
                      +.++++....++.+..
T Consensus        87 ~~~~~~~~~~~~~~~~  102 (203)
T cd00268          87 EVARKLGKHTNLKVVV  102 (203)
T ss_pred             HHHHHHhccCCceEEE
Confidence            9999998766666554

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.

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.48  E-value=1.9e-13  Score=109.34  Aligned_cols=91  Identities=14%  Similarity=0.203  Sum_probs=79.5

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~  121 (138)
                      |...+.+.+.+.++..++++|.++++.+.+ +++++.+|||+|||+++.+++++.+..  ...+++|++|+++|+.|+++
T Consensus        13 L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PTreLa~Qv~~   92 (629)
T PRK11634         13 LKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRELAVQVAE   92 (629)
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCcHHHHHHHHH
Confidence            567788888888999999999999998888 999999999999999999999988765  34689999999999999999


Q ss_pred             HHHHHhhhc-Cceee
Q psy2029         122 SLAKAAEEF-KFYLE  135 (138)
Q Consensus       122 ~~~~~~~~~-~~~v~  135 (138)
                      .+.++.... ++.+.
T Consensus        93 ~l~~~~~~~~~i~v~  107 (629)
T PRK11634         93 AMTDFSKHMRGVNVV  107 (629)
T ss_pred             HHHHHHhhcCCceEE
Confidence            999987665 55543

>PRK01172 ski2-like helicase; Provisional

Probab=99.46  E-value=2.4e-13  Score=109.69  Aligned_cols=89  Identities=24%  Similarity=0.392  Sum_probs=73.2

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSL  123 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~  123 (138)
                      |.++..+.+.+.++. ++++|.++++.+.+ +|+++++|||+|||+++++++++.+.. +.+++|++|+++|+.|+++++
T Consensus         8 l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~-~~k~v~i~P~raLa~q~~~~~   85 (674)
T PRK01172          8 YDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLA-GLKSIYIVPLRSLAMEKYEEL   85 (674)
T ss_pred             CCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHh-CCcEEEEechHHHHHHHHHHH
Confidence            445666666665554 89999999988877 999999999999999999999887765 678999999999999999999


Q ss_pred             HHHhhhcCceeee
Q psy2029         124 AKAAEEFKFYLEV  136 (138)
Q Consensus       124 ~~~~~~~~~~v~~  136 (138)
                      +++ ...|.+|..
T Consensus        86 ~~l-~~~g~~v~~   97 (674)
T PRK01172         86 SRL-RSLGMRVKI   97 (674)
T ss_pred             HHH-hhcCCeEEE
Confidence            985 345666543

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

Probab=99.44  E-value=4.8e-13  Score=108.30  Aligned_cols=87  Identities=17%  Similarity=0.182  Sum_probs=75.8

Q ss_pred             HHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCC-------CeEEEEccchhHHHHH
Q psy2029          48 EKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQ-------KSAIFILPYISLVHEK  119 (138)
Q Consensus        48 q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~-------~~~~~i~P~~~l~~q~  119 (138)
                      ...+.|.+. +..+.+.|..++|.+.+ +|+++.+|||+|||+.|.++++.++...+       -.++||.|++||.+++
T Consensus        11 ~v~~~~~~~-~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkALn~Di   89 (814)
T COG1201          11 RVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKALNNDI   89 (814)
T ss_pred             HHHHHHHHh-cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHHHHHH
Confidence            334444444 67799999999999999 99999999999999999999999998741       3699999999999999


Q ss_pred             HHHHHHHhhhcCceee
Q psy2029         120 YQSLAKAAEEFKFYLE  135 (138)
Q Consensus       120 ~~~~~~~~~~~~~~v~  135 (138)
                      .+.+..++..+|+.|.
T Consensus        90 ~~rL~~~~~~~G~~v~  105 (814)
T COG1201          90 RRRLEEPLRELGIEVA  105 (814)
T ss_pred             HHHHHHHHHHcCCccc
Confidence            9999999999998873

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

Probab=99.43  E-value=5.4e-13  Score=104.65  Aligned_cols=91  Identities=18%  Similarity=0.186  Sum_probs=80.6

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCC-e-EEEEccchhHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQK-S-AIFILPYISLVHEK  119 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~-~-~~~i~P~~~l~~q~  119 (138)
                      |.....+.+.+.++..+.++|..++|.+.. ++++..++||+|||+++.+|+++.+..  ... . +++++||++|+.|+
T Consensus        36 l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aLil~PTRELA~Qi  115 (513)
T COG0513          36 LSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAVQI  115 (513)
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccccCCCceEEECCCHHHHHHH
Confidence            567888999999999999999999999988 999999999999999999999999873  222 2 99999999999999


Q ss_pred             HHHHHHHhhhc-Cceee
Q psy2029         120 YQSLAKAAEEF-KFYLE  135 (138)
Q Consensus       120 ~~~~~~~~~~~-~~~v~  135 (138)
                      ++.++++.... ++++.
T Consensus       116 ~~~~~~~~~~~~~~~~~  132 (513)
T COG0513         116 AEELRKLGKNLGGLRVA  132 (513)
T ss_pred             HHHHHHHHhhcCCccEE
Confidence            99999999987 56643

>KOG0952|consensus

Probab=99.40  E-value=1.1e-12  Score=106.88  Aligned_cols=56  Identities=27%  Similarity=0.488  Sum_probs=49.0

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh---------cCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI---------KQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~---------~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ..+|++||||||||||.+|++++++.+.+         .+-|++|++|++||+.++++.+.+...
T Consensus       125 SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~~~~kkl~  189 (1230)
T KOG0952|consen  125 SNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDKFSKKLA  189 (1230)
T ss_pred             CCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHHHHhhhcc
Confidence            46799999999999999999999998775         345999999999999999998777644

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

Probab=99.38  E-value=9.5e-13  Score=102.25  Aligned_cols=82  Identities=21%  Similarity=0.360  Sum_probs=74.7

Q ss_pred             HHHHHHhhhhhhhhHHH-hhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhc
Q psy2029          53 LAKAAEEFKFYLEGKCL-EMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEF  130 (138)
Q Consensus        53 l~~~~~~~~~~~Q~~~~-~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~  130 (138)
                      +...|...+.|+|..+. ..+.+ +|.++.++|++|||++++++-+.++...++|.+|++|+.||++|++++|++...++
T Consensus       209 lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~~g~KmlfLvPLVALANQKy~dF~~rYs~L  288 (830)
T COG1202         209 LKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSGGKKMLFLVPLVALANQKYEDFKERYSKL  288 (830)
T ss_pred             HHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHhCCCeEEEEehhHHhhcchHHHHHHHhhcc
Confidence            33346788999999998 66777 99999999999999999999999999989999999999999999999999999999


Q ss_pred             Ccee
Q psy2029         131 KFYL  134 (138)
Q Consensus       131 ~~~v  134 (138)
                      |+.+
T Consensus       289 glkv  292 (830)
T COG1202         289 GLKV  292 (830)
T ss_pred             cceE
Confidence            8876

>KOG0348|consensus

Probab=99.37  E-value=2.1e-12  Score=99.43  Aligned_cols=88  Identities=17%  Similarity=0.278  Sum_probs=75.6

Q ss_pred             HHHHHHHHHH-HHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--------CCCeEEEEccchhHH
Q psy2029          47 HEKYQSLAKA-AEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--------KQKSAIFILPYISLV  116 (138)
Q Consensus        47 ~q~~~~l~~~-~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--------~~~~~~~i~P~~~l~  116 (138)
                      ......++.. ..+.+..+|.+++|.+.+ ++.++.++||+|||+++.+|+.+.+..        .+.-+++|+|||+|+
T Consensus       145 ~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~ALVivPTREL~  224 (708)
T KOG0348|consen  145 PHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYALVIVPTRELA  224 (708)
T ss_pred             HHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccccccCCceEEEEechHHHH
Confidence            3445556554 566789999999999998 999999999999999999999999976        245799999999999


Q ss_pred             HHHHHHHHHHhhhcCcee
Q psy2029         117 HEKYQSLAKAAEEFKFYL  134 (138)
Q Consensus       117 ~q~~~~~~~~~~~~~~~v  134 (138)
                      .|.++.++++..++.|-|
T Consensus       225 ~Q~y~~~qKLl~~~hWIV  242 (708)
T KOG0348|consen  225 LQIYETVQKLLKPFHWIV  242 (708)
T ss_pred             HHHHHHHHHHhcCceEEe
Confidence            999999999998876654

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

Probab=99.37  E-value=4.5e-12  Score=85.29  Aligned_cols=75  Identities=24%  Similarity=0.353  Sum_probs=64.3

Q ss_pred             hhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC-CCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          62 FYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK-QKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        62 ~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~-~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      .++|.++++.+.+ +++++.+|||+|||.++.++++..+.+. ..++++++|+++|++|.++++++++...+.++..
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~   77 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEGKDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVL   77 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTTSSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEE
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccCCCceEEEEeeccccccccccccccccccccccccc
Confidence            3689999977766 9999999999999999999999888774 3599999999999999999999998875555443

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 ....

>KOG0350|consensus

Probab=99.37  E-value=1.6e-12  Score=99.32  Aligned_cols=86  Identities=23%  Similarity=0.278  Sum_probs=72.4

Q ss_pred             HHHHHHHHhhhhhhhhHHHhhh---------hc-cceEEEeecCCCchHhHHHHHHHHHHhC---CCeEEEEccchhHHH
Q psy2029          51 QSLAKAAEEFKFYLEGKCLEMI---------QN-KNCVLSIPTSGGKTLVGEILIMKELKIK---QKSAIFILPYISLVH  117 (138)
Q Consensus        51 ~~l~~~~~~~~~~~Q~~~~~~~---------~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~---~~~~~~i~P~~~l~~  117 (138)
                      +.+.+.+.+.++|+|..++|-+         .. +++.+.+|||+|||+++.+|+++.+.++   .-|+++|+|++.|+.
T Consensus       150 q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v~~LRavVivPtr~L~~  229 (620)
T KOG0350|consen  150 QLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTRELAL  229 (620)
T ss_pred             HHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHHHccCCccceEEEEEeeHHHHHH
Confidence            3455566778999998887322         23 7889999999999999999999988763   358999999999999


Q ss_pred             HHHHHHHHHhhhcCceeee
Q psy2029         118 EKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus       118 q~~~~~~~~~~~~~~~v~~  136 (138)
                      |++..|.++..+.|+.|..
T Consensus       230 QV~~~f~~~~~~tgL~V~~  248 (620)
T KOG0350|consen  230 QVYDTFKRLNSGTGLAVCS  248 (620)
T ss_pred             HHHHHHHHhccCCceEEEe
Confidence            9999999999999988754

>KOG0345|consensus

Probab=99.35  E-value=5.1e-12  Score=95.98  Aligned_cols=85  Identities=18%  Similarity=0.168  Sum_probs=75.7

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC-----CC--eEEEEccchhHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK-----QK--SAIFILPYISLV  116 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~-----~~--~~~~i~P~~~l~  116 (138)
                      |..++...+.+.|+...+|+|..++|.+.. +++++.+|||+|||+++++|+++-+..+     +.  -+++|+|||+|+
T Consensus        13 L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalIIsPTRELa   92 (567)
T KOG0345|consen   13 LSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALIISPTRELA   92 (567)
T ss_pred             ccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEEEecCcHHHH
Confidence            557888999999999999999999999988 9999999999999999999999988441     22  589999999999


Q ss_pred             HHHHHHHHHHhhh
Q psy2029         117 HEKYQSLAKAAEE  129 (138)
Q Consensus       117 ~q~~~~~~~~~~~  129 (138)
                      .|+.+....+.+.
T Consensus        93 ~QI~~V~~~F~~~  105 (567)
T KOG0345|consen   93 RQIREVAQPFLEH  105 (567)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999888777

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.35  E-value=1.3e-12  Score=100.26  Aligned_cols=59  Identities=17%  Similarity=0.126  Sum_probs=50.9

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhh---------cCCeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKI---------KQKSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~---------~~~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      +++|+|++++||||||||++|.++++..+..         .+.++++++|+++|+.|+++.+..+...
T Consensus        42 il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~lil~PtreLa~Qi~~~~~~l~~~  109 (423)
T PRK04837         42 TLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQA  109 (423)
T ss_pred             HhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEEEECCcHHHHHHHHHHHHHHhcc
Confidence            3789999999999999999999999987754         1357999999999999999988877543

>KOG0338|consensus

Probab=99.35  E-value=1.8e-12  Score=99.39  Aligned_cols=91  Identities=12%  Similarity=0.090  Sum_probs=79.4

Q ss_pred             hhHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC-----CCeEEEEccchhHHH
Q psy2029          44 SLVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK-----QKSAIFILPYISLVH  117 (138)
Q Consensus        44 aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~-----~~~~~~i~P~~~l~~  117 (138)
                      .|..++++.+...|+..+.|+|..++|...- +++..++-||+|||.++.+|++++++.+     ..|+++++||++|+.
T Consensus       187 NLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~PTRELai  266 (691)
T KOG0338|consen  187 NLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKKVAATRVLVLVPTRELAI  266 (691)
T ss_pred             ccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCcccCcceeEEEEeccHHHHH
Confidence            3556778888888888999999999997777 9999999999999999999999999873     248999999999999


Q ss_pred             HHHHHHHHHhhhcCcee
Q psy2029         118 EKYQSLAKAAEEFKFYL  134 (138)
Q Consensus       118 q~~~~~~~~~~~~~~~v  134 (138)
                      |.+...++++...++.|
T Consensus       267 Qv~sV~~qlaqFt~I~~  283 (691)
T KOG0338|consen  267 QVHSVTKQLAQFTDITV  283 (691)
T ss_pred             HHHHHHHHHHhhcccee
Confidence            99999999987765443

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.34  E-value=3.4e-12  Score=105.49  Aligned_cols=75  Identities=23%  Similarity=0.284  Sum_probs=62.6

Q ss_pred             HHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--------CCCeEEEEccchhHHHHHHH
Q psy2029          51 QSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--------KQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        51 ~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--------~~~~~~~i~P~~~l~~q~~~  121 (138)
                      +++.+.++..++++|.++++.+.+ +|+++++|||+|||+++.+++++.+..        .+.+++|++|++||++|+++
T Consensus        23 ~~~~~~~~~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtraLa~di~~  102 (876)
T PRK13767         23 REWFKEKFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRALNNDIHR  102 (876)
T ss_pred             HHHHHHccCCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHHHHHHHHHH
Confidence            333333456699999999988887 999999999999999999999998864        13469999999999999998


Q ss_pred             HHHH
Q psy2029         122 SLAK  125 (138)
Q Consensus       122 ~~~~  125 (138)
                      .+.+
T Consensus       103 ~L~~  106 (876)
T PRK13767        103 NLEE  106 (876)
T ss_pred             HHHH
Confidence            7664

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

Probab=99.33  E-value=2e-12  Score=105.18  Aligned_cols=56  Identities=16%  Similarity=0.359  Sum_probs=51.3

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|+|+++++|||||||++|.+|+++.+.+ .+.+++|++|+++|.+|+++.+.+++
T Consensus        49 l~G~nvvv~apTGSGKTla~~LPiL~~l~~~~~~~aL~l~PtraLa~q~~~~l~~l~  105 (742)
T TIGR03817        49 HAGRHVVVATGTASGKSLAYQLPVLSALADDPRATALYLAPTKALAADQLRAVRELT  105 (742)
T ss_pred             HCCCCEEEECCCCCcHHHHHHHHHHHHHhhCCCcEEEEEcChHHHHHHHHHHHHHhc
Confidence            689999999999999999999999998866 45699999999999999999999875

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=99.33  E-value=2.3e-12  Score=102.27  Aligned_cols=60  Identities=18%  Similarity=0.216  Sum_probs=52.0

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhhc---------CCeEEEEcchhhhHHHHHHHHHHHHHhh
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKIK---------QKSAIFILPYISLVHEKYQSLAKAAEEF   60 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~---------~~~~l~v~P~~aL~~q~~~~l~~~~~~~   60 (138)
                      +++|+|++++||||||||++|+++++.++..+         ..+++|++|+++|+.|+++.+..++...
T Consensus        43 ~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raLIl~PTreLa~Qi~~~~~~l~~~~  111 (572)
T PRK04537         43 ALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADL  111 (572)
T ss_pred             HhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEEEEeCcHHHHHHHHHHHHHHhccC
Confidence            47899999999999999999999999877541         3589999999999999999998876543

>KOG0331|consensus

Probab=99.32  E-value=3.7e-12  Score=98.60  Aligned_cols=89  Identities=15%  Similarity=0.122  Sum_probs=78.4

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC--------CCeEEEEccchhH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK--------QKSAIFILPYISL  115 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~--------~~~~~~i~P~~~l  115 (138)
                      |..+....+...++..++++|++.+|.+.+ ++++..+-||+|||+.+++|++.++...        ++++++++|||+|
T Consensus        98 ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~PTREL  177 (519)
T KOG0331|consen   98 LSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPTREL  177 (519)
T ss_pred             ccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEEcCcHHH
Confidence            344556666777888999999999999998 9999999999999999999999999862        5689999999999


Q ss_pred             HHHHHHHHHHHhhhcCce
Q psy2029         116 VHEKYQSLAKAAEEFKFY  133 (138)
Q Consensus       116 ~~q~~~~~~~~~~~~~~~  133 (138)
                      +.|+.+++.++...++++
T Consensus       178 A~QV~~~~~~~~~~~~~~  195 (519)
T KOG0331|consen  178 AVQVQAEAREFGKSLRLR  195 (519)
T ss_pred             HHHHHHHHHHHcCCCCcc
Confidence            999999999999888754

>KOG0340|consensus

Probab=99.31  E-value=5.3e-12  Score=93.10  Aligned_cols=89  Identities=16%  Similarity=0.183  Sum_probs=80.0

Q ss_pred             HHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHHHHH
Q psy2029          48 EKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLA  124 (138)
Q Consensus        48 q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~~~~  124 (138)
                      =..+.+...+.+.+.|+|..|+|.+.+ ++++-++-||+|||..+.+++++++.+  .+.-++++.||++|+.|++++|.
T Consensus        17 Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTPTrELA~QiaEQF~   96 (442)
T KOG0340|consen   17 WLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTPTRELALQIAEQFI   96 (442)
T ss_pred             HHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCCCcceEEEecchHHHHHHHHHHHH
Confidence            345667777888999999999999999 999999999999999999999999987  35689999999999999999999


Q ss_pred             HHhhhcCceeee
Q psy2029         125 KAAEEFKFYLEV  136 (138)
Q Consensus       125 ~~~~~~~~~v~~  136 (138)
                      ..++..++++..
T Consensus        97 alGk~l~lK~~v  108 (442)
T KOG0340|consen   97 ALGKLLNLKVSV  108 (442)
T ss_pred             HhcccccceEEE
Confidence            999998887654

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.30  E-value=3.3e-12  Score=99.43  Aligned_cols=57  Identities=23%  Similarity=0.226  Sum_probs=50.6

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhc---------CCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIK---------QKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~---------~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|+++++|||||||++|.++++..+.+.         +.+++|++|+++|+.|+++.+..+..
T Consensus       122 ~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~aLil~PtreLa~Q~~~~~~~l~~  187 (475)
T PRK01297        122 LAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAAALTK  187 (475)
T ss_pred             hCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceEEEEeCcHHHHHHHHHHHHHhhc
Confidence            6899999999999999999999999887653         35899999999999999999888753

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.30  E-value=4.2e-12  Score=98.40  Aligned_cols=58  Identities=16%  Similarity=0.227  Sum_probs=50.2

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhhc--------CCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKIK--------QKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~--------~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      +++|+|++++||||||||++|.++++..+...        ..++++++|+++|+.|+.+.+..+..
T Consensus        35 il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil~PtreLa~Qi~~~~~~~~~  100 (456)
T PRK10590         35 VLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSK  100 (456)
T ss_pred             HhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEEeCcHHHHHHHHHHHHHHhc
Confidence            36899999999999999999999999887542        13799999999999999999988754

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.29  E-value=7.7e-11  Score=97.59  Aligned_cols=55  Identities=27%  Similarity=0.425  Sum_probs=47.9

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh--------cCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI--------KQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--------~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ++|+|++++||||||||++|.+++++++..        ++.+++|++|+++|.+|+++++...
T Consensus        45 l~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtraLa~di~~~L~~~  107 (876)
T PRK13767         45 HEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRALNNDIHRNLEEP  107 (876)
T ss_pred             HcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHHHHHHHHHHHHHHH
Confidence            679999999999999999999999988764        1347999999999999999887654

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.29  E-value=4.6e-12  Score=97.49  Aligned_cols=58  Identities=17%  Similarity=0.184  Sum_probs=50.8

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh------cCCeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI------KQKSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~------~~~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      ++|+|++++||||+|||++|++++++++.+      ...++++++|+++|+.|.++.+..++..
T Consensus        36 ~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~Pt~eLa~Q~~~~~~~l~~~   99 (434)
T PRK11192         36 LDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELAMQVADQARELAKH   99 (434)
T ss_pred             hCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEECCcHHHHHHHHHHHHHHHcc
Confidence            578999999999999999999999998764      1358999999999999999998887543

>PTZ00110 helicase; Provisional

Probab=99.29  E-value=5.1e-12  Score=99.84  Aligned_cols=58  Identities=14%  Similarity=0.150  Sum_probs=50.7

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhh-------cCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKI-------KQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-------~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      +++|+|++++||||||||++|.+|++.++..       .+..+++++|+++|+.|+.+++..++.
T Consensus       164 ~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp~~LIL~PTreLa~Qi~~~~~~~~~  228 (545)
T PTZ00110        164 ALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGA  228 (545)
T ss_pred             HhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCcEEEEECChHHHHHHHHHHHHHHhc
Confidence            3689999999999999999999999987754       245789999999999999999988754

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

Probab=99.29  E-value=3.7e-12  Score=100.15  Aligned_cols=57  Identities=16%  Similarity=0.151  Sum_probs=49.4

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh---------cCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI---------KQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~---------~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|++++||||||||++|+++++.++.+         .+.++++++|+++|+.|+.+.+..++.
T Consensus       156 l~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~~~aLIL~PTreLa~Qi~~~~~~l~~  221 (518)
T PLN00206        156 LSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGK  221 (518)
T ss_pred             hcCCCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCCceEEEEeCCHHHHHHHHHHHHHHhC
Confidence            689999999999999999999999987653         345899999999999999888877643

>PRK02362 ski2-like helicase; Provisional

Probab=99.29  E-value=6.1e-12  Score=102.50  Aligned_cols=54  Identities=31%  Similarity=0.649  Sum_probs=49.8

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ++|+|++++||||||||++|++++++++. ++++++|++|+++|++|+++.+.++
T Consensus        37 ~~g~nvlv~APTGSGKTlia~lail~~l~-~~~kal~i~P~raLa~q~~~~~~~~   90 (737)
T PRK02362         37 LDGKNLLAAIPTASGKTLIAELAMLKAIA-RGGKALYIVPLRALASEKFEEFERF   90 (737)
T ss_pred             hCCCcEEEECCCcchHHHHHHHHHHHHHh-cCCcEEEEeChHHHHHHHHHHHHHh
Confidence            57899999999999999999999998875 5889999999999999999999876

>PRK00254 ski2-like helicase; Provisional

Probab=99.28  E-value=8.4e-12  Score=101.49  Aligned_cols=55  Identities=38%  Similarity=0.661  Sum_probs=50.8

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ++|+|++++||||||||++|++++++++.+.+++++|++|+++|++|+++.+.++
T Consensus        37 ~~g~nvlv~apTGsGKT~~~~l~il~~l~~~~~~~l~l~P~~aLa~q~~~~~~~~   91 (720)
T PRK00254         37 LEGKNLVLAIPTASGKTLVAEIVMVNKLLREGGKAVYLVPLKALAEEKYREFKDW   91 (720)
T ss_pred             hCCCcEEEECCCCcHHHHHHHHHHHHHHHhcCCeEEEEeChHHHHHHHHHHHHHH
Confidence            5789999999999999999999999988777889999999999999999988764

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.28  E-value=2.3e-11  Score=98.33  Aligned_cols=89  Identities=18%  Similarity=0.200  Sum_probs=72.2

Q ss_pred             HHHHHHHHHHHhhhhhhhhHHHhhhhc-------cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHH
Q psy2029          48 EKYQSLAKAAEEFKFYLEGKCLEMIQN-------KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKY  120 (138)
Q Consensus        48 q~~~~l~~~~~~~~~~~Q~~~~~~~~~-------~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~  120 (138)
                      ...+++.+.....+++.|..+++.+.+       .+.++.+|||+|||+++.++++..+. .+.++++++|+++|+.|.+
T Consensus       249 ~~~~~~~~~l~f~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~-~g~q~lilaPT~~LA~Q~~  327 (681)
T PRK10917        249 ELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIE-AGYQAALMAPTEILAEQHY  327 (681)
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHH-cCCeEEEEeccHHHHHHHH
Confidence            334444444344588999999965543       37899999999999999999988765 4789999999999999999


Q ss_pred             HHHHHHhhhcCceeeec
Q psy2029         121 QSLAKAAEEFKFYLEVL  137 (138)
Q Consensus       121 ~~~~~~~~~~~~~v~~~  137 (138)
                      +.+++++.++|+++..+
T Consensus       328 ~~l~~l~~~~~i~v~ll  344 (681)
T PRK10917        328 ENLKKLLEPLGIRVALL  344 (681)
T ss_pred             HHHHHHHhhcCcEEEEE
Confidence            99999999988887654

>PRK09401 reverse gyrase; Reviewed

Probab=99.27  E-value=4.4e-11  Score=101.07  Aligned_cols=86  Identities=23%  Similarity=0.268  Sum_probs=69.0

Q ss_pred             HHHHHHHHHHHh----hhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHH
Q psy2029          48 EKYQSLAKAAEE----FKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQS  122 (138)
Q Consensus        48 q~~~~l~~~~~~----~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~  122 (138)
                      +.++++++++..    .++++|..+++.+.. +++++.+|||+|||..++. +...+...+.++++++||++|+.|+++.
T Consensus        64 ~~~~~~~~~f~~~~G~~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~f~l~-~~~~l~~~g~~alIL~PTreLa~Qi~~~  142 (1176)
T PRK09401         64 EEYKEFEKFFKKKTGSKPWSLQRTWAKRLLLGESFAIIAPTGVGKTTFGLV-MSLYLAKKGKKSYIIFPTRLLVEQVVEK  142 (1176)
T ss_pred             HHHHHHHHHHHHhcCCCCcHHHHHHHHHHHCCCcEEEEcCCCCCHHHHHHH-HHHHHHhcCCeEEEEeccHHHHHHHHHH
Confidence            455666655432    479999999988887 9999999999999976544 4444555678999999999999999999


Q ss_pred             HHHHhhhcCcee
Q psy2029         123 LAKAAEEFKFYL  134 (138)
Q Consensus       123 ~~~~~~~~~~~v  134 (138)
                      +++++...++.+
T Consensus       143 l~~l~~~~~~~~  154 (1176)
T PRK09401        143 LEKFGEKVGCGV  154 (1176)
T ss_pred             HHHHhhhcCceE
Confidence            999998877664

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.27  E-value=2.2e-11  Score=94.39  Aligned_cols=58  Identities=19%  Similarity=0.330  Sum_probs=50.3

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhhc--CCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~--~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      +++|+|++++||||||||++|.++++.++...  ..++++++|+++|+.|..+++..++.
T Consensus        38 ~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~   97 (460)
T PRK11776         38 ILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRELADQVAKEIRRLAR   97 (460)
T ss_pred             HhcCCCEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCHHHHHHHHHHHHHHHh
Confidence            36899999999999999999999999887542  34799999999999999999888753

>KOG0330|consensus

Probab=99.26  E-value=2.2e-11  Score=90.80  Aligned_cols=82  Identities=12%  Similarity=0.148  Sum_probs=67.3

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhc--CCeEEEEcchhhhHHHHHHHHHHHHHhhhhh---------hhhHHHh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQSLAKAAEEFKFY---------LEGKCLE   70 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~--~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~---------~Q~~~~~   70 (138)
                      +.|+++|..|.||||||.+|.+|++++|+++  ...+++++|+++|..|+.+.++..+...+..         .+.+..+
T Consensus        96 L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVLtPtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~~~  175 (476)
T KOG0330|consen   96 LGGRDVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVLTPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQ  175 (476)
T ss_pred             hCCCcEEEEeccCCCchhhhHHHHHHHHHcCCCCceEEEecCcHHHHHHHHHHHHHhccccCeEEEEEecCchHHHHHHH
Confidence            7899999999999999999999999999884  3489999999999999999999987665444         4444444


Q ss_pred             hhhccceEEEeec
Q psy2029          71 MIQNKNCVLSIPT   83 (138)
Q Consensus        71 ~~~~~~~ii~~pt   83 (138)
                      ..++.++++.+|.
T Consensus       176 L~kkPhilVaTPG  188 (476)
T KOG0330|consen  176 LSKKPHILVATPG  188 (476)
T ss_pred             hhcCCCEEEeCcH
Confidence            4445888888884

>TIGR01054 rgy reverse gyrase

Probab=99.25  E-value=5e-11  Score=100.81  Aligned_cols=86  Identities=20%  Similarity=0.203  Sum_probs=69.6

Q ss_pred             HHHHHHHHHHH----hhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHH
Q psy2029          48 EKYQSLAKAAE----EFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQS  122 (138)
Q Consensus        48 q~~~~l~~~~~----~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~  122 (138)
                      +.++++.+++.    ..++++|..+++.+.. +++++.+|||+|||..+ +++...+...+.++++++||++|+.|+++.
T Consensus        62 ~~~~~f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~f~-l~~~~~l~~~g~~vLIL~PTreLa~Qi~~~  140 (1171)
T TIGR01054        62 EELKEFEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTTFG-LAMSLFLAKKGKRCYIILPTTLLVIQVAEK  140 (1171)
T ss_pred             HHHHHHHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHHHH-HHHHHHHHhcCCeEEEEeCHHHHHHHHHHH
Confidence            35556666543    2589999999988887 99999999999999855 555555555678999999999999999999


Q ss_pred             HHHHhhhcCcee
Q psy2029         123 LAKAAEEFKFYL  134 (138)
Q Consensus       123 ~~~~~~~~~~~v  134 (138)
                      +++++...|+.+
T Consensus       141 l~~l~~~~~i~~  152 (1171)
T TIGR01054       141 ISSLAEKAGVGT  152 (1171)
T ss_pred             HHHHHHhcCCce
Confidence            999998777653

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.

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

Probab=99.25  E-value=1.1e-11  Score=101.89  Aligned_cols=60  Identities=20%  Similarity=0.287  Sum_probs=53.9

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHHHHHhhh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAAEEFK   61 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~   61 (138)
                      .+|+|++|+.|||||||.+|++|++.+++. ...++||+.|++||.+++.++++++....+
T Consensus        83 ~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a~AL~lYPtnALa~DQ~~rl~~~~~~~~  143 (851)
T COG1205          83 REGRNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTNALANDQAERLRELISDLP  143 (851)
T ss_pred             HCCCCEEEECCCCCchhHHHHHHHHHHHhhCcCccEEEEechhhhHhhHHHHHHHHHHhCC
Confidence            578999999999999999999999999887 455889999999999999999999866544

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

Probab=99.25  E-value=2e-11  Score=82.10  Aligned_cols=58  Identities=26%  Similarity=0.429  Sum_probs=51.0

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhc-CCeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIK-QKSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~-~~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      .+|+|+++++|||+|||+++..+++..+.+. ..++++++|+++|.+|..+++.+++..
T Consensus        12 ~~~~~~li~aptGsGKT~~~~~~~l~~~~~~~~~~~lii~P~~~l~~q~~~~~~~~~~~   70 (169)
T PF00270_consen   12 ISGKNVLISAPTGSGKTLAYILPALNRLQEGKDARVLIIVPTRALAEQQFERLRKFFSN   70 (169)
T ss_dssp             HTTSEEEEECSTTSSHHHHHHHHHHHHHHTTSSSEEEEEESSHHHHHHHHHHHHHHTTT
T ss_pred             HcCCCEEEECCCCCccHHHHHHHHHhhhccCCCceEEEEeecccccccccccccccccc
Confidence            3688999999999999999999999877664 349999999999999999999888653

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 ....

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.24  E-value=4.9e-11  Score=98.80  Aligned_cols=88  Identities=17%  Similarity=0.137  Sum_probs=71.9

Q ss_pred             HHHHHHHHHHHhhhhhhhhHHHhhhhc-------cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHH
Q psy2029          48 EKYQSLAKAAEEFKFYLEGKCLEMIQN-------KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKY  120 (138)
Q Consensus        48 q~~~~l~~~~~~~~~~~Q~~~~~~~~~-------~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~  120 (138)
                      +..+.+.+.+...+++.|..+++.+.+       .+.++++|||+|||.++++++++.+.. +.++++++||++|+.|.+
T Consensus       439 ~~~~~~~~~~~f~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~-g~qvlvLvPT~~LA~Q~~  517 (926)
T TIGR00580       439 EWQQEFEDSFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLD-GKQVAVLVPTTLLAQQHF  517 (926)
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHh-CCeEEEEeCcHHHHHHHH
Confidence            445556554333588999999965543       578999999999999999999887764 689999999999999999


Q ss_pred             HHHHHHhhhcCceeee
Q psy2029         121 QSLAKAAEEFKFYLEV  136 (138)
Q Consensus       121 ~~~~~~~~~~~~~v~~  136 (138)
                      +.|++++.+.++++..
T Consensus       518 ~~f~~~~~~~~i~v~~  533 (926)
T TIGR00580       518 ETFKERFANFPVTIEL  533 (926)
T ss_pred             HHHHHHhccCCcEEEE
Confidence            9999999888877654

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.

>PTZ00424 helicase 45; Provisional

Probab=99.23  E-value=4.1e-11  Score=91.17  Aligned_cols=57  Identities=12%  Similarity=0.158  Sum_probs=49.4

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|++++||||||||++|.++++..+..  ++.++++++|+++|+.|..+.+...+.
T Consensus        63 ~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~  121 (401)
T PTZ00424         63 LDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTRELAQQIQKVVLALGD  121 (401)
T ss_pred             hCCCCEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECCCHHHHHHHHHHHHHHhh
Confidence            678999999999999999999999987643  456899999999999999888877653

>KOG0951|consensus

Probab=99.23  E-value=3.8e-11  Score=99.71  Aligned_cols=81  Identities=25%  Similarity=0.308  Sum_probs=70.2

Q ss_pred             HhhhhhhhhHHHhhhhc--cceEEEeecCCCchHhHHHHHHHHHHhCC----------CeEEEEccchhHHHHHHHHHHH
Q psy2029          58 EEFKFYLEGKCLEMIQN--KNCVLSIPTSGGKTLVGEILIMKELKIKQ----------KSAIFILPYISLVHEKYQSLAK  125 (138)
Q Consensus        58 ~~~~~~~Q~~~~~~~~~--~~~ii~~ptg~GKt~~~~~~~l~~~~~~~----------~~~~~i~P~~~l~~q~~~~~~~  125 (138)
                      ...+.++|.........  .|+++|+|||+|||.+|++.+++++..+.          .+++|++|++||+.++...|.+
T Consensus       307 ~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKaLvqE~VgsfSk  386 (1674)
T KOG0951|consen  307 KQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKALVQEMVGSFSK  386 (1674)
T ss_pred             chhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeHHHHHHHHHHHHHh
Confidence            34477888877754443  99999999999999999999999998742          2899999999999999999999


Q ss_pred             HhhhcCceeeecC
Q psy2029         126 AAEEFKFYLEVLE  138 (138)
Q Consensus       126 ~~~~~~~~v~~~~  138 (138)
                      +..++|+.|.+.+
T Consensus       387 Rla~~GI~V~ElT  399 (1674)
T KOG0951|consen  387 RLAPLGITVLELT  399 (1674)
T ss_pred             hccccCcEEEEec
Confidence            9999999998863

>KOG0348|consensus

Probab=99.23  E-value=1.6e-11  Score=94.71  Aligned_cols=58  Identities=22%  Similarity=0.391  Sum_probs=51.4

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhh--------cCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKI--------KQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--------~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      +|+|+|++|.++||||||++|.+|+.+++..        .|.-+++++||++|+.|+|+.+.+.-.
T Consensus       171 lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~ALVivPTREL~~Q~y~~~qKLl~  236 (708)
T KOG0348|consen  171 LLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYALVIVPTRELALQIYETVQKLLK  236 (708)
T ss_pred             hhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccccccCCceEEEEechHHHHHHHHHHHHHHhc
Confidence            4789999999999999999999999998865        255889999999999999999888743

>KOG0354|consensus

Probab=99.22  E-value=1.1e-11  Score=99.09  Aligned_cols=57  Identities=19%  Similarity=0.455  Sum_probs=51.5

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      | |+|+++++|||+|||.+|.+.|.+|+.+ .++|+++.+|++.|+.|+.+.+..++..
T Consensus        75 L-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~~KiVF~aP~~pLv~QQ~a~~~~~~~~  132 (746)
T KOG0354|consen   75 L-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPKGKVVFLAPTRPLVNQQIACFSIYLIP  132 (746)
T ss_pred             h-cCCeEEEeecCCCccchHHHHHHHHHhcCCcceEEEeeCCchHHHHHHHHHhhccCc
Confidence            6 9999999999999999999999999988 5679999999999999998888777643

>KOG0350|consensus

Probab=99.22  E-value=2.3e-11  Score=93.10  Aligned_cols=114  Identities=18%  Similarity=0.271  Sum_probs=82.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhc---CCeEEEEcchhhhHHHHHHHHHHHHHhhhhhh-----hhHHH---hh
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIK---QKSAIFILPYISLVHEKYQSLAKAAEEFKFYL-----EGKCL---EM   71 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~---~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~-----Q~~~~---~~   71 (138)
                      .++++.|.||||||||++|.+|+.+.+..+   .-|+++++|++.|..|.++.|.++....+..+     |...-   .+
T Consensus       182 r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v~~LRavVivPtr~L~~QV~~~f~~~~~~tgL~V~~~sgq~sl~~E~~q  261 (620)
T KOG0350|consen  182 RPRDICVNAPTGSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTRELALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQ  261 (620)
T ss_pred             CCCceEEecCCCCCceeeehhHHHHHHccCCccceEEEEEeeHHHHHHHHHHHHHHhccCCceEEEecccccchHHHHHH
Confidence            367999999999999999999999977664   34899999999999999999999865443222     21111   11


Q ss_pred             h-hc-c----ceEEEeecCCCchHhHHHHHHHHHHh------CCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          72 I-QN-K----NCVLSIPTSGGKTLVGEILIMKELKI------KQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        72 ~-~~-~----~~ii~~ptg~GKt~~~~~~~l~~~~~------~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      + .+ .    ++++++|          -..+.++.+      .+-|.++|.-.--|.+|.++++-..
T Consensus       262 L~~~~~~~~~DIlVaTP----------GRLVDHl~~~k~f~Lk~LrfLVIDEADRll~qsfQ~Wl~~  318 (620)
T KOG0350|consen  262 LASDPPECRIDILVATP----------GRLVDHLNNTKSFDLKHLRFLVIDEADRLLDQSFQEWLDT  318 (620)
T ss_pred             HhcCCCccccceEEcCc----------hHHHHhccCCCCcchhhceEEEechHHHHHHHHHHHHHHH
Confidence            2 22 3    8888888          445556653      2347888888877888877665443

>KOG0343|consensus

Probab=99.22  E-value=2.2e-11  Score=94.26  Aligned_cols=89  Identities=18%  Similarity=0.208  Sum_probs=74.9

Q ss_pred             HHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh------CCCeEEEEccchhHHHHH
Q psy2029          47 HEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI------KQKSAIFILPYISLVHEK  119 (138)
Q Consensus        47 ~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~------~~~~~~~i~P~~~l~~q~  119 (138)
                      ......+.+..+..+..+|.+++|.... ++++-.+-||+|||+++++|+++.+..      .+--+++|.|||+|+.|+
T Consensus        78 ~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGalIISPTRELA~Qt  157 (758)
T KOG0343|consen   78 QKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGALIISPTRELALQT  157 (758)
T ss_pred             hHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCCCCCCceeEEecchHHHHHHH
Confidence            3344455555555678899999988887 999999999999999999999999976      245689999999999999


Q ss_pred             HHHHHHHhhhcCceee
Q psy2029         120 YQSLAKAAEEFKFYLE  135 (138)
Q Consensus       120 ~~~~~~~~~~~~~~v~  135 (138)
                      ++.+.+++..++++.+
T Consensus       158 FevL~kvgk~h~fSaG  173 (758)
T KOG0343|consen  158 FEVLNKVGKHHDFSAG  173 (758)
T ss_pred             HHHHHHHhhccccccc
Confidence            9999999999877654

>KOG0346|consensus

Probab=99.21  E-value=3.2e-11  Score=91.17  Aligned_cols=87  Identities=21%  Similarity=0.271  Sum_probs=75.9

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--------CCCeEEEEccchhH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--------KQKSAIFILPYISL  115 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--------~~~~~~~i~P~~~l  115 (138)
                      |...+.+.+.+.|+..+.-+|..++|.+.+ ++++..+.||+|||.++++|+++.+.+        .+..+++++||++|
T Consensus        26 LD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~iLvPTkEL  105 (569)
T KOG0346|consen   26 LDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVILVPTKEL  105 (569)
T ss_pred             CCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcccccccceeEEEechHHH
Confidence            445566777778888889999999999988 999999999999999999999999976        24579999999999


Q ss_pred             HHHHHHHHHHHhhhcC
Q psy2029         116 VHEKYQSLAKAAEEFK  131 (138)
Q Consensus       116 ~~q~~~~~~~~~~~~~  131 (138)
                      +.|.+..+.++....+
T Consensus       106 ~qQvy~viekL~~~c~  121 (569)
T KOG0346|consen  106 AQQVYKVIEKLVEYCS  121 (569)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            9999999998876653

>KOG0342|consensus

Probab=99.21  E-value=4e-11  Score=91.49  Aligned_cols=90  Identities=14%  Similarity=0.145  Sum_probs=79.3

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh------CCCeEEEEccchhHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI------KQKSAIFILPYISLVH  117 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~------~~~~~~~i~P~~~l~~  117 (138)
                      |.......+.+.++....++|...++.+.. ++++..+-||+|||+++++++++.+..      ++..+++++|||+|+.
T Consensus        89 LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi~PTRELA~  168 (543)
T KOG0342|consen   89 LSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLIICPTRELAM  168 (543)
T ss_pred             cCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCCCCCeeEEEecccHHHHH
Confidence            456778889999999999999999977777 999999999999999999999999876      2457999999999999


Q ss_pred             HHHHHHHHHhhhc-Ccee
Q psy2029         118 EKYQSLAKAAEEF-KFYL  134 (138)
Q Consensus       118 q~~~~~~~~~~~~-~~~v  134 (138)
                      |.+.+.+++...+ ++.|
T Consensus       169 Q~~~eak~Ll~~h~~~~v  186 (543)
T KOG0342|consen  169 QIFAEAKELLKYHESITV  186 (543)
T ss_pred             HHHHHHHHHHhhCCCcce
Confidence            9999999998887 4443

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.20  E-value=7.4e-11  Score=94.74  Aligned_cols=77  Identities=18%  Similarity=0.242  Sum_probs=65.7

Q ss_pred             hhhhhhhHHHhhhhc-------cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCc
Q psy2029          60 FKFYLEGKCLEMIQN-------KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF  132 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~-------~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~  132 (138)
                      .+++.|..+++.+..       .|.++.+|||+|||+++.++++..+. .+.+++|++|+++|+.|.++.+++++.++|+
T Consensus       235 ~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~-~g~qvlilaPT~~LA~Q~~~~~~~l~~~~gi  313 (630)
T TIGR00643       235 KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIE-AGYQVALMAPTEILAEQHYNSLRNLLAPLGI  313 (630)
T ss_pred             CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHH-cCCcEEEECCHHHHHHHHHHHHHHHhcccCc
Confidence            588899999855432       36799999999999999998887665 4789999999999999999999999998888


Q ss_pred             eeeec
Q psy2029         133 YLEVL  137 (138)
Q Consensus       133 ~v~~~  137 (138)
                      ++..+
T Consensus       314 ~v~ll  318 (630)
T TIGR00643       314 EVALL  318 (630)
T ss_pred             EEEEE
Confidence            87643

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

Probab=99.20  E-value=2.2e-11  Score=100.44  Aligned_cols=56  Identities=29%  Similarity=0.430  Sum_probs=50.6

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ..|+++++|||||||||+++++++...+.+ +.+++|+.|++||.+|+++++...+.
T Consensus       132 er~esVlV~ApTssGKTvVaeyAi~~al~~-~qrviYTsPIKALsNQKyrdl~~~fg  187 (1041)
T COG4581         132 ERGESVLVCAPTSSGKTVVAEYAIALALRD-GQRVIYTSPIKALSNQKYRDLLAKFG  187 (1041)
T ss_pred             hCCCcEEEEccCCCCcchHHHHHHHHHHHc-CCceEeccchhhhhhhHHHHHHHHhh
Confidence            468999999999999999999999987765 77799999999999999999888654

>KOG0344|consensus

Probab=99.20  E-value=2.7e-11  Score=93.91  Aligned_cols=88  Identities=18%  Similarity=0.255  Sum_probs=75.7

Q ss_pred             HHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCC-------CeEEEEccchhHHHHH
Q psy2029          48 EKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQ-------KSAIFILPYISLVHEK  119 (138)
Q Consensus        48 q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~-------~~~~~i~P~~~l~~q~  119 (138)
                      +..+++.+.++..+.++|.+++|...+ ++++.++|||+|||+.+.+|+++++....       -+++++.|+++|++|.
T Consensus       146 ~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~~~gl~a~Il~ptreLa~Qi  225 (593)
T KOG0344|consen  146 RLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQEKHKVGLRALILSPTRELAAQI  225 (593)
T ss_pred             HHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhhcccCccceEEEEecchHHHHHHH
Confidence            445667777788899999999998888 99999999999999999999999998633       5899999999999999


Q ss_pred             HHHHHHHh--hhcCceee
Q psy2029         120 YQSLAKAA--EEFKFYLE  135 (138)
Q Consensus       120 ~~~~~~~~--~~~~~~v~  135 (138)
                      +++.+++.  ...+.+++
T Consensus       226 ~re~~k~~~~~~t~~~a~  243 (593)
T KOG0344|consen  226 YREMRKYSIDEGTSLRAA  243 (593)
T ss_pred             HHHHHhcCCCCCCchhhh
Confidence            99999998  55555443

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.19  E-value=4.7e-11  Score=92.94  Aligned_cols=67  Identities=19%  Similarity=0.319  Sum_probs=59.7

Q ss_pred             HHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          56 AAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        56 ~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      ++++.+.++|.++++.+.+ +++++.+|||+|||+++.++++.    .++.+++++|+++|+.|+++.++..
T Consensus         7 ~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~----~~~~~lVi~P~~~L~~dq~~~l~~~   74 (470)
T TIGR00614         7 FGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALC----SDGITLVISPLISLMEDQVLQLKAS   74 (470)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHH----cCCcEEEEecHHHHHHHHHHHHHHc
Confidence            4667789999999988887 99999999999999999999875    3678999999999999999998865

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

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

Probab=99.19  E-value=1e-10  Score=91.93  Aligned_cols=60  Identities=17%  Similarity=0.257  Sum_probs=51.7

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhh--cCC-e-EEEEcchhhhHHHHHHHHHHHHHhh
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQK-S-AIFILPYISLVHEKYQSLAKAAEEF   60 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~-~-~l~v~P~~aL~~q~~~~l~~~~~~~   60 (138)
                      +++|+|++..|+||+|||++|.+|+++++..  ... . +++++||++|+.|+++++..++...
T Consensus        63 ~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aLil~PTRELA~Qi~~~~~~~~~~~  126 (513)
T COG0513          63 ILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNL  126 (513)
T ss_pred             HhCCCCEEEECCCCChHHHHHHHHHHHHHhcccccCCCceEEECCCHHHHHHHHHHHHHHHhhc
Confidence            4789999999999999999999999998762  222 2 8999999999999999999987654

>KOG0343|consensus

Probab=99.19  E-value=4.9e-11  Score=92.44  Aligned_cols=82  Identities=22%  Similarity=0.253  Sum_probs=67.1

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhh------cCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhhhhHHH-----
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKI------KQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCL-----   69 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~------~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~-----   69 (138)
                      .|+|++++-.|.||||||+++++|++++|-.      .|--++++.||++|..|++..+.+.+..+.++..-..+     
T Consensus       103 aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGalIISPTRELA~QtFevL~kvgk~h~fSaGLiiGG~~~k  182 (758)
T KOG0343|consen  103 ALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGALIISPTRELALQTFEVLNKVGKHHDFSAGLIIGGKDVK  182 (758)
T ss_pred             hccCcccccccccCCCceeeehHHHHHHHHHcCCCCCCCceeEEecchHHHHHHHHHHHHHHhhccccccceeecCchhH
Confidence            3789999999999999999999999998755      35588999999999999999999998766555433222     


Q ss_pred             ---hhhhccceEEEee
Q psy2029          70 ---EMIQNKNCVLSIP   82 (138)
Q Consensus        70 ---~~~~~~~~ii~~p   82 (138)
                         ..+.+.|+++|+|
T Consensus       183 ~E~eRi~~mNILVCTP  198 (758)
T KOG0343|consen  183 FELERISQMNILVCTP  198 (758)
T ss_pred             HHHHhhhcCCeEEech
Confidence               2344489999999

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.18  E-value=8.3e-11  Score=94.11  Aligned_cols=80  Identities=20%  Similarity=0.305  Sum_probs=65.2

Q ss_pred             chhhhHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHH
Q psy2029          41 PYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEK  119 (138)
Q Consensus        41 P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~  119 (138)
                      |..++..+..++.  ++++.+.++|.++++.+.+ +++++.+|||+|||+++.++++..    .+.+++++|+++|+.|+
T Consensus         8 ~~~~~~~~~l~~~--fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~----~g~tlVisPl~sL~~dq   81 (607)
T PRK11057          8 NLESLAKQVLQET--FGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL----DGLTLVVSPLISLMKDQ   81 (607)
T ss_pred             CchhHHHHHHHHH--cCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc----CCCEEEEecHHHHHHHH
Confidence            3444444444432  4677788999999988888 999999999999999999998853    56799999999999999


Q ss_pred             HHHHHHH
Q psy2029         120 YQSLAKA  126 (138)
Q Consensus       120 ~~~~~~~  126 (138)
                      .+.++..
T Consensus        82 v~~l~~~   88 (607)
T PRK11057         82 VDQLLAN   88 (607)
T ss_pred             HHHHHHc
Confidence            9998876

>KOG0331|consensus

Probab=99.18  E-value=7e-11  Score=91.62  Aligned_cols=60  Identities=15%  Similarity=0.130  Sum_probs=53.7

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhh--------cCCeEEEEcchhhhHHHHHHHHHHHHHhh
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKI--------KQKSAIFILPYISLVHEKYQSLAKAAEEF   60 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--------~~~~~l~v~P~~aL~~q~~~~l~~~~~~~   60 (138)
                      +++|+|++..|.||||||++|.+|++.++.+        ++.++|+++||++|+.|+.+++.+++...
T Consensus       125 ~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~PTRELA~QV~~~~~~~~~~~  192 (519)
T KOG0331|consen  125 ALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPTRELAVQVQAEAREFGKSL  192 (519)
T ss_pred             eccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEEcCcHHHHHHHHHHHHHHcCCC
Confidence            3789999999999999999999999999875        25589999999999999999999987644

>KOG0346|consensus

Probab=99.17  E-value=1.7e-10  Score=87.32  Aligned_cols=82  Identities=23%  Similarity=0.316  Sum_probs=63.5

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhh--------cCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhhhhHHH---
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKI--------KQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCL---   69 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--------~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~---   69 (138)
                      +|+|+|++..|.||||||.+|++|+++.+++        .+..+++++|+++|+.|.|..++.....+...++..-+   
T Consensus        53 aLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~iLvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~  132 (569)
T KOG0346|consen   53 ALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVILVPTKELAQQVYKVIEKLVEYCSKDLRAINLASS  132 (569)
T ss_pred             hhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcccccccceeEEEechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcc
Confidence            4799999999999999999999999998876        24488999999999999999988875554433322211   


Q ss_pred             -------hhhhc-cceEEEee
Q psy2029          70 -------EMIQN-KNCVLSIP   82 (138)
Q Consensus        70 -------~~~~~-~~~ii~~p   82 (138)
                             ..+.+ .++++.+|
T Consensus       133 ~sdsv~~~~L~d~pdIvV~TP  153 (569)
T KOG0346|consen  133 MSDSVNSVALMDLPDIVVATP  153 (569)
T ss_pred             cchHHHHHHHccCCCeEEeCh
Confidence                   23345 78888888

>PRK01172 ski2-like helicase; Provisional

Probab=99.17  E-value=5e-11  Score=96.37  Aligned_cols=54  Identities=33%  Similarity=0.564  Sum_probs=48.6

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .+|+|++++||||||||++++.++++++.+ +++++|++|+++|++|+++++.++
T Consensus        35 ~~~~nvlv~apTGSGKTl~a~lail~~l~~-~~k~v~i~P~raLa~q~~~~~~~l   88 (674)
T PRK01172         35 RKGENVIVSVPTAAGKTLIAYSAIYETFLA-GLKSIYIVPLRSLAMEKYEELSRL   88 (674)
T ss_pred             hcCCcEEEECCCCchHHHHHHHHHHHHHHh-CCcEEEEechHHHHHHHHHHHHHH
Confidence            468899999999999999999999987654 789999999999999999998764

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.16  E-value=1.3e-10  Score=93.12  Aligned_cols=57  Identities=14%  Similarity=0.225  Sum_probs=49.5

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|++++||||+|||++|.++++..+..  ...++++++|+++|+.|..+.+.++..
T Consensus        41 l~g~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PTreLa~Qv~~~l~~~~~   99 (629)
T PRK11634         41 LNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRELAVQVAEAMTDFSK   99 (629)
T ss_pred             HcCCCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCcHHHHHHHHHHHHHHHh
Confidence            678999999999999999999999877644  345899999999999999999888743

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.15  E-value=3.4e-10  Score=90.65  Aligned_cols=52  Identities=25%  Similarity=0.532  Sum_probs=45.9

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|+|+++++|||+|||++|.++++.    .++.+++++|+++|..|+.+.+...+
T Consensus        38 l~g~dvlv~apTGsGKTl~y~lpal~----~~g~tlVisPl~sL~~dqv~~l~~~g   89 (607)
T PRK11057         38 LSGRDCLVVMPTGGGKSLCYQIPALV----LDGLTLVVSPLISLMKDQVDQLLANG   89 (607)
T ss_pred             HcCCCEEEEcCCCchHHHHHHHHHHH----cCCCEEEEecHHHHHHHHHHHHHHcC
Confidence            68899999999999999999999875    35789999999999999988887653

>KOG0335|consensus

Probab=99.15  E-value=5.1e-11  Score=91.30  Aligned_cols=90  Identities=17%  Similarity=0.108  Sum_probs=75.8

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC------------CCeEEEEcc
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK------------QKSAIFILP  111 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~------------~~~~~~i~P  111 (138)
                      |.+....++...+...+.|+|..++|.+.+ ++.+++++||+|||..+++|++.++...            .+++++++|
T Consensus        81 l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~lIlap  160 (482)
T KOG0335|consen   81 LGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRALILAP  160 (482)
T ss_pred             hhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccCCCCCCceEEEeC
Confidence            334444555555667799999999999998 9999999999999999999999999862            268999999


Q ss_pred             chhHHHHHHHHHHHHhhhcCcee
Q psy2029         112 YISLVHEKYQSLAKAAEEFKFYL  134 (138)
Q Consensus       112 ~~~l~~q~~~~~~~~~~~~~~~v  134 (138)
                      |++|+.|.+++.+++.-..++++
T Consensus       161 TReL~~Qi~nea~k~~~~s~~~~  183 (482)
T KOG0335|consen  161 TRELVDQIYNEARKFSYLSGMKS  183 (482)
T ss_pred             cHHHhhHHHHHHHhhccccccee
Confidence            99999999999999977666554

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.15  E-value=2.3e-10  Score=89.06  Aligned_cols=52  Identities=25%  Similarity=0.514  Sum_probs=46.0

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|+|+++++|||+|||++|.+|++.    .++.+++++|+++|..|+++.+...+
T Consensus        24 l~g~dvlv~apTGsGKTl~y~lp~l~----~~~~~lVi~P~~~L~~dq~~~l~~~g   75 (470)
T TIGR00614        24 LLGRDCFVVMPTGGGKSLCYQLPALC----SDGITLVISPLISLMEDQVLQLKASG   75 (470)
T ss_pred             HcCCCEEEEcCCCCcHhHHHHHHHHH----cCCcEEEEecHHHHHHHHHHHHHHcC
Confidence            67899999999999999999999875    36789999999999999988887654

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

>cd00268 DEADc DEAD-box helicases

Probab=99.15  E-value=1.5e-10  Score=80.32  Aligned_cols=57  Identities=19%  Similarity=0.216  Sum_probs=49.6

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhc----CCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIK----QKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~----~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      .+|+|+++++|||+|||+++.++++..+...    +.++++++|+++|..|..+.++++..
T Consensus        34 ~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~L~~q~~~~~~~~~~   94 (203)
T cd00268          34 LSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQIAEVARKLGK   94 (203)
T ss_pred             hcCCcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHHHHHHHHHHHHHHhc
Confidence            4689999999999999999999988877653    45899999999999999998888743

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.

>PRK14701 reverse gyrase; Provisional

Probab=99.14  E-value=3.2e-10  Score=98.19  Aligned_cols=72  Identities=21%  Similarity=0.285  Sum_probs=61.3

Q ss_pred             hhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCc
Q psy2029          60 FKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF  132 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~  132 (138)
                      .+++.|..+++.+.. +++++.+|||+|||+++.++.+.. ...+.++++++|+++|+.|+++.+++++...++
T Consensus        79 ~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~-~~~g~~aLVl~PTreLa~Qi~~~l~~l~~~~~~  151 (1638)
T PRK14701         79 EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFL-ALKGKKCYIILPTTLLVKQTVEKIESFCEKANL  151 (1638)
T ss_pred             CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHH-HhcCCeEEEEECHHHHHHHHHHHHHHHHhhcCC
Confidence            589999999988888 999999999999999766655543 234678999999999999999999999877643

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.13  E-value=4.7e-10  Score=89.56  Aligned_cols=52  Identities=25%  Similarity=0.487  Sum_probs=46.1

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|+|++++||||+|||++|.++++.    +++.+++++|+++|..|+.+.+...+
T Consensus        26 l~g~dvlv~~PTG~GKTl~y~lpal~----~~g~~lVisPl~sL~~dq~~~l~~~g   77 (591)
T TIGR01389        26 LDGRDVLVVMPTGGGKSLCYQVPALL----LKGLTVVISPLISLMKDQVDQLRAAG   77 (591)
T ss_pred             HcCCCEEEEcCCCccHhHHHHHHHHH----cCCcEEEEcCCHHHHHHHHHHHHHcC
Confidence            68999999999999999999998874    36788999999999999999887764

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.

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.12  E-value=1.5e-10  Score=92.32  Aligned_cols=67  Identities=19%  Similarity=0.292  Sum_probs=60.0

Q ss_pred             HHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          56 AAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        56 ~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      ++++.+.+.|.++++.+.+ +++++.+|||+|||+++.++++.    .++.++|++|+++|+.|+++.+++.
T Consensus         9 fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~----~~g~~lVisPl~sL~~dq~~~l~~~   76 (591)
T TIGR01389         9 FGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALL----LKGLTVVISPLISLMKDQVDQLRAA   76 (591)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHH----cCCcEEEEcCCHHHHHHHHHHHHHc
Confidence            4677788999999988888 99999999999999999999875    3567899999999999999999876

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.

>KOG0347|consensus

Probab=99.11  E-value=6.4e-11  Score=91.69  Aligned_cols=92  Identities=22%  Similarity=0.189  Sum_probs=79.6

Q ss_pred             HHHHHHHHHHHHHhhhhhhhhHHHhhh-hc-cceEEEeecCCCchHhHHHHHHHHHHh-------------CCCe--EEE
Q psy2029          46 VHEKYQSLAKAAEEFKFYLEGKCLEMI-QN-KNCVLSIPTSGGKTLVGEILIMKELKI-------------KQKS--AIF  108 (138)
Q Consensus        46 ~~q~~~~l~~~~~~~~~~~Q~~~~~~~-~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~-------------~~~~--~~~  108 (138)
                      ..++++.+...+++.+.++|...+|.+ ++ .+++-.+.||+|||+++-+|++.++.+             ...+  +++
T Consensus       189 p~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~~~k~~k~~~LV  268 (731)
T KOG0347|consen  189 PMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELSNTSAKYVKPIALV  268 (731)
T ss_pred             CHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhhhhHHhccCcceeEE
Confidence            368889999999999999999999655 55 889999999999999999999996543             2334  899


Q ss_pred             EccchhHHHHHHHHHHHHhhhcCceeeec
Q psy2029         109 ILPYISLVHEKYQSLAKAAEEFKFYLEVL  137 (138)
Q Consensus       109 i~P~~~l~~q~~~~~~~~~~~~~~~v~~~  137 (138)
                      ++|||+||.|+.+.+..++...++++..+
T Consensus       269 ~tPTRELa~QV~~Hl~ai~~~t~i~v~si  297 (731)
T KOG0347|consen  269 VTPTRELAHQVKQHLKAIAEKTQIRVASI  297 (731)
T ss_pred             ecChHHHHHHHHHHHHHhccccCeEEEEe
Confidence            99999999999999999999999987643

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.11  E-value=3.5e-10  Score=85.26  Aligned_cols=63  Identities=19%  Similarity=0.308  Sum_probs=53.1

Q ss_pred             hhhHHHhhhhc-c--ceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhc
Q psy2029          64 LEGKCLEMIQN-K--NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEF  130 (138)
Q Consensus        64 ~Q~~~~~~~~~-~--~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~  130 (138)
                      +|.++++.+.+ .  ++++++|||+|||.++.++++.    .+.+++|++|+++|++|+++.+++++...
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~----~~~~~~~~~P~~aL~~~~~~~~~~~~~~~   66 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLH----GENDTIALYPTNALIEDQTEAIKEFVDVF   66 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHH----cCCCEEEEeChHHHHHHHHHHHHHHHHhc
Confidence            47778877766 3  4688999999999999998885    35688999999999999999999998543

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.

>KOG0345|consensus

Probab=99.07  E-value=7.7e-10  Score=84.35  Aligned_cols=58  Identities=22%  Similarity=0.259  Sum_probs=49.4

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhc-----CC--eEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIK-----QK--SAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~-----~~--~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      ++++|+++-+|||||||++|.+|+++-+.++     .+  -++++.|+++|+.|+.+....+..+
T Consensus        41 l~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalIIsPTRELa~QI~~V~~~F~~~  105 (567)
T KOG0345|consen   41 LKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALIISPTRELARQIREVAQPFLEH  105 (567)
T ss_pred             hcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEEEecCcHHHHHHHHHHHHHHHHh
Confidence            6789999999999999999999999866332     22  5799999999999999998888655

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.07  E-value=4.3e-10  Score=84.48  Aligned_cols=51  Identities=24%  Similarity=0.322  Sum_probs=45.1

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +++++||||||||.++..+++..+.+ .+.+++|+.|+++|.+|+++.+.+.
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~~~~~ii~v~P~~~L~~q~~~~l~~~   52 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQKADRVIIALPTRATINAMYRRAKEL   52 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhCCCCeEEEEeehHHHHHHHHHHHHHH
Confidence            47999999999999999999977544 4579999999999999999988886

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.

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

Probab=99.07  E-value=1.6e-09  Score=90.58  Aligned_cols=51  Identities=24%  Similarity=0.432  Sum_probs=44.9

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ++|+|++++||||+|||++|.+|++.    .++.++++.|+++|..++...+...
T Consensus       473 L~GrDVLVimPTGSGKSLcYQLPAL~----~~GiTLVISPLiSLmqDQV~~L~~~  523 (1195)
T PLN03137        473 MSGYDVFVLMPTGGGKSLTYQLPALI----CPGITLVISPLVSLIQDQIMNLLQA  523 (1195)
T ss_pred             HcCCCEEEEcCCCccHHHHHHHHHHH----cCCcEEEEeCHHHHHHHHHHHHHhC
Confidence            68999999999999999999999885    3678999999999998877776654

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.06  E-value=8.5e-10  Score=93.28  Aligned_cols=88  Identities=14%  Similarity=0.184  Sum_probs=70.0

Q ss_pred             HHHHHHHHHHHhhhhhhhhHHHhhhhc-------cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHH
Q psy2029          48 EKYQSLAKAAEEFKFYLEGKCLEMIQN-------KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKY  120 (138)
Q Consensus        48 q~~~~l~~~~~~~~~~~Q~~~~~~~~~-------~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~  120 (138)
                      ..++++...+...+.+.|.++++.+.+       .+.++++|||+|||.+++.+++..+. .+.++++++|+++|+.|.+
T Consensus       588 ~~~~~~~~~~~~~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~-~g~qvlvLvPT~eLA~Q~~  666 (1147)
T PRK10689        588 EQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE-NHKQVAVLVPTTLLAQQHY  666 (1147)
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHH-cCCeEEEEeCcHHHHHHHH
Confidence            344555555444688999999965442       68899999999999999887776544 5789999999999999999


Q ss_pred             HHHHHHhhhcCceeee
Q psy2029         121 QSLAKAAEEFKFYLEV  136 (138)
Q Consensus       121 ~~~~~~~~~~~~~v~~  136 (138)
                      +.|++.+...++++..
T Consensus       667 ~~f~~~~~~~~v~i~~  682 (1147)
T PRK10689        667 DNFRDRFANWPVRIEM  682 (1147)
T ss_pred             HHHHHhhccCCceEEE
Confidence            9999988877766543

>KOG0333|consensus

Probab=99.06  E-value=3.9e-10  Score=86.99  Aligned_cols=92  Identities=13%  Similarity=0.063  Sum_probs=80.5

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh-----------CCCeEEEEccc
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI-----------KQKSAIFILPY  112 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~-----------~~~~~~~i~P~  112 (138)
                      +..+.++.+.+.+...+.|+|.+++|...+ ++.+..+-||||||+.+.++++..+.+           .++.+++++||
T Consensus       252 ~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~~~~en~~~gpyaiilapt  331 (673)
T KOG0333|consen  252 FPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNIEGPYAIILAPT  331 (673)
T ss_pred             CCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccCCccccchhhHHHHHHcCCCcchhhhcccCceeeeechH
Confidence            456777777777888899999999986666 999999999999999999999888765           36789999999


Q ss_pred             hhHHHHHHHHHHHHhhhcCceeee
Q psy2029         113 ISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus       113 ~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      ++|+.|+.++-.+++.++|+++..
T Consensus       332 ReLaqqIeeEt~kf~~~lg~r~vs  355 (673)
T KOG0333|consen  332 RELAQQIEEETNKFGKPLGIRTVS  355 (673)
T ss_pred             HHHHHHHHHHHHHhcccccceEEE
Confidence            999999999999999999988754

>KOG0948|consensus

Probab=99.06  E-value=2.4e-10  Score=91.24  Aligned_cols=56  Identities=29%  Similarity=0.434  Sum_probs=50.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      .++.+++|+|.|++|||++|++++...|++ +.|++|..|.++|.+|+|+++.+-+.
T Consensus       142 dr~eSVLVSAHTSAGKTVVAeYAIA~sLr~-kQRVIYTSPIKALSNQKYREl~~EF~  197 (1041)
T KOG0948|consen  142 DRGESVLVSAHTSAGKTVVAEYAIAMSLRE-KQRVIYTSPIKALSNQKYRELLEEFK  197 (1041)
T ss_pred             cCCceEEEEeecCCCcchHHHHHHHHHHHh-cCeEEeeChhhhhcchhHHHHHHHhc
Confidence            467899999999999999999999998775 78999999999999999999887644

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

Probab=99.05  E-value=5.3e-10  Score=85.87  Aligned_cols=52  Identities=27%  Similarity=0.421  Sum_probs=48.7

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +|+++++|||-|||.+|...+.+.+.+.+++++++.|++.|+.|..+.+.+.
T Consensus        30 ~NtLvvlPTGLGKT~IA~~V~~~~l~~~~~kvlfLAPTKPLV~Qh~~~~~~v   81 (542)
T COG1111          30 KNTLVVLPTGLGKTFIAAMVIANRLRWFGGKVLFLAPTKPLVLQHAEFCRKV   81 (542)
T ss_pred             cCeEEEecCCccHHHHHHHHHHHHHHhcCCeEEEecCCchHHHHHHHHHHHH
Confidence            5999999999999999999999999887779999999999999999998886

>PRK09401 reverse gyrase; Reviewed

Probab=99.04  E-value=7.7e-10  Score=93.74  Aligned_cols=58  Identities=28%  Similarity=0.328  Sum_probs=47.8

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEF   60 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~   60 (138)
                      ++|+|++++||||+|||.++. ++...+..++.++++++|+++|+.|+++.+..++...
T Consensus        93 l~g~dv~i~ApTGsGKT~f~l-~~~~~l~~~g~~alIL~PTreLa~Qi~~~l~~l~~~~  150 (1176)
T PRK09401         93 LLGESFAIIAPTGVGKTTFGL-VMSLYLAKKGKKSYIIFPTRLLVEQVVEKLEKFGEKV  150 (1176)
T ss_pred             HCCCcEEEEcCCCCCHHHHHH-HHHHHHHhcCCeEEEEeccHHHHHHHHHHHHHHhhhc
Confidence            689999999999999997554 3333344467899999999999999999999987643

>KOG0334|consensus

Probab=99.03  E-value=6.9e-10  Score=90.87  Aligned_cols=91  Identities=16%  Similarity=0.180  Sum_probs=80.4

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh-------CCCeEEEEccchhHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI-------KQKSAIFILPYISLV  116 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~-------~~~~~~~i~P~~~l~  116 (138)
                      +...+...+++.+...+.++|.+++|.+.. +++|..+-||+|||+.+.+|+++....       .++-+++++|+++|+
T Consensus       372 l~~~il~tlkkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi~li~aPtrela  451 (997)
T KOG0334|consen  372 LSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILAPTRELA  451 (997)
T ss_pred             chHHHHHHHHHhcCCCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCChhhCCCceEEEEcCCHHHH
Confidence            445677788777788899999999999999 999999999999999999999977764       255789999999999


Q ss_pred             HHHHHHHHHHhhhcCceee
Q psy2029         117 HEKYQSLAKAAEEFKFYLE  135 (138)
Q Consensus       117 ~q~~~~~~~~~~~~~~~v~  135 (138)
                      .|++++++++...+|+++.
T Consensus       452 ~QI~r~~~kf~k~l~ir~v  470 (997)
T KOG0334|consen  452 MQIHREVRKFLKLLGIRVV  470 (997)
T ss_pred             HHHHHHHHHHHhhcCceEE
Confidence            9999999999999888764

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

Probab=99.02  E-value=7.4e-10  Score=91.66  Aligned_cols=69  Identities=23%  Similarity=0.406  Sum_probs=61.4

Q ss_pred             hhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhc
Q psy2029          61 KFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEF  130 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~  130 (138)
                      +.++|.+++..+-. +++++++|||+|||+++++++...+. ++.+++|..|.+||.+|++++|...+.++
T Consensus       120 LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~-~~qrviYTsPIKALsNQKyrdl~~~fgdv  189 (1041)
T COG4581         120 LDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALR-DGQRVIYTSPIKALSNQKYRDLLAKFGDV  189 (1041)
T ss_pred             cCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHH-cCCceEeccchhhhhhhHHHHHHHHhhhh
Confidence            56789999987777 99999999999999999998876555 46779999999999999999999998866

>KOG0950|consensus

Probab=99.00  E-value=9.1e-10  Score=89.62  Aligned_cols=83  Identities=35%  Similarity=0.596  Sum_probs=77.1

Q ss_pred             HHHHhhhhhhhhHHH--hhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcC
Q psy2029          55 KAAEEFKFYLEGKCL--EMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFK  131 (138)
Q Consensus        55 ~~~~~~~~~~Q~~~~--~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~  131 (138)
                      ..+....+.||++|.  +.+.+ +|+++.+||+.|||+++++.+++++....+.++.++|+.+.+.+....+...+.++|
T Consensus       218 ~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~rr~~llilp~vsiv~Ek~~~l~~~~~~~G  297 (1008)
T KOG0950|consen  218 DKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCRRRNVLLILPYVSIVQEKISALSPFSIDLG  297 (1008)
T ss_pred             hhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHHhhceeEecceeehhHHHHhhhhhhccccC
Confidence            346677899999999  77778 999999999999999999999999998889999999999999999999999999999


Q ss_pred             ceeeec
Q psy2029         132 FYLEVL  137 (138)
Q Consensus       132 ~~v~~~  137 (138)
                      +.|.+|
T Consensus       298 ~~ve~y  303 (1008)
T KOG0950|consen  298 FPVEEY  303 (1008)
T ss_pred             Ccchhh
Confidence            999887

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.00  E-value=6.1e-09  Score=83.40  Aligned_cols=75  Identities=12%  Similarity=0.005  Sum_probs=67.3

Q ss_pred             hhhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          60 FKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      .++++|..+++.+...+ +..+.||+|||+++.++++..+.. +..+++++|++.|+.|.++.+..++..+|++|..
T Consensus       103 ~p~~VQ~~~~~~ll~G~-Iae~~TGeGKTla~~lp~~~~al~-G~~v~VvTptreLA~qdae~~~~l~~~lGlsv~~  177 (656)
T PRK12898        103 RHFDVQLMGGLALLSGR-LAEMQTGEGKTLTATLPAGTAALA-GLPVHVITVNDYLAERDAELMRPLYEALGLTVGC  177 (656)
T ss_pred             CCChHHHHHHHHHhCCC-eeeeeCCCCcHHHHHHHHHHHhhc-CCeEEEEcCcHHHHHHHHHHHHHHHhhcCCEEEE
Confidence            47899999998888744 999999999999999999987664 7889999999999999999999999999998864

>KOG0342|consensus

Probab=99.00  E-value=5.4e-10  Score=85.40  Aligned_cols=83  Identities=14%  Similarity=0.181  Sum_probs=62.4

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhh------cCCeEEEEcchhhhHHHHHHHHHHHHHhh-hhhhhhHHH----
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKI------KQKSAIFILPYISLVHEKYQSLAKAAEEF-KFYLEGKCL----   69 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~------~~~~~l~v~P~~aL~~q~~~~l~~~~~~~-~~~~Q~~~~----   69 (138)
                      ++.|+|+++.|.||+|||++|++|+++.+..      .+..+++++|+++|..|++.+..+....+ ...+|...+    
T Consensus       116 ll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~  195 (543)
T KOG0342|consen  116 LLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLIICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNF  195 (543)
T ss_pred             cCCCccceeeeccCCCceeeehhHHHHHHHhcccCCCCCeeEEEecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccc
Confidence            4789999999999999999999999998766      23488999999999999999998875443 222222221    


Q ss_pred             ----hhhhc-cceEEEeec
Q psy2029          70 ----EMIQN-KNCVLSIPT   83 (138)
Q Consensus        70 ----~~~~~-~~~ii~~pt   83 (138)
                          ..+.. -|+++.+|.
T Consensus       196 ~~e~~kl~k~~niliATPG  214 (543)
T KOG0342|consen  196 SVEADKLVKGCNILIATPG  214 (543)
T ss_pred             hHHHHHhhccccEEEeCCc
Confidence                22233 677788874

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

Probab=98.99  E-value=3.1e-10  Score=88.53  Aligned_cols=64  Identities=23%  Similarity=0.497  Sum_probs=56.9

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhh
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYL   64 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~   64 (138)
                      +++|+|.+|..+|+||||++++++=+..+++.++|.+|++|+.+|.+|++++|.+...+.+..+
T Consensus       229 LLeG~nllVVSaTasGKTLIgElAGi~~~l~~g~KmlfLvPLVALANQKy~dF~~rYs~Lglkv  292 (830)
T COG1202         229 LLEGENLLVVSATASGKTLIGELAGIPRLLSGGKKMLFLVPLVALANQKYEDFKERYSKLGLKV  292 (830)
T ss_pred             cccCCceEEEeccCCCcchHHHhhCcHHHHhCCCeEEEEehhHHhhcchHHHHHHHhhcccceE
Confidence            4789999999999999999999998888888899999999999999999999998766555443

>PHA02558 uvsW UvsW helicase; Provisional

Probab=98.99  E-value=1.7e-09  Score=84.92  Aligned_cols=69  Identities=20%  Similarity=0.231  Sum_probs=55.6

Q ss_pred             hhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhh
Q psy2029          60 FKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE  128 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~  128 (138)
                      .+.++|.++++...+ .+.++.+|||+|||+++...+...+...+.++++++|+++|++|..++++++..
T Consensus       114 ~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~~~~~~~~~~~vLilvpt~eL~~Q~~~~l~~~~~  183 (501)
T PHA02558        114 EPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLSRYYLENYEGKVLIIVPTTSLVTQMIDDFVDYRL  183 (501)
T ss_pred             CCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHHHHHHhcCCCeEEEEECcHHHHHHHHHHHHHhcc
Confidence            578899999976666 889999999999999886543322333345999999999999999999998763

>KOG0335|consensus

Probab=98.99  E-value=9.4e-10  Score=84.44  Aligned_cols=57  Identities=23%  Similarity=0.237  Sum_probs=50.8

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhhc------------CCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKIK------------QKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~------------~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +.+|++.+.|||||||||.+|++|++.+++++            ..+++++.||++|+.|++++-+++.
T Consensus       108 i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~lIlapTReL~~Qi~nea~k~~  176 (482)
T KOG0335|consen  108 ISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRALILAPTRELVDQIYNEARKFS  176 (482)
T ss_pred             eecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccCCCCCCceEEEeCcHHHhhHHHHHHHhhc
Confidence            35789999999999999999999999988773            2588999999999999999998874

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=98.99  E-value=2.3e-09  Score=88.01  Aligned_cols=74  Identities=15%  Similarity=0.101  Sum_probs=66.1

Q ss_pred             hhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          62 FYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        62 ~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      .|+|.++++.+.. ++.+..++||+|||+++.+|++..+.. +..+++++|+++||.|.++.+..++..+|+++..
T Consensus        94 tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~-g~~v~IVTpTrELA~Qdae~m~~L~k~lGLsV~~  168 (970)
T PRK12899         94 VPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALT-GKPVHLVTVNDYLAQRDCEWVGSVLRWLGLTTGV  168 (970)
T ss_pred             ChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhh-cCCeEEEeCCHHHHHHHHHHHHHHHhhcCCeEEE
Confidence            7889999988777 899999999999999999999988875 4458899999999999999999999988888754

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

Probab=98.99  E-value=1.1e-09  Score=91.49  Aligned_cols=67  Identities=18%  Similarity=0.254  Sum_probs=58.5

Q ss_pred             HHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          56 AAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        56 ~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      +|.+.+.+.|.++++.+.. +++++.+|||+|||+++.+|++..    .+.+|+|+|+++|+.|+...+...
T Consensus       456 FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~----~GiTLVISPLiSLmqDQV~~L~~~  523 (1195)
T PLN03137        456 FGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC----PGITLVISPLVSLIQDQIMNLLQA  523 (1195)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc----CCcEEEEeCHHHHHHHHHHHHHhC
Confidence            3566789999999988888 999999999999999999999863    568999999999999888777654

>TIGR01054 rgy reverse gyrase

Probab=98.98  E-value=1.9e-09  Score=91.41  Aligned_cols=57  Identities=28%  Similarity=0.349  Sum_probs=47.6

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      ++|+|++++||||+|||..+ +++...+...+.++++++|+++|+.|.++.+..++..
T Consensus        91 l~G~d~vi~ApTGsGKT~f~-l~~~~~l~~~g~~vLIL~PTreLa~Qi~~~l~~l~~~  147 (1171)
T TIGR01054        91 LRGDSFAIIAPTGVGKTTFG-LAMSLFLAKKGKRCYIILPTTLLVIQVAEKISSLAEK  147 (1171)
T ss_pred             hCCCeEEEECCCCCCHHHHH-HHHHHHHHhcCCeEEEEeCHHHHHHHHHHHHHHHHHh
Confidence            68999999999999999854 4554445556789999999999999999999988653

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.

>KOG0344|consensus

Probab=98.94  E-value=1.2e-09  Score=84.88  Aligned_cols=59  Identities=24%  Similarity=0.392  Sum_probs=52.6

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhhcC-------CeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKIKQ-------KSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~-------~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      ++++++++.|||||+|||+++.+|++.++....       -+++++.|+++|..|+++++.++..+
T Consensus       170 fl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~~~gl~a~Il~ptreLa~Qi~re~~k~~~~  235 (593)
T KOG0344|consen  170 FLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQEKHKVGLRALILSPTRELAAQIYREMRKYSID  235 (593)
T ss_pred             hhcccceEEeccCCCcchhhhhhHHHHHHHHhhcccCccceEEEEecchHHHHHHHHHHHHhcCCC
Confidence            367899999999999999999999999987743       48899999999999999999998743

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=98.93  E-value=3.2e-09  Score=79.80  Aligned_cols=52  Identities=23%  Similarity=0.316  Sum_probs=46.7

Q ss_pred             eEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHHHHHHHHHHHHhh
Q psy2029          77 CVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAAE  128 (138)
Q Consensus        77 ~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~~q~~~~~~~~~~  128 (138)
                      +++.+|||+|||.++++++++.+.. ...+++|++|+++|++|+++.+.+++.
T Consensus         2 vvi~apTGsGKT~~~~~~~l~~~~~~~~~~ii~v~P~~~L~~q~~~~l~~~f~   54 (358)
T TIGR01587         2 LVIEAPTGYGKTEAALLWALHSIKSQKADRVIIALPTRATINAMYRRAKELFG   54 (358)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhhCCCCeEEEEeehHHHHHHHHHHHHHHhC
Confidence            6799999999999999999987754 457999999999999999999999864

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.

>KOG0947|consensus

Probab=98.92  E-value=9.5e-10  Score=89.68  Aligned_cols=57  Identities=23%  Similarity=0.363  Sum_probs=50.1

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      ..|+++.|.|+|++|||++|++++..... ++.|++|..|.++|.+|++++|+..+..
T Consensus       310 erg~SVFVAAHTSAGKTvVAEYAialaq~-h~TR~iYTSPIKALSNQKfRDFk~tF~D  366 (1248)
T KOG0947|consen  310 ERGDSVFVAAHTSAGKTVVAEYAIALAQK-HMTRTIYTSPIKALSNQKFRDFKETFGD  366 (1248)
T ss_pred             HcCCeEEEEecCCCCcchHHHHHHHHHHh-hccceEecchhhhhccchHHHHHHhccc
Confidence            46899999999999999999999876443 5889999999999999999999987543

>KOG0354|consensus

Probab=98.91  E-value=4.6e-09  Score=84.32  Aligned_cols=72  Identities=15%  Similarity=0.325  Sum_probs=60.6

Q ss_pred             hhhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHHHHHHHHHHHHhhhcC
Q psy2029          60 FKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAAEEFK  131 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~  131 (138)
                      .+.+.|.+.......+|+++++|||+|||++|...++.++.. ++.|+|+++|++-|++|+...+..++.+.+
T Consensus        62 ~lR~YQ~eivq~ALgkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~~KiVF~aP~~pLv~QQ~a~~~~~~~~~~  134 (746)
T KOG0354|consen   62 ELRNYQEELVQPALGKNTIIALPTGSGKTFIAAVIMKNHFEWRPKGKVVFLAPTRPLVNQQIACFSIYLIPYS  134 (746)
T ss_pred             cccHHHHHHhHHhhcCCeEEEeecCCCccchHHHHHHHHHhcCCcceEEEeeCCchHHHHHHHHHhhccCccc
Confidence            356677777633338999999999999999999999988876 458999999999999999999988876643

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=98.91  E-value=2.9e-09  Score=86.31  Aligned_cols=53  Identities=25%  Similarity=0.347  Sum_probs=47.3

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      .|.++++|||||||++|.++++..+. .+.++++++|+++|+.|.++.+.++..
T Consensus       283 ~~~Ll~~~TGSGKT~va~~~il~~~~-~g~q~lilaPT~~LA~Q~~~~l~~l~~  335 (681)
T PRK10917        283 MNRLLQGDVGSGKTVVAALAALAAIE-AGYQAALMAPTEILAEQHYENLKKLLE  335 (681)
T ss_pred             ceEEEECCCCCcHHHHHHHHHHHHHH-cCCeEEEEeccHHHHHHHHHHHHHHHh
Confidence            47899999999999999999987654 588999999999999999999988753

>KOG0337|consensus

Probab=98.91  E-value=2.8e-09  Score=80.43  Aligned_cols=96  Identities=17%  Similarity=0.166  Sum_probs=85.3

Q ss_pred             cchhhhHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC---CCeEEEEccchhH
Q psy2029          40 LPYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK---QKSAIFILPYISL  115 (138)
Q Consensus        40 ~P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~---~~~~~~i~P~~~l  115 (138)
                      .+.-.|....++++.+.+++.+.|+|...+|.+.+ ++++-.+-||+|||.++.+++++.+..+   +.|++++.|+++|
T Consensus        23 fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s~~g~RalilsptreL  102 (529)
T KOG0337|consen   23 FQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHSQTGLRALILSPTREL  102 (529)
T ss_pred             ccccCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhccccccceeeccCcHHH
Confidence            45556777888999999999999999999999999 9999999999999999999999999874   3699999999999


Q ss_pred             HHHHHHHHHHHhhhcCceee
Q psy2029         116 VHEKYQSLAKAAEEFKFYLE  135 (138)
Q Consensus       116 ~~q~~~~~~~~~~~~~~~v~  135 (138)
                      +.|..+.+++.+...+++..
T Consensus       103 a~qtlkvvkdlgrgt~lr~s  122 (529)
T KOG0337|consen  103 ALQTLKVVKDLGRGTKLRQS  122 (529)
T ss_pred             HHHHHHHHHHhccccchhhh
Confidence            99999999999987776643

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=98.90  E-value=2.8e-09  Score=88.56  Aligned_cols=52  Identities=15%  Similarity=0.191  Sum_probs=46.8

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      .|.++++|||+|||.+|..+++..+. .+.++++++|+++|+.|.++.+.+..
T Consensus       473 ~d~Ll~adTGsGKT~val~a~l~al~-~g~qvlvLvPT~~LA~Q~~~~f~~~~  524 (926)
T TIGR00580       473 MDRLVCGDVGFGKTEVAMRAAFKAVL-DGKQVAVLVPTTLLAQQHFETFKERF  524 (926)
T ss_pred             CCEEEECCCCccHHHHHHHHHHHHHH-hCCeEEEEeCcHHHHHHHHHHHHHHh
Confidence            68999999999999999999988665 47899999999999999999988754

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.

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=98.90  E-value=3.3e-09  Score=80.03  Aligned_cols=48  Identities=19%  Similarity=0.299  Sum_probs=42.1

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +++++||||||||.++.++++.    .+.+++|+.|+++|.+|+++.+.++.
T Consensus        16 ~~~i~apTGsGKT~~~~~~~l~----~~~~~~~~~P~~aL~~~~~~~~~~~~   63 (357)
T TIGR03158        16 IIFNTAPTGAGKTLAWLTPLLH----GENDTIALYPTNALIEDQTEAIKEFV   63 (357)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH----cCCCEEEEeChHHHHHHHHHHHHHHH
Confidence            4789999999999999888774    35688999999999999999888875

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.

>PRK14701 reverse gyrase; Provisional

Probab=98.90  E-value=9e-09  Score=89.48  Aligned_cols=57  Identities=25%  Similarity=0.390  Sum_probs=47.4

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      ++|+|++++||||+|||+++..+++.. ..++.++++++|+++|+.|+.+.+..++..
T Consensus        92 l~G~d~li~APTGsGKTl~~~~~al~~-~~~g~~aLVl~PTreLa~Qi~~~l~~l~~~  148 (1638)
T PRK14701         92 LRGKSFSIVAPTGMGKSTFGAFIALFL-ALKGKKCYIILPTTLLVKQTVEKIESFCEK  148 (1638)
T ss_pred             HcCCCEEEEEcCCCCHHHHHHHHHHHH-HhcCCeEEEEECHHHHHHHHHHHHHHHHhh
Confidence            689999999999999999665555543 335779999999999999999999987653

>KOG0951|consensus

Probab=98.88  E-value=2.6e-09  Score=89.14  Aligned_cols=80  Identities=26%  Similarity=0.378  Sum_probs=59.9

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhc----------CCeEEEEcchhhhHHHHHHHHHHHHHhhhhhhhhHHH----
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIK----------QKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCL----   69 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~----------~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~----   69 (138)
                      .+|+++|||||+|||++|+..+++.+.++          ..++.|++|+++|+++....|.+.....+..+-....    
T Consensus       325 ~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKaLvqE~VgsfSkRla~~GI~V~ElTgD~~l  404 (1674)
T KOG0951|consen  325 DENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKALVQEMVGSFSKRLAPLGITVLELTGDSQL  404 (1674)
T ss_pred             cCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeHHHHHHHHHHHHHhhccccCcEEEEecccccc
Confidence            46999999999999999999999877552          2289999999999999999988875555444433332    


Q ss_pred             --hhhhccceEEEeec
Q psy2029          70 --EMIQNKNCVLSIPT   83 (138)
Q Consensus        70 --~~~~~~~~ii~~pt   83 (138)
                        ..+...++++++|-
T Consensus       405 ~~~qieeTqVIV~TPE  420 (1674)
T KOG0951|consen  405 GKEQIEETQVIVTTPE  420 (1674)
T ss_pred             hhhhhhcceeEEeccc
Confidence              12222667777773

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=98.88  E-value=3.8e-09  Score=85.02  Aligned_cols=52  Identities=23%  Similarity=0.321  Sum_probs=46.1

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      |.++++|||||||++|.++++..+ +.+.++++++|+++|+.|.++.+.++..
T Consensus       258 ~~Ll~g~TGSGKT~va~l~il~~~-~~g~qvlilaPT~~LA~Q~~~~~~~l~~  309 (630)
T TIGR00643       258 NRLLQGDVGSGKTLVAALAMLAAI-EAGYQVALMAPTEILAEQHYNSLRNLLA  309 (630)
T ss_pred             cEEEECCCCCcHHHHHHHHHHHHH-HcCCcEEEECCHHHHHHHHHHHHHHHhc
Confidence            689999999999999999988765 4588999999999999999999988643

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

Probab=98.87  E-value=1.5e-08  Score=80.13  Aligned_cols=53  Identities=26%  Similarity=0.460  Sum_probs=47.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|+++.+|||+||+++|.+|++-    ..+-+++|.|+.+|..++.+.+...|.
T Consensus        30 l~g~d~lvvmPTGgGKSlCyQiPAll----~~G~TLVVSPLiSLM~DQV~~l~~~Gi   82 (590)
T COG0514          30 LSGKDTLVVMPTGGGKSLCYQIPALL----LEGLTLVVSPLISLMKDQVDQLEAAGI   82 (590)
T ss_pred             HcCCcEEEEccCCCCcchHhhhHHHh----cCCCEEEECchHHHHHHHHHHHHHcCc
Confidence            67899999999999999999999885    256889999999999999999988863

>PRK13766 Hef nuclease; Provisional

Probab=98.87  E-value=1.1e-08  Score=84.08  Aligned_cols=69  Identities=20%  Similarity=0.237  Sum_probs=58.4

Q ss_pred             hhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhh
Q psy2029          61 KFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEE  129 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~  129 (138)
                      +.++|........++|.++++|||+|||.++.+.+...+...+.++++++|+++|++|+.+.+++++..
T Consensus        16 ~r~yQ~~~~~~~l~~n~lv~~ptG~GKT~~a~~~i~~~l~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~   84 (773)
T PRK13766         16 ARLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIAERLHKKGGKVLILAPTKPLVEQHAEFFRKFLNI   84 (773)
T ss_pred             ccHHHHHHHHHHhcCCeEEEcCCCccHHHHHHHHHHHHHHhCCCeEEEEeCcHHHHHHHHHHHHHHhCC
Confidence            455677776666667999999999999999988888777556789999999999999999999988643

>KOG0947|consensus

Probab=98.87  E-value=6.4e-09  Score=84.97  Aligned_cols=72  Identities=17%  Similarity=0.274  Sum_probs=62.5

Q ss_pred             hhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCce
Q psy2029          61 KFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFY  133 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~  133 (138)
                      +-++|.+++-.+.. .++++.++|++|||++|+.++.- ...++.|++|..|.+||.+|++++|++-|.+.|+-
T Consensus       298 lD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAial-aq~h~TR~iYTSPIKALSNQKfRDFk~tF~DvgLl  370 (1248)
T KOG0947|consen  298 LDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIAL-AQKHMTRTIYTSPIKALSNQKFRDFKETFGDVGLL  370 (1248)
T ss_pred             ccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHH-HHhhccceEecchhhhhccchHHHHHHhcccccee
Confidence            55689999977766 99999999999999999998754 34468999999999999999999999999888643

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=98.86  E-value=3.5e-08  Score=80.64  Aligned_cols=76  Identities=13%  Similarity=0.100  Sum_probs=65.0

Q ss_pred             hhhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeeec
Q psy2029          60 FKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEVL  137 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~~  137 (138)
                      .++++|..++..+.+.+ +..+.||+|||+++.++++..... +..+.+++|++.||.|.++.+..++..+|++|..+
T Consensus        78 ~p~~vQl~~~~~l~~G~-Iaem~TGeGKTL~a~lp~~l~al~-G~~v~VvTpt~~LA~qd~e~~~~l~~~lGl~v~~i  153 (790)
T PRK09200         78 RPYDVQLIGALVLHEGN-IAEMQTGEGKTLTATMPLYLNALE-GKGVHLITVNDYLAKRDAEEMGQVYEFLGLTVGLN  153 (790)
T ss_pred             CCchHHHHhHHHHcCCc-eeeecCCCcchHHHHHHHHHHHHc-CCCeEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEE
Confidence            46778877776565533 999999999999999999866664 78899999999999999999999999999988753

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

Probab=98.85  E-value=1.5e-08  Score=78.05  Aligned_cols=65  Identities=22%  Similarity=0.280  Sum_probs=56.1

Q ss_pred             hhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhh
Q psy2029          64 LEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE  128 (138)
Q Consensus        64 ~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~  128 (138)
                      .|.........+|.++++|||=|||.+|.+-+..++...++++++++||+.||.|.++.+++...
T Consensus        19 YQ~~i~a~al~~NtLvvlPTGLGKT~IA~~V~~~~l~~~~~kvlfLAPTKPLV~Qh~~~~~~v~~   83 (542)
T COG1111          19 YQLNIAAKALFKNTLVVLPTGLGKTFIAAMVIANRLRWFGGKVLFLAPTKPLVLQHAEFCRKVTG   83 (542)
T ss_pred             HHHHHHHHHhhcCeEEEecCCccHHHHHHHHHHHHHHhcCCeEEEecCCchHHHHHHHHHHHHhC
Confidence            45555555556899999999999999999999988888777999999999999999999998853

>PHA02558 uvsW UvsW helicase; Provisional

Probab=98.84  E-value=7e-09  Score=81.44  Aligned_cols=56  Identities=27%  Similarity=0.402  Sum_probs=44.0

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +++++.++++|||+|||+++...+...+.....++++++|+++|.+|..+++.+++
T Consensus       127 l~~~~~il~apTGsGKT~i~~~l~~~~~~~~~~~vLilvpt~eL~~Q~~~~l~~~~  182 (501)
T PHA02558        127 LKNNRRLLNLPTSAGKSLIQYLLSRYYLENYEGKVLIIVPTTSLVTQMIDDFVDYR  182 (501)
T ss_pred             HhcCceEEEeCCCCCHHHHHHHHHHHHHhcCCCeEEEEECcHHHHHHHHHHHHHhc
Confidence            45678999999999999987554433222334499999999999999999998864

>KOG0340|consensus

Probab=98.83  E-value=2.2e-09  Score=79.50  Aligned_cols=60  Identities=17%  Similarity=0.259  Sum_probs=52.8

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhhc--CCeEEEEcchhhhHHHHHHHHHHHHHhh
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQSLAKAAEEF   60 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~--~~~~l~v~P~~aL~~q~~~~l~~~~~~~   60 (138)
                      ||+|+||+-+|.||||||.++.+++++.+.+.  +.=+++++|+++|.-|+.+.|.-.+...
T Consensus        41 ILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTPTrELA~QiaEQF~alGk~l  102 (442)
T KOG0340|consen   41 ILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTPTRELALQIAEQFIALGKLL  102 (442)
T ss_pred             HhcccccccccccCCCcchhhhHHHHHhhccCCCcceEEEecchHHHHHHHHHHHHHhcccc
Confidence            58999999999999999999999999988773  4577899999999999999988876543

>PRK10689 transcription-repair coupling factor; Provisional

Probab=98.83  E-value=1.3e-08  Score=86.28  Aligned_cols=53  Identities=15%  Similarity=0.169  Sum_probs=46.6

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      .|.++++|||+|||.+|..+++..+ .++.++++++|+++|+.|+++.+.+.+.
T Consensus       622 ~d~Ll~a~TGsGKT~val~aa~~~~-~~g~qvlvLvPT~eLA~Q~~~~f~~~~~  674 (1147)
T PRK10689        622 MDRLVCGDVGFGKTEVAMRAAFLAV-ENHKQVAVLVPTTLLAQQHYDNFRDRFA  674 (1147)
T ss_pred             CCEEEEcCCCcCHHHHHHHHHHHHH-HcCCeEEEEeCcHHHHHHHHHHHHHhhc
Confidence            6899999999999999988887654 4588999999999999999999987643

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

Probab=98.83  E-value=1.5e-08  Score=83.04  Aligned_cols=70  Identities=16%  Similarity=0.119  Sum_probs=54.8

Q ss_pred             hhhhhhHHHhhhhc-c-ceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHHHHHHHhhhc
Q psy2029          61 KFYLEGKCLEMIQN-K-NCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAEEF  130 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~-~-~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~~~~~~~~~~  130 (138)
                      ++++|.++++.+.+ + ++++.+|||+|||.++..+.+.....  ...+.+|++|+++|+.|+++.++++.+.+
T Consensus        16 PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~~~~~~~~~rLv~~vPtReLa~Qi~~~~~~~~k~l   89 (844)
T TIGR02621        16 PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAVEIGAKVPRRLVYVVNRRTVVDQVTEEAEKIGERL   89 (844)
T ss_pred             CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccccccccccceEEEeCchHHHHHHHHHHHHHHHHHh
Confidence            99999999988887 5 57778999999998654434322111  23467788899999999999999999865

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.

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=98.81  E-value=4.7e-08  Score=79.43  Aligned_cols=74  Identities=16%  Similarity=0.190  Sum_probs=59.3

Q ss_pred             hhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          62 FYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        62 ~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      .|+|.+.+..+.. ...++.++||+|||+++.++++..+.. +..+++++|+++|+.|.++.+..++..+|+.|..
T Consensus        70 rpydVQlig~l~l~~G~Iaem~TGeGKTLta~Lpa~l~aL~-g~~V~VVTpn~yLA~Rdae~m~~l~~~LGLsv~~  144 (762)
T TIGR03714        70 FPYDVQVLGAIVLHQGNIAEMKTGEGKTLTATMPLYLNALT-GKGAMLVTTNDYLAKRDAEEMGPVYEWLGLTVSL  144 (762)
T ss_pred             CccHHHHHHHHHhcCCceeEecCCcchHHHHHHHHHHHhhc-CCceEEeCCCHHHHHHHHHHHHHHHhhcCCcEEE
Confidence            4444444433332 446999999999999999998776664 6679999999999999999999999999988764

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.

>KOG0326|consensus

Probab=98.81  E-value=2.6e-09  Score=78.35  Aligned_cols=92  Identities=15%  Similarity=0.161  Sum_probs=80.8

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC--CCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~--~~~~~~i~P~~~l~~q~~~  121 (138)
                      |..+.+..+.+.|+..+-|+|++.+|.... ++++..+-.|+|||.++.+|.++.+...  .-.+++++|+++|+-|..+
T Consensus        92 Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPtrelALQtSq  171 (459)
T KOG0326|consen   92 LKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPTRELALQTSQ  171 (459)
T ss_pred             hhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCccccceeEEEEeecchhhHHHHH
Confidence            445666777778888899999999998887 9999999999999999999999988753  3578999999999999999


Q ss_pred             HHHHHhhhcCceeee
Q psy2029         122 SLAKAAEEFKFYLEV  136 (138)
Q Consensus       122 ~~~~~~~~~~~~v~~  136 (138)
                      ...+..+++|+.|..
T Consensus       172 vc~~lskh~~i~vmv  186 (459)
T KOG0326|consen  172 VCKELSKHLGIKVMV  186 (459)
T ss_pred             HHHHHhcccCeEEEE
Confidence            999999999988753

>KOG0948|consensus

Probab=98.79  E-value=1.4e-08  Score=81.44  Aligned_cols=74  Identities=23%  Similarity=0.354  Sum_probs=66.3

Q ss_pred             hhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceee
Q psy2029          61 KFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLE  135 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~  135 (138)
                      +-++|..++..+-+ .++++++.|++|||.+|++++...+.+ +.|++|..|.+||.+|+++++..=|++.|+.-+
T Consensus       130 LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~-kQRVIYTSPIKALSNQKYREl~~EF~DVGLMTG  204 (1041)
T KOG0948|consen  130 LDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLRE-KQRVIYTSPIKALSNQKYRELLEEFKDVGLMTG  204 (1041)
T ss_pred             cCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHh-cCeEEeeChhhhhcchhHHHHHHHhcccceeec
Confidence            56789999888887 999999999999999999999887765 889999999999999999999999999887543

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=98.78  E-value=9.5e-09  Score=88.35  Aligned_cols=47  Identities=23%  Similarity=0.334  Sum_probs=41.1

Q ss_pred             EEccCCcchHHHHHHHHHHHHhhc------------CCeEEEEcchhhhHHHHHHHHHH
Q psy2029           9 LSIPTSGGKTLVGEILIMKELKIK------------QKSAIFILPYISLVHEKYQSLAK   55 (138)
Q Consensus         9 ~~~ptg~GKt~~~~~~~~~~~~~~------------~~~~l~v~P~~aL~~q~~~~l~~   55 (138)
                      |+||||||||++|.++++..+...            +.+++|+.|+++|.+|++++++.
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~~~~~~~~~~~~~~~raLYISPLKALa~Dv~~~L~~   59 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQI   59 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhcccccccccccCCCCEEEEEeChHHHHHHHHHHHHH
Confidence            589999999999999998877642            35899999999999999998865

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

Probab=98.78  E-value=5.4e-08  Score=80.22  Aligned_cols=81  Identities=25%  Similarity=0.309  Sum_probs=66.8

Q ss_pred             HHHHHHHHH----hhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHH
Q psy2029          50 YQSLAKAAE----EFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLA  124 (138)
Q Consensus        50 ~~~l~~~~~----~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~  124 (138)
                      ++++.+++.    ..+|..|..|...+.. +++.+.+|||.|||...+++.+.-.. .+++++||+||+.|+.|.++.++
T Consensus        68 ~e~~~~fF~k~~G~~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~a~-kgkr~yii~PT~~Lv~Q~~~kl~  146 (1187)
T COG1110          68 YEEFEEFFKKATGFRPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLAK-KGKRVYIIVPTTTLVRQVYERLK  146 (1187)
T ss_pred             HHHHHHHHHHhhCCCchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHHHHh-cCCeEEEEecCHHHHHHHHHHHH
Confidence            445555433    2589999999866666 99999999999999999888876544 47899999999999999999999


Q ss_pred             HHhhhcC
Q psy2029         125 KAAEEFK  131 (138)
Q Consensus       125 ~~~~~~~  131 (138)
                      ++....|
T Consensus       147 ~~~e~~~  153 (1187)
T COG1110         147 KFAEDAG  153 (1187)
T ss_pred             HHHhhcC
Confidence            9998776

>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=98.77  E-value=3.8e-08  Score=66.67  Aligned_cols=64  Identities=22%  Similarity=0.374  Sum_probs=49.3

Q ss_pred             hhhhhhHHHhhhh-------c-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhh
Q psy2029          61 KFYLEGKCLEMIQ-------N-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE  128 (138)
Q Consensus        61 ~~~~Q~~~~~~~~-------~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~  128 (138)
                      +.++|.+++..+.       + ++.++.+|||+|||.++...+.+. ..   ++++++|+..|++|..+++..+..
T Consensus         4 lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l-~~---~~l~~~p~~~l~~Q~~~~~~~~~~   75 (184)
T PF04851_consen    4 LRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILEL-AR---KVLIVAPNISLLEQWYDEFDDFGS   75 (184)
T ss_dssp             E-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHH-HC---EEEEEESSHHHHHHHHHHHHHHST
T ss_pred             CCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcc-cc---ceeEecCHHHHHHHHHHHHHHhhh
Confidence            4667777774333       2 788999999999999997655543 32   999999999999999999965543

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 ....

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=98.76  E-value=1.1e-07  Score=77.04  Aligned_cols=75  Identities=11%  Similarity=0.030  Sum_probs=61.9

Q ss_pred             hhhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          60 FKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      .++++|...+..+.+ ..+..++||+|||+++.++++-.... +..+.+++|+..||.|.++.+..++..+|++|..
T Consensus        56 ~p~~vQlig~~~l~~-G~Iaem~TGeGKTLva~lpa~l~aL~-G~~V~VvTpt~~LA~qdae~~~~l~~~LGLsv~~  130 (745)
T TIGR00963        56 RPFDVQLIGGIALHK-GKIAEMKTGEGKTLTATLPAYLNALT-GKGVHVVTVNDYLAQRDAEWMGQVYRFLGLSVGL  130 (745)
T ss_pred             CccchHHhhhhhhcC-CceeeecCCCccHHHHHHHHHHHHHh-CCCEEEEcCCHHHHHHHHHHHHHHhccCCCeEEE
Confidence            366777776665544 33899999999999999999654554 6679999999999999999999999999998864

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.

>KOG0338|consensus

Probab=98.76  E-value=1.1e-08  Score=78.96  Aligned_cols=78  Identities=15%  Similarity=0.221  Sum_probs=58.9

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhc-----CCeEEEEcchhhhHHHHHHHHHHHHHhh-----------hhhhh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIK-----QKSAIFILPYISLVHEKYQSLAKAAEEF-----------KFYLE   65 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~-----~~~~l~v~P~~aL~~q~~~~l~~~~~~~-----------~~~~Q   65 (138)
                      |-|++++-||-||||||.+|.+|++.+++=+     ..|+|+++|+++|.-|.+..........           ....|
T Consensus       216 llgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~Q  295 (691)
T KOG0338|consen  216 LLGKDICACAATGSGKTAAFALPILERLLYRPKKVAATRVLVLVPTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQ  295 (691)
T ss_pred             hhcchhhheecccCCchhhhHHHHHHHHhcCcccCcceeEEEEeccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHH
Confidence            5789999999999999999999999998763     2399999999999998887766653321           23334


Q ss_pred             hHHHhhhhc-cceEEEee
Q psy2029          66 GKCLEMIQN-KNCVLSIP   82 (138)
Q Consensus        66 ~~~~~~~~~-~~~ii~~p   82 (138)
                      ..+   ++. .++++.+|
T Consensus       296 E~~---LRs~PDIVIATP  310 (691)
T KOG0338|consen  296 EAV---LRSRPDIVIATP  310 (691)
T ss_pred             HHH---HhhCCCEEEecc
Confidence            433   334 67777777

>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=98.75  E-value=3.5e-08  Score=66.83  Aligned_cols=50  Identities=26%  Similarity=0.524  Sum_probs=41.9

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +.++++.+|||||||.++...+.+...    ++++++|..+|.+|..+++..+.
T Consensus        25 ~~~~ll~~~tGsGKT~~~~~~~~~l~~----~~l~~~p~~~l~~Q~~~~~~~~~   74 (184)
T PF04851_consen   25 ERRVLLNAPTGSGKTIIALALILELAR----KVLIVAPNISLLEQWYDEFDDFG   74 (184)
T ss_dssp             CSEEEEEESTTSSHHHHHHHHHHHHHC----EEEEEESSHHHHHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCcChhhhhhhhcccc----ceeEecCHHHHHHHHHHHHHHhh
Confidence            578999999999999999766665332    99999999999999999986553

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 ....

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=98.75  E-value=4.2e-08  Score=62.99  Aligned_cols=54  Identities=24%  Similarity=0.365  Sum_probs=45.5

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      +++++.+|||+|||..+...+...... ..+++++++|...+.++..+.+.....
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~~~~~~lv~~p~~~l~~~~~~~~~~~~~   55 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFG   55 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhcccCCCEEEEcCcHHHHHHHHHHHHHHhh
Confidence            478999999999999998888775544 567999999999999999888877653

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

>KOG0328|consensus

Probab=98.74  E-value=8e-09  Score=74.72  Aligned_cols=93  Identities=13%  Similarity=0.191  Sum_probs=83.2

Q ss_pred             hhHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHH
Q psy2029          44 SLVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKY  120 (138)
Q Consensus        44 aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~  120 (138)
                      .|.++.++.+..+|+..+-.+|..+++.+.. ++++..+..|+|||..+.+.+++.+..  +...++++.|+|+|+.|.-
T Consensus        33 gl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~lilsPTRELa~Qi~  112 (400)
T KOG0328|consen   33 GLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDISVRETQALILSPTRELAVQIQ  112 (400)
T ss_pred             CchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccccceeeEEEecChHHHHHHHH
Confidence            4778999999999999999999999988888 999999999999999998888886654  3468999999999999999


Q ss_pred             HHHHHHhhhcCceeee
Q psy2029         121 QSLAKAAEEFKFYLEV  136 (138)
Q Consensus       121 ~~~~~~~~~~~~~v~~  136 (138)
                      +.+..++.+.++.+..
T Consensus       113 ~vi~alg~~mnvq~ha  128 (400)
T KOG0328|consen  113 KVILALGDYMNVQCHA  128 (400)
T ss_pred             HHHHHhcccccceEEE
Confidence            9999999999888764

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

Probab=98.74  E-value=2.3e-07  Score=76.64  Aligned_cols=59  Identities=34%  Similarity=0.465  Sum_probs=50.1

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFK   61 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~   61 (138)
                      +.|+++-+.||||.|||...++..+. +...++|+++++||+.|+.|.++.+..++...+
T Consensus        95 ~rg~SFaiiAPTGvGKTTfg~~~sl~-~a~kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~  153 (1187)
T COG1110          95 VRGKSFAIIAPTGVGKTTFGLLMSLY-LAKKGKRVYIIVPTTTLVRQVYERLKKFAEDAG  153 (1187)
T ss_pred             HcCCceEEEcCCCCchhHHHHHHHHH-HHhcCCeEEEEecCHHHHHHHHHHHHHHHhhcC
Confidence            57899999999999999888766554 334689999999999999999999999875544

>KOG4284|consensus

Probab=98.73  E-value=9.2e-09  Score=81.43  Aligned_cols=94  Identities=18%  Similarity=0.240  Sum_probs=81.3

Q ss_pred             hhHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHH
Q psy2029          44 SLVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKY  120 (138)
Q Consensus        44 aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~  120 (138)
                      +|-.+....+++.++..+.++|..++|.... .++++.+-.|+|||+++...+++.+..  ....+++++|||+++-|+.
T Consensus        31 ~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~PTREiaVQI~  110 (980)
T KOG4284|consen   31 ALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTPTREIAVQIK  110 (980)
T ss_pred             HHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcccCcceeEEEecchhhhhHHH
Confidence            3455666777777888899999999999998 999999999999999999999988865  3578999999999999999


Q ss_pred             HHHHHHhhhc-Cceeeec
Q psy2029         121 QSLAKAAEEF-KFYLEVL  137 (138)
Q Consensus       121 ~~~~~~~~~~-~~~v~~~  137 (138)
                      +.+.+++..+ |+++..|
T Consensus       111 ~tv~~v~~sf~g~~csvf  128 (980)
T KOG4284|consen  111 ETVRKVAPSFTGARCSVF  128 (980)
T ss_pred             HHHHHhcccccCcceEEE
Confidence            9999998876 7777654

>PRK13766 Hef nuclease; Provisional

Probab=98.73  E-value=3.1e-08  Score=81.40  Aligned_cols=53  Identities=26%  Similarity=0.382  Sum_probs=46.9

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +|+++++|||+|||.++.+.+...+.+.++++++++|+++|.+|..+.+.++.
T Consensus        30 ~n~lv~~ptG~GKT~~a~~~i~~~l~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~   82 (773)
T PRK13766         30 KNTLVVLPTGLGKTAIALLVIAERLHKKGGKVLILAPTKPLVEQHAEFFRKFL   82 (773)
T ss_pred             CCeEEEcCCCccHHHHHHHHHHHHHHhCCCeEEEEeCcHHHHHHHHHHHHHHh
Confidence            38999999999999999888887775568899999999999999998888763

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=98.72  E-value=2.3e-08  Score=86.12  Aligned_cols=48  Identities=23%  Similarity=0.329  Sum_probs=42.1

Q ss_pred             EEeecCCCchHhHHHHHHHHHHhC------------CCeEEEEccchhHHHHHHHHHHHH
Q psy2029          79 LSIPTSGGKTLVGEILIMKELKIK------------QKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        79 i~~ptg~GKt~~~~~~~l~~~~~~------------~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      +++|||+|||+++.++++..+...            +.+++||+|++||++|+.+.++..
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~~~~~~~~~~~~~~~raLYISPLKALa~Dv~~~L~~p   60 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIP   60 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhcccccccccccCCCCEEEEEeChHHHHHHHHHHHHHH
Confidence            478999999999999999988642            358999999999999999998763

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

Probab=98.71  E-value=4.1e-08  Score=78.65  Aligned_cols=55  Identities=22%  Similarity=0.297  Sum_probs=48.0

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++..+++.||||+|||++|+++++..+.. .+.++++.+|+++|.+|.++++....
T Consensus        15 ~~~~lliEA~TGtGKTlAYLlpal~~~~~~~~~rvlIstpT~~Lq~Ql~~~l~~l~   70 (636)
T TIGR03117        15 QKRIGMLEASTGVGKTLAMIMAALTMLKERPDQKIAIAVPTLALMGQLWSELERLT   70 (636)
T ss_pred             cCCeEEEEcCCCCcHHHHHHHHHHHHHHhccCceEEEECCcHHHHHHHHHHHHHHH
Confidence            56788999999999999999999877664 47899999999999999998777664

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.

>KOG0334|consensus

Probab=98.70  E-value=9.6e-08  Score=78.64  Aligned_cols=59  Identities=17%  Similarity=0.216  Sum_probs=52.0

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhh-------cCCeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKI-------KQKSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-------~~~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      |..|+++|..|-||||||+.|.+|++.|...       +|.-+++++|+++|..|+.+++..+...
T Consensus       399 ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi~li~aPtrela~QI~r~~~kf~k~  464 (997)
T KOG0334|consen  399 IMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILAPTRELAMQIHREVRKFLKL  464 (997)
T ss_pred             hccCcceEEeeccCCccchhhhcchhhhhhcCCChhhCCCceEEEEcCCHHHHHHHHHHHHHHHhh
Confidence            4689999999999999999999999988765       3557899999999999999999988543

>KOG0341|consensus

Probab=98.70  E-value=1.6e-08  Score=76.04  Aligned_cols=83  Identities=14%  Similarity=0.108  Sum_probs=69.5

Q ss_pred             HHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh----------CCCeEEEEccchhHH
Q psy2029          48 EKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI----------KQKSAIFILPYISLV  116 (138)
Q Consensus        48 q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~----------~~~~~~~i~P~~~l~  116 (138)
                      .+++.+.+.+...+.|+|.+-+|.+.. ++++-.+-||+|||+++.+|++-...+          .++-.++|+|.++|+
T Consensus       180 ~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~gLiicPSRELA  259 (610)
T KOG0341|consen  180 PLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEGPYGLIICPSRELA  259 (610)
T ss_pred             HHHHHHHhcCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCCCeeEEEcCcHHHH
Confidence            445666666777899999999998888 999999999999999999988655543          256789999999999


Q ss_pred             HHHHHHHHHHhhhc
Q psy2029         117 HEKYQSLAKAAEEF  130 (138)
Q Consensus       117 ~q~~~~~~~~~~~~  130 (138)
                      .|.++-+..++..+
T Consensus       260 rQt~~iie~~~~~L  273 (610)
T KOG0341|consen  260 RQTHDIIEQYVAAL  273 (610)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999998887655

>PRK05580 primosome assembly protein PriA; Validated

Probab=98.66  E-value=1.1e-07  Score=77.20  Aligned_cols=66  Identities=23%  Similarity=0.187  Sum_probs=54.6

Q ss_pred             hhhhhhHHHhhhhc----cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHh
Q psy2029          61 KFYLEGKCLEMIQN----KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA  127 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~----~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~  127 (138)
                      +++.|.++++.+.+    .+.++.+|||+|||.+++.++.+.+. .++++++++|+++|+.|.++.|++.+
T Consensus       145 Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~-~g~~vLvLvPt~~L~~Q~~~~l~~~f  214 (679)
T PRK05580        145 LNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLA-QGKQALVLVPEIALTPQMLARFRARF  214 (679)
T ss_pred             CCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHH-cCCeEEEEeCcHHHHHHHHHHHHHHh
Confidence            66788888855542    67899999999999999776655444 47899999999999999999999875

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=98.66  E-value=4.6e-08  Score=80.56  Aligned_cols=82  Identities=12%  Similarity=0.073  Sum_probs=59.9

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhhhhHHH-----hh--hhc
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCL-----EM--IQN   74 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~-----~~--~~~   74 (138)
                      +.+++++..|+||+|||++|.+|++.+++. +..+++++|++.|+.|..+.+...+...+..+.....     ..  ...
T Consensus       105 ~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~-g~~v~IVTpTrELA~Qdae~m~~L~k~lGLsV~~i~GG~~~~eq~~~y~  183 (970)
T PRK12899        105 AMHKGFITEMQTGEGKTLTAVMPLYLNALT-GKPVHLVTVNDYLAQRDCEWVGSVLRWLGLTTGVLVSGSPLEKRKEIYQ  183 (970)
T ss_pred             hcCCCeEEEeCCCCChHHHHHHHHHHHHhh-cCCeEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHHcC
Confidence            457889999999999999999999987765 4568899999999999999998876544333322111     11  112


Q ss_pred             cceEEEeecC
Q psy2029          75 KNCVLSIPTS   84 (138)
Q Consensus        75 ~~~ii~~ptg   84 (138)
                      .++++.+|..
T Consensus       184 ~DIVygTPgR  193 (970)
T PRK12899        184 CDVVYGTASE  193 (970)
T ss_pred             CCEEEECCCh
Confidence            5677777754

>PRK05580 primosome assembly protein PriA; Validated

Probab=98.64  E-value=1e-07  Score=77.44  Aligned_cols=52  Identities=25%  Similarity=0.222  Sum_probs=45.4

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +.++++.+|||||||.++..++...+ ..++++++++|+++|..|.++.+.+.
T Consensus       162 ~~~~Ll~~~TGSGKT~v~l~~i~~~l-~~g~~vLvLvPt~~L~~Q~~~~l~~~  213 (679)
T PRK05580        162 FSPFLLDGVTGSGKTEVYLQAIAEVL-AQGKQALVLVPEIALTPQMLARFRAR  213 (679)
T ss_pred             CCcEEEECCCCChHHHHHHHHHHHHH-HcCCeEEEEeCcHHHHHHHHHHHHHH
Confidence            46799999999999999987776654 45889999999999999999999875

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=98.64  E-value=9.5e-08  Score=70.23  Aligned_cols=55  Identities=25%  Similarity=0.286  Sum_probs=45.3

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCC-----eEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQK-----SAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~-----~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .+|.++++.||||+|||++++.+++..+...+.     +++|.+++.++..+...++++.
T Consensus        25 ~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00488       25 DRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             HcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            367899999999999999999999876665443     8999999999887777776654

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=98.64  E-value=9.5e-08  Score=70.23  Aligned_cols=55  Identities=25%  Similarity=0.286  Sum_probs=45.3

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCC-----eEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQK-----SAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~-----~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .+|.++++.||||+|||++++.+++..+...+.     +++|.+++.++..+...++++.
T Consensus        25 ~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00489       25 DRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             HcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            367899999999999999999999876665443     8999999999887777776654

>KOG0327|consensus

Probab=98.62  E-value=2.6e-08  Score=74.30  Aligned_cols=93  Identities=13%  Similarity=0.211  Sum_probs=80.3

Q ss_pred             hhHHHHHHHHHHHHHhhhhhhhhHHH-hhhhccceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHH
Q psy2029          44 SLVHEKYQSLAKAAEEFKFYLEGKCL-EMIQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKY  120 (138)
Q Consensus        44 aL~~q~~~~l~~~~~~~~~~~Q~~~~-~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~  120 (138)
                      .|.+..++.+..+|+..+..+|..++ |.+...|....+.+|+|||.++..++++.+..  ....+++++|+++|+.|..
T Consensus        32 ~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~ke~qalilaPtreLa~qi~  111 (397)
T KOG0327|consen   32 NLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILAPTRELAQQIQ  111 (397)
T ss_pred             CCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcchHHHHHHHhcchHHHHHHHH
Confidence            46678888888899999999999998 55555999999999999999999999998754  3467999999999999999


Q ss_pred             HHHHHHhhhcCceeee
Q psy2029         121 QSLAKAAEEFKFYLEV  136 (138)
Q Consensus       121 ~~~~~~~~~~~~~v~~  136 (138)
                      +....++...+.+|..
T Consensus       112 ~v~~~lg~~~~~~v~~  127 (397)
T KOG0327|consen  112 KVVRALGDHMDVSVHA  127 (397)
T ss_pred             HHHHhhhcccceeeee
Confidence            9999998888877753

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=98.61  E-value=2.5e-07  Score=59.28  Aligned_cols=55  Identities=25%  Similarity=0.380  Sum_probs=47.3

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHHHHHHHHHHHHhhh
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAAEE  129 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~~q~~~~~~~~~~~  129 (138)
                      +++++..|||+|||..+...+.+.... ..+++++++|++++++|..+.+..+...
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~~~~~~lv~~p~~~l~~~~~~~~~~~~~~   56 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGE   56 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhcccCCCEEEEcCcHHHHHHHHHHHHHHhhC
Confidence            468899999999999998888776654 4579999999999999999999988753

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

>TIGR00595 priA primosomal protein N'

Probab=98.61  E-value=7.4e-08  Score=75.75  Aligned_cols=49  Identities=29%  Similarity=0.196  Sum_probs=41.4

Q ss_pred             EEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           8 VLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++.+|||||||.++...+.. .++.++++++++|+++|..|.++.+++.+
T Consensus         1 LL~g~TGsGKT~v~l~~i~~-~l~~g~~vLvlvP~i~L~~Q~~~~l~~~f   49 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEK-VLALGKSVLVLVPEIALTPQMIQRFKYRF   49 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHH-HHHcCCeEEEEeCcHHHHHHHHHHHHHHh
Confidence            46899999999999766554 45568899999999999999999998753

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).

>KOG0347|consensus

Probab=98.60  E-value=8.9e-08  Score=74.68  Aligned_cols=124  Identities=20%  Similarity=0.233  Sum_probs=76.4

Q ss_pred             CC-ccEEEEccCCcchHHHHHHHHHHHHhh-------------cCCe--EEEEcchhhhHHHHHHHHHHHHHhhh-----
Q psy2029           3 QN-KNCVLSIPTSGGKTLVGEILIMKELKI-------------KQKS--AIFILPYISLVHEKYQSLAKAAEEFK-----   61 (138)
Q Consensus         3 ~~-~~~~~~~ptg~GKt~~~~~~~~~~~~~-------------~~~~--~l~v~P~~aL~~q~~~~l~~~~~~~~-----   61 (138)
                      .| .+++--|.||||||++|-+|++..+.+             +..+  +|+++||++|+.|+.+.+.......+     
T Consensus       217 ~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~s  296 (731)
T KOG0347|consen  217 RGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELSNTSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVAS  296 (731)
T ss_pred             ccchhcccccccCCCceeeecchhhhhhhhccchHhhhhhHHhccCcceeEEecChHHHHHHHHHHHHHhccccCeEEEE
Confidence            45 688999999999999999999983322             2335  89999999999999999988755433     


Q ss_pred             ----hhhhhHHHhhhh-ccceEEEeecCCCchHhHHHHHHHH-HHh-CCCeEEEEccchhHHHH-HHHHHHHHhhhcC
Q psy2029          62 ----FYLEGKCLEMIQ-NKNCVLSIPTSGGKTLVGEILIMKE-LKI-KQKSAIFILPYISLVHE-KYQSLAKAAEEFK  131 (138)
Q Consensus        62 ----~~~Q~~~~~~~~-~~~~ii~~ptg~GKt~~~~~~~l~~-~~~-~~~~~~~i~P~~~l~~q-~~~~~~~~~~~~~  131 (138)
                          ..+|.+-- .+. ..++++.+|.. -+.+..   --.+ +.+ .+-+.+++.-.--+++. -+++|.++.+.++
T Consensus       297 i~GGLavqKQqR-lL~~~p~IVVATPGR-lweli~---e~n~~l~~~k~vkcLVlDEaDRmvekghF~Els~lL~~L~  369 (731)
T KOG0347|consen  297 ITGGLAVQKQQR-LLNQRPDIVVATPGR-LWELIE---EDNTHLGNFKKVKCLVLDEADRMVEKGHFEELSKLLKHLN  369 (731)
T ss_pred             eechhHHHHHHH-HHhcCCCEEEecchH-HHHHHH---hhhhhhhhhhhceEEEEccHHHHhhhccHHHHHHHHHHhh
Confidence                33333221 122 26777777721 111111   0000 000 23467777777667644 3466776665543

>KOG0339|consensus

Probab=98.59  E-value=1.5e-07  Score=72.99  Aligned_cols=90  Identities=11%  Similarity=0.117  Sum_probs=76.2

Q ss_pred             HHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh-------CCCeEEEEccchhHHH
Q psy2029          46 VHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI-------KQKSAIFILPYISLVH  117 (138)
Q Consensus        46 ~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~-------~~~~~~~i~P~~~l~~  117 (138)
                      ..|+...++...+..++++|.+++|-... ++++-.+-||+|||.++..+++-++..       .++-.+|++|+++|+.
T Consensus       231 DkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL~~g~gPi~vilvPTrela~  310 (731)
T KOG0339|consen  231 DKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVILVPTRELAS  310 (731)
T ss_pred             hHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhhcCCCCCeEEEEeccHHHHH
Confidence            34666666666666789999999987766 999999999999999999999888865       2467899999999999


Q ss_pred             HHHHHHHHHhhhcCceee
Q psy2029         118 EKYQSLAKAAEEFKFYLE  135 (138)
Q Consensus       118 q~~~~~~~~~~~~~~~v~  135 (138)
                      |++.+.+++++..|+++.
T Consensus       311 Qi~~eaKkf~K~ygl~~v  328 (731)
T KOG0339|consen  311 QIFSEAKKFGKAYGLRVV  328 (731)
T ss_pred             HHHHHHHHhhhhccceEE
Confidence            999999999999988864

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

Probab=98.59  E-value=2.7e-07  Score=74.10  Aligned_cols=56  Identities=20%  Similarity=0.301  Sum_probs=49.9

Q ss_pred             hhc-cceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHHHHHHHHHHHHh
Q psy2029          72 IQN-KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAA  127 (138)
Q Consensus        72 ~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~~q~~~~~~~~~  127 (138)
                      +.+ ...++.+|||+|||++++++++..+.. .+.++++.+||++|.+|.++++..+.
T Consensus        13 l~~~~~lliEA~TGtGKTlAYLlpal~~~~~~~~~rvlIstpT~~Lq~Ql~~~l~~l~   70 (636)
T TIGR03117        13 LRQKRIGMLEASTGVGKTLAMIMAALTMLKERPDQKIAIAVPTLALMGQLWSELERLT   70 (636)
T ss_pred             HhcCCeEEEEcCCCCcHHHHHHHHHHHHHHhccCceEEEECCcHHHHHHHHHHHHHHH
Confidence            344 778899999999999999999988764 47899999999999999999999887

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.

>TIGR00603 rad25 DNA repair helicase rad25

Probab=98.56  E-value=2.9e-07  Score=74.73  Aligned_cols=63  Identities=19%  Similarity=0.236  Sum_probs=51.9

Q ss_pred             hhhhhhHHHhhhhc----cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHh
Q psy2029          61 KFYLEGKCLEMIQN----KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA  127 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~----~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~  127 (138)
                      +.++|.+++..+..    ++.++++|||+|||++++..+. .+   +.++|+++|++.|++|..++|.+|+
T Consensus       256 LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~-~l---~k~tLILvps~~Lv~QW~~ef~~~~  322 (732)
T TIGR00603       256 IRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAAC-TV---KKSCLVLCTSAVSVEQWKQQFKMWS  322 (732)
T ss_pred             cCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHH-Hh---CCCEEEEeCcHHHHHHHHHHHHHhc
Confidence            56789988855542    4789999999999999965543 32   5679999999999999999999986

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=98.55  E-value=6e-07  Score=60.89  Aligned_cols=71  Identities=23%  Similarity=0.318  Sum_probs=59.6

Q ss_pred             hhhhhhhhHHHhhhhc--cceEEEeecCCCchHhHHHHHHHHHHhC-CCeEEEEccchhHHHHHHHHHHHHhhh
Q psy2029          59 EFKFYLEGKCLEMIQN--KNCVLSIPTSGGKTLVGEILIMKELKIK-QKSAIFILPYISLVHEKYQSLAKAAEE  129 (138)
Q Consensus        59 ~~~~~~Q~~~~~~~~~--~~~ii~~ptg~GKt~~~~~~~l~~~~~~-~~~~~~i~P~~~l~~q~~~~~~~~~~~  129 (138)
                      ..+.++|.++++.+.+  +++++..|+|+|||..+...+++.+... ..++++++|+.+++.|....+.+.+..
T Consensus         7 ~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~~~~~l~~~p~~~~~~~~~~~~~~~~~~   80 (201)
T smart00487        7 EPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAEQWAEELKKLGPS   80 (201)
T ss_pred             CCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccCCCcEEEEeCCHHHHHHHHHHHHHHhcc
Confidence            4467889989866654  7889999999999998888888877653 478999999999999999999988754

>KOG0949|consensus

Probab=98.55  E-value=1.6e-07  Score=77.22  Aligned_cols=55  Identities=27%  Similarity=0.390  Sum_probs=49.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      .+++++++|||++|||.+..+++-.++++ ..+-++|++|+++|++|...++...+
T Consensus       525 r~eSavIVAPTSaGKTfisfY~iEKVLResD~~VVIyvaPtKaLVnQvsa~VyaRF  580 (1330)
T KOG0949|consen  525 RNESAVIVAPTSAGKTFISFYAIEKVLRESDSDVVIYVAPTKALVNQVSANVYARF  580 (1330)
T ss_pred             cccceEEEeeccCCceeccHHHHHHHHhhcCCCEEEEecchHHHhhhhhHHHHHhh
Confidence            56899999999999999999999999888 56788999999999999988887765

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

Probab=98.55  E-value=1.5e-07  Score=78.20  Aligned_cols=49  Identities=16%  Similarity=0.154  Sum_probs=43.1

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQ   51 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~   51 (138)
                      .+|+++++.||||+|||++|++|++.... ++.++++.+|+++|.+|...
T Consensus       262 ~~~~~~~~eA~TG~GKT~ayLlp~~~~~~-~~~~vvi~t~t~~Lq~Ql~~  310 (850)
T TIGR01407       262 THSEKSLIEAPTGTGKTLGYLLPALYYAI-TEKPVVISTNTKVLQSQLLE  310 (850)
T ss_pred             ccCCcEEEECCCCCchhHHHHHHHHHHhc-CCCeEEEEeCcHHHHHHHHH
Confidence            35788999999999999999999988665 57799999999999998865

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.

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=98.54  E-value=1.4e-07  Score=75.72  Aligned_cols=56  Identities=14%  Similarity=0.093  Sum_probs=48.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEF   60 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~   60 (138)
                      ++|+  +..|.||+|||+++.+|++.+.. .+..+++++|+..|+.|.++.+.++....
T Consensus       116 l~G~--Iae~~TGeGKTla~~lp~~~~al-~G~~v~VvTptreLA~qdae~~~~l~~~l  171 (656)
T PRK12898        116 LSGR--LAEMQTGEGKTLTATLPAGTAAL-AGLPVHVITVNDYLAERDAELMRPLYEAL  171 (656)
T ss_pred             hCCC--eeeeeCCCCcHHHHHHHHHHHhh-cCCeEEEEcCcHHHHHHHHHHHHHHHhhc
Confidence            5665  89999999999999999998765 47899999999999999999999876543

>KOG0329|consensus

Probab=98.54  E-value=1.4e-07  Score=67.57  Aligned_cols=92  Identities=13%  Similarity=0.134  Sum_probs=78.6

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC--CCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~--~~~~~~i~P~~~l~~q~~~  121 (138)
                      |..+..+.+-+.|+.++-.+|.+|+|+.-- .++++.+-.|-|||.++.+..++++..-  .-.+++++.+|+|+-|+.+
T Consensus        49 lkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtrelafqi~~  128 (387)
T KOG0329|consen   49 LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTRELAFQISK  128 (387)
T ss_pred             cCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCCCCeEEEEEEeccHHHHHHHHH
Confidence            456888999999999999999999977655 9999999999999999999999988762  2468999999999999999


Q ss_pred             HHHHHhhhc-Cceeee
Q psy2029         122 SLAKAAEEF-KFYLEV  136 (138)
Q Consensus       122 ~~~~~~~~~-~~~v~~  136 (138)
                      ++.++.+.+ +++|..
T Consensus       129 ey~rfskymP~vkvaV  144 (387)
T KOG0329|consen  129 EYERFSKYMPSVKVSV  144 (387)
T ss_pred             HHHHHHhhCCCceEEE
Confidence            999888776 555543

>KOG0337|consensus

Probab=98.54  E-value=2.9e-07  Score=69.84  Aligned_cols=58  Identities=19%  Similarity=0.243  Sum_probs=52.4

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhhc---CCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKIK---QKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~---~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ||+|++++-.+-||||||.++.++|++++...   +.|++++.|+++|..|..+-..+.+.
T Consensus        55 iLe~~dvv~martgsgktaaf~ipm~e~Lk~~s~~g~RalilsptreLa~qtlkvvkdlgr  115 (529)
T KOG0337|consen   55 ILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHSQTGLRALILSPTRELALQTLKVVKDLGR  115 (529)
T ss_pred             eeeccccceeeecCCcchhhHHHHHHHHHhhccccccceeeccCcHHHHHHHHHHHHHhcc
Confidence            57899999999999999999999999998774   46999999999999999998888764

>KOG0352|consensus

Probab=98.53  E-value=4.7e-07  Score=69.02  Aligned_cols=49  Identities=24%  Similarity=0.431  Sum_probs=42.6

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ..++.|++|||+||+++|.+|++-+    ++-.+++.|+.+|..++.+.+...
T Consensus        36 k~DVyVsMPTGaGKSLCyQLPaL~~----~gITIV~SPLiALIkDQiDHL~~L   84 (641)
T KOG0352|consen   36 KCDVYVSMPTGAGKSLCYQLPALVH----GGITIVISPLIALIKDQIDHLKRL   84 (641)
T ss_pred             cCcEEEeccCCCchhhhhhchHHHh----CCeEEEehHHHHHHHHHHHHHHhc
Confidence            3589999999999999999998863    456788899999999999998775

>KOG0339|consensus

Probab=98.51  E-value=7.7e-07  Score=69.11  Aligned_cols=58  Identities=12%  Similarity=0.158  Sum_probs=51.4

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh-------cCCeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI-------KQKSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-------~~~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      +.|++++-.|-||||||.++..+++.|+++       .+.-.+|++|+++|+.|++.+..+++.-
T Consensus       258 lsgrdvigIAktgSgktaAfi~pm~~himdq~eL~~g~gPi~vilvPTrela~Qi~~eaKkf~K~  322 (731)
T KOG0339|consen  258 LSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVILVPTRELASQIFSEAKKFGKA  322 (731)
T ss_pred             cccccchheeeccCcchhHHHHHHHHHhcchhhhcCCCCCeEEEEeccHHHHHHHHHHHHHhhhh
Confidence            678999999999999999999999999877       2446788999999999999999888653

>KOG0950|consensus

Probab=98.50  E-value=2e-07  Score=76.32  Aligned_cols=68  Identities=38%  Similarity=0.662  Sum_probs=62.2

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhhhhHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCL   69 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~   69 (138)
                      ++++|++.++||++|||+++++.++..++.+++.+++++|+.+.+.++...+..++...++++....+
T Consensus       238 ~e~~nliys~Pts~gktlvaeilml~~~l~~rr~~llilp~vsiv~Ek~~~l~~~~~~~G~~ve~y~g  305 (1008)
T KOG0950|consen  238 LERKNLIYSLPTSAGKTLVAEILMLREVLCRRRNVLLILPYVSIVQEKISALSPFSIDLGFPVEEYAG  305 (1008)
T ss_pred             hcccceEEeCCCccchHHHHHHHHHHHHHHHhhceeEecceeehhHHHHhhhhhhccccCCcchhhcc
Confidence            57899999999999999999999999999889999999999999999999999988888888777665

>PRK09694 helicase Cas3; Provisional

Probab=98.50  E-value=5.8e-07  Score=74.57  Aligned_cols=70  Identities=19%  Similarity=0.153  Sum_probs=53.0

Q ss_pred             hhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC-CCeEEEEccchhHHHHHHHHHHHHhhh
Q psy2029          60 FKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK-QKSAIFILPYISLVHEKYQSLAKAAEE  129 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~-~~~~~~i~P~~~l~~q~~~~~~~~~~~  129 (138)
                      .+.+.|..+...... ..+++.+|||+|||.+++..+.+-+... ..+++|.+|++++++|.++++++++..
T Consensus       286 ~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~~~~~~~gi~~aLPT~Atan~m~~Rl~~~~~~  357 (878)
T PRK09694        286 QPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLIDQGLADSIIFALPTQATANAMLSRLEALASK  357 (878)
T ss_pred             CChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHHHhCCCCeEEEECcHHHHHHHHHHHHHHHHHH
Confidence            356777766433233 6678999999999999977665433332 368999999999999999999886654

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

Probab=98.48  E-value=8.3e-07  Score=73.84  Aligned_cols=70  Identities=14%  Similarity=0.080  Sum_probs=55.6

Q ss_pred             hhhhhhHHH----hhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHH-HHHHHhhhcC
Q psy2029          61 KFYLEGKCL----EMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQ-SLAKAAEEFK  131 (138)
Q Consensus        61 ~~~~Q~~~~----~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~-~~~~~~~~~~  131 (138)
                      ..+.|.+..    +.+.+ +++++.+|||+|||+.++++++..+. .+.++++.+||++|.+|... ++..+.+.++
T Consensus       246 ~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~-~~~~vvi~t~t~~Lq~Ql~~~~~~~l~~~~~  321 (850)
T TIGR01407       246 YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI-TEKPVVISTNTKVLQSQLLEKDIPLLNEILN  321 (850)
T ss_pred             cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc-CCCeEEEEeCcHHHHHHHHHHHHHHHHHHcC
Confidence            456777655    34445 78899999999999999999988776 56799999999999999865 6666655555

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.

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=98.48  E-value=1.3e-06  Score=72.00  Aligned_cols=74  Identities=15%  Similarity=0.067  Sum_probs=59.1

Q ss_pred             hhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          61 KFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      ++++|....-. ....-+..++||+|||+++.++++..+.. +..+.+++|++.||.|.++.+..++..+|+.|..
T Consensus        83 ~ydvQliGg~~-Lh~G~Iaem~TGeGKTL~a~Lpa~~~al~-G~~V~VvTpn~yLA~qd~e~m~~l~~~lGLtv~~  156 (896)
T PRK13104         83 HFDVQLIGGMV-LHEGNIAEMRTGEGKTLVATLPAYLNAIS-GRGVHIVTVNDYLAKRDSQWMKPIYEFLGLTVGV  156 (896)
T ss_pred             cchHHHhhhhh-hccCccccccCCCCchHHHHHHHHHHHhc-CCCEEEEcCCHHHHHHHHHHHHHHhcccCceEEE
Confidence            34444433322 23444789999999999999999987765 5679999999999999999999999999988764

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=98.46  E-value=5.5e-07  Score=61.07  Aligned_cols=53  Identities=26%  Similarity=0.418  Sum_probs=45.2

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhc-CCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIK-QKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~-~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +++++++|||+|||.++...+...+... ..++++++|+.++..|..+.+....
T Consensus        25 ~~~~i~~~~GsGKT~~~~~~~~~~~~~~~~~~~l~~~p~~~~~~~~~~~~~~~~   78 (201)
T smart00487       25 RDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAEQWAEELKKLG   78 (201)
T ss_pred             CcEEEECCCCCchhHHHHHHHHHHhcccCCCcEEEEeCCHHHHHHHHHHHHHHh
Confidence            6899999999999998888888766542 4789999999999999888887765

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=98.46  E-value=7.2e-07  Score=65.60  Aligned_cols=67  Identities=21%  Similarity=0.292  Sum_probs=53.5

Q ss_pred             hhhhhhHHH----hhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCC-----eEEEEccchhHHHHHHHHHHHHh
Q psy2029          61 KFYLEGKCL----EMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQK-----SAIFILPYISLVHEKYQSLAKAA  127 (138)
Q Consensus        61 ~~~~Q~~~~----~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~-----~~~~i~P~~~l~~q~~~~~~~~~  127 (138)
                      +.+.|.+..    ..+.+ .++++.+|||+|||+.++.+++..+...+.     +++|.+++.++.+|...++++..
T Consensus         9 ~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~~   85 (289)
T smart00488        9 PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKLM   85 (289)
T ss_pred             CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhcc
Confidence            355666644    33444 889999999999999999999887776443     89999999999999888888763

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=98.46  E-value=7.2e-07  Score=65.60  Aligned_cols=67  Identities=21%  Similarity=0.292  Sum_probs=53.5

Q ss_pred             hhhhhhHHH----hhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCC-----eEEEEccchhHHHHHHHHHHHHh
Q psy2029          61 KFYLEGKCL----EMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQK-----SAIFILPYISLVHEKYQSLAKAA  127 (138)
Q Consensus        61 ~~~~Q~~~~----~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~-----~~~~i~P~~~l~~q~~~~~~~~~  127 (138)
                      +.+.|.+..    ..+.+ .++++.+|||+|||+.++.+++..+...+.     +++|.+++.++.+|...++++..
T Consensus         9 ~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~~   85 (289)
T smart00489        9 PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKLM   85 (289)
T ss_pred             CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhcc
Confidence            355666644    33444 889999999999999999999887776443     89999999999999888888763

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

Probab=98.46  E-value=6.6e-07  Score=69.41  Aligned_cols=66  Identities=24%  Similarity=0.327  Sum_probs=51.4

Q ss_pred             hhhhhhhHHHhhhh-----ccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhh
Q psy2029          60 FKFYLEGKCLEMIQ-----NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEE  129 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~-----~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~  129 (138)
                      .+.+.|.+++..+.     ++..++.+|||+|||.++...+- ++   +.++++++|+++|+.|..+.+.+.+..
T Consensus        36 ~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~-~~---~~~~Lvlv~~~~L~~Qw~~~~~~~~~~  106 (442)
T COG1061          36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIA-EL---KRSTLVLVPTKELLDQWAEALKKFLLL  106 (442)
T ss_pred             CCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHH-Hh---cCCEEEEECcHHHHHHHHHHHHHhcCC
Confidence            36778888884332     37889999999999999965554 33   445999999999999999888877653

>PRK09694 helicase Cas3; Provisional

Probab=98.46  E-value=7.2e-07  Score=74.01  Aligned_cols=52  Identities=23%  Similarity=0.255  Sum_probs=43.2

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhc--CCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~--~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +..+++.||||+|||.+++.++.. +...  ..+++|.+|+.+..++.++++.++
T Consensus       301 pgl~ileApTGsGKTEAAL~~A~~-l~~~~~~~gi~~aLPT~Atan~m~~Rl~~~  354 (878)
T PRK09694        301 PGLTIIEAPTGSGKTEAALAYAWR-LIDQGLADSIIFALPTQATANAMLSRLEAL  354 (878)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHH-HHHhCCCCeEEEECcHHHHHHHHHHHHHHH
Confidence            457899999999999999887775 4333  358999999999999999998764

>KOG0332|consensus

Probab=98.44  E-value=3.5e-07  Score=68.48  Aligned_cols=90  Identities=12%  Similarity=0.098  Sum_probs=77.4

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc---cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN---KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEK  119 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~---~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~  119 (138)
                      |..+..+.+...++..+..+|+.++|.+..   +|.+..+..|+|||.++.+.++.++..  ..+.++-++|+++||.|+
T Consensus        97 LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~~~~PQ~iCLaPtrELA~Q~  176 (477)
T KOG0332|consen   97 LKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPDVVVPQCICLAPTRELAPQT  176 (477)
T ss_pred             CCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCccccCCCceeeCchHHHHHHH
Confidence            556788888888888899999999987764   899999999999999999999998875  346777889999999999


Q ss_pred             HHHHHHHhhhcCcee
Q psy2029         120 YQSLAKAAEEFKFYL  134 (138)
Q Consensus       120 ~~~~~~~~~~~~~~v  134 (138)
                      -+.+.+.++..++.+
T Consensus       177 ~eVv~eMGKf~~ita  191 (477)
T KOG0332|consen  177 GEVVEEMGKFTELTA  191 (477)
T ss_pred             HHHHHHhcCceeeeE
Confidence            999999988775554

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

Probab=98.43  E-value=3.1e-07  Score=75.50  Aligned_cols=59  Identities=17%  Similarity=0.170  Sum_probs=42.7

Q ss_pred             CCCc-cEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHHHhh
Q psy2029           2 VQNK-NCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAEEF   60 (138)
Q Consensus         2 ~~~~-~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~~~~   60 (138)
                      ++|+ ++++.+|||||||.++.++.+....+  ...+.+|++|+++|++|+++++++++...
T Consensus        28 l~G~~~v~~~apTGSGKTaa~aafll~~~~~~~~~~rLv~~vPtReLa~Qi~~~~~~~~k~l   89 (844)
T TIGR02621        28 VAGQPPESCSTPTGLGKTSIIAAWLLAVEIGAKVPRRLVYVVNRRTVVDQVTEEAEKIGERL   89 (844)
T ss_pred             HcCCCcceEecCCCCcccHHHHHhhccccccccccceEEEeCchHHHHHHHHHHHHHHHHHh
Confidence            5677 57778999999998765444421111  12366778899999999999999987643

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.

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=98.41  E-value=5.1e-07  Score=73.99  Aligned_cols=55  Identities=16%  Similarity=0.146  Sum_probs=47.4

Q ss_pred             EEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhhh
Q psy2029           8 VLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFY   63 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~   63 (138)
                      +..+.||+|||++|.+|++.+.++ |..+.+++|+..|+.|.++.+.++....+.+
T Consensus        95 Iaem~TGeGKTL~a~lp~~l~al~-G~~v~VvTpt~~LA~qd~e~~~~l~~~lGl~  149 (790)
T PRK09200         95 IAEMQTGEGKTLTATMPLYLNALE-GKGVHLITVNDYLAKRDAEEMGQVYEFLGLT  149 (790)
T ss_pred             eeeecCCCcchHHHHHHHHHHHHc-CCCeEEEeCCHHHHHHHHHHHHHHHhhcCCe
Confidence            999999999999999998865554 8899999999999999999998886654433

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

Probab=98.40  E-value=6.6e-07  Score=70.96  Aligned_cols=67  Identities=21%  Similarity=0.306  Sum_probs=58.7

Q ss_pred             HHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHh
Q psy2029          57 AEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA  127 (138)
Q Consensus        57 ~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~  127 (138)
                      |.....+-|.+++..+.+ ++.++.+|||+||++++-+|++-.    .+-+++|.|+.+|..++.+.++..+
T Consensus        14 Gy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~----~G~TLVVSPLiSLM~DQV~~l~~~G   81 (590)
T COG0514          14 GYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL----EGLTLVVSPLISLMKDQVDQLEAAG   81 (590)
T ss_pred             CccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc----CCCEEEECchHHHHHHHHHHHHHcC
Confidence            455566779999988888 999999999999999999999753    5578999999999999999999884

>KOG0336|consensus

Probab=98.40  E-value=2.5e-07  Score=70.15  Aligned_cols=80  Identities=13%  Similarity=0.098  Sum_probs=67.5

Q ss_pred             HHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--------CCCeEEEEccchhHHHH
Q psy2029          48 EKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--------KQKSAIFILPYISLVHE  118 (138)
Q Consensus        48 q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--------~~~~~~~i~P~~~l~~q  118 (138)
                      +..+++.+.++..+.|+|.++.|-+.. .+++..+.||+|||+.++++.+..+..        .+..+++++|+++|+.|
T Consensus       230 evmenIkK~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~ptreLalq  309 (629)
T KOG0336|consen  230 EVMENIKKTGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTRELALQ  309 (629)
T ss_pred             HHHHHHHhccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhccCCCceEEEeccHHHHHH
Confidence            445667777888999999999998887 999999999999999999988766643        35689999999999999


Q ss_pred             HHHHHHHHh
Q psy2029         119 KYQSLAKAA  127 (138)
Q Consensus       119 ~~~~~~~~~  127 (138)
                      +-.+..++.
T Consensus       310 ie~e~~kys  318 (629)
T KOG0336|consen  310 IEGEVKKYS  318 (629)
T ss_pred             HHhHHhHhh
Confidence            887777663

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=98.39  E-value=7.3e-07  Score=72.65  Aligned_cols=79  Identities=16%  Similarity=0.179  Sum_probs=57.9

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhhhhHHH------------hhhhc
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCL------------EMIQN   74 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~------------~~~~~   74 (138)
                      .++.++||+|||++|.+|++.+.+. +..+++++|+..|+.+..+.+.++....+..+.....            .....
T Consensus        86 ~Iaem~TGeGKTLta~Lpa~l~aL~-g~~V~VVTpn~yLA~Rdae~m~~l~~~LGLsv~~~~~~s~~~~~~~~~rr~~y~  164 (762)
T TIGR03714        86 NIAEMKTGEGKTLTATMPLYLNALT-GKGAMLVTTNDYLAKRDAEEMGPVYEWLGLTVSLGVVDDPDEEYDANEKRKIYN  164 (762)
T ss_pred             ceeEecCCcchHHHHHHHHHHHhhc-CCceEEeCCCHHHHHHHHHHHHHHHhhcCCcEEEEECCCCccccCHHHHHHhCC
Confidence            6999999999999999998776654 6789999999999999999988876555444332111            11112


Q ss_pred             cceEEEeecCCC
Q psy2029          75 KNCVLSIPTSGG   86 (138)
Q Consensus        75 ~~~ii~~ptg~G   86 (138)
                      .++++++|..-|
T Consensus       165 ~dIvygTp~~Lg  176 (762)
T TIGR03714       165 SDIVYTTNSALG  176 (762)
T ss_pred             CCEEEECchhhh
Confidence            677788885544

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.

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

Probab=98.39  E-value=7.1e-07  Score=73.87  Aligned_cols=52  Identities=15%  Similarity=0.157  Sum_probs=43.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHH-HHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKY-QSLAKA   56 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~-~~l~~~   56 (138)
                      +++.+++.||||+|||++|.+|++...  ++.++++.+|+++|.+|.. +.+...
T Consensus       263 ~~~~~~~eA~tGtGKT~ayllp~l~~~--~~~~vvI~t~T~~Lq~Ql~~~~i~~l  315 (820)
T PRK07246        263 DGPASFIEAQTGIGKTYGYLLPLLAQS--DQRQIIVSVPTKILQDQIMAEEVKAI  315 (820)
T ss_pred             CCCcEEEECCCCCcHHHHHHHHHHHhc--CCCcEEEEeCcHHHHHHHHHHHHHHH
Confidence            567889999999999999999988643  4679999999999999995 445444

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

Probab=98.39  E-value=7.4e-07  Score=74.70  Aligned_cols=49  Identities=16%  Similarity=0.153  Sum_probs=43.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQ   51 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~   51 (138)
                      ++..+++.||||+|||++|++|++......++++++.++|++|-+|...
T Consensus       275 ~~~~~~iEA~TGtGKTlaYLlpa~~~a~~~~~~vvIsT~T~~LQ~Ql~~  323 (928)
T PRK08074        275 DSEHALIEAGTGTGKSLAYLLPAAYFAKKKEEPVVISTYTIQLQQQLLE  323 (928)
T ss_pred             cCCCEEEECCCCCchhHHHHHHHHHHhhccCCeEEEEcCCHHHHHHHHH
Confidence            4678899999999999999999987766678899999999999998765

>KOG0351|consensus

Probab=98.38  E-value=3.2e-07  Score=76.24  Aligned_cols=52  Identities=29%  Similarity=0.542  Sum_probs=44.8

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +.|+++.+.+|||+||+++|.+|++.    .++-.++|.|+.+|.+++...+...+
T Consensus       277 l~Gkd~fvlmpTG~GKSLCYQlPA~l----~~gitvVISPL~SLm~DQv~~L~~~~  328 (941)
T KOG0351|consen  277 LSGKDCFVLMPTGGGKSLCYQLPALL----LGGVTVVISPLISLMQDQVTHLSKKG  328 (941)
T ss_pred             HcCCceEEEeecCCceeeEeeccccc----cCCceEEeccHHHHHHHHHHhhhhcC
Confidence            68999999999999999999999875    25677889999999999888885543

>TIGR00595 priA primosomal protein N'

Probab=98.38  E-value=8.2e-07  Score=69.93  Aligned_cols=49  Identities=24%  Similarity=0.177  Sum_probs=41.0

Q ss_pred             EEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhh
Q psy2029          79 LSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE  128 (138)
Q Consensus        79 i~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~  128 (138)
                      +..|||+|||.+++.. +..+...+++++|++|+++|+.|.++.|++.+.
T Consensus         2 L~g~TGsGKT~v~l~~-i~~~l~~g~~vLvlvP~i~L~~Q~~~~l~~~f~   50 (505)
T TIGR00595         2 LFGVTGSGKTEVYLQA-IEKVLALGKSVLVLVPEIALTPQMIQRFKYRFG   50 (505)
T ss_pred             ccCCCCCCHHHHHHHH-HHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhC
Confidence            5689999999999655 444555688999999999999999999998763

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).

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.37  E-value=9.1e-07  Score=72.15  Aligned_cols=48  Identities=17%  Similarity=0.126  Sum_probs=42.4

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQ   51 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~   51 (138)
                      ++.+++.||||+|||+.|++|+.......++++++-+.|++|-+|...
T Consensus        49 ~~~lviEAgTGtGKTlaYLlPai~~A~~~~k~vVIST~T~~LQeQL~~   96 (697)
T PRK11747         49 GRILVIEAGTGVGKTLSYLLAGIPIARAEKKKLVISTATVALQEQLVS   96 (697)
T ss_pred             cceEEEECCCCcchhHHHHHHHHHHHHHcCCeEEEEcCCHHHHHHHHh
Confidence            467899999999999999999987766678899999999999988864

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=98.33  E-value=1.1e-06  Score=71.50  Aligned_cols=55  Identities=13%  Similarity=0.077  Sum_probs=45.9

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhh
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF   62 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~   62 (138)
                      .+..++||+|||+++.++++-+.+. +..+.+++|+..|+.|.++.+.++....+.
T Consensus        72 ~Iaem~TGeGKTLva~lpa~l~aL~-G~~V~VvTpt~~LA~qdae~~~~l~~~LGL  126 (745)
T TIGR00963        72 KIAEMKTGEGKTLTATLPAYLNALT-GKGVHVVTVNDYLAQRDAEWMGQVYRFLGL  126 (745)
T ss_pred             ceeeecCCCccHHHHHHHHHHHHHh-CCCEEEEcCCHHHHHHHHHHHHHHhccCCC
Confidence            3899999999999999998644444 678999999999999999999988654433

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.

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

Probab=98.33  E-value=1.2e-06  Score=70.95  Aligned_cols=54  Identities=17%  Similarity=0.127  Sum_probs=47.6

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +|+.+++.||||+|||+.++.+++......+.++++.++++++.+|.+++..+.
T Consensus        33 ~~~~~~iEapTGtGKTl~yL~~al~~~~~~~~~viist~t~~lq~q~~~~~~~~   86 (654)
T COG1199          33 GGEGLLIEAPTGTGKTLAYLLPALAYAREEGKKVIISTRTKALQEQLLEEDLPI   86 (654)
T ss_pred             CCCcEEEECCCCccHHHHHHHHHHHHHHHcCCcEEEECCCHHHHHHHHHhhcch
Confidence            455699999999999999999999887777899999999999999998876664

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

Probab=98.32  E-value=1.5e-06  Score=67.48  Aligned_cols=49  Identities=27%  Similarity=0.445  Sum_probs=40.7

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ++..++++|||+|||.++...+..    .+.++++++|+..|..|-.+.+...
T Consensus        55 ~~~gvivlpTGaGKT~va~~~~~~----~~~~~Lvlv~~~~L~~Qw~~~~~~~  103 (442)
T COG1061          55 ERRGVIVLPTGAGKTVVAAEAIAE----LKRSTLVLVPTKELLDQWAEALKKF  103 (442)
T ss_pred             CCceEEEeCCCCCHHHHHHHHHHH----hcCCEEEEECcHHHHHHHHHHHHHh
Confidence            678899999999999999777665    2345999999999999988776665

>PHA02653 RNA helicase NPH-II; Provisional

Probab=98.30  E-value=9.7e-07  Score=71.51  Aligned_cols=54  Identities=26%  Similarity=0.226  Sum_probs=40.8

Q ss_pred             CCCccEEEEccCCcchHHHH---------HHHHHHHHh----h-cCCeEEEEcchhhhHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVG---------EILIMKELK----I-KQKSAIFILPYISLVHEKYQSLAK   55 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~---------~~~~~~~~~----~-~~~~~l~v~P~~aL~~q~~~~l~~   55 (138)
                      ++|++++++|+||||||...         .++.+..+.    + .+++++++.|+++|+.|...++.+
T Consensus       177 ~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~  244 (675)
T PHA02653        177 ISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLK  244 (675)
T ss_pred             HhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHH
Confidence            57899999999999999862         222333221    1 356899999999999998888765

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=98.29  E-value=2e-06  Score=70.54  Aligned_cols=52  Identities=27%  Similarity=0.429  Sum_probs=45.7

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhh---cCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKI---KQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~---~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      .+++.||||+|||.+++..+...+.+   ...|++++.|++++.+++++.+.+++
T Consensus       216 ~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie~~~~r~~~~~  270 (733)
T COG1203         216 LVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIF  270 (733)
T ss_pred             cEEEEeCCCCChHHHHHHHHHHHhhccccccceEEEEccHHHHHHHHHHHHHhhh
Confidence            67899999999999999998876665   36799999999999999999988753

>PHA02653 RNA helicase NPH-II; Provisional

Probab=98.29  E-value=2e-06  Score=69.78  Aligned_cols=66  Identities=24%  Similarity=0.147  Sum_probs=50.7

Q ss_pred             hhhhhHHHhhhhc-cceEEEeecCCCchHh---------HHHHHHHHHH----h-CCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          62 FYLEGKCLEMIQN-KNCVLSIPTSGGKTLV---------GEILIMKELK----I-KQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        62 ~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~---------~~~~~l~~~~----~-~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      ..+|.+.++.+.+ +++++.++||+|||..         ++++.+..+.    . ...+++++.|+++|+.|...++.+.
T Consensus       166 ~~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~~  245 (675)
T PHA02653        166 PDVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLKS  245 (675)
T ss_pred             HHHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHHH
Confidence            3467878888877 9999999999999986         2233444332    1 3468999999999999999988765


Q ss_pred             h
Q psy2029         127 A  127 (138)
Q Consensus       127 ~  127 (138)
                      .
T Consensus       246 v  246 (675)
T PHA02653        246 L  246 (675)
T ss_pred             h
Confidence            4

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=98.29  E-value=2.2e-06  Score=70.28  Aligned_cols=75  Identities=27%  Similarity=0.414  Sum_probs=60.5

Q ss_pred             hhhhhhhhHHHhhh---hc-c-ceEEEeecCCCchHhHHHHHHHHHHh---CCCeEEEEccchhHHHHHHHHHHHHhhhc
Q psy2029          59 EFKFYLEGKCLEMI---QN-K-NCVLSIPTSGGKTLVGEILIMKELKI---KQKSAIFILPYISLVHEKYQSLAKAAEEF  130 (138)
Q Consensus        59 ~~~~~~Q~~~~~~~---~~-~-~~ii~~ptg~GKt~~~~~~~l~~~~~---~~~~~~~i~P~~~l~~q~~~~~~~~~~~~  130 (138)
                      ..+.+.|..+....   .. . .+++.+|||+|||.+++.+++..+..   ...+.+|+.|++++++++++.+++++...
T Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie~~~~r~~~~~~~~  273 (733)
T COG1203         194 HEGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGLF  273 (733)
T ss_pred             chhhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhccccccceEEEEccHHHHHHHHHHHHHhhhccc
Confidence            34577787777322   23 4 67899999999999999999888777   36899999999999999999999987665


Q ss_pred             Cce
Q psy2029         131 KFY  133 (138)
Q Consensus       131 ~~~  133 (138)
                      +..
T Consensus       274 ~~~  276 (733)
T COG1203         274 SVI  276 (733)
T ss_pred             ccc
Confidence            443

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

Probab=98.29  E-value=2.6e-06  Score=72.51  Aligned_cols=66  Identities=15%  Similarity=0.269  Sum_probs=51.9

Q ss_pred             hhhhhhHHHhhh----h-c-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHHHHHHHh
Q psy2029          61 KFYLEGKCLEMI----Q-N-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAA  127 (138)
Q Consensus        61 ~~~~Q~~~~~~~----~-~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~~~~~~~  127 (138)
                      +.+.|..++..+    . . ++.++.+|||+|||+.+...+ .++..  ..+++++++|.++|+.|..+.|..+.
T Consensus       414 lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~li-~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~~~~  487 (1123)
T PRK11448        414 LRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIALM-YRLLKAKRFRRILFLVDRSALGEQAEDAFKDTK  487 (1123)
T ss_pred             CCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHHHH-HHHHhcCccCeEEEEecHHHHHHHHHHHHHhcc
Confidence            577898888433    2 2 678999999999999975544 44443  34799999999999999999999874

>KOG0341|consensus

Probab=98.28  E-value=2.1e-06  Score=64.95  Aligned_cols=57  Identities=16%  Similarity=0.146  Sum_probs=47.2

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhh----------cCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKI----------KQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~----------~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +|.|+++|-.|-||||||++|.+|+..-.++          .+.-.++++|.++|..|.++-+..+.
T Consensus       204 vLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~gLiicPSRELArQt~~iie~~~  270 (610)
T KOG0341|consen  204 VLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEGPYGLIICPSRELARQTHDIIEQYV  270 (610)
T ss_pred             EeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCCCeeEEEcCcHHHHHHHHHHHHHHH
Confidence            3789999999999999999998886654333          35688999999999999988777764

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=98.27  E-value=1.6e-06  Score=71.68  Aligned_cols=52  Identities=19%  Similarity=0.206  Sum_probs=44.1

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK   55 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~   55 (138)
                      ++.+++++||||||||..+..++++... .+++++++.|++.++.|..+.+.+
T Consensus        19 ~~~~vvv~A~TGSGKTt~~pl~lL~~~~-~~~~ilvlqPrR~aA~qia~rva~   70 (812)
T PRK11664         19 TAPQVLLKAPTGAGKSTWLPLQLLQHGG-INGKIIMLEPRRLAARNVAQRLAE   70 (812)
T ss_pred             hCCCEEEEcCCCCCHHHHHHHHHHHcCC-cCCeEEEECChHHHHHHHHHHHHH
Confidence            4678999999999999999988886532 346899999999999999888754

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

Probab=98.26  E-value=2.7e-06  Score=72.41  Aligned_cols=53  Identities=19%  Similarity=0.320  Sum_probs=42.5

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +++++++|||||||.++...+...+.. ..+++|+++|.++|.+|..++|..++
T Consensus       434 r~~Ll~maTGSGKT~tai~li~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~~~~  487 (1123)
T PRK11448        434 REILLAMATGTGKTRTAIALMYRLLKAKRFRRILFLVDRSALGEQAEDAFKDTK  487 (1123)
T ss_pred             CCeEEEeCCCCCHHHHHHHHHHHHHhcCccCeEEEEecHHHHHHHHHHHHHhcc
Confidence            578999999999999875555443322 34699999999999999999988763

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

Probab=98.25  E-value=2.5e-06  Score=69.27  Aligned_cols=53  Identities=17%  Similarity=0.202  Sum_probs=44.4

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++.++++|||||||+.+...+...+.. ...++++++|...|.+|..++|..++
T Consensus       264 ~~gli~~~TGsGKT~t~~~la~~l~~~~~~~~vl~lvdR~~L~~Q~~~~f~~~~  317 (667)
T TIGR00348       264 RGGLIWHTQGSGKTLTMLFAARKALELLKNPKVFFVVDRRELDYQLMKEFQSLQ  317 (667)
T ss_pred             ceeEEEEecCCCccHHHHHHHHHHHhhcCCCeEEEEECcHHHHHHHHHHHHhhC
Confidence            578999999999999987777654322 45699999999999999999998875

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

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

Probab=98.24  E-value=6.1e-06  Score=68.44  Aligned_cols=72  Identities=15%  Similarity=0.116  Sum_probs=54.7

Q ss_pred             hhhhhHHH----hhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHH-HHHHHHhhhcCceee
Q psy2029          62 FYLEGKCL----EMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKY-QSLAKAAEEFKFYLE  135 (138)
Q Consensus        62 ~~~Q~~~~----~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~-~~~~~~~~~~~~~v~  135 (138)
                      .+-|.+..    ..+.+ ..+++.++||+|||+.++++++...  .+.++++.+||++|.+|.. +++..+.+.+++++.
T Consensus       247 R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~--~~~~vvI~t~T~~Lq~Ql~~~~i~~l~~~~~~~~~  324 (820)
T PRK07246        247 RPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS--DQRQIIVSVPTKILQDQIMAEEVKAIQEVFHIDCH  324 (820)
T ss_pred             CHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc--CCCcEEEEeCcHHHHHHHHHHHHHHHHHhcCCcEE
Confidence            34455533    33444 7788999999999999999988754  3678999999999999994 777777666666543

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=98.22  E-value=3.1e-06  Score=70.03  Aligned_cols=52  Identities=19%  Similarity=0.227  Sum_probs=44.8

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK   55 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~   55 (138)
                      ++.+++++||||||||..+..+++.... .+++++++.|++.++.|..+.+.+
T Consensus        16 ~~~~vIi~a~TGSGKTT~vpl~lL~~~~-~~~~ilvlqPrR~aA~qiA~rva~   67 (819)
T TIGR01970        16 AHPQVVLEAPPGAGKSTAVPLALLDAPG-IGGKIIMLEPRRLAARSAAQRLAS   67 (819)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHHHhhc-cCCeEEEEeCcHHHHHHHHHHHHH
Confidence            4568999999999999999999887653 467999999999999999988754

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.

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

Probab=98.21  E-value=6e-06  Score=66.09  Aligned_cols=77  Identities=21%  Similarity=0.253  Sum_probs=61.7

Q ss_pred             hhhhhhhHHHhhhh-----c--cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCc
Q psy2029          60 FKFYLEGKCLEMIQ-----N--KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF  132 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~-----~--~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~  132 (138)
                      .++..|..++.-+.     .  .|-++--.-|||||++|.++++..+. .+.++..++||-=||+|-++.+.+|+.++|+
T Consensus       262 ~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~-~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i  340 (677)
T COG1200         262 KLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIE-AGYQAALMAPTEILAEQHYESLRKWLEPLGI  340 (677)
T ss_pred             CccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHH-cCCeeEEeccHHHHHHHHHHHHHHHhhhcCC
Confidence            35566777763222     1  45567888999999999998887655 4888999999999999999999999999999


Q ss_pred             eeeec
Q psy2029         133 YLEVL  137 (138)
Q Consensus       133 ~v~~~  137 (138)
                      +|.-+
T Consensus       341 ~V~lL  345 (677)
T COG1200         341 RVALL  345 (677)
T ss_pred             eEEEe
Confidence            88654

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=98.20  E-value=1.5e-05  Score=65.70  Aligned_cols=74  Identities=15%  Similarity=0.084  Sum_probs=57.6

Q ss_pred             hhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          61 KFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      ++++|....-.+ ...-+..+.||+|||+++.++++-.... +..+-+++|+..||.|.++.+..++..+|+.|..
T Consensus        82 ~~dvQlig~l~L-~~G~Iaem~TGeGKTLva~lpa~l~aL~-G~~V~IvTpn~yLA~rd~e~~~~l~~~LGlsv~~  155 (830)
T PRK12904         82 HFDVQLIGGMVL-HEGKIAEMKTGEGKTLVATLPAYLNALT-GKGVHVVTVNDYLAKRDAEWMGPLYEFLGLSVGV  155 (830)
T ss_pred             CCccHHHhhHHh-cCCchhhhhcCCCcHHHHHHHHHHHHHc-CCCEEEEecCHHHHHHHHHHHHHHHhhcCCeEEE
Confidence            455555443323 3334789999999999999999644444 5567799999999999999999999999998864

>TIGR00603 rad25 DNA repair helicase rad25

Probab=98.19  E-value=3.5e-06  Score=68.64  Aligned_cols=49  Identities=20%  Similarity=0.287  Sum_probs=41.5

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++.++++|||+|||+++..++..    .++++|+++|+..|++|-.++|.++.
T Consensus       274 r~GIIvLPtGaGKTlvai~aa~~----l~k~tLILvps~~Lv~QW~~ef~~~~  322 (732)
T TIGR00603       274 RSGIIVLPCGAGKSLVGVTAACT----VKKSCLVLCTSAVSVEQWKQQFKMWS  322 (732)
T ss_pred             CCcEEEeCCCCChHHHHHHHHHH----hCCCEEEEeCcHHHHHHHHHHHHHhc
Confidence            47899999999999999766543    25789999999999999999998874

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).

>KOG0336|consensus

Probab=98.18  E-value=1e-06  Score=66.95  Aligned_cols=58  Identities=16%  Similarity=0.107  Sum_probs=48.8

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhh--------cCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKI--------KQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--------~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      +|+|.+++..|.||+|||++++.+.+.|+..        .+..+++++|+++|..|+.-+...+..
T Consensus       254 ~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~ptreLalqie~e~~kysy  319 (629)
T KOG0336|consen  254 LLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTRELALQIEGEVKKYSY  319 (629)
T ss_pred             eecCcceEEEEecCCCcCHHHhccceeeeeccchhhhccCCCceEEEeccHHHHHHHHhHHhHhhh
Confidence            4899999999999999999999998876533        245889999999999998877777644

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=98.17  E-value=2.4e-06  Score=70.51  Aligned_cols=54  Identities=17%  Similarity=0.110  Sum_probs=46.5

Q ss_pred             EEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhh
Q psy2029           8 VLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF   62 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~   62 (138)
                      +..++||+|||++|.+|++.+++. +..+++++|+..|+.|.++.+.++....+.
T Consensus        99 Iaem~TGeGKTL~a~Lpa~~~al~-G~~V~VvTpn~yLA~qd~e~m~~l~~~lGL  152 (896)
T PRK13104         99 IAEMRTGEGKTLVATLPAYLNAIS-GRGVHIVTVNDYLAKRDSQWMKPIYEFLGL  152 (896)
T ss_pred             cccccCCCCchHHHHHHHHHHHhc-CCCEEEEcCCHHHHHHHHHHHHHHhcccCc
Confidence            789999999999999999977664 677999999999999999999988654443

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=98.14  E-value=9e-06  Score=67.36  Aligned_cols=64  Identities=17%  Similarity=0.167  Sum_probs=49.9

Q ss_pred             hhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHH-hhhcCceee
Q psy2029          71 MIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA-AEEFKFYLE  135 (138)
Q Consensus        71 ~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~-~~~~~~~v~  135 (138)
                      .+.+ .++++.+|||+|||..+.+++++... .+.+++++.|++.++.|.++.+.+. ....|..|+
T Consensus        16 ~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~-~~~~ilvlqPrR~aA~qia~rva~~l~~~~g~~VG   81 (812)
T PRK11664         16 ALKTAPQVLLKAPTGAGKSTWLPLQLLQHGG-INGKIIMLEPRRLAARNVAQRLAEQLGEKPGETVG   81 (812)
T ss_pred             HHHhCCCEEEEcCCCCCHHHHHHHHHHHcCC-cCCeEEEECChHHHHHHHHHHHHHHhCcccCceEE
Confidence            3444 78999999999999999988887543 2458999999999999999998654 344454443

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=98.13  E-value=3.2e-05  Score=63.55  Aligned_cols=75  Identities=11%  Similarity=0.055  Sum_probs=61.3

Q ss_pred             hhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeeec
Q psy2029          61 KFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEVL  137 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~~  137 (138)
                      ++++|....-.+.+ .-+..+.||+|||+++.+++...+.. +..+-+++|+--||.+-++.+..++..+|++|...
T Consensus        81 ~~dvQlig~l~l~~-G~iaEm~TGEGKTLvA~l~a~l~al~-G~~v~vvT~neyLA~Rd~e~~~~~~~~LGl~vg~i  155 (796)
T PRK12906         81 PFDVQIIGGIVLHE-GNIAEMKTGEGKTLTATLPVYLNALT-GKGVHVVTVNEYLSSRDATEMGELYRWLGLTVGLN  155 (796)
T ss_pred             CchhHHHHHHHHhc-CCcccccCCCCCcHHHHHHHHHHHHc-CCCeEEEeccHHHHHhhHHHHHHHHHhcCCeEEEe
Confidence            55666555433333 33889999999999999999887775 77788999999999999999999999999998754

>PF13245 AAA_19: Part of AAA domain

Probab=98.12  E-value=1.8e-05  Score=46.84  Aligned_cols=49  Identities=22%  Similarity=0.182  Sum_probs=36.4

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhh---cCCeEEEEcchhhhHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKI---KQKSAIFILPYISLVHEKYQSL   53 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~---~~~~~l~v~P~~aL~~q~~~~l   53 (138)
                      .-++|.+|.|||||....-.+...+..   .+.+++++.|++...+++.+.+
T Consensus        11 ~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen   11 PLFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCCHHHHHHHHHHH
Confidence            345669999999996665555543321   2679999999999888877776

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=98.11  E-value=2.4e-05  Score=64.82  Aligned_cols=61  Identities=16%  Similarity=0.090  Sum_probs=54.5

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      ..-+..++||.|||+++.++++..+.. +..+.+++|+..||.+.++.+..++..+|++|..
T Consensus        96 ~G~IaEm~TGEGKTL~a~lp~~l~al~-g~~VhIvT~ndyLA~RD~e~m~~l~~~lGlsv~~  156 (908)
T PRK13107         96 SNRIAEMRTGEGKTLTATLPAYLNALT-GKGVHVITVNDYLARRDAENNRPLFEFLGLTVGI  156 (908)
T ss_pred             CCccccccCCCCchHHHHHHHHHHHhc-CCCEEEEeCCHHHHHHHHHHHHHHHHhcCCeEEE
Confidence            455789999999999999999877765 5669999999999999999999999999999864

>KOG0352|consensus

Probab=98.11  E-value=7.3e-06  Score=62.73  Aligned_cols=64  Identities=25%  Similarity=0.422  Sum_probs=53.2

Q ss_pred             hhhhhhhHHHhhhhc--cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHh
Q psy2029          60 FKFYLEGKCLEMIQN--KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA  127 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~--~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~  127 (138)
                      .-.+.|++++..+.+  .++.+++|||+||++++-+|.+-    .++-.+++.|+.||+.++...+.++-
T Consensus        20 FKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~----~~gITIV~SPLiALIkDQiDHL~~LK   85 (641)
T KOG0352|consen   20 FKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALV----HGGITIVISPLIALIKDQIDHLKRLK   85 (641)
T ss_pred             hcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHH----hCCeEEEehHHHHHHHHHHHHHHhcC
Confidence            345679988865544  88899999999999999999875    25577899999999999999888763

>KOG0333|consensus

Probab=98.09  E-value=3.6e-06  Score=65.60  Aligned_cols=57  Identities=21%  Similarity=0.179  Sum_probs=48.1

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh-----------cCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI-----------KQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-----------~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++.+|+|..|.||||||+++.++++.-+.+           .+++++++.|+++|..|+.++-..++.
T Consensus       280 lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~~~~en~~~gpyaiilaptReLaqqIeeEt~kf~~  347 (673)
T KOG0333|consen  280 LQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNIEGPYAIILAPTRELAQQIEEETNKFGK  347 (673)
T ss_pred             hccCCeeeEEeccCCccccchhhHHHHHHcCCCcchhhhcccCceeeeechHHHHHHHHHHHHHHhcc
Confidence            678899999999999999999887754322           367999999999999999998777754

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.09  E-value=8.1e-06  Score=66.79  Aligned_cols=55  Identities=22%  Similarity=0.273  Sum_probs=45.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcC--CeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQ--KSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~--~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .+|+++++.+|||+|||++.+.+++....+.+  .+++|.+.+.+=..|..+++++.
T Consensus        27 ~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~~~~kIiy~sRThsQl~q~i~Elk~~   83 (705)
T TIGR00604        27 DRGDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRKL   83 (705)
T ss_pred             ccCCceEEeCCCCCCccHHHHHHHHHHHHhccccccEEEEcccchHHHHHHHHHHhh
Confidence            46789999999999999999999888766444  69999999987667777887774

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).

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=98.09  E-value=1.9e-05  Score=65.52  Aligned_cols=64  Identities=17%  Similarity=0.195  Sum_probs=50.7

Q ss_pred             hhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHh-hhcCcee
Q psy2029          70 EMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA-EEFKFYL  134 (138)
Q Consensus        70 ~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~-~~~~~~v  134 (138)
                      ..+.+ .++++.+|||+|||..+.+++++... .+.+++++.|++.++.|.++.+.+.. ...|..|
T Consensus        12 ~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~-~~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~V   77 (819)
T TIGR01970        12 DALAAHPQVVLEAPPGAGKSTAVPLALLDAPG-IGGKIIMLEPRRLAARSAAQRLASQLGEAVGQTV   77 (819)
T ss_pred             HHHHcCCcEEEECCCCCCHHHHHHHHHHHhhc-cCCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEE
Confidence            33444 78899999999999999999988763 35689999999999999999986443 3444444

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.

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

Probab=98.09  E-value=1.9e-05  Score=66.58  Aligned_cols=89  Identities=18%  Similarity=0.164  Sum_probs=71.6

Q ss_pred             HHHHHHHHHHHhhhhhhhhHHHhhhh-----c--cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHH
Q psy2029          48 EKYQSLAKAAEEFKFYLEGKCLEMIQ-----N--KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKY  120 (138)
Q Consensus        48 q~~~~l~~~~~~~~~~~Q~~~~~~~~-----~--~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~  120 (138)
                      +.+++|.+.+....++=|..++..+.     .  .+-++|-.-|-|||-+|+-+++..+.. ++++.+++||+-|++|.+
T Consensus       582 ~~q~~F~~~FPyeET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~-GKQVAvLVPTTlLA~QHy  660 (1139)
T COG1197         582 EWQEEFEASFPYEETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMD-GKQVAVLVPTTLLAQQHY  660 (1139)
T ss_pred             HHHHHHHhcCCCcCCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhcC-CCeEEEEcccHHhHHHHH
Confidence            44556655544455666877874333     1  566899999999999999998887665 789999999999999999


Q ss_pred             HHHHHHhhhcCceeeec
Q psy2029         121 QSLAKAAEEFKFYLEVL  137 (138)
Q Consensus       121 ~~~~~~~~~~~~~v~~~  137 (138)
                      +.|++.|.++.++|..+
T Consensus       661 ~tFkeRF~~fPV~I~~L  677 (1139)
T COG1197         661 ETFKERFAGFPVRIEVL  677 (1139)
T ss_pred             HHHHHHhcCCCeeEEEe
Confidence            99999999999998765

>KOG0328|consensus

Probab=98.08  E-value=1.6e-06  Score=63.09  Aligned_cols=61  Identities=13%  Similarity=0.300  Sum_probs=50.8

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHh--hcCCeEEEEcchhhhHHHHHHHHHHHHHhhh
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELK--IKQKSAIFILPYISLVHEKYQSLAKAAEEFK   61 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~--~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~   61 (138)
                      |++|+|++..|..|+|||..+.+.+++.+-  .+...++++.|+++|..|+.+.+...+...+
T Consensus        61 IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~lilsPTRELa~Qi~~vi~alg~~mn  123 (400)
T KOG0328|consen   61 ILKGRDVIAQAQSGTGKTATFSISVLQSLDISVRETQALILSPTRELAVQIQKVILALGDYMN  123 (400)
T ss_pred             hhcccceEEEecCCCCceEEEEeeeeeecccccceeeEEEecChHHHHHHHHHHHHHhccccc
Confidence            589999999999999999999888886432  2456889999999999999998888765443

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

Probab=98.05  E-value=0.00014  Score=61.48  Aligned_cols=52  Identities=17%  Similarity=0.201  Sum_probs=47.2

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      |=++|+.-|-|||.+|+=+++....+ |+.+.+++||+-|++|.+++|.+.+.
T Consensus       617 DRLiCGDVGFGKTEVAmRAAFkAV~~-GKQVAvLVPTTlLA~QHy~tFkeRF~  668 (1139)
T COG1197         617 DRLICGDVGFGKTEVAMRAAFKAVMD-GKQVAVLVPTTLLAQQHYETFKERFA  668 (1139)
T ss_pred             hheeecCcCCcHHHHHHHHHHHHhcC-CCeEEEEcccHHhHHHHHHHHHHHhc
Confidence            44899999999999999999998775 89999999999999999999998765

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=98.01  E-value=0.0004  Score=49.63  Aligned_cols=53  Identities=13%  Similarity=0.163  Sum_probs=39.1

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ..|..+++.+|.|+|||..+...+...+ .++.+++|+.- -.-..+..+++..+
T Consensus        19 ~~gs~~lI~G~pGsGKT~la~~~l~~~~-~~ge~~lyvs~-ee~~~~i~~~~~~~   71 (237)
T TIGR03877        19 PERNVVLLSGGPGTGKSIFSQQFLWNGL-QMGEPGIYVAL-EEHPVQVRRNMAQF   71 (237)
T ss_pred             cCCeEEEEEcCCCCCHHHHHHHHHHHHH-HcCCcEEEEEe-eCCHHHHHHHHHHh
Confidence            3578899999999999999988887766 45889999863 22334555655544

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.

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

Probab=98.00  E-value=0.0003  Score=49.67  Aligned_cols=121  Identities=13%  Similarity=0.104  Sum_probs=65.0

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhhhhHHHhhhhccce-EEEe
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIQNKNC-VLSI   81 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~-ii~~   81 (138)
                      .|..+++.+|+|+|||..+...+.+.+.+.+.+++|+.-... ..+..+++..+    ++++....    .+.++ ++..
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs~ee~-~~~l~~~~~s~----g~d~~~~~----~~g~l~~~d~   88 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVSFEEP-PEELIENMKSF----GWDLEEYE----DSGKLKIIDA   88 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEESSS--HHHHHHHHHTT----TS-HHHHH----HTTSEEEEES
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEEecCC-HHHHHHHHHHc----CCcHHHHh----hcCCEEEEec
Confidence            578899999999999999988888766544788888764221 23444444433    44333211    11112 2222


Q ss_pred             ecCC----CchHhHHHHHHHHHHh-CCCeEEEEccchhH--------HHHHHHHHHHHhhhcCc
Q psy2029          82 PTSG----GKTLVGEILIMKELKI-KQKSAIFILPYISL--------VHEKYQSLAKAAEEFKF  132 (138)
Q Consensus        82 ptg~----GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l--------~~q~~~~~~~~~~~~~~  132 (138)
                      .+..    ....-.++..+....+ .+.+.++|.+..++        .....+.+.+.....|.
T Consensus        89 ~~~~~~~~~~~~~~l~~~i~~~i~~~~~~~vVIDsls~l~~~~~~~~~r~~l~~l~~~l~~~~~  152 (226)
T PF06745_consen   89 FPERIGWSPNDLEELLSKIREAIEELKPDRVVIDSLSALLLYDDPEELRRFLRALIKFLKSRGV  152 (226)
T ss_dssp             SGGGST-TSCCHHHHHHHHHHHHHHHTSSEEEEETHHHHTTSSSGGGHHHHHHHHHHHHHHTTE
T ss_pred             ccccccccccCHHHHHHHHHHHHHhcCCCEEEEECHHHHhhcCCHHHHHHHHHHHHHHHHHCCC
Confidence            2221    2233333333333332 35578889988888        23344455555555554

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 ....

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=97.98  E-value=0.00054  Score=49.68  Aligned_cols=106  Identities=14%  Similarity=0.114  Sum_probs=59.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhhhhHHHhhhhccceEEEee
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIQNKNCVLSIP   82 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~ii~~p   82 (138)
                      .|.-++|.+|+|+|||..+...+...+. ++.+++|+.-- .=.++..+++.......+++++..      ..++++.-+
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~~~a~-~Ge~vlyis~E-e~~~~~~~~l~~~a~~~g~d~~~~------~~~l~~id~  106 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAVTQAS-RGNPVLFVTVE-SPANFVYTSLKERAKAMGVDFDKI------EENIILIDA  106 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHh-CCCcEEEEEec-CCchHHHHHHHHHHHHcCCCHHHH------hCCEEEEEC
Confidence            4677899999999999999887776554 47799997632 111333344444444445554421      123444333


Q ss_pred             cCCC---chHhHHHHHHHHHH-hCCCeEEEEccchhHH
Q psy2029          83 TSGG---KTLVGEILIMKELK-IKQKSAIFILPYISLV  116 (138)
Q Consensus        83 tg~G---Kt~~~~~~~l~~~~-~~~~~~~~i~P~~~l~  116 (138)
                      ...-   ...-.++..+.+.. +.+.+.++|.+..++-
T Consensus       107 ~~~~~~~~~~~~l~~~l~~~i~~~~~~~vVIDSls~l~  144 (259)
T TIGR03878       107 ASSTELRENVPNLLATLAYAIKEYKVKNTVIDSITGLY  144 (259)
T ss_pred             CCchhhhhhHHHHHHHHHHHHHhhCCCEEEEcCchHhc
Confidence            3211   12222222233222 3467788898887653

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

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

Probab=97.96  E-value=4.5e-05  Score=62.12  Aligned_cols=54  Identities=17%  Similarity=0.206  Sum_probs=44.5

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHHHHHHHHHHHHhh
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAAE  128 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~~q~~~~~~~~~~  128 (138)
                      ++.++.+|||+|||+.+...+..-+.. ...++++++|...|..|..+.|.++..
T Consensus       264 ~~gli~~~TGsGKT~t~~~la~~l~~~~~~~~vl~lvdR~~L~~Q~~~~f~~~~~  318 (667)
T TIGR00348       264 RGGLIWHTQGSGKTLTMLFAARKALELLKNPKVFFVVDRRELDYQLMKEFQSLQK  318 (667)
T ss_pred             ceeEEEEecCCCccHHHHHHHHHHHhhcCCCeEEEEECcHHHHHHHHHHHHhhCC
Confidence            578999999999999997666443322 347899999999999999999998863

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

>KOG0332|consensus

Probab=97.94  E-value=1e-05  Score=60.84  Aligned_cols=56  Identities=13%  Similarity=0.124  Sum_probs=47.4

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHHHhh
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAEEF   60 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~~~~   60 (138)
                      .|+|..+..|+|||.+|.+.|+.+.-.  ....++.++|+++|+.|..+.+.+.|...
T Consensus       130 ~nlIaQsqsGtGKTaaFvL~MLsrvd~~~~~PQ~iCLaPtrELA~Q~~eVv~eMGKf~  187 (477)
T KOG0332|consen  130 QNLIAQSQSGTGKTAAFVLTMLSRVDPDVVVPQCICLAPTRELAPQTGEVVEEMGKFT  187 (477)
T ss_pred             hhhhhhhcCCCchhHHHHHHHHHhcCccccCCCceeeCchHHHHHHHHHHHHHhcCce
Confidence            578889999999999999999986532  34578888999999999999999987654

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=97.93  E-value=3.7e-05  Score=63.00  Aligned_cols=66  Identities=18%  Similarity=0.256  Sum_probs=54.5

Q ss_pred             hhhhhHHH----hhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCC--CeEEEEccchhHHHHHHHHHHHHh
Q psy2029          62 FYLEGKCL----EMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQ--KSAIFILPYISLVHEKYQSLAKAA  127 (138)
Q Consensus        62 ~~~Q~~~~----~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~--~~~~~i~P~~~l~~q~~~~~~~~~  127 (138)
                      ++.|.+..    ..+.+ .+.++.+|||+|||+..+.+++....+.+  .|++|.+.|.+-..|..+++++..
T Consensus        12 y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~~~~kIiy~sRThsQl~q~i~Elk~~~   84 (705)
T TIGR00604        12 YPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRKLM   84 (705)
T ss_pred             CHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhccccccEEEEcccchHHHHHHHHHHhhh
Confidence            45565554    33445 88999999999999999999999877544  799999999999999999999853

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

>KOG0353|consensus

Probab=97.93  E-value=3.8e-05  Score=58.23  Aligned_cols=53  Identities=26%  Similarity=0.432  Sum_probs=46.1

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ..|+++++.+|||.||++++.+|++-    ..+-++++.|+.+|.+++.-.++..+.
T Consensus       107 ma~ed~~lil~tgggkslcyqlpal~----adg~alvi~plislmedqil~lkqlgi  159 (695)
T KOG0353|consen  107 MAGEDAFLILPTGGGKSLCYQLPALC----ADGFALVICPLISLMEDQILQLKQLGI  159 (695)
T ss_pred             hccCceEEEEeCCCccchhhhhhHHh----cCCceEeechhHHHHHHHHHHHHHhCc
Confidence            46889999999999999999999875    367789999999999998888887764

>KOG0353|consensus

Probab=97.93  E-value=3.9e-05  Score=58.14  Aligned_cols=65  Identities=23%  Similarity=0.321  Sum_probs=54.6

Q ss_pred             hhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhh
Q psy2029          61 KFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEE  129 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~  129 (138)
                      ..|.|..++..... ++.++.+|||+||++++-+|++-    ..+-+++|.|+.+|++++.-++++++..
T Consensus        95 frplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~----adg~alvi~plislmedqil~lkqlgi~  160 (695)
T KOG0353|consen   95 FRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALC----ADGFALVICPLISLMEDQILQLKQLGID  160 (695)
T ss_pred             cChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHh----cCCceEeechhHHHHHHHHHHHHHhCcc
Confidence            45667777766666 88899999999999999999875    3678899999999999999999988543

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=97.91  E-value=0.00011  Score=60.93  Aligned_cols=75  Identities=15%  Similarity=0.093  Sum_probs=59.6

Q ss_pred             hhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeeec
Q psy2029          61 KFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEVL  137 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~~  137 (138)
                      ++++|....- +....-+..+.||+|||+++.++++-.+.. +..+-+++|+..||.+-++.+..++..+|+.|...
T Consensus        83 ~ydVQliGg~-~Lh~G~iaEM~TGEGKTLvA~l~a~l~al~-G~~VhvvT~ndyLA~RD~e~m~~l~~~lGl~v~~i  157 (913)
T PRK13103         83 HFDVQLIGGM-TLHEGKIAEMRTGEGKTLVGTLAVYLNALS-GKGVHVVTVNDYLARRDANWMRPLYEFLGLSVGIV  157 (913)
T ss_pred             cchhHHHhhh-HhccCccccccCCCCChHHHHHHHHHHHHc-CCCEEEEeCCHHHHHHHHHHHHHHhcccCCEEEEE
Confidence            3445543322 223555789999999999999999876665 77888999999999999999999999999998754

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=97.90  E-value=0.00014  Score=59.33  Aligned_cols=74  Identities=16%  Similarity=0.069  Sum_probs=60.0

Q ss_pred             hhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          61 KFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      ++++|....-.+. ..-+..+.||+|||+++.+++...+.. +..+-+++|+.-||.+-++.+..++..+|++|..
T Consensus        79 ~ydvQlig~l~Ll-~G~VaEM~TGEGKTLvA~l~a~l~AL~-G~~VhvvT~NdyLA~RDae~m~~ly~~LGLsvg~  152 (764)
T PRK12326         79 PFDVQLLGALRLL-AGDVIEMATGEGKTLAGAIAAAGYALQ-GRRVHVITVNDYLARRDAEWMGPLYEALGLTVGW  152 (764)
T ss_pred             cchHHHHHHHHHh-CCCcccccCCCCHHHHHHHHHHHHHHc-CCCeEEEcCCHHHHHHHHHHHHHHHHhcCCEEEE
Confidence            4555554443333 344679999999999999999877765 7788999999999999999999999999999875

>KOG0949|consensus

Probab=97.87  E-value=4.4e-05  Score=63.51  Aligned_cols=67  Identities=22%  Similarity=0.301  Sum_probs=53.3

Q ss_pred             hhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHHHHHHHHHHHHh
Q psy2029          61 KFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAA  127 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~~q~~~~~~~~~  127 (138)
                      +..||.+....+-. ++.++.+||++|||.++..++=.-+.. ...-++|++|+++|++|...+....+
T Consensus       512 Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfisfY~iEKVLResD~~VVIyvaPtKaLVnQvsa~VyaRF  580 (1330)
T KOG0949|consen  512 PDEWQRELLDSVDRNESAVIVAPTSAGKTFISFYAIEKVLRESDSDVVIYVAPTKALVNQVSANVYARF  580 (1330)
T ss_pred             CcHHHHHHhhhhhcccceEEEeeccCCceeccHHHHHHHHhhcCCCEEEEecchHHHhhhhhHHHHHhh
Confidence            44577766654444 888999999999999997766555544 34678999999999999999998887

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

Probab=97.87  E-value=3.7e-05  Score=62.36  Aligned_cols=67  Identities=15%  Similarity=0.075  Sum_probs=56.3

Q ss_pred             hhhhhhhHHH----hhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          60 FKFYLEGKCL----EMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        60 ~~~~~Q~~~~----~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      .+.+.|.+..    ....+ +..++.+|||+|||+.++.+++......+.++++.+++.++-+|..++...+
T Consensus        15 ~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~~~~viist~t~~lq~q~~~~~~~~   86 (654)
T COG1199          15 EPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEGKKVIISTRTKALQEQLLEEDLPI   86 (654)
T ss_pred             CCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHcCCcEEEECCCHHHHHHHHHhhcch
Confidence            4666777766    23334 5589999999999999999999998887899999999999999999888765

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

Probab=97.83  E-value=6.4e-05  Score=61.50  Aligned_cols=67  Identities=22%  Similarity=0.316  Sum_probs=52.4

Q ss_pred             hhhhhhHHH----hhhhc--cceEEEeecCCCchHhHHHHHHHHHHhC--CCeEEEEccchhHHHHHHHHHHHHhh
Q psy2029          61 KFYLEGKCL----EMIQN--KNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQSLAKAAE  128 (138)
Q Consensus        61 ~~~~Q~~~~----~~~~~--~~~ii~~ptg~GKt~~~~~~~l~~~~~~--~~~~~~i~P~~~l~~q~~~~~~~~~~  128 (138)
                      +...|..++    +.+.+  ...++.+.||+|||..| +.++.++...  -+|+|+++..++|+.|.+..|.++..
T Consensus       166 ~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTA-iaii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P  240 (875)
T COG4096         166 PRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTA-IAIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLP  240 (875)
T ss_pred             chHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeH-HHHHHHHHhcchhheeeEEechHHHHHHHHHHHHHhCC
Confidence            455677777    33433  66899999999999999 5555566653  37999999999999999999888753

>PRK04328 hypothetical protein; Provisional

Probab=97.82  E-value=0.0013  Score=47.33  Aligned_cols=52  Identities=10%  Similarity=0.174  Sum_probs=36.7

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .|..+++.+|+|+|||..+...+...+. ++.+++|+.- -+-.++..+++..+
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~~~~-~ge~~lyis~-ee~~~~i~~~~~~~   73 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWNGLQ-MGEPGVYVAL-EEHPVQVRRNMRQF   73 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHh-cCCcEEEEEe-eCCHHHHHHHHHHc
Confidence            5778899999999999999888777654 4788888763 22233444444444

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

Probab=97.81  E-value=6.1e-05  Score=61.53  Aligned_cols=52  Identities=25%  Similarity=0.216  Sum_probs=45.7

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +..++.+-||||||.+|+-.+.+.+. .|+.+|+++|-++|..|..++|+..+
T Consensus       218 ~~~Ll~GvTGSGKTEvYl~~i~~~L~-~GkqvLvLVPEI~Ltpq~~~rf~~rF  269 (730)
T COG1198         218 APFLLDGVTGSGKTEVYLEAIAKVLA-QGKQVLVLVPEIALTPQLLARFKARF  269 (730)
T ss_pred             cceeEeCCCCCcHHHHHHHHHHHHHH-cCCEEEEEeccccchHHHHHHHHHHh
Confidence            45799999999999999888887654 58999999999999999999998864

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

Probab=97.80  E-value=7.7e-05  Score=62.86  Aligned_cols=61  Identities=15%  Similarity=0.127  Sum_probs=49.5

Q ss_pred             hhhhhhHHH----hhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHH
Q psy2029          61 KFYLEGKCL----EMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        61 ~~~~Q~~~~----~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~  121 (138)
                      ..+-|.+..    ..+.+ ...++.+|||.|||+.+++|++..+...+.++++-++|++|-+|..+
T Consensus       258 ~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~~~~~vvIsT~T~~LQ~Ql~~  323 (928)
T PRK08074        258 KREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKKKEEPVVISTYTIQLQQQLLE  323 (928)
T ss_pred             CCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhccCCeEEEEcCCHHHHHHHHH
Confidence            344565544    33344 77889999999999999999998777678999999999999999865

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=97.79  E-value=0.002  Score=46.72  Aligned_cols=131  Identities=14%  Similarity=0.065  Sum_probs=68.3

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhh---------hhhhh--HHHh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFK---------FYLEG--KCLE   70 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~---------~~~Q~--~~~~   70 (138)
                      ..|+.+++.+|+|+|||..+...+.......+.+++|+.---. .++..+.+........         +..+.  .+..
T Consensus        28 ~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~g~~vl~iS~E~~-~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  106 (271)
T cd01122          28 RKGELIILTAGTGVGKTTFLREYALDLITQHGVRVGTISLEEP-VVRTARRLLGQYAGKRLHLPDTVFIYTLEEFDAAFD  106 (271)
T ss_pred             cCCcEEEEEcCCCCCHHHHHHHHHHHHHHhcCceEEEEEcccC-HHHHHHHHHHHHhCCCcccCCccccccHHHHHHHHH
Confidence            4577889999999999998877766544444778888753111 1333333322211100         11111  0111


Q ss_pred             hhhc-cceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHHH-------------HHHHHHHHHhhhcCcee
Q psy2029          71 MIQN-KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVH-------------EKYQSLAKAAEEFKFYL  134 (138)
Q Consensus        71 ~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~~-------------q~~~~~~~~~~~~~~~v  134 (138)
                      ...+ .++.+. .....-+.-.+...++.+.. .+.+.++|.+...+..             +..+.+++++...++.|
T Consensus       107 ~~~~~~~l~i~-d~~~~~~~~~i~~~i~~~~~~~~~~~vvID~l~~l~~~~~~~~~~~~~~~~~~~~L~~la~~~~vtv  184 (271)
T cd01122         107 EFEGTGRLFMY-DSFGEYSMDSVLEKVRYMAVSHGIQHIIIDNLSIMVSDERASGDERKALDEIMTKLRGFATEHGIHI  184 (271)
T ss_pred             HhcCCCcEEEE-cCCCccCHHHHHHHHHHHHhcCCceEEEECCHHHHhccCCCchhHHHHHHHHHHHHHHHHHHhCCEE
Confidence            2222 233333 22222244444455554443 4678888888766642             33455666667766654

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.79  E-value=0.0019  Score=45.00  Aligned_cols=40  Identities=20%  Similarity=0.203  Sum_probs=30.8

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcch
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPY   42 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~   42 (138)
                      ..|.-+.+.+|+|+|||..+...+.... ..+.+++|+.-.
T Consensus        10 ~~g~i~~i~G~~GsGKT~l~~~~~~~~~-~~g~~v~yi~~e   49 (209)
T TIGR02237        10 ERGTITQIYGPPGSGKTNICMILAVNAA-RQGKKVVYIDTE   49 (209)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHH-hCCCeEEEEECC
Confidence            3567789999999999999977666543 457789987653

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

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=97.79  E-value=0.0011  Score=52.32  Aligned_cols=104  Identities=16%  Similarity=0.079  Sum_probs=60.8

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhhhhHHHhhhhccceE-E-
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIQNKNCV-L-   79 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~i-i-   79 (138)
                      ..|..+++.+|+|+|||..+...+...+ .++.+++|+.-- +=.+|+.++.+.+    +++.+..    ..+..+. + 
T Consensus       261 ~~gs~~li~G~~G~GKt~l~~~f~~~~~-~~ge~~~y~s~e-Es~~~i~~~~~~l----g~~~~~~----~~~g~l~~~~  330 (484)
T TIGR02655       261 FKDSIILATGATGTGKTLLVSKFLENAC-ANKERAILFAYE-ESRAQLLRNAYSW----GIDFEEM----EQQGLLKIIC  330 (484)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHH-HCCCeEEEEEee-CCHHHHHHHHHHc----CCChHHH----hhCCcEEEEE
Confidence            4678889999999999999988877654 457899997642 2234555555444    4433221    1111121 1 


Q ss_pred             EeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHH
Q psy2029          80 SIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLV  116 (138)
Q Consensus        80 ~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~  116 (138)
                      .-|...+.. -.+-.+++.+.+.+.+.++|.+..++.
T Consensus       331 ~~p~~~~~~-~~~~~i~~~i~~~~~~~vvIDsi~~~~  366 (484)
T TIGR02655       331 AYPESAGLE-DHLQIIKSEIADFKPARIAIDSLSALA  366 (484)
T ss_pred             cccccCChH-HHHHHHHHHHHHcCCCEEEEcCHHHHH
Confidence            224333311 122333444445677889999988773

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.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=97.75  E-value=0.0014  Score=46.69  Aligned_cols=39  Identities=18%  Similarity=0.141  Sum_probs=31.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      ..|+-+++.+|+|+|||..+...+...+.+.+.+++|+.
T Consensus        11 ~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s   49 (242)
T cd00984          11 QPGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFS   49 (242)
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEe
Confidence            457788999999999999988777776655578888876

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.

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=97.73  E-value=0.00039  Score=57.00  Aligned_cols=57  Identities=16%  Similarity=0.082  Sum_probs=46.9

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHH-HHHHHHhhhcC
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKY-QSLAKAAEEFK  131 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~-~~~~~~~~~~~  131 (138)
                      +..++.+|||.|||+.+++|++..+...++++++=+.|++|=+|.. +++-.+.+-+|
T Consensus        50 ~~lviEAgTGtGKTlaYLlPai~~A~~~~k~vVIST~T~~LQeQL~~kDlP~l~~~l~  107 (697)
T PRK11747         50 RILVIEAGTGVGKTLSYLLAGIPIARAEKKKLVISTATVALQEQLVSKDLPLLLKISG  107 (697)
T ss_pred             ceEEEECCCCcchhHHHHHHHHHHHHHcCCeEEEEcCCHHHHHHHHhhhhhHHHHHcC
Confidence            4578999999999999999999888877899999999999999986 55554444344

>KOG0327|consensus

Probab=97.71  E-value=1.2e-05  Score=60.25  Aligned_cols=65  Identities=14%  Similarity=0.287  Sum_probs=52.0

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhhh
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLE   65 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q   65 (138)
                      +++|.|+.+.+++|+|||.++.++++.++--  ....++.++|+++|..|..+.....+...+..++
T Consensus        60 ~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~ke~qalilaPtreLa~qi~~v~~~lg~~~~~~v~  126 (397)
T KOG0327|consen   60 CIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILAPTRELAQQIQKVVRALGDHMDVSVH  126 (397)
T ss_pred             cccCCceeEeeeccccchhhhHHHHHhhcCcchHHHHHHHhcchHHHHHHHHHHHHhhhcccceeee
Confidence            3689999999999999999999999876421  3457788999999999999887777665544444

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=97.71  E-value=5.1e-05  Score=62.66  Aligned_cols=55  Identities=16%  Similarity=0.099  Sum_probs=45.0

Q ss_pred             EEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhhh
Q psy2029           8 VLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFY   63 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~   63 (138)
                      +..++||+|||+++.++++-..+. +..+.+++|+..|+.+.++.+.+++...+..
T Consensus        98 Iaem~TGeGKTLva~lpa~l~aL~-G~~V~IvTpn~yLA~rd~e~~~~l~~~LGls  152 (830)
T PRK12904         98 IAEMKTGEGKTLVATLPAYLNALT-GKGVHVVTVNDYLAKRDAEWMGPLYEFLGLS  152 (830)
T ss_pred             hhhhhcCCCcHHHHHHHHHHHHHc-CCCEEEEecCHHHHHHHHHHHHHHHhhcCCe
Confidence            789999999999999998643443 6678899999999999999999886654443

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=97.70  E-value=6.4e-05  Score=62.36  Aligned_cols=57  Identities=16%  Similarity=0.060  Sum_probs=47.6

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhh
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYL   64 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~   64 (138)
                      -+..++||.|||+++.+|++.+.+. +..+.+++|+..|+.+-.+.+.++....+..+
T Consensus        98 ~IaEm~TGEGKTL~a~lp~~l~al~-g~~VhIvT~ndyLA~RD~e~m~~l~~~lGlsv  154 (908)
T PRK13107         98 RIAEMRTGEGKTLTATLPAYLNALT-GKGVHVITVNDYLARRDAENNRPLFEFLGLTV  154 (908)
T ss_pred             ccccccCCCCchHHHHHHHHHHHhc-CCCEEEEeCCHHHHHHHHHHHHHHHHhcCCeE
Confidence            4779999999999999999876664 66799999999999999998888866555443

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=97.69  E-value=0.00073  Score=53.21  Aligned_cols=60  Identities=15%  Similarity=0.205  Sum_probs=42.1

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhhhh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEG   66 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q~   66 (138)
                      ..|+..++.+|+|+|||..+...+...+.+.+.+++|+.-- +=.++..++    ....+|+.+.
T Consensus        19 p~g~~~Li~G~pGsGKT~la~qfl~~g~~~~ge~~lyvs~e-E~~~~l~~~----~~~~G~~~~~   78 (484)
T TIGR02655        19 PIGRSTLVSGTSGTGKTLFSIQFLYNGIIHFDEPGVFVTFE-ESPQDIIKN----ARSFGWDLQK   78 (484)
T ss_pred             CCCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEEe-cCHHHHHHH----HHHcCCCHHH
Confidence            35788999999999999999888887766557788998742 222344444    4444555554

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.

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

Probab=97.64  E-value=9.3e-05  Score=48.93  Aligned_cols=54  Identities=20%  Similarity=0.239  Sum_probs=38.9

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +|+-.++-.++|+|||.--+--+.+..++++.|+|++.|++.+.++..+.++..
T Consensus         3 kg~~~~~d~hpGaGKTr~vlp~~~~~~i~~~~rvLvL~PTRvva~em~~aL~~~   56 (148)
T PF07652_consen    3 KGELTVLDLHPGAGKTRRVLPEIVREAIKRRLRVLVLAPTRVVAEEMYEALKGL   56 (148)
T ss_dssp             TTEEEEEE--TTSSTTTTHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHTTTS
T ss_pred             CCceeEEecCCCCCCcccccHHHHHHHHHccCeEEEecccHHHHHHHHHHHhcC
Confidence            566778999999999975444444445667999999999999998888887654

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 ....

>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=97.61  E-value=0.0022  Score=43.66  Aligned_cols=49  Identities=14%  Similarity=0.148  Sum_probs=33.8

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ++++.+|+|+|||..+.-.+...+ ..+.+++|+... .-.++..+.+..+
T Consensus         1 ~~li~G~~G~GKT~l~~~~~~~~~-~~g~~v~~~s~e-~~~~~~~~~~~~~   49 (187)
T cd01124           1 STLLSGGPGTGKTTFALQFLYAGL-ARGEPGLYVTLE-ESPEELIENAESL   49 (187)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHH-HCCCcEEEEECC-CCHHHHHHHHHHc
Confidence            368999999999999877777655 457888887643 2234444544443

A related protein is found in archaea.

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=97.61  E-value=0.0028  Score=44.72  Aligned_cols=52  Identities=15%  Similarity=0.077  Sum_probs=36.9

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .|+.+++.+|+|+|||..+...+...+. ++.+++|+..--. .++..+++..+
T Consensus        15 ~g~~~li~G~~G~GKt~~~~~~~~~~~~-~g~~~~y~s~e~~-~~~l~~~~~~~   66 (224)
T TIGR03880        15 EGHVIVVIGEYGTGKTTFSLQFLYQGLK-NGEKAMYISLEER-EERILGYAKSK   66 (224)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHh-CCCeEEEEECCCC-HHHHHHHHHHc
Confidence            4678899999999999998877776554 4888999764332 34445554443

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.

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

Probab=97.60  E-value=0.00018  Score=49.32  Aligned_cols=45  Identities=29%  Similarity=0.324  Sum_probs=29.1

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEK   49 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~   49 (138)
                      ++.|+++.+|+|+|||..+... ...+.+.+.+++|+ +...|.++.
T Consensus        46 ~~~~l~l~G~~G~GKThLa~ai-~~~~~~~g~~v~f~-~~~~L~~~l   90 (178)
T PF01695_consen   46 NGENLILYGPPGTGKTHLAVAI-ANEAIRKGYSVLFI-TASDLLDEL   90 (178)
T ss_dssp             C--EEEEEESTTSSHHHHHHHH-HHHHHHTT--EEEE-EHHHHHHHH
T ss_pred             cCeEEEEEhhHhHHHHHHHHHH-HHHhccCCcceeEe-ecCceeccc
Confidence            5789999999999999998444 44466667777774 444554443

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.

>KOG0326|consensus

Probab=97.59  E-value=2e-05  Score=58.33  Aligned_cols=60  Identities=17%  Similarity=0.227  Sum_probs=50.9

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhc--CCeEEEEcchhhhHHHHHHHHHHHHHhhh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQSLAKAAEEFK   61 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~--~~~~l~v~P~~aL~~q~~~~l~~~~~~~~   61 (138)
                      |.|+|++..|..|+|||.++.+|+++.+-..  .-.+++++|+++|..|..+...+.+.+.+
T Consensus       120 LtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPtrelALQtSqvc~~lskh~~  181 (459)
T KOG0326|consen  120 LTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPTRELALQTSQVCKELSKHLG  181 (459)
T ss_pred             ecchhhhhhccCCCCCccceechhhhhcCccccceeEEEEeecchhhHHHHHHHHHHhcccC
Confidence            7899999999999999999999999865442  33779999999999999988888876554

>PF13245 AAA_19: Part of AAA domain

Probab=97.56  E-value=0.00039  Score=41.04  Aligned_cols=49  Identities=22%  Similarity=0.182  Sum_probs=37.2

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHh---CCCeEEEEccchhHHHHHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKI---KQKSAIFILPYISLVHEKYQSL  123 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~---~~~~~~~i~P~~~l~~q~~~~~  123 (138)
                      .-+++..|.|+|||....-.+...+..   .+.+++++.|++..+++..+.+
T Consensus        11 ~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen   11 PLFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCCHHHHHHHHHHH
Confidence            445679999999997765555444421   2678999999999999888887

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=97.56  E-value=0.0067  Score=42.84  Aligned_cols=38  Identities=16%  Similarity=0.160  Sum_probs=29.8

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      .|+.+++.+|+|+|||..+...+...+ .++.+++|+..
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~~~~-~~g~~~~~is~   56 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAYKGL-RDGDPVIYVTT   56 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHHH-hcCCeEEEEEc
Confidence            578899999999999998876665544 45778888764

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.

>KOG0351|consensus

Probab=97.56  E-value=8.8e-05  Score=62.16  Aligned_cols=67  Identities=22%  Similarity=0.318  Sum_probs=56.2

Q ss_pred             HHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          56 AAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        56 ~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      ++.+...+-|.+++..... ++.++.+|||+||++++-+|++-.    ++-.++|.|+.+|+.++...+...
T Consensus       260 Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~----~gitvVISPL~SLm~DQv~~L~~~  327 (941)
T KOG0351|consen  260 FGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLL----GGVTVVISPLISLMQDQVTHLSKK  327 (941)
T ss_pred             hccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeecccccc----CCceEEeccHHHHHHHHHHhhhhc
Confidence            3556677889999987777 999999999999999998888752    457899999999999999888444

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=97.55  E-value=0.00013  Score=60.17  Aligned_cols=54  Identities=13%  Similarity=0.110  Sum_probs=46.0

Q ss_pred             EEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhh
Q psy2029           8 VLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF   62 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~   62 (138)
                      +..+.||+|||+++.+++..+.+. |..+.+++|+--|..+-++.+.++....+.
T Consensus        97 iaEm~TGEGKTLvA~l~a~l~al~-G~~v~vvT~neyLA~Rd~e~~~~~~~~LGl  150 (796)
T PRK12906         97 IAEMKTGEGKTLTATLPVYLNALT-GKGVHVVTVNEYLSSRDATEMGELYRWLGL  150 (796)
T ss_pred             cccccCCCCCcHHHHHHHHHHHHc-CCCeEEEeccHHHHHhhHHHHHHHHHhcCC
Confidence            889999999999999998876664 888999999999999999998887654443

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

Probab=97.52  E-value=0.00023  Score=47.05  Aligned_cols=51  Identities=22%  Similarity=0.233  Sum_probs=39.9

Q ss_pred             ceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          76 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        76 ~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      -.++...+|+|||---+-..+++....+.|+|++.|++.++++..+.++..
T Consensus         6 ~~~~d~hpGaGKTr~vlp~~~~~~i~~~~rvLvL~PTRvva~em~~aL~~~   56 (148)
T PF07652_consen    6 LTVLDLHPGAGKTRRVLPEIVREAIKRRLRVLVLAPTRVVAEEMYEALKGL   56 (148)
T ss_dssp             EEEEE--TTSSTTTTHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHTTTS
T ss_pred             eeEEecCCCCCCcccccHHHHHHHHHccCeEEEecccHHHHHHHHHHHhcC
Confidence            346889999999998777777777778899999999999999999888654

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 ....

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.51  E-value=0.0041  Score=47.48  Aligned_cols=38  Identities=18%  Similarity=0.089  Sum_probs=26.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcC-CeEEEEc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQ-KSAIFIL   40 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~-~~~l~v~   40 (138)
                      +|+.+++.+|||+|||....-.+.......+ .++.++.
T Consensus       136 ~g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit  174 (374)
T PRK14722        136 RGGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLT  174 (374)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEe
Confidence            4778999999999999877555554333334 3555543

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

Probab=97.51  E-value=0.00018  Score=57.93  Aligned_cols=51  Identities=25%  Similarity=0.294  Sum_probs=44.7

Q ss_pred             EEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           8 VLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      ++.+.-|||||++|.++++.. .+.|..+..-+||--|.+|.++++.++...
T Consensus       287 LlQGDVGSGKTvVA~laml~a-i~~G~Q~ALMAPTEILA~QH~~~~~~~l~~  337 (677)
T COG1200         287 LLQGDVGSGKTVVALLAMLAA-IEAGYQAALMAPTEILAEQHYESLRKWLEP  337 (677)
T ss_pred             HhccCcCCCHHHHHHHHHHHH-HHcCCeeEEeccHHHHHHHHHHHHHHHhhh
Confidence            678899999999999999975 455888888899999999999999998653

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.48  E-value=0.0033  Score=47.19  Aligned_cols=41  Identities=34%  Similarity=0.356  Sum_probs=30.0

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLV   46 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~   46 (138)
                      ++++++++|||+|||..+. ++...+.+++.+++|+. ...|.
T Consensus       183 ~~~Lll~G~~GtGKThLa~-aIa~~l~~~g~~V~y~t-~~~l~  223 (329)
T PRK06835        183 NENLLFYGNTGTGKTFLSN-CIAKELLDRGKSVIYRT-ADELI  223 (329)
T ss_pred             CCcEEEECCCCCcHHHHHH-HHHHHHHHCCCeEEEEE-HHHHH
Confidence            4789999999999998874 45555667777888754 33443

>cd01394 radB RadB

Probab=97.47  E-value=0.012  Score=41.30  Aligned_cols=37  Identities=19%  Similarity=0.154  Sum_probs=29.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      .|+-+.+.+|.|+|||..+...+.... ..+.+++|+.
T Consensus        18 ~g~i~~i~G~~GsGKT~l~~~~a~~~~-~~g~~v~yi~   54 (218)
T cd01394          18 RGTVTQVYGPPGTGKTNIAIQLAVETA-GQGKKVAYID   54 (218)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH-hcCCeEEEEE
Confidence            466789999999999999987776543 4578898874

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

>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=97.44  E-value=0.002  Score=46.94  Aligned_cols=74  Identities=12%  Similarity=0.082  Sum_probs=56.0

Q ss_pred             hhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          61 KFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      ++++|...+-.+ ...-+..+.||.|||+++.+++.-.... +..+=++.....|+..-++++..++..+|+.|..
T Consensus        78 p~~vQll~~l~L-~~G~laEm~TGEGKTli~~l~a~~~AL~-G~~V~vvT~NdyLA~RD~~~~~~~y~~LGlsv~~  151 (266)
T PF07517_consen   78 PYDVQLLGALAL-HKGRLAEMKTGEGKTLIAALPAALNALQ-GKGVHVVTSNDYLAKRDAEEMRPFYEFLGLSVGI  151 (266)
T ss_dssp             --HHHHHHHHHH-HTTSEEEESTTSHHHHHHHHHHHHHHTT-SS-EEEEESSHHHHHHHHHHHHHHHHHTT--EEE
T ss_pred             ccHHHHhhhhhc-ccceeEEecCCCCcHHHHHHHHHHHHHh-cCCcEEEeccHHHhhccHHHHHHHHHHhhhcccc
Confidence            555665554333 3455899999999999999888776664 6778888999999999999999999999999864

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 ....

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=97.42  E-value=0.0085  Score=42.14  Aligned_cols=43  Identities=12%  Similarity=0.010  Sum_probs=31.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhc-----CCeEEEEcchhhh
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIK-----QKSAIFILPYISL   45 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~-----~~~~l~v~P~~aL   45 (138)
                      .|+-+.+.+|.|+|||..+...+...+...     +.+++|+..-..+
T Consensus        18 ~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~~~   65 (226)
T cd01393          18 TGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGAF   65 (226)
T ss_pred             CCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCCCC
Confidence            466789999999999999877766644332     2788888764433

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.

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.42  E-value=0.011  Score=41.75  Aligned_cols=38  Identities=21%  Similarity=0.203  Sum_probs=30.1

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      .|+-+.+.+|.|+|||..+...+...+ ..+.+++|+.-
T Consensus        22 ~g~i~~i~G~~GsGKT~l~~~la~~~~-~~~~~v~yi~~   59 (225)
T PRK09361         22 RGTITQIYGPPGSGKTNICLQLAVEAA-KNGKKVIYIDT   59 (225)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH-HCCCeEEEEEC
Confidence            467789999999999999977776644 45788888754

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

Probab=97.41  E-value=0.00043  Score=48.38  Aligned_cols=53  Identities=19%  Similarity=0.217  Sum_probs=37.3

Q ss_pred             CCcc-EEEEccCCcchHHHHHHHHHHH-------HhhcCCeEEEEcchhhhHHHHHHHHHH
Q psy2029           3 QNKN-CVLSIPTSGGKTLVGEILIMKE-------LKIKQKSAIFILPYISLVHEKYQSLAK   55 (138)
Q Consensus         3 ~~~~-~~~~~ptg~GKt~~~~~~~~~~-------~~~~~~~~l~v~P~~aL~~q~~~~l~~   55 (138)
                      +... .+|++|.|+|||.+....+...       ....+.+++++.|+.+-+++..+.+.+
T Consensus        15 ~~~~~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen   15 SSNGITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             TSSE-EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             cCCCCEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            3344 8999999999995543333332       134678999999999888888888777

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=97.41  E-value=0.01  Score=40.65  Aligned_cols=130  Identities=19%  Similarity=0.176  Sum_probs=57.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh---------cCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhhhhHHHhhhh
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI---------KQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIQ   73 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~---------~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~   73 (138)
                      .|.=+++.+|+|+|||.++...+......         ++.+++|+..--. ..+..+.+........ ..+...+....
T Consensus        31 ~g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~~~~~~-~~~~~~~~~~~  108 (193)
T PF13481_consen   31 RGELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRALLQDYD-DDANLFFVDLS  108 (193)
T ss_dssp             TTSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHHHHTTS--HHHHHHHHHH-
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHHHhcccC-CccceEEeecc
Confidence            46668999999999999887766654431         3568898865333 2344455554432210 01111111111


Q ss_pred             c-cceEEEeecCCCchHhHHHHHHHH-HHh-CCCeEEEEccchhHHH----------HHHHHHHHHhhhcCcee
Q psy2029          74 N-KNCVLSIPTSGGKTLVGEILIMKE-LKI-KQKSAIFILPYISLVH----------EKYQSLAKAAEEFKFYL  134 (138)
Q Consensus        74 ~-~~~ii~~ptg~GKt~~~~~~~l~~-~~~-~~~~~~~i~P~~~l~~----------q~~~~~~~~~~~~~~~v  134 (138)
                      + ...-+..+...+...-..+.-+.+ +.. .+.+.++|.|...+..          +..+.+++++...|+.|
T Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~lvviD~l~~~~~~~~~~~~~~~~~~~~l~~la~~~~~~v  182 (193)
T PF13481_consen  109 NWGCIRLFEPDSGGPLLDEDLEELEAALKELYGPDLVVIDPLQSLHDGDENSNSAVAQLMQELKRLAKEYGVAV  182 (193)
T ss_dssp             -E-EE---TTS---TTSHHHHHHHHHHHTT----SEEEEE-GGGG--S-TT-HHHHHHHHHHHHHHHHHH--EE
T ss_pred             ccccceeeecccccccchHHHHHHHHHHhhcCCCcEEEEcCHHHHhcCCCCCHHHHHHHHHHHHHHHHHcCCEE
Confidence            1 111222222222222223333333 333 4678999998766654          34555666666666654

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=97.39  E-value=0.00024  Score=59.07  Aligned_cols=52  Identities=19%  Similarity=0.128  Sum_probs=44.4

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      -|..+.||.|||+++.++++...+. |..+.+++|+.-|..+-++.+.++...
T Consensus        98 ~iaEM~TGEGKTLvA~l~a~l~al~-G~~VhvvT~ndyLA~RD~e~m~~l~~~  149 (913)
T PRK13103         98 KIAEMRTGEGKTLVGTLAVYLNALS-GKGVHVVTVNDYLARRDANWMRPLYEF  149 (913)
T ss_pred             ccccccCCCCChHHHHHHHHHHHHc-CCCEEEEeCCHHHHHHHHHHHHHHhcc
Confidence            4678999999999999998876654 888999999999999999988887543

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

Probab=97.39  E-value=0.00062  Score=57.24  Aligned_cols=50  Identities=18%  Similarity=0.155  Sum_probs=39.3

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLA   54 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~   54 (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            588999999999999998888764333 33588999999998877665544

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=97.38  E-value=0.0016  Score=54.08  Aligned_cols=74  Identities=14%  Similarity=0.072  Sum_probs=58.5

Q ss_pred             hhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          61 KFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      ++++|....- +.....+..+.||.|||+++.+++.-.... +..+-+|++...|+..-++.+..++..+|+.|+.
T Consensus        77 ~ydvQlig~l-~L~~G~IaEm~TGEGKTL~a~l~ayl~aL~-G~~VhVvT~NdyLA~RD~e~m~pvy~~LGLsvg~  150 (870)
T CHL00122         77 HFDVQLIGGL-VLNDGKIAEMKTGEGKTLVATLPAYLNALT-GKGVHIVTVNDYLAKRDQEWMGQIYRFLGLTVGL  150 (870)
T ss_pred             CCchHhhhhH-hhcCCccccccCCCCchHHHHHHHHHHHhc-CCceEEEeCCHHHHHHHHHHHHHHHHHcCCceee
Confidence            4445543321 223667889999999999999999655553 7778899999999999999999999999999874

>PRK08181 transposase; Validated

Probab=97.36  E-value=0.00056  Score=49.95  Aligned_cols=45  Identities=22%  Similarity=0.286  Sum_probs=31.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEK   49 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~   49 (138)
                      ++.|+++++|+|+|||..+...+. .+.+.+.+++|+ +...|.++.
T Consensus       105 ~~~nlll~Gp~GtGKTHLa~Aia~-~a~~~g~~v~f~-~~~~L~~~l  149 (269)
T PRK08181        105 KGANLLLFGPPGGGKSHLAAAIGL-ALIENGWRVLFT-RTTDLVQKL  149 (269)
T ss_pred             cCceEEEEecCCCcHHHHHHHHHH-HHHHcCCceeee-eHHHHHHHH
Confidence            567999999999999988754444 345567777774 444555444

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

Probab=97.34  E-value=0.00073  Score=48.90  Aligned_cols=50  Identities=24%  Similarity=0.216  Sum_probs=35.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLA   54 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~   54 (138)
                      +++|+++.+|.|.|||..+...+. .+...+.+++| +++.+|..+....+.
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~-~l~~~g~sv~f-~~~~el~~~Lk~~~~  153 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGN-ELLKAGISVLF-ITAPDLLSKLKAAFD  153 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHH-HHHHcCCeEEE-EEHHHHHHHHHHHHh
Confidence            578999999999999999844444 45555667766 566666655555444

>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=0.0013  Score=48.01  Aligned_cols=67  Identities=12%  Similarity=-0.007  Sum_probs=51.9

Q ss_pred             hhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhC---CCeEEEEccchhHHHHHHHHHHHHhhhc
Q psy2029          63 YLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIK---QKSAIFILPYISLVHEKYQSLAKAAEEF  130 (138)
Q Consensus        63 ~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~---~~~~~~i~P~~~l~~q~~~~~~~~~~~~  130 (138)
                      +-|..++.. .+.+++|.++.|+|||.+....+.+-+...   ..++++++++++.+.+..+.+.+.+...
T Consensus         3 ~eQ~~~i~~-~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~~aa~e~~~ri~~~l~~~   72 (315)
T PF00580_consen    3 DEQRRIIRS-TEGPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTNAAAQEMRERIRELLEEE   72 (315)
T ss_dssp             HHHHHHHHS--SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHhC-CCCCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCHHHHHHHHHHHHHhcCcc
Confidence            345666554 448899999999999999887777666553   4689999999999999999999876554

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 ....

>PRK08116 hypothetical protein; Validated

Probab=97.30  E-value=0.025  Score=41.32  Aligned_cols=43  Identities=26%  Similarity=0.286  Sum_probs=29.7

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKY   50 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~   50 (138)
                      .+++++|+|+|||..+. ++.+.+.+.+.+++|+ +...|.+++.
T Consensus       116 gl~l~G~~GtGKThLa~-aia~~l~~~~~~v~~~-~~~~ll~~i~  158 (268)
T PRK08116        116 GLLLWGSVGTGKTYLAA-CIANELIEKGVPVIFV-NFPQLLNRIK  158 (268)
T ss_pred             eEEEECCCCCCHHHHHH-HHHHHHHHcCCeEEEE-EHHHHHHHHH
Confidence            48999999999999885 4555666666677665 4444444433

>KOG4284|consensus

Probab=97.29  E-value=6.9e-05  Score=60.13  Aligned_cols=57  Identities=18%  Similarity=0.297  Sum_probs=47.4

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhc--CCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~--~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      +.+.++||.|..|+|||++|.+.+...+-.+  ....++++|++++.-|+.+.+...+.
T Consensus        60 ~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~PTREiaVQI~~tv~~v~~  118 (980)
T KOG4284|consen   60 FSKMDLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTPTREIAVQIKETVRKVAP  118 (980)
T ss_pred             hcccceEEEecCCCCceEEEEeeeehhcCcccCcceeEEEecchhhhhHHHHHHHHhcc
Confidence            4567999999999999999988888776543  34778899999999999988877654

>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=97.29  E-value=0.00088  Score=48.98  Aligned_cols=53  Identities=11%  Similarity=-0.013  Sum_probs=40.6

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhc---CCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIK---QKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~---~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ..+++|.|+.|||||.+...-+...+...   ..++++++++++.+.+..+.+.+.
T Consensus        13 ~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~~aa~e~~~ri~~~   68 (315)
T PF00580_consen   13 EGPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTNAAAQEMRERIREL   68 (315)
T ss_dssp             SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCHHHHHHHHHHHHHh
Confidence            56899999999999998866665544332   348999999999888887777775

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 ....

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=97.29  E-value=0.00051  Score=56.08  Aligned_cols=50  Identities=22%  Similarity=0.166  Sum_probs=43.0

Q ss_pred             EEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           8 VLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      +..+.||.|||+++.+++..+.+. |..+.+++|+--|+.+-++.+.++..
T Consensus        95 VaEM~TGEGKTLvA~l~a~l~AL~-G~~VhvvT~NdyLA~RDae~m~~ly~  144 (764)
T PRK12326         95 VIEMATGEGKTLAGAIAAAGYALQ-GRRVHVITVNDYLARRDAEWMGPLYE  144 (764)
T ss_pred             cccccCCCCHHHHHHHHHHHHHHc-CCCeEEEcCCHHHHHHHHHHHHHHHH
Confidence            568999999999999998876654 88899999999999998888887654

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.29  E-value=0.012  Score=41.66  Aligned_cols=40  Identities=15%  Similarity=0.013  Sum_probs=29.8

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhc-----CCeEEEEcch
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIK-----QKSAIFILPY   42 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~-----~~~~l~v~P~   42 (138)
                      .|+-+.+.+|.|+|||..+...+...+...     +.+++|+..-
T Consensus        18 ~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e   62 (235)
T cd01123          18 TGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTE   62 (235)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCC
Confidence            467789999999999999977766544332     3688888643

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 .

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=97.28  E-value=0.01  Score=47.00  Aligned_cols=52  Identities=12%  Similarity=0.020  Sum_probs=36.8

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .|..+++.+|+|+|||..+...+...+ ..+.+++|+.... -.+++.+++..+
T Consensus       272 ~g~~~li~G~~G~GKT~l~~~~~~~~~-~~g~~~~yis~e~-~~~~i~~~~~~~  323 (509)
T PRK09302        272 RGSIILVSGATGTGKTLLASKFAEAAC-RRGERCLLFAFEE-SRAQLIRNARSW  323 (509)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHH-hCCCcEEEEEecC-CHHHHHHHHHHc
Confidence            467789999999999999977776654 4578999985432 244555555443

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

Probab=97.28  E-value=0.00051  Score=56.42  Aligned_cols=51  Identities=24%  Similarity=0.308  Sum_probs=42.1

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ..++++|-||+|||..|...+.. |+.  .-+|+|+++--++|.+|-+..+.++
T Consensus       186 ~raLlvMATGTGKTrTAiaii~r-L~r~~~~KRVLFLaDR~~Lv~QA~~af~~~  238 (875)
T COG4096         186 NRALLVMATGTGKTRTAIAIIDR-LIKSGWVKRVLFLADRNALVDQAYGAFEDF  238 (875)
T ss_pred             ceEEEEEecCCCcceeHHHHHHH-HHhcchhheeeEEechHHHHHHHHHHHHHh
Confidence            35899999999999998666554 444  3569999999999999999887776

>KOG0329|consensus

Probab=97.28  E-value=0.00019  Score=51.86  Aligned_cols=58  Identities=10%  Similarity=0.094  Sum_probs=48.2

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhc-C-CeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIK-Q-KSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~-~-~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      +-|.+++..|.+|+|||.++.++.++.+-.- | -.+++.+-+++|.-|+.+++.+++..
T Consensus        77 ilgmdvlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtrelafqi~~ey~rfsky  136 (387)
T KOG0329|consen   77 ILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTRELAFQISKEYERFSKY  136 (387)
T ss_pred             hhcchhheecccCCCceeeeehhhhhhcCCCCCeEEEEEEeccHHHHHHHHHHHHHHHhh
Confidence            4578999999999999999999988865442 2 26788899999999999999888543

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=97.26  E-value=0.015  Score=41.49  Aligned_cols=53  Identities=11%  Similarity=0.107  Sum_probs=36.5

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      -.|+.+++.+|+|+|||..+...+.. +.+++.+++|+...- -..+..+++..+
T Consensus        22 ~~g~~~~i~G~~G~GKTtl~~~~~~~-~~~~g~~~~yi~~e~-~~~~~~~~~~~~   74 (230)
T PRK08533         22 PAGSLILIEGDESTGKSILSQRLAYG-FLQNGYSVSYVSTQL-TTTEFIKQMMSL   74 (230)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH-HHhCCCcEEEEeCCC-CHHHHHHHHHHh
Confidence            35778899999999999998666665 445678888887432 234555555443

>TIGR00665 DnaB replicative DNA helicase

Probab=97.20  E-value=0.033  Score=43.27  Aligned_cols=130  Identities=16%  Similarity=0.059  Sum_probs=68.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhh---------hh--hhhh--HHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEF---------KF--YLEG--KCL   69 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~---------~~--~~Q~--~~~   69 (138)
                      .|.-+++.|++|+|||..+.-.+.....+.+.+++|+..--. ..+..+++.......         ..  .++.  .+.
T Consensus       194 ~G~l~vi~g~pg~GKT~~~l~~a~~~a~~~g~~vl~~SlEm~-~~~i~~R~~~~~~~v~~~~~~~g~l~~~~~~~~~~a~  272 (434)
T TIGR00665       194 PSDLIILAARPSMGKTAFALNIAENAAIKEGKPVAFFSLEMS-AEQLAMRMLSSESRVDSQKLRTGKLSDEDWEKLTSAA  272 (434)
T ss_pred             CCeEEEEEeCCCCChHHHHHHHHHHHHHhCCCeEEEEeCcCC-HHHHHHHHHHHhcCCCHHHhccCCCCHHHHHHHHHHH
Confidence            456679999999999999877776645445667877653111 123333333321100         00  1111  111


Q ss_pred             hhhhccceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhH------------HHHHHHHHHHHhhhcCceee
Q psy2029          70 EMIQNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISL------------VHEKYQSLAKAAEEFKFYLE  135 (138)
Q Consensus        70 ~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l------------~~q~~~~~~~~~~~~~~~v~  135 (138)
                      ..+.+.++.+.-  ..+-+..-+...++++.. .+.+.++|.+...+            +.+..+.++.++..+++.|.
T Consensus       273 ~~l~~~~l~i~d--~~~~~~~~i~~~i~~~~~~~~~~~vvID~l~~i~~~~~~~~r~~~i~~i~~~Lk~lA~e~~i~vi  349 (434)
T TIGR00665       273 GKLSEAPLYIDD--TPGLTITELRAKARRLKREHGLGLIVIDYLQLMSGSGRSENRQQEVSEISRSLKALAKELNVPVI  349 (434)
T ss_pred             HHHhcCCEEEEC--CCCCCHHHHHHHHHHHHHhcCCCEEEEcchHhcCCCCCCCCHHHHHHHHHHHHHHHHHHhCCeEE
Confidence            222223333322  234455555555555543 45677777765433            23345667777777777654

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.

>PRK06921 hypothetical protein; Provisional

Probab=97.19  E-value=0.0017  Score=47.39  Aligned_cols=44  Identities=16%  Similarity=0.181  Sum_probs=30.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhc-CCeEEEEcchhhhHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIK-QKSAIFILPYISLVHE   48 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~-~~~~l~v~P~~aL~~q   48 (138)
                      .+.++++++|+|+|||..+. ++...+.++ +.+++|+. ...+..+
T Consensus       116 ~~~~l~l~G~~G~GKThLa~-aia~~l~~~~g~~v~y~~-~~~l~~~  160 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLT-AAANELMRKKGVPVLYFP-FVEGFGD  160 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHH-HHHHHHhhhcCceEEEEE-HHHHHHH
Confidence            35789999999999998874 444556665 67777754 3344333

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

Probab=97.19  E-value=0.0017  Score=45.33  Aligned_cols=63  Identities=17%  Similarity=0.206  Sum_probs=46.1

Q ss_pred             hhhhhHHHhhhhc-cc-eEEEeecCCCchHhHHHHHHHHH--------HhCCCeEEEEccchhHHHHHHHHHHH
Q psy2029          62 FYLEGKCLEMIQN-KN-CVLSIPTSGGKTLVGEILIMKEL--------KIKQKSAIFILPYISLVHEKYQSLAK  125 (138)
Q Consensus        62 ~~~Q~~~~~~~~~-~~-~ii~~ptg~GKt~~~~~~~l~~~--------~~~~~~~~~i~P~~~l~~q~~~~~~~  125 (138)
                      .+.|..++..... .. .++..|.|+|||....-.+ ..+        ...+.++++++|+.+-+++..+.+.+
T Consensus         3 n~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~~~i-~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    3 NESQREAIQSALSSNGITLIQGPPGTGKTTTLASII-AQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             -HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHHHHH-HHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHcCCCCEEEECCCCCChHHHHHHHH-HHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            4568888866666 55 7899999999996554333 333        33578999999999999999999888

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=97.18  E-value=0.0065  Score=43.17  Aligned_cols=52  Identities=12%  Similarity=0.141  Sum_probs=37.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .|..+++.+|+|+|||..+...+...+. ++.+++|+.--.. .++..+++..+
T Consensus        24 ~g~~~~i~G~~GsGKt~l~~~~~~~~~~-~g~~~~y~~~e~~-~~~~~~~~~~~   75 (234)
T PRK06067         24 FPSLILIEGDHGTGKSVLSQQFVYGALK-QGKKVYVITTENT-SKSYLKQMESV   75 (234)
T ss_pred             CCcEEEEECCCCCChHHHHHHHHHHHHh-CCCEEEEEEcCCC-HHHHHHHHHHC
Confidence            5678899999999999999888776554 5889999764322 24555555444

>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=97.17  E-value=0.0029  Score=46.02  Aligned_cols=61  Identities=21%  Similarity=0.255  Sum_probs=39.8

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhC-C----CeEEEEccchhHHHHHHHHHHHHhhhcCceeeec
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIK-Q----KSAIFILPYISLVHEKYQSLAKAAEEFKFYLEVL  137 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~-~----~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~~  137 (138)
                      +.++++-..|.|||..++..+ ..+... .    .++++++|. ++..+..+++.+++.+...++..+
T Consensus        26 ~g~lL~de~GlGKT~~~i~~~-~~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~~~~~~~~~v~~~   91 (299)
T PF00176_consen   26 RGGLLADEMGLGKTITAIALI-SYLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEKWFDPDSLRVIIY   91 (299)
T ss_dssp             -EEEE---TTSSHHHHHHHHH-HHHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHHHSGT-TS-EEEE
T ss_pred             CCEEEEECCCCCchhhhhhhh-hhhhhccccccccceeEeecc-chhhhhhhhhcccccccccccccc
Confidence            778899999999999985544 444432 1    259999999 888999999999986644455443

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.

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=97.15  E-value=0.013  Score=37.39  Aligned_cols=26  Identities=27%  Similarity=0.245  Sum_probs=17.6

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKE   28 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~   28 (138)
                      +++.+++++|+|+|||.+....+...
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~~~~~   28 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRLARQL   28 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHHHHHHHh
Confidence            45678999999999999887666653

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

Probab=97.14  E-value=0.031  Score=42.24  Aligned_cols=55  Identities=18%  Similarity=0.173  Sum_probs=43.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      +.++.+++|=||+|||..- +......++.|+++.+..|-...+.+.+.++...+.
T Consensus       115 ~k~~~lv~AV~GaGKTEMi-f~~i~~al~~G~~vciASPRvDVclEl~~Rlk~aF~  169 (441)
T COG4098         115 QKEDTLVWAVTGAGKTEMI-FQGIEQALNQGGRVCIASPRVDVCLELYPRLKQAFS  169 (441)
T ss_pred             hcCcEEEEEecCCCchhhh-HHHHHHHHhcCCeEEEecCcccchHHHHHHHHHhhc
Confidence            4568999999999999875 344444566799999999988888888888877644

>PRK09354 recA recombinase A; Provisional

Probab=97.10  E-value=0.018  Score=43.64  Aligned_cols=92  Identities=23%  Similarity=0.180  Sum_probs=56.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhhhhHHHhhhhccceEEEee
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIQNKNCVLSIP   82 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~ii~~p   82 (138)
                      .|.-+.+.+|.|+|||..++..+..... .+++++|+..--++..+   .++..    +++.          .++++.-|
T Consensus        59 ~G~IteI~G~~GsGKTtLal~~~~~~~~-~G~~~~yId~E~s~~~~---~a~~l----Gvdl----------d~lli~qp  120 (349)
T PRK09354         59 RGRIVEIYGPESSGKTTLALHAIAEAQK-AGGTAAFIDAEHALDPV---YAKKL----GVDI----------DNLLVSQP  120 (349)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH-cCCcEEEECCccchHHH---HHHHc----CCCH----------HHeEEecC
Confidence            4567789999999999999888776543 58899998775554432   11111    2221          34445545


Q ss_pred             cCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHH
Q psy2029          83 TSGGKTLVGEILIMKELKI-KQKSAIFILPYISLV  116 (138)
Q Consensus        83 tg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~  116 (138)
                      . ++...   +.++..+.. ...+.++|.+..+|.
T Consensus       121 ~-~~Eq~---l~i~~~li~s~~~~lIVIDSvaaL~  151 (349)
T PRK09354        121 D-TGEQA---LEIADTLVRSGAVDLIVVDSVAALV  151 (349)
T ss_pred             C-CHHHH---HHHHHHHhhcCCCCEEEEeChhhhc
Confidence            3 33333   333444443 456778887777775

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=97.08  E-value=0.025  Score=44.91  Aligned_cols=53  Identities=15%  Similarity=0.208  Sum_probs=38.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .|+.+++.+++|+|||..+...+...+.+.+.+++|+.- -+-.+++.+++..+
T Consensus        30 ~Gs~~li~G~pGsGKT~l~~qf~~~~~~~~ge~~lyis~-ee~~~~i~~~~~~~   82 (509)
T PRK09302         30 KGRPTLVSGTAGTGKTLFALQFLVNGIKRFDEPGVFVTF-EESPEDIIRNVASF   82 (509)
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCEEEEEc-cCCHHHHHHHHHHc
Confidence            577889999999999999988877766554788888753 22234555555544

>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=97.07  E-value=0.051  Score=37.83  Aligned_cols=49  Identities=24%  Similarity=0.122  Sum_probs=26.9

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc--chhhhHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL--PYISLVHEKYQSLAK   55 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~--P~~aL~~q~~~~l~~   55 (138)
                      -+++.+|||+|||....-.+.....+ +.++.+++  .++.=..++.+.+.+
T Consensus         3 vi~lvGptGvGKTTt~aKLAa~~~~~-~~~v~lis~D~~R~ga~eQL~~~a~   53 (196)
T PF00448_consen    3 VIALVGPTGVGKTTTIAKLAARLKLK-GKKVALISADTYRIGAVEQLKTYAE   53 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHT-T--EEEEEESTSSTHHHHHHHHHHH
T ss_pred             EEEEECCCCCchHhHHHHHHHHHhhc-cccceeecCCCCCccHHHHHHHHHH
Confidence            36789999999996654444433333 66665554  344433444444433

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 ....

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=97.07  E-value=0.0014  Score=47.34  Aligned_cols=52  Identities=10%  Similarity=0.200  Sum_probs=38.0

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .|+.+++.++.|+|||..+...+.+.+. .+.+++|+.- .+-..+..+++..+
T Consensus        22 ~g~~~lI~G~pGsGKT~f~~qfl~~~~~-~ge~vlyvs~-~e~~~~l~~~~~~~   73 (260)
T COG0467          22 RGSVVLITGPPGTGKTIFALQFLYEGAR-EGEPVLYVST-EESPEELLENARSF   73 (260)
T ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHHHh-cCCcEEEEEe-cCCHHHHHHHHHHc
Confidence            5788999999999999999888887554 4888999764 33334455554443

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=97.06  E-value=0.0077  Score=50.44  Aligned_cols=74  Identities=12%  Similarity=0.068  Sum_probs=58.9

Q ss_pred             hhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          61 KFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      ++++|....- +....-+..+.||.|||+++.+++.-..+. ++.+-+|++..-||..-++.+..++..+|+.|+.
T Consensus        86 ~ydVQliGgl-~Lh~G~IAEM~TGEGKTL~atlpaylnAL~-GkgVhVVTvNdYLA~RDae~m~~vy~~LGLtvg~  159 (939)
T PRK12902         86 HFDVQLIGGM-VLHEGQIAEMKTGEGKTLVATLPSYLNALT-GKGVHVVTVNDYLARRDAEWMGQVHRFLGLSVGL  159 (939)
T ss_pred             cchhHHHhhh-hhcCCceeeecCCCChhHHHHHHHHHHhhc-CCCeEEEeCCHHHHHhHHHHHHHHHHHhCCeEEE
Confidence            4445543332 223555789999999999999999876665 6778889999999999999999999999999874

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=97.05  E-value=0.024  Score=42.88  Aligned_cols=50  Identities=10%  Similarity=-0.049  Sum_probs=34.0

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh-----cCCeEEEEcchhhhHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI-----KQKSAIFILPYISLVHEKYQS   52 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-----~~~~~l~v~P~~aL~~q~~~~   52 (138)
                      .|+-..+++|.|+|||..+...+....+.     .+++++|+..--.+..+...+
T Consensus       125 ~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~  179 (344)
T PLN03187        125 TRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVP  179 (344)
T ss_pred             CCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHH
Confidence            45667899999999999987766654432     236999987644444444433

>PRK05973 replicative DNA helicase; Provisional

Probab=97.05  E-value=0.0017  Score=46.55  Aligned_cols=53  Identities=19%  Similarity=0.261  Sum_probs=37.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ..|.-++|.+++|+|||..++..+.+... ++.+++|+.---. .+++.+++...
T Consensus        62 ~~Gsl~LIaG~PG~GKT~lalqfa~~~a~-~Ge~vlyfSlEes-~~~i~~R~~s~  114 (237)
T PRK05973         62 KPGDLVLLGARPGHGKTLLGLELAVEAMK-SGRTGVFFTLEYT-EQDVRDRLRAL  114 (237)
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHHHh-cCCeEEEEEEeCC-HHHHHHHHHHc
Confidence            35677899999999999999888777654 4778888753211 24556665554

>PRK06526 transposase; Provisional

Probab=97.05  E-value=0.0012  Score=47.88  Aligned_cols=44  Identities=20%  Similarity=0.163  Sum_probs=30.0

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHE   48 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q   48 (138)
                      .+.|+++++|+|+|||..+...... +...+.+++|.. ...+.++
T Consensus        97 ~~~nlll~Gp~GtGKThLa~al~~~-a~~~g~~v~f~t-~~~l~~~  140 (254)
T PRK06526         97 GKENVVFLGPPGTGKTHLAIGLGIR-ACQAGHRVLFAT-AAQWVAR  140 (254)
T ss_pred             cCceEEEEeCCCCchHHHHHHHHHH-HHHCCCchhhhh-HHHHHHH
Confidence            4679999999999999888555443 445577776643 3334433

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=97.04  E-value=0.022  Score=42.60  Aligned_cols=50  Identities=10%  Similarity=-0.017  Sum_probs=34.1

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh-----cCCeEEEEcchhhhHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI-----KQKSAIFILPYISLVHEKYQS   52 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-----~~~~~l~v~P~~aL~~q~~~~   52 (138)
                      .|.-..+++|.|+|||..+...+....+.     .+++++|+.---.+..+...+
T Consensus        95 ~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~~  149 (313)
T TIGR02238        95 SMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRA  149 (313)
T ss_pred             CCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHHH
Confidence            45667899999999999987766654432     356999987544444444433

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.

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

Probab=97.04  E-value=0.0032  Score=49.81  Aligned_cols=53  Identities=21%  Similarity=0.194  Sum_probs=42.0

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcC
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFK  131 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~  131 (138)
                      +...+.--||+|||+.-.--+ ..   -.+++++++|.+.|+.|.+.+|+++|.+.-
T Consensus        33 ~~QtLLGvTGSGKTfT~AnVI-~~---~~rPtLV~AhNKTLAaQLy~Efk~fFP~Na   85 (663)
T COG0556          33 KHQTLLGVTGSGKTFTMANVI-AK---VQRPTLVLAHNKTLAAQLYSEFKEFFPENA   85 (663)
T ss_pred             eeeEEeeeccCCchhHHHHHH-HH---hCCCeEEEecchhHHHHHHHHHHHhCcCcc
Confidence            566788899999997653322 22   357889999999999999999999987663

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=97.01  E-value=0.029  Score=41.80  Aligned_cols=40  Identities=15%  Similarity=0.060  Sum_probs=29.9

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhc-----CCeEEEEcch
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIK-----QKSAIFILPY   42 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~-----~~~~l~v~P~   42 (138)
                      .|.-+.+++|+|+|||..+...+.......     +.+++|+.--
T Consensus       101 ~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te  145 (317)
T PRK04301        101 TQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTE  145 (317)
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCC
Confidence            456678999999999999988777654431     3588898643

>PRK12377 putative replication protein; Provisional

Probab=97.01  E-value=0.0024  Score=46.08  Aligned_cols=45  Identities=22%  Similarity=0.221  Sum_probs=30.1

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQ   51 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~   51 (138)
                      .++++++|+|+|||..+. ++...+.+.+.+++|+ +...|..++..
T Consensus       102 ~~l~l~G~~GtGKThLa~-AIa~~l~~~g~~v~~i-~~~~l~~~l~~  146 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAA-AIGNRLLAKGRSVIVV-TVPDVMSRLHE  146 (248)
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHHHHcCCCeEEE-EHHHHHHHHHH
Confidence            578999999999998874 4444566656667664 44445444433

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=97.00  E-value=0.0011  Score=46.59  Aligned_cols=41  Identities=20%  Similarity=0.259  Sum_probs=28.0

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhc-CCeEEEEcchhh
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIK-QKSAIFILPYIS   44 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~-~~~~l~v~P~~a   44 (138)
                      ...+++.+|.|+|||+.+...++..+.+. -.+++++-|..+
T Consensus        19 ~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~   60 (205)
T PF02562_consen   19 NDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVE   60 (205)
T ss_dssp             -SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCC
Confidence            35679999999999999999999877662 247788777664

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

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=96.99  E-value=0.0006  Score=50.80  Aligned_cols=25  Identities=36%  Similarity=0.501  Sum_probs=20.5

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      |.-+|+++.+|||||||+.|...+.
T Consensus        95 L~KSNILLiGPTGsGKTlLAqTLAk  119 (408)
T COG1219          95 LSKSNILLIGPTGSGKTLLAQTLAK  119 (408)
T ss_pred             eeeccEEEECCCCCcHHHHHHHHHH
Confidence            3457999999999999999865544

>PRK08760 replicative DNA helicase; Provisional

Probab=96.98  E-value=0.082  Score=41.78  Aligned_cols=131  Identities=14%  Similarity=0.041  Sum_probs=71.0

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH-------hhh----hhhhh--HHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE-------EFK----FYLEG--KCL   69 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~-------~~~----~~~Q~--~~~   69 (138)
                      .|.=+++.|++|+|||..++-.+.....+.+.+++|+..--. ..|...++.....       ..+    ..|..  .+.
T Consensus       228 ~G~LivIaarPg~GKTafal~iA~~~a~~~g~~V~~fSlEMs-~~ql~~Rl~a~~s~i~~~~i~~g~l~~~e~~~~~~a~  306 (476)
T PRK08760        228 PTDLIILAARPAMGKTTFALNIAEYAAIKSKKGVAVFSMEMS-ASQLAMRLISSNGRINAQRLRTGALEDEDWARVTGAI  306 (476)
T ss_pred             CCceEEEEeCCCCChhHHHHHHHHHHHHhcCCceEEEeccCC-HHHHHHHHHHhhCCCcHHHHhcCCCCHHHHHHHHHHH
Confidence            355668899999999999977776654444667777643111 1344444332210       000    01111  111


Q ss_pred             hhhhccceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhH------------HHHHHHHHHHHhhhcCceeee
Q psy2029          70 EMIQNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISL------------VHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        70 ~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l------------~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      ..+.+.++.+.  ...+-|.-.+...++++.. ++.+.++|.....+            +.+..+.++.+++.+++.|.-
T Consensus       307 ~~l~~~~l~I~--d~~~~t~~~I~~~~r~l~~~~~~~lVvIDyLql~~~~~~~~~r~~ei~~Isr~LK~lAkel~ipVi~  384 (476)
T PRK08760        307 KMLKETKIFID--DTPGVSPEVLRSKCRRLKREHDLGLIVIDYLQLMSVPGNSENRATEISEISRSLKGLAKELNVPVIA  384 (476)
T ss_pred             HHHhcCCEEEe--CCCCCCHHHHHHHHHHHHHhcCCCEEEEecHHhcCCCCCCcccHHHHHHHHHHHHHHHHHhCCEEEE
Confidence            22223343333  2344566555556666654 34566666543222            346778888898888887753

>PRK10867 signal recognition particle protein; Provisional

Probab=96.95  E-value=0.059  Score=42.06  Aligned_cols=44  Identities=23%  Similarity=0.215  Sum_probs=28.8

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhc-CCeEEEEc--chhhhHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIK-QKSAIFIL--PYISLVHEKY   50 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~-~~~~l~v~--P~~aL~~q~~   50 (138)
                      -+++++|+|+|||..+.-.+.. +..+ +.+++++.  ++++-..+++
T Consensus       102 vI~~vG~~GsGKTTtaakLA~~-l~~~~G~kV~lV~~D~~R~aa~eQL  148 (433)
T PRK10867        102 VIMMVGLQGAGKTTTAGKLAKY-LKKKKKKKVLLVAADVYRPAAIEQL  148 (433)
T ss_pred             EEEEECCCCCcHHHHHHHHHHH-HHHhcCCcEEEEEccccchHHHHHH
Confidence            4689999999999877555553 4445 67777764  4554333333

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=96.90  E-value=0.053  Score=40.21  Aligned_cols=43  Identities=14%  Similarity=0.003  Sum_probs=31.0

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh-----cCCeEEEEcchhhh
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI-----KQKSAIFILPYISL   45 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-----~~~~~l~v~P~~aL   45 (138)
                      .|.-+.+++|.|+|||..+...+....++     .+++++|+.---.+
T Consensus        94 ~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f  141 (310)
T TIGR02236        94 TQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTF  141 (310)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCC
Confidence            45667899999999999998877765442     23589998744333

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.

>PRK14873 primosome assembly protein PriA; Provisional

Probab=96.90  E-value=0.0014  Score=53.42  Aligned_cols=49  Identities=12%  Similarity=-0.016  Sum_probs=40.3

Q ss_pred             EEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           8 VLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++.+.+|||||.+++-.+...+ ..|+.+|+++|..+|..|..+.|.+.+
T Consensus       164 i~~~~~GSGKTevyl~~i~~~l-~~Gk~vLvLvPEi~lt~q~~~rl~~~f  212 (665)
T PRK14873        164 VWQALPGEDWARRLAAAAAATL-RAGRGALVVVPDQRDVDRLEAALRALL  212 (665)
T ss_pred             HhhcCCCCcHHHHHHHHHHHHH-HcCCeEEEEecchhhHHHHHHHHHHHc
Confidence            3344469999999977777654 458899999999999999999998864

>PRK05748 replicative DNA helicase; Provisional

Probab=96.86  E-value=0.12  Score=40.52  Aligned_cols=131  Identities=14%  Similarity=0.015  Sum_probs=69.7

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH-HH---h-----h--hhhhh--hHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA-AE---E-----F--KFYLE--GKCL   69 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~-~~---~-----~--~~~~Q--~~~~   69 (138)
                      .|.-+++.|++|+|||..+.-.+.....+.+.+++|+..- .=..|+..++... +.   .     .  ...|+  ..+.
T Consensus       202 ~G~livIaarpg~GKT~~al~ia~~~a~~~g~~v~~fSlE-ms~~~l~~R~l~~~~~v~~~~i~~~~l~~~e~~~~~~a~  280 (448)
T PRK05748        202 PNDLIIVAARPSVGKTAFALNIAQNVATKTDKNVAIFSLE-MGAESLVMRMLCAEGNIDAQRLRTGQLTDDDWPKLTIAM  280 (448)
T ss_pred             CCceEEEEeCCCCCchHHHHHHHHHHHHhCCCeEEEEeCC-CCHHHHHHHHHHHhcCCCHHHhhcCCCCHHHHHHHHHHH
Confidence            4567799999999999999777766444456777776421 1113444443211 10   0     0  01111  1111


Q ss_pred             hhhhccceEEEeecCCCchHhHHHHHHHHHHh-C-CCeEEEEccchhH-------------HHHHHHHHHHHhhhcCcee
Q psy2029          70 EMIQNKNCVLSIPTSGGKTLVGEILIMKELKI-K-QKSAIFILPYISL-------------VHEKYQSLAKAAEEFKFYL  134 (138)
Q Consensus        70 ~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~-~-~~~~~~i~P~~~l-------------~~q~~~~~~~~~~~~~~~v  134 (138)
                      ....+.++.+.-  ..+-|..-+...++++.. . +.+.++|.....+             +.+..+.++.+++.+++.|
T Consensus       281 ~~l~~~~~~i~d--~~~~ti~~i~~~~r~~~~~~~~~~~vvIDyL~li~~~~~~~~~r~~~i~~i~~~LK~lAke~~i~v  358 (448)
T PRK05748        281 GSLSDAPIYIDD--TPGIKVTEIRARCRRLAQEHGGLGLILIDYLQLIQGSGRSGENRQQEVSEISRSLKALAKELKVPV  358 (448)
T ss_pred             HHHhcCCEEEEC--CCCCCHHHHHHHHHHHHHhcCCCCEEEEccchhcCCCCCCCcCHHHHHHHHHHHHHHHHHHhCCeE
Confidence            222234444432  334555555555555544 3 4566666654433             2345667888888888876


Q ss_pred             ee
Q psy2029         135 EV  136 (138)
Q Consensus       135 ~~  136 (138)
                      .-
T Consensus       359 i~  360 (448)
T PRK05748        359 IA  360 (448)
T ss_pred             EE
Confidence            53

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

Probab=96.85  E-value=0.0036  Score=52.84  Aligned_cols=50  Identities=18%  Similarity=0.155  Sum_probs=40.3

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHHHHHHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLA  124 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~~q~~~~~~  124 (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            678899999999999997777654444 34789999999999988776655

>PRK11823 DNA repair protein RadA; Provisional

Probab=96.84  E-value=0.046  Score=42.82  Aligned_cols=39  Identities=8%  Similarity=0.030  Sum_probs=30.2

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      ..|.-+++.+|+|+|||..+...+.... .++.+++|+.-
T Consensus        78 ~~Gs~~lI~G~pG~GKTtL~lq~a~~~a-~~g~~vlYvs~  116 (446)
T PRK11823         78 VPGSVVLIGGDPGIGKSTLLLQVAARLA-AAGGKVLYVSG  116 (446)
T ss_pred             cCCEEEEEECCCCCCHHHHHHHHHHHHH-hcCCeEEEEEc
Confidence            3467789999999999998877666533 45779999864

>TIGR00416 sms DNA repair protein RadA

Probab=96.83  E-value=0.036  Score=43.52  Aligned_cols=40  Identities=13%  Similarity=0.070  Sum_probs=30.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcch
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPY   42 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~   42 (138)
                      ..|.-+++.+++|+|||..+...+.. +..++.+++|+..-
T Consensus        92 ~~GsvilI~G~pGsGKTTL~lq~a~~-~a~~g~kvlYvs~E  131 (454)
T TIGR00416        92 VPGSLILIGGDPGIGKSTLLLQVACQ-LAKNQMKVLYVSGE  131 (454)
T ss_pred             cCCeEEEEEcCCCCCHHHHHHHHHHH-HHhcCCcEEEEECc
Confidence            35677899999999999998776655 34456789998753

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)).

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

Probab=96.82  E-value=0.0034  Score=51.61  Aligned_cols=67  Identities=18%  Similarity=0.133  Sum_probs=51.6

Q ss_pred             hhhhhhHHHhhh----hc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhh
Q psy2029          61 KFYLEGKCLEMI----QN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE  128 (138)
Q Consensus        61 ~~~~Q~~~~~~~----~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~  128 (138)
                      +.+-|..+...+    .. ...++..-||+|||-+++- ++......++.+++++|..+|-.|..+.|+..|.
T Consensus       199 Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~-~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg  270 (730)
T COG1198         199 LNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLE-AIAKVLAQGKQVLVLVPEIALTPQLLARFKARFG  270 (730)
T ss_pred             cCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHH-HHHHHHHcCCEEEEEeccccchHHHHHHHHHHhC
Confidence            344455555332    22 6678999999999999954 4455566689999999999999999999999975

>PRK10536 hypothetical protein; Provisional

Probab=96.82  E-value=0.0023  Score=46.36  Aligned_cols=42  Identities=17%  Similarity=0.151  Sum_probs=30.7

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcC-CeEEEEcchhh
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQ-KSAIFILPYIS   44 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~-~~~l~v~P~~a   44 (138)
                      ++..+++.+|+|+|||+.+...+...+.+.. .++++.-|..+
T Consensus        73 ~~~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI~RP~v~  115 (262)
T PRK10536         73 SKQLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRPVLQ  115 (262)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEEeCCCCC
Confidence            4567899999999999999888887665533 34555556544

>PRK09183 transposase/IS protein; Provisional

Probab=96.80  E-value=0.0047  Score=44.83  Aligned_cols=38  Identities=26%  Similarity=0.161  Sum_probs=27.9

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      -.|.++++.+|+|+|||..+...... +...+.+++|+.
T Consensus       100 ~~~~~v~l~Gp~GtGKThLa~al~~~-a~~~G~~v~~~~  137 (259)
T PRK09183        100 ERNENIVLLGPSGVGKTHLAIALGYE-AVRAGIKVRFTT  137 (259)
T ss_pred             hcCCeEEEEeCCCCCHHHHHHHHHHH-HHHcCCeEEEEe
Confidence            35789999999999999887655443 334566777753

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.80  E-value=0.043  Score=42.71  Aligned_cols=38  Identities=26%  Similarity=0.145  Sum_probs=25.9

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHH-hhcCCeEEEEc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKEL-KIKQKSAIFIL   40 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~-~~~~~~~l~v~   40 (138)
                      .|+.+.+.+|||+|||..+...+.... ...+.++.++.
T Consensus       220 ~~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~  258 (424)
T PRK05703        220 QGGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALIT  258 (424)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEE
Confidence            356789999999999977655444332 33456776654

>PHA02542 41 41 helicase; Provisional

Probab=96.78  E-value=0.081  Score=41.79  Aligned_cols=130  Identities=15%  Similarity=0.040  Sum_probs=66.6

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhH-HHHHHHHHHH----HHhhhh-----hhh--hHHHhh
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLV-HEKYQSLAKA----AEEFKF-----YLE--GKCLEM   71 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~-~q~~~~l~~~----~~~~~~-----~~Q--~~~~~~   71 (138)
                      |.-+++.|++|+|||.++.-.+.... ..+.+++|+.-  ++. +|...++...    ..+...     .|.  ......
T Consensus       190 G~LiiIaarPgmGKTtfalniA~~~a-~~g~~Vl~fSL--EM~~~ql~~Rl~a~~~~i~~~~l~~l~~~~~~~~~~~~~~  266 (473)
T PHA02542        190 KTLNVLLAGVNVGKSLGLCSLAADYL-QQGYNVLYISM--EMAEEVIAKRIDANLLDVSLDDIDDLSKAEYKAKMEKLRS  266 (473)
T ss_pred             CcEEEEEcCCCccHHHHHHHHHHHHH-hcCCcEEEEec--cCCHHHHHHHHHHHHcCCCHHHHhhcCHHHHHHHHHHHHH
Confidence            45568899999999999977776544 45677777641  111 2333333211    111110     011  111122


Q ss_pred             hhccceEEEeecCCCchHhHHHHHHHHHHh-CC--CeEEEEccchhH---------------HHHHHHHHHHHhhhcCce
Q psy2029          72 IQNKNCVLSIPTSGGKTLVGEILIMKELKI-KQ--KSAIFILPYISL---------------VHEKYQSLAKAAEEFKFY  133 (138)
Q Consensus        72 ~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~--~~~~~i~P~~~l---------------~~q~~~~~~~~~~~~~~~  133 (138)
                      ....++.+.....++-|..-+...++++.. ++  ...|+|....-+               +.+..+.++.+++.+++.
T Consensus       267 ~~~~~l~I~~~d~~~lt~~~ir~~~rrlk~~~g~~~dlVvIDYLqL~~~~~~~~~~~nr~~ei~~Isr~LK~lAkel~vp  346 (473)
T PHA02542        267 KTQGKLIIKQYPTGGAHAGHFRALLNELKLKKNFKPDVIIVDYLGICASSRLRVSSENSYTYVKAIAEELRGLAVEHDVV  346 (473)
T ss_pred             HhCCCceeecCCCCCCCHHHHHHHHHHHHHhcCCCCCEEEEechhhccCCcccCCCCChHHHHHHHHHHHHHHHHHhCCe
Confidence            222344333323344555444555555553 22  345554433222               234668888888888887


Q ss_pred             eee
Q psy2029         134 LEV  136 (138)
Q Consensus       134 v~~  136 (138)
                      |.-
T Consensus       347 Vi~  349 (473)
T PHA02542        347 VWT  349 (473)
T ss_pred             EEE
Confidence            753

>TIGR00376 DNA helicase, putative

Probab=96.72  E-value=0.0056  Score=49.90  Aligned_cols=50  Identities=22%  Similarity=0.147  Sum_probs=38.6

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK   55 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~   55 (138)
                      ...+|.+|.|+|||....-.+. ++...+.+++++.|+..-+++..+.+.+
T Consensus       174 ~~~lI~GpPGTGKT~t~~~ii~-~~~~~g~~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       174 DLFLIHGPPGTGKTRTLVELIR-QLVKRGLRVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHH-HHHHcCCCEEEEcCcHHHHHHHHHHHHh
Confidence            5789999999999977644333 3555678999999998777777777765

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.

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=96.72  E-value=0.062  Score=41.63  Aligned_cols=130  Identities=15%  Similarity=0.088  Sum_probs=68.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH----h-----hh--hhhhh--HHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE----E-----FK--FYLEG--KCL   69 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~----~-----~~--~~~Q~--~~~   69 (138)
                      .|.-+++.|++|+|||..+.-.+.....+.+.+++|+..-- =..+...++.....    .     ..  ..++.  ...
T Consensus       193 ~g~liviag~pg~GKT~~al~ia~~~a~~~g~~v~~fSlEm-~~~~l~~Rl~~~~~~v~~~~~~~~~l~~~~~~~~~~~~  271 (421)
T TIGR03600       193 KGDLIVIGARPSMGKTTLALNIAENVALREGKPVLFFSLEM-SAEQLGERLLASKSGINTGNIRTGRFNDSDFNRLLNAV  271 (421)
T ss_pred             CCceEEEEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEECCC-CHHHHHHHHHHHHcCCCHHHHhcCCCCHHHHHHHHHHH
Confidence            46667999999999999987777664445577787765210 01233333222110    0     00  01111  111


Q ss_pred             hhhhccceEEEeecCCCchHhHHHHHHHHHHh-C-CCeEEEEccchhH-----------HHHHHHHHHHHhhhcCceee
Q psy2029          70 EMIQNKNCVLSIPTSGGKTLVGEILIMKELKI-K-QKSAIFILPYISL-----------VHEKYQSLAKAAEEFKFYLE  135 (138)
Q Consensus        70 ~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~-~-~~~~~~i~P~~~l-----------~~q~~~~~~~~~~~~~~~v~  135 (138)
                      ..+.+.++.+.-  .++-|.--+...++++.. . +.+.++|.....+           +.+..+.++.++..+++.|.
T Consensus       272 ~~l~~~~l~i~d--~~~~t~~~i~~~~r~~~~~~~~~~lvvIDyLql~~~~~~~~~~~~~~~i~~~Lk~lAke~~i~Vi  348 (421)
T TIGR03600       272 DRLSEKDLYIDD--TGGLTVAQIRSIARRIKRKKGGLDLIVVDYIQLMAPTRGRDRNEELGGISRGLKALAKELDVPVV  348 (421)
T ss_pred             HHHhcCCEEEEC--CCCCCHHHHHHHHHHHHHhcCCCCEEEEecccccCCCCCCCHHHHHHHHHHHHHHHHHHhCCcEE
Confidence            222234443332  234455555555555543 2 4566666654332           22466778888888887764

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.

>PF12846 AAA_10: AAA-like domain

Probab=96.71  E-value=0.0039  Score=45.30  Aligned_cols=40  Identities=15%  Similarity=0.160  Sum_probs=30.3

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhh
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISL   45 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL   45 (138)
                      .++++.++||+|||.... .++..+...+..++++-|..+.
T Consensus         2 ~h~~i~G~tGsGKT~~~~-~l~~~~~~~g~~~~i~D~~g~~   41 (304)
T PF12846_consen    2 PHTLILGKTGSGKTTLLK-NLLEQLIRRGPRVVIFDPKGDY   41 (304)
T ss_pred             CeEEEECCCCCcHHHHHH-HHHHHHHHcCCCEEEEcCCchH
Confidence            588999999999998876 5555566667788887765443

>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=96.71  E-value=0.0053  Score=43.08  Aligned_cols=52  Identities=17%  Similarity=0.223  Sum_probs=37.6

Q ss_pred             hhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCC-CeEEEEccchh
Q psy2029          63 YLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQ-KSAIFILPYIS  114 (138)
Q Consensus        63 ~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~-~~~~~i~P~~~  114 (138)
                      .-|..++..+.+ ..+++..|.|+|||+.|...+++.+.+.. .+.+|+-|..+
T Consensus         7 ~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~   60 (205)
T PF02562_consen    7 EEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVE   60 (205)
T ss_dssp             HHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--
T ss_pred             HHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCC
Confidence            446666666667 77789999999999999999998887643 68888888764

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

>KOG1802|consensus

Probab=96.68  E-value=0.0064  Score=49.38  Aligned_cols=74  Identities=9%  Similarity=0.095  Sum_probs=59.0

Q ss_pred             hhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          59 EFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        59 ~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      ..+...|..+...+.. .=.++.-|.|+|||+.+.-.+.+-+..+..++++.+|..--+.|.++.+.+-    |++|.+
T Consensus       409 pkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~~~~~VLvcApSNiAVDqLaeKIh~t----gLKVvR  483 (935)
T KOG1802|consen  409 PKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQHAGPVLVCAPSNIAVDQLAEKIHKT----GLKVVR  483 (935)
T ss_pred             hhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHhcCCceEEEcccchhHHHHHHHHHhc----CceEee
Confidence            3466788888877776 6668999999999999988777766667789999999988888877777665    666654

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=96.67  E-value=0.0031  Score=39.89  Aligned_cols=40  Identities=20%  Similarity=0.159  Sum_probs=27.7

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhh
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYIS   44 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~a   44 (138)
                      +.++++.+|+|+|||..+...+.. +......++++.+...
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~-~~~~~~~~~~~~~~~~   41 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARE-LGPPGGGVIYIDGEDI   41 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhc-cCCCCCCEEEECCEEc
Confidence            568999999999999998655544 2222235777776543

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.

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=96.66  E-value=0.13  Score=39.44  Aligned_cols=38  Identities=8%  Similarity=0.073  Sum_probs=29.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      .|+-+++.+|.|+|||..+...+.. +...+.+++|+.-
T Consensus        81 ~GslvLI~G~pG~GKStLllq~a~~-~a~~g~~VlYvs~  118 (372)
T cd01121          81 PGSVILIGGDPGIGKSTLLLQVAAR-LAKRGGKVLYVSG  118 (372)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHH-HHhcCCeEEEEEC
Confidence            4677899999999999988766654 3345679999864

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.

>TIGR00959 ffh signal recognition particle protein

Probab=96.64  E-value=0.16  Score=39.65  Aligned_cols=45  Identities=18%  Similarity=0.101  Sum_probs=28.6

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc--chhhhHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL--PYISLVHEKY   50 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~--P~~aL~~q~~   50 (138)
                      .+++++|+|+|||..+.-.+.......+.+++++.  ++++-..+++
T Consensus       101 vi~~vG~~GsGKTTtaakLA~~l~~~~g~kV~lV~~D~~R~~a~~QL  147 (428)
T TIGR00959       101 VILMVGLQGSGKTTTCGKLAYYLKKKQGKKVLLVACDLYRPAAIEQL  147 (428)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHhCCCeEEEEeccccchHHHHHH
Confidence            46899999999998876655542223566777764  3444333333

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.

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=96.62  E-value=0.028  Score=47.13  Aligned_cols=74  Identities=12%  Similarity=0.077  Sum_probs=56.7

Q ss_pred             hhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          61 KFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      ++++|...+-.+ ...-+..+.||.|||+++.+++.-.++. ++.+-++...--||.--++....++..+|+.|+.
T Consensus        79 ~ydVQliGglvL-h~G~IAEMkTGEGKTLvAtLpayLnAL~-GkgVhVVTvNdYLA~RDae~mg~vy~fLGLsvG~  152 (925)
T PRK12903         79 PYDVQIIGGIIL-DLGSVAEMKTGEGKTITSIAPVYLNALT-GKGVIVSTVNEYLAERDAEEMGKVFNFLGLSVGI  152 (925)
T ss_pred             cCchHHHHHHHH-hcCCeeeecCCCCccHHHHHHHHHHHhc-CCceEEEecchhhhhhhHHHHHHHHHHhCCceee
Confidence            455665444333 3344689999999999999998765554 6666777888889999999999999999998764

>PRK08727 hypothetical protein; Validated

Probab=96.59  E-value=0.0092  Score=42.57  Aligned_cols=39  Identities=21%  Similarity=0.169  Sum_probs=27.0

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLV   46 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~   46 (138)
                      .+++++|+|+|||..+...... +.+.+.++.|+. ...+.
T Consensus        43 ~l~l~G~~G~GKThL~~a~~~~-~~~~~~~~~y~~-~~~~~   81 (233)
T PRK08727         43 WLYLSGPAGTGKTHLALALCAA-AEQAGRSSAYLP-LQAAA   81 (233)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH-HHHcCCcEEEEe-HHHhh
Confidence            4899999999999877544443 455677888854 43433

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.57  E-value=0.12  Score=40.23  Aligned_cols=48  Identities=25%  Similarity=0.139  Sum_probs=31.1

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc--chhhhHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL--PYISLVHEKYQS   52 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~--P~~aL~~q~~~~   52 (138)
                      .-+++++|+|+|||..+.-.+.......+.++.++.  +++....++.+.
T Consensus       224 ~vi~lvGptGvGKTTtaaKLA~~~~~~~G~~V~Lit~Dt~R~aA~eQLk~  273 (432)
T PRK12724        224 KVVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLYTTDNYRIAAIEQLKR  273 (432)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEecccchhhhHHHHHHH
Confidence            447899999999998886666543344566776654  445544443333

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.54  E-value=0.11  Score=33.94  Aligned_cols=37  Identities=19%  Similarity=0.170  Sum_probs=27.1

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhh
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYIS   44 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~a   44 (138)
                      +++++|+|+|||..+...+... ...+.+++|+.....
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~-~~~~~~v~~~~~e~~   38 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNI-ATKGGKVVYVDIEEE   38 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHH-HhcCCEEEEEECCcc
Confidence            5789999999999886665543 335778888765433

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.

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

Probab=96.54  E-value=0.0071  Score=45.71  Aligned_cols=50  Identities=20%  Similarity=0.211  Sum_probs=39.2

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHH--hhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKEL--KIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~--~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      -++|.+..|||||+++...+.. +  .+.+.+++++++..+|.+...+.+...
T Consensus         3 v~~I~G~aGTGKTvla~~l~~~-l~~~~~~~~~~~l~~n~~l~~~l~~~l~~~   54 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALNLAKE-LQNSEEGKKVLYLCGNHPLRNKLREQLAKK   54 (352)
T ss_pred             EEEEEecCCcCHHHHHHHHHHH-hhccccCCceEEEEecchHHHHHHHHHhhh
Confidence            4689999999999999666655 4  446778999999999887777666554

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

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=96.51  E-value=0.098  Score=37.28  Aligned_cols=36  Identities=14%  Similarity=0.180  Sum_probs=26.1

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHh-----------hcCCeEEEEc
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELK-----------IKQKSAIFIL   40 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~-----------~~~~~~l~v~   40 (138)
                      .-.++.+|.|+|||..++..++....           .++++++|+.
T Consensus         2 ~~~ll~g~~G~GKS~lal~la~~va~G~~~~g~~~~~~~~~~Vlyi~   48 (239)
T cd01125           2 YVSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLS   48 (239)
T ss_pred             ceeEEEcCCCCCHHHHHHHHHHHHhcCccccCCccccCCCceEEEEE
Confidence            34589999999999998776664221           1356889986

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.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.51  E-value=0.044  Score=43.84  Aligned_cols=37  Identities=19%  Similarity=0.155  Sum_probs=24.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhc-CCeEEEE
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIK-QKSAIFI   39 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~-~~~~l~v   39 (138)
                      +|+.+.+.+|||+|||..+...+....... +.++.++
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLI  386 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALV  386 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEE
Confidence            567889999999999977644444322222 3456554

>PTZ00035 Rad51 protein; Provisional

Probab=96.47  E-value=0.13  Score=38.90  Aligned_cols=39  Identities=15%  Similarity=0.014  Sum_probs=27.9

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh-----cCCeEEEEcc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI-----KQKSAIFILP   41 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-----~~~~~l~v~P   41 (138)
                      .|+-+.+++|.|+|||..+...+....+.     .+++++|+.-
T Consensus       117 ~G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdt  160 (337)
T PTZ00035        117 TGSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDT  160 (337)
T ss_pred             CCeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEc
Confidence            45667899999999998886665543321     3568888764

>PRK07773 replicative DNA helicase; Validated

Probab=96.46  E-value=0.22  Score=42.41  Aligned_cols=131  Identities=12%  Similarity=0.013  Sum_probs=68.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHh----h-------hhhhhh--HHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEE----F-------KFYLEG--KCL   69 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~----~-------~~~~Q~--~~~   69 (138)
                      .|.-+++.|++|+|||..+.-.+.....+.+.+++|+.-- -=..|+..++......    .       ...|+.  .+.
T Consensus       216 ~G~livIagrPg~GKT~fal~ia~~~a~~~~~~V~~fSlE-ms~~ql~~R~~s~~~~i~~~~i~~g~l~~~~~~~~~~a~  294 (886)
T PRK07773        216 PGQLIIVAARPSMGKTTFGLDFARNCAIRHRLAVAIFSLE-MSKEQLVMRLLSAEAKIKLSDMRSGRMSDDDWTRLARAM  294 (886)
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHHHHhcCCeEEEEecC-CCHHHHHHHHHHHhcCCCHHHHhcCCCCHHHHHHHHHHH
Confidence            4555789999999999999777776555556677765421 0013444443332110    0       011111  111


Q ss_pred             hhhhccceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhH------------HHHHHHHHHHHhhhcCceeee
Q psy2029          70 EMIQNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISL------------VHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        70 ~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l------------~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      ..+.+.++.+.  ...+-++.-+...++++.. .+.+.++|.....+            +.+..+.++.+++++++.|.-
T Consensus       295 ~~l~~~~i~i~--d~~~~~i~~i~~~~r~~~~~~~~~lvvIDyLql~~~~~~~~~r~~ei~~isr~LK~lAkel~vpvi~  372 (886)
T PRK07773        295 GEISEAPIFID--DTPNLTVMEIRAKARRLRQEANLGLIVVDYLQLMTSGKKYENRQQEVSEISRHLKLLAKELEVPVVA  372 (886)
T ss_pred             HHHhcCCEEEE--CCCCCCHHHHHHHHHHHHHhcCCCEEEEcchhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHCCcEEE
Confidence            22222343332  2333444444444444443 34566666553322            345677888888888887653

>PRK08506 replicative DNA helicase; Provisional

Probab=96.46  E-value=0.18  Score=39.87  Aligned_cols=129  Identities=15%  Similarity=0.098  Sum_probs=70.0

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH----hh-------hhhhh--hHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE----EF-------KFYLE--GKCL   69 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~----~~-------~~~~Q--~~~~   69 (138)
                      .|.-+++.|++|+|||..+.-.+... ...+.+++|+..--. ..|...++.....    ..       ...|+  .++.
T Consensus       191 ~G~LivIaarpg~GKT~fal~ia~~~-~~~g~~V~~fSlEMs-~~ql~~Rlla~~s~v~~~~i~~~~l~~~e~~~~~~a~  268 (472)
T PRK08506        191 KGDLIIIAARPSMGKTTLCLNMALKA-LNQDKGVAFFSLEMP-AEQLMLRMLSAKTSIPLQNLRTGDLDDDEWERLSDAC  268 (472)
T ss_pred             CCceEEEEcCCCCChHHHHHHHHHHH-HhcCCcEEEEeCcCC-HHHHHHHHHHHhcCCCHHHHhcCCCCHHHHHHHHHHH
Confidence            45667899999999999997777664 345667777643111 1344444322211    00       00111  1111


Q ss_pred             hhhhccceEEEeecCCCchHhHHHHHHHHHHhC--CCeEEEEccchhH------------HHHHHHHHHHHhhhcCceee
Q psy2029          70 EMIQNKNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISL------------VHEKYQSLAKAAEEFKFYLE  135 (138)
Q Consensus        70 ~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~--~~~~~~i~P~~~l------------~~q~~~~~~~~~~~~~~~v~  135 (138)
                      ..+.+.++.+  ...++-|..-+...++++...  +.+.++|.....+            +.+..+.++.+++.+++.|.
T Consensus       269 ~~l~~~~l~I--~d~~~~ti~~I~~~~r~l~~~~~~~~lvvIDyLql~~~~~~~~~r~~ev~~isr~LK~lAkel~ipVi  346 (472)
T PRK08506        269 DELSKKKLFV--YDSGYVNIHQVRAQLRKLKSQHPEIGLAVIDYLQLMSGSGNFKDRHLQISEISRGLKLLARELDIPII  346 (472)
T ss_pred             HHHHcCCeEE--ECCCCCCHHHHHHHHHHHHHhCCCCCEEEEcChhhccCCCCCCCHHHHHHHHHHHHHHHHHHhCCcEE
Confidence            2233344433  233456766666666666542  3456665543322            23556678888888888765

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.46  E-value=0.11  Score=43.36  Aligned_cols=37  Identities=19%  Similarity=0.117  Sum_probs=23.3

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcC-CeEEEEc
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQ-KSAIFIL   40 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~-~~~l~v~   40 (138)
                      |+-+.+.+|||+|||......+.......+ +++.++.
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit  222 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAREGADQLALLT  222 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEec
Confidence            456789999999998665444433223344 3665544

>TIGR00376 DNA helicase, putative

Probab=96.46  E-value=0.018  Score=47.05  Aligned_cols=65  Identities=17%  Similarity=0.110  Sum_probs=49.4

Q ss_pred             hhhhhhHHHhhhhc--cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          61 KFYLEGKCLEMIQN--KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~--~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      +.+.|..++.....  ...++.-|.|+|||....-.+ ..+...+.++++++|+..-+.+..+.+.+.
T Consensus       158 ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii-~~~~~~g~~VLv~a~sn~Avd~l~e~l~~~  224 (637)
T TIGR00376       158 LNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVELI-RQLVKRGLRVLVTAPSNIAVDNLLERLALC  224 (637)
T ss_pred             CCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHHHH-HHHHHcCCCEEEEcCcHHHHHHHHHHHHhC
Confidence            46678888755544  667899999999997774444 344455779999999999998888888764

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.

>PRK05636 replicative DNA helicase; Provisional

Probab=96.44  E-value=0.28  Score=39.09  Aligned_cols=129  Identities=16%  Similarity=0.058  Sum_probs=66.2

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhH-HHHHHHHHHHH----Hhh-------hhhhhhH--HH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLV-HEKYQSLAKAA----EEF-------KFYLEGK--CL   69 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~-~q~~~~l~~~~----~~~-------~~~~Q~~--~~   69 (138)
                      |.=+++.|++|+|||..++-.+.....+.+.+++|+..  ++. .|...++....    ...       ...|+..  +.
T Consensus       265 G~Liiiaarpg~GKT~~al~~a~~~a~~~g~~v~~fSl--EMs~~ql~~R~ls~~s~v~~~~i~~g~l~~~e~~~~~~a~  342 (505)
T PRK05636        265 GQMIIVAARPGVGKSTLALDFMRSASIKHNKASVIFSL--EMSKSEIVMRLLSAEAEVRLSDMRGGKMDEDAWEKLVQRL  342 (505)
T ss_pred             CceEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEEe--eCCHHHHHHHHHHHhcCCCHHHHhcCCCCHHHHHHHHHHH
Confidence            44558899999999998876666544445667766532  111 23333321110    000       0111110  11


Q ss_pred             hhhhccceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhH------------HHHHHHHHHHHhhhcCceeee
Q psy2029          70 EMIQNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISL------------VHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        70 ~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l------------~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      ..+.+.++.+  ....+-|+.-+....+++.. ++.+.++|.....+            +.+..+.++.+++.+++.|..
T Consensus       343 ~~l~~~~l~I--~d~~~~ti~~I~~~~r~~~~~~~~~lvvIDYLql~~~~~~~~~r~~ei~~isr~LK~lAkel~ipVi~  420 (505)
T PRK05636        343 GKIAQAPIFI--DDSANLTMMEIRSKARRLKQKHDLKLIVVDYLQLMSSGKRVESRQQEVSEFSRQLKLLAKELDVPLIA  420 (505)
T ss_pred             HHHhcCCEEE--ECCCCCCHHHHHHHHHHHHHhcCCCEEEEcchHhcCCCCCCCcHHHHHHHHHHHHHHHHHHhCCeEEE
Confidence            1122233333  23334455555555555543 34566666553322            234667788888888887754

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=96.42  E-value=0.008  Score=40.90  Aligned_cols=45  Identities=16%  Similarity=0.166  Sum_probs=33.5

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK   55 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~   55 (138)
                      .++.+|+|||||..++..+..    .+.+++|+....++..+..+.+..
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~----~~~~~~y~at~~~~d~em~~rI~~   46 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAE----LGGPVTYIATAEAFDDEMAERIAR   46 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHh----cCCCeEEEEccCcCCHHHHHHHHH
Confidence            578999999999999876554    467899988776765555555444

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.

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.40  E-value=0.015  Score=41.95  Aligned_cols=40  Identities=23%  Similarity=0.344  Sum_probs=28.0

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLV   46 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~   46 (138)
                      .++++++|+|+|||..+. ++..++...+.+++|+ +...|.
T Consensus       100 ~~~~l~G~~GtGKThLa~-aia~~l~~~g~~v~~i-t~~~l~  139 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAA-AICNELLLRGKSVLII-TVADIM  139 (244)
T ss_pred             ceEEEECCCCCCHHHHHH-HHHHHHHhcCCeEEEE-EHHHHH
Confidence            468999999999998874 4444566667777775 443443

>COG4889 Predicted helicase [General function prediction only]

Probab=96.39  E-value=0.0084  Score=50.30  Aligned_cols=64  Identities=17%  Similarity=0.284  Sum_probs=47.7

Q ss_pred             hhhhhhhHHHhh----hhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          60 FKFYLEGKCLEM----IQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        60 ~~~~~Q~~~~~~----~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      .+.++|.+++..    ..+ .+.-+.+.-|+|||+.+ +-+.+++-  ..+++|++|..+|..|..+++..-
T Consensus       161 k~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTs-LkisEala--~~~iL~LvPSIsLLsQTlrew~~~  229 (1518)
T COG4889         161 KPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTS-LKISEALA--AARILFLVPSISLLSQTLREWTAQ  229 (1518)
T ss_pred             CCChhHHHHHHHHHhhcccccCCcEEEecCCCccchH-HHHHHHHh--hhheEeecchHHHHHHHHHHHhhc
Confidence            467889988843    333 44556677899999998 44555554  378999999999999998877654

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=96.38  E-value=0.15  Score=39.41  Aligned_cols=108  Identities=19%  Similarity=0.178  Sum_probs=52.6

Q ss_pred             CCccEEEEccCCcchHH-HHHHHHHHHHhhcCCeEEE-Ecc-hhhhHHHHHHHHHHHHHhhhhhhh--------hHHHhh
Q psy2029           3 QNKNCVLSIPTSGGKTL-VGEILIMKELKIKQKSAIF-ILP-YISLVHEKYQSLAKAAEEFKFYLE--------GKCLEM   71 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~-~~~~~~~~~~~~~~~~~l~-v~P-~~aL~~q~~~~l~~~~~~~~~~~Q--------~~~~~~   71 (138)
                      +++.+.+.+|||.|||. .|-+++.........++-+ .+- +|-   --.++++.++.-.+.|+-        .+++..
T Consensus       202 ~~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRI---GA~EQLk~Ya~im~vp~~vv~~~~el~~ai~~  278 (407)
T COG1419         202 QKRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRI---GAVEQLKTYADIMGVPLEVVYSPKELAEAIEA  278 (407)
T ss_pred             cCcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchh---hHHHHHHHHHHHhCCceEEecCHHHHHHHHHH
Confidence            46788999999999994 4445555443343444433 332 332   222334444433333321        112233


Q ss_pred             hhccceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccch
Q psy2029          72 IQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYI  113 (138)
Q Consensus        72 ~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~  113 (138)
                      ..+.++++.=..|-+=--...+.-+.++..  +.-....+++..
T Consensus       279 l~~~d~ILVDTaGrs~~D~~~i~el~~~~~~~~~i~~~Lvlsat  322 (407)
T COG1419         279 LRDCDVILVDTAGRSQYDKEKIEELKELIDVSHSIEVYLVLSAT  322 (407)
T ss_pred             hhcCCEEEEeCCCCCccCHHHHHHHHHHHhccccceEEEEEecC
Confidence            444555555555544333333444555544  233445555543

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=96.38  E-value=0.0075  Score=50.34  Aligned_cols=54  Identities=15%  Similarity=0.100  Sum_probs=43.1

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhh
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEF   60 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~   60 (138)
                      .-+..+.||.|||+++.+++.-+.+ .|..+.++++..-|+..-.+.+.+.....
T Consensus        91 G~IaEm~TGEGKTL~a~l~ayl~aL-~G~~VhVvT~NdyLA~RD~e~m~pvy~~L  144 (870)
T CHL00122         91 GKIAEMKTGEGKTLVATLPAYLNAL-TGKGVHIVTVNDYLAKRDQEWMGQIYRFL  144 (870)
T ss_pred             CccccccCCCCchHHHHHHHHHHHh-cCCceEEEeCCHHHHHHHHHHHHHHHHHc
Confidence            4678999999999999998865444 48888999999999988777777764433

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=96.37  E-value=0.012  Score=43.27  Aligned_cols=38  Identities=26%  Similarity=0.127  Sum_probs=24.9

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcC-CeEEEEc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQ-KSAIFIL   40 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~-~~~l~v~   40 (138)
                      ++..+.+++|||+|||..+.-.+.......+ .++.++.
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~  231 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALIT  231 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEE
Confidence            3567889999999999777555444322223 5666653

>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=96.37  E-value=0.19  Score=36.29  Aligned_cols=131  Identities=15%  Similarity=0.044  Sum_probs=69.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHh-------hh--h--hhhh--HHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEE-------FK--F--YLEG--KCL   69 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~-------~~--~--~~Q~--~~~   69 (138)
                      .|.=+++.|++|+|||..+.-.+...+.+.+..++|+..--. .++...++......       .+  .  .++.  ...
T Consensus        18 ~g~L~vi~a~pg~GKT~~~l~ia~~~a~~~~~~vly~SlEm~-~~~l~~R~la~~s~v~~~~i~~g~l~~~e~~~~~~~~   96 (259)
T PF03796_consen   18 PGELTVIAARPGVGKTAFALQIALNAALNGGYPVLYFSLEMS-EEELAARLLARLSGVPYNKIRSGDLSDEEFERLQAAA   96 (259)
T ss_dssp             TT-EEEEEESTTSSHHHHHHHHHHHHHHTTSSEEEEEESSS--HHHHHHHHHHHHHTSTHHHHHCCGCHHHHHHHHHHHH
T ss_pred             cCcEEEEEecccCCchHHHHHHHHHHHHhcCCeEEEEcCCCC-HHHHHHHHHHHhhcchhhhhhccccCHHHHHHHHHHH
Confidence            345568999999999999988888766654678888764111 12333332222110       00  0  1111  111


Q ss_pred             hhhhccceEEEeecCCCchHhHHHHHHHHHHhC--CCeEEEEcc------------chhHHHHHHHHHHHHhhhcCceee
Q psy2029          70 EMIQNKNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILP------------YISLVHEKYQSLAKAAEEFKFYLE  135 (138)
Q Consensus        70 ~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~--~~~~~~i~P------------~~~l~~q~~~~~~~~~~~~~~~v~  135 (138)
                      ..+.+..+. ..+++ +-+.-.+...++.+...  +.++++|..            ...-+.+.++.+++++..+++.|.
T Consensus        97 ~~l~~~~l~-i~~~~-~~~~~~i~~~i~~~~~~~~~~~~v~IDyl~ll~~~~~~~~~~~~~~~i~~~Lk~lA~~~~i~vi  174 (259)
T PF03796_consen   97 EKLSDLPLY-IEDTP-SLTIDDIESKIRRLKREGKKVDVVFIDYLQLLKSEDSSDNRRQEIGEISRELKALAKELNIPVI  174 (259)
T ss_dssp             HHHHTSEEE-EEESS-S-BHHHHHHHHHHHHHHSTTEEEEEEEEGGGSBTSCSSSCCHHHHHHHHHHHHHHHHHHTSEEE
T ss_pred             HHHhhCcEE-EECCC-CCCHHHHHHHHHHHHhhccCCCEEEechHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHcCCeEE
Confidence            223333333 33333 23555555555555442  345555543            233455677889999988888765


Q ss_pred             e
Q psy2029         136 V  136 (138)
Q Consensus       136 ~  136 (138)
                      .
T Consensus       175 ~  175 (259)
T PF03796_consen  175 A  175 (259)
T ss_dssp             E
T ss_pred             E
Confidence            3

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 ....

>TIGR02012 tigrfam_recA protein RecA

Probab=96.36  E-value=0.013  Score=43.88  Aligned_cols=43  Identities=26%  Similarity=0.186  Sum_probs=33.1

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLV   46 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~   46 (138)
                      .|.-+.+.+|.|+|||..++..+..... .+++++|+..-.++.
T Consensus        54 ~G~iteI~G~~GsGKTtLaL~~~~~~~~-~g~~v~yId~E~~~~   96 (321)
T TIGR02012        54 RGRIIEIYGPESSGKTTLALHAIAEAQK-AGGTAAFIDAEHALD   96 (321)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH-cCCcEEEEcccchhH
Confidence            4567789999999999999887776544 588999986654443

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.

>PRK08939 primosomal protein DnaI; Reviewed

Probab=96.36  E-value=0.013  Score=43.67  Aligned_cols=36  Identities=25%  Similarity=0.157  Sum_probs=26.8

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      +++++++.+|+|+|||..+. ++...+.+.+.++.|+
T Consensus       155 ~~~gl~L~G~~G~GKThLa~-Aia~~l~~~g~~v~~~  190 (306)
T PRK08939        155 KVKGLYLYGDFGVGKSYLLA-AIANELAKKGVSSTLL  190 (306)
T ss_pred             CCCeEEEECCCCCCHHHHHH-HHHHHHHHcCCCEEEE
Confidence            35689999999999998875 4444466667777665

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=96.36  E-value=0.0038  Score=47.19  Aligned_cols=42  Identities=26%  Similarity=0.288  Sum_probs=27.8

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLV   46 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~   46 (138)
                      .+.|+++++|||||||...-. ++.. +....+++.+-...+|.
T Consensus       161 ~~~nilI~G~tGSGKTTll~a-Ll~~-i~~~~rivtiEd~~El~  202 (344)
T PRK13851        161 GRLTMLLCGPTGSGKTTMSKT-LISA-IPPQERLITIEDTLELV  202 (344)
T ss_pred             cCCeEEEECCCCccHHHHHHH-HHcc-cCCCCCEEEECCCcccc
Confidence            468999999999999987533 3332 33455666665555543

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

Probab=96.35  E-value=0.018  Score=40.02  Aligned_cols=45  Identities=24%  Similarity=0.204  Sum_probs=31.0

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQ   51 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~   51 (138)
                      -.++.+|.|+|||.+. ..+.+.+...+.+++++.|+..-..+..+
T Consensus        20 ~~~l~G~aGtGKT~~l-~~~~~~~~~~g~~v~~~apT~~Aa~~L~~   64 (196)
T PF13604_consen   20 VSVLQGPAGTGKTTLL-KALAEALEAAGKRVIGLAPTNKAAKELRE   64 (196)
T ss_dssp             EEEEEESTTSTHHHHH-HHHHHHHHHTT--EEEEESSHHHHHHHHH
T ss_pred             EEEEEECCCCCHHHHH-HHHHHHHHhCCCeEEEECCcHHHHHHHHH
Confidence            4678899999999864 33555555567899999999765554333

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=96.35  E-value=0.14  Score=38.79  Aligned_cols=51  Identities=12%  Similarity=0.014  Sum_probs=33.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh-----cCCeEEEEcchhhhHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI-----KQKSAIFILPYISLVHEKYQSL   53 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-----~~~~~l~v~P~~aL~~q~~~~l   53 (138)
                      .|.-+.++++.|+|||..+...+....+.     .+++++|+.---.+..+...++
T Consensus       122 ~g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl~qi  177 (342)
T PLN03186        122 TGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRLIQI  177 (342)
T ss_pred             CceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHHHHH
Confidence            35567899999999999886655443322     2358999875544444444433

>PRK05595 replicative DNA helicase; Provisional

Probab=96.33  E-value=0.19  Score=39.29  Aligned_cols=130  Identities=15%  Similarity=0.037  Sum_probs=67.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhH-HHHHHHHHHHHH----hh-------hhhhhhHH--
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLV-HEKYQSLAKAAE----EF-------KFYLEGKC--   68 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~-~q~~~~l~~~~~----~~-------~~~~Q~~~--   68 (138)
                      .|.-+++.|++|+|||..+.-.+.....+.+.+++|+..  ++. .|...++.....    ..       ...|+...  
T Consensus       200 ~g~liviaarpg~GKT~~al~ia~~~a~~~g~~vl~fSl--Ems~~~l~~R~~a~~~~v~~~~~~~~~l~~~e~~~~~~~  277 (444)
T PRK05595        200 KGDMILIAARPSMGKTTFALNIAEYAALREGKSVAIFSL--EMSKEQLAYKLLCSEANVDMLRLRTGNLEDKDWENIARA  277 (444)
T ss_pred             CCcEEEEEecCCCChHHHHHHHHHHHHHHcCCcEEEEec--CCCHHHHHHHHHHHhcCCCHHHHhcCCCCHHHHHHHHHH
Confidence            455668899999999999877666534445778877643  111 233333222211    00       00111100  


Q ss_pred             HhhhhccceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchh------------HHHHHHHHHHHHhhhcCceee
Q psy2029          69 LEMIQNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYIS------------LVHEKYQSLAKAAEEFKFYLE  135 (138)
Q Consensus        69 ~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~------------l~~q~~~~~~~~~~~~~~~v~  135 (138)
                      ...+.+.++.+.  ...+-|..-....++++.. ++.+.++|.....            -+.+..+.++.+++.+++.|.
T Consensus       278 ~~~l~~~~l~i~--d~~~~t~~~i~~~~r~~~~~~~~~~vvIDylql~~~~~~~~~r~~~v~~is~~LK~lAke~~i~vi  355 (444)
T PRK05595        278 SGPLAAAKIFID--DTAGVSVMEMRSKCRRLKIEHGIDMILIDYLQLMSGGKGSESRQQEVSEISRSIKALAKEMECPVI  355 (444)
T ss_pred             HHHHhcCCEEEE--CCCCCCHHHHHHHHHHHHHhcCCCEEEEeHHHhccCCCCCccHHHHHHHHHHHHHHHHHHhCCeEE
Confidence            011222344333  3344555555555555543 3455555543221            134566778888888888765


Q ss_pred             e
Q psy2029         136 V  136 (138)
Q Consensus       136 ~  136 (138)
                      -
T Consensus       356 ~  356 (444)
T PRK05595        356 A  356 (444)
T ss_pred             E
Confidence            3

>PRK07004 replicative DNA helicase; Provisional

Probab=96.33  E-value=0.28  Score=38.68  Aligned_cols=130  Identities=11%  Similarity=-0.002  Sum_probs=66.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhH-HHHHHHHHHH-H---Hh---h----hhhhhh--HH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLV-HEKYQSLAKA-A---EE---F----KFYLEG--KC   68 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~-~q~~~~l~~~-~---~~---~----~~~~Q~--~~   68 (138)
                      .|.=+++.|.+|+|||..+.-.+.....+.+..++++..  ++. .|...++-.. +   .+   .    ...|+.  .+
T Consensus       212 ~g~liviaarpg~GKT~~al~ia~~~a~~~~~~v~~fSl--EM~~~ql~~R~la~~~~v~~~~i~~g~l~~~e~~~~~~a  289 (460)
T PRK07004        212 GGELIIVAGRPSMGKTAFSMNIGEYVAVEYGLPVAVFSM--EMPGTQLAMRMLGSVGRLDQHRMRTGRLTDEDWPKLTHA  289 (460)
T ss_pred             CCceEEEEeCCCCCccHHHHHHHHHHHHHcCCeEEEEeC--CCCHHHHHHHHHHhhcCCCHHHHhcCCCCHHHHHHHHHH
Confidence            466678999999999999877666544455667766532  111 2333333211 0   00   0    111111  11


Q ss_pred             HhhhhccceEEEeecCCCchHhHHHHHHHHHHhC-C-CeEEEEccchhH------------HHHHHHHHHHHhhhcCcee
Q psy2029          69 LEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIK-Q-KSAIFILPYISL------------VHEKYQSLAKAAEEFKFYL  134 (138)
Q Consensus        69 ~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~-~-~~~~~i~P~~~l------------~~q~~~~~~~~~~~~~~~v  134 (138)
                      ...+.+.++.+.  ..++-+..-+....+++... + ...++|.....+            +.++.+.++.+++.+++.|
T Consensus       290 ~~~l~~~~l~I~--d~~~~~~~~i~~~~r~l~~~~~~~~lviIDYLql~~~~~~~~~r~~ei~~Isr~LK~lAkel~ipV  367 (460)
T PRK07004        290 VQKMSEAQLFID--ETGGLNPMELRSRARRLARQCGKLGLIIIDYLQLMSGSSQGENRATEISEISRSLKSLAKELDVPV  367 (460)
T ss_pred             HHHHhcCCEEEE--CCCCCCHHHHHHHHHHHHHhCCCCCEEEEChhhhccCCCCCCcHHHHHHHHHHHHHHHHHHhCCeE
Confidence            122223333332  22234444444555555432 2 455555432211            3467788888888888877


Q ss_pred             ee
Q psy2029         135 EV  136 (138)
Q Consensus       135 ~~  136 (138)
                      ..
T Consensus       368 i~  369 (460)
T PRK07004        368 IA  369 (460)
T ss_pred             EE
Confidence            53

>PRK08084 DNA replication initiation factor; Provisional

Probab=96.32  E-value=0.0095  Score=42.54  Aligned_cols=36  Identities=8%  Similarity=0.079  Sum_probs=26.1

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      +.++++++|+|+|||..+...... +.+.+.++.|+.
T Consensus        45 ~~~l~l~Gp~G~GKThLl~a~~~~-~~~~~~~v~y~~   80 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLLHAACAE-LSQRGRAVGYVP   80 (235)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH-HHhCCCeEEEEE
Confidence            357899999999999887554443 344567777754

>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=96.30  E-value=0.017  Score=36.79  Aligned_cols=37  Identities=22%  Similarity=0.248  Sum_probs=25.9

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      +..+++.+|+|+|||..+...+.. +.+.+..++++..
T Consensus        19 ~~~v~i~G~~G~GKT~l~~~i~~~-~~~~~~~v~~~~~   55 (151)
T cd00009          19 PKNLLLYGPPGTGKTTLARAIANE-LFRPGAPFLYLNA   55 (151)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH-hhcCCCCeEEEeh
Confidence            568999999999999877555443 3334566666544

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.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.26  E-value=0.12  Score=39.79  Aligned_cols=50  Identities=22%  Similarity=0.071  Sum_probs=29.7

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhh---cCCeEEEEc--chhhhHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKI---KQKSAIFIL--PYISLVHEKYQSL   53 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~---~~~~~l~v~--P~~aL~~q~~~~l   53 (138)
                      +..+++.+|||+|||..+.-.+......   ++.++.++.  +++.-..++.+.+
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~  228 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTY  228 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHH
Confidence            4578999999999997775444432222   355666653  4444333334443

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=96.26  E-value=0.0084  Score=44.45  Aligned_cols=42  Identities=21%  Similarity=0.260  Sum_probs=27.6

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhh
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISL   45 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL   45 (138)
                      .+.|+++++|||||||...-. ++..+.+  .+.+++.+-...++
T Consensus       131 ~~~~ilI~G~tGSGKTTll~a-l~~~i~~~~~~~ri~tiEd~~El  174 (299)
T TIGR02782       131 ARKNILVVGGTGSGKTTLANA-LLAEIAKNDPTDRVVIIEDTREL  174 (299)
T ss_pred             cCCeEEEECCCCCCHHHHHHH-HHHHhhccCCCceEEEECCchhh
Confidence            457999999999999987633 3333322  24577666555444

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.

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

Probab=96.25  E-value=0.016  Score=43.48  Aligned_cols=44  Identities=23%  Similarity=0.143  Sum_probs=34.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVH   47 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~   47 (138)
                      .|.-+.+.+|.|+|||..++..+..... .+++++|+.+--++..
T Consensus        54 ~G~iteI~Gp~GsGKTtLal~~~~~~~~-~g~~~vyId~E~~~~~   97 (325)
T cd00983          54 KGRIIEIYGPESSGKTTLALHAIAEAQK-LGGTVAFIDAEHALDP   97 (325)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH-cCCCEEEECccccHHH
Confidence            3567789999999999999887776543 5889999987655543

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK09165 replicative DNA helicase; Provisional

Probab=96.25  E-value=0.23  Score=39.55  Aligned_cols=130  Identities=13%  Similarity=0.054  Sum_probs=68.0

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh--------------cCCeEEEEcchhhhH-HHHHHHHHHHHHhh-------
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI--------------KQKSAIFILPYISLV-HEKYQSLAKAAEEF-------   60 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--------------~~~~~l~v~P~~aL~-~q~~~~l~~~~~~~-------   60 (138)
                      .|.-+++.|++|+|||..++-.+.....+              .+.+++|+..  ++. .|...++.......       
T Consensus       216 ~g~livIaarpg~GKT~~al~ia~~~a~~~~~~~~~~~~~~~~~g~~vl~fSl--EMs~~ql~~R~la~~s~v~~~~i~~  293 (497)
T PRK09165        216 PSDLIILAGRPSMGKTALATNIAFNAAKAYRREAQPDGSKKAVNGGVVGFFSL--EMSAEQLATRILSEQSEISSSKIRR  293 (497)
T ss_pred             CCceEEEEeCCCCChHHHHHHHHHHHHHhhcccccccccccccCCCeEEEEeC--cCCHHHHHHHHHHHhcCCCHHHHhc
Confidence            45567899999999999887666654332              2457777642  111 34444432221100       


Q ss_pred             --h--hhhhh--HHHhhhhccceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhH--------------HHHH
Q psy2029          61 --K--FYLEG--KCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISL--------------VHEK  119 (138)
Q Consensus        61 --~--~~~Q~--~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l--------------~~q~  119 (138)
                        .  ..|+.  .+...+.+.++.+.-  .++-|+.-+...++++.. ++.+.++|.....+              +.+.
T Consensus       294 ~~l~~~e~~~l~~a~~~l~~~~l~I~d--~~~~ti~~i~~~ir~l~~~~~~~lvvIDyLqli~~~~~~~~~~r~~ev~~i  371 (497)
T PRK09165        294 GKISEEDFEKLVDASQELQKLPLYIDD--TPALSISQLRARARRLKRQHGLDLLVVDYLQLIRGSSKRSSDNRVQEISEI  371 (497)
T ss_pred             CCCCHHHHHHHHHHHHHHhcCCeEEeC--CCCCCHHHHHHHHHHHHHhcCCCEEEEcchHhccCCCCCCCCchHHHHHHH
Confidence              0  01111  001122223444332  335566666666666554 34566666554322              2346


Q ss_pred             HHHHHHHhhhcCceeee
Q psy2029         120 YQSLAKAAEEFKFYLEV  136 (138)
Q Consensus       120 ~~~~~~~~~~~~~~v~~  136 (138)
                      .+.++.+++.+++.|.-
T Consensus       372 s~~LK~lAkel~ipVi~  388 (497)
T PRK09165        372 TQGLKALAKELNIPVIA  388 (497)
T ss_pred             HHHHHHHHHHhCCeEEE
Confidence            67788888888887653

>PRK05642 DNA replication initiation factor; Validated

Probab=96.23  E-value=0.0096  Score=42.51  Aligned_cols=40  Identities=10%  Similarity=0.082  Sum_probs=27.3

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLV   46 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~   46 (138)
                      ..+++++|+|+|||..+... ...+.+++.+++|+.. ..+.
T Consensus        46 ~~l~l~G~~G~GKTHLl~a~-~~~~~~~~~~v~y~~~-~~~~   85 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQAA-CLRFEQRGEPAVYLPL-AELL   85 (234)
T ss_pred             CeEEEECCCCCCHHHHHHHH-HHHHHhCCCcEEEeeH-HHHH
Confidence            46789999999999885433 3344555778888543 4443

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=96.22  E-value=0.03  Score=47.64  Aligned_cols=66  Identities=14%  Similarity=0.180  Sum_probs=49.9

Q ss_pred             hhhhhhHHHhhh-hc--cceEEEeecCCCchHhHHHHHHHHHHhC-CCeEEEEccchhHHHHHHHHHHHHh
Q psy2029          61 KFYLEGKCLEMI-QN--KNCVLSIPTSGGKTLVGEILIMKELKIK-QKSAIFILPYISLVHEKYQSLAKAA  127 (138)
Q Consensus        61 ~~~~Q~~~~~~~-~~--~~~ii~~ptg~GKt~~~~~~~l~~~~~~-~~~~~~i~P~~~l~~q~~~~~~~~~  127 (138)
                      ++|+|......+ ..  .++++.-..|-|||..+.+.+-+.+... ..++++|+|. +|..|...++.+++
T Consensus       153 l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g~~~rvLIVvP~-sL~~QW~~El~~kF  222 (956)
T PRK04914        153 LIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTGRAERVLILVPE-TLQHQWLVEMLRRF  222 (956)
T ss_pred             CCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcCCCCcEEEEcCH-HHHHHHHHHHHHHh
Confidence            678888776433 22  6788999999999999965554433333 3689999997 79999999997765

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.20  E-value=0.0067  Score=47.67  Aligned_cols=28  Identities=25%  Similarity=0.328  Sum_probs=20.5

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCC
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQK   34 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~   34 (138)
                      =+++.+|||||||.. ++++++.+.....
T Consensus       260 liLvTGPTGSGKTTT-LY~~L~~ln~~~~  287 (500)
T COG2804         260 LILVTGPTGSGKTTT-LYAALSELNTPER  287 (500)
T ss_pred             EEEEeCCCCCCHHHH-HHHHHHHhcCCCc
Confidence            468999999999987 4666766544333

>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=96.18  E-value=0.009  Score=43.32  Aligned_cols=117  Identities=13%  Similarity=0.071  Sum_probs=53.6

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhhhhHHH-hhhhc-cceEEE
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCL-EMIQN-KNCVLS   80 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~-~~~~~-~~~ii~   80 (138)
                      .+.++++++|||||||... -+++..+-+...+++.+-...++........ .........-..+.+ ..++. .+.++.
T Consensus       126 ~~~~ili~G~tGSGKTT~l-~all~~i~~~~~~iv~iEd~~E~~l~~~~~~-~~~~~~~~~~~~~~l~~~LR~~pD~iii  203 (270)
T PF00437_consen  126 GRGNILISGPTGSGKTTLL-NALLEEIPPEDERIVTIEDPPELRLPGPNQI-QIQTRRDEISYEDLLKSALRQDPDVIII  203 (270)
T ss_dssp             TTEEEEEEESTTSSHHHHH-HHHHHHCHTTTSEEEEEESSS-S--SCSSEE-EEEEETTTBSHHHHHHHHTTS--SEEEE
T ss_pred             cceEEEEECCCccccchHH-HHHhhhccccccceEEeccccceeecccceE-EEEeecCcccHHHHHHHHhcCCCCcccc
Confidence            3679999999999999876 3334433333367777765444322100000 000000111122223 33344 777777


Q ss_pred             eecCCCchHhHHHHHHHHHHhCCCeE-EEEccchhHHHHHHHHHHHHh
Q psy2029          81 IPTSGGKTLVGEILIMKELKIKQKSA-IFILPYISLVHEKYQSLAKAA  127 (138)
Q Consensus        81 ~ptg~GKt~~~~~~~l~~~~~~~~~~-~~i~P~~~l~~q~~~~~~~~~  127 (138)
                      .--.++.+..+ +.++.    .+.+. +--.... -+.+....+..++
T Consensus       204 gEiR~~e~~~~-~~a~~----tGh~~~~tT~Ha~-s~~~~i~Rl~~l~  245 (270)
T PF00437_consen  204 GEIRDPEAAEA-IQAAN----TGHLGSLTTLHAN-SAEDAIERLADLG  245 (270)
T ss_dssp             SCE-SCHHHHH-HHHHH----TT-EEEEEEEE-S-SHHHHHHHHHHHC
T ss_pred             cccCCHhHHHH-HHhhc----cCCceeeeeeecC-CHHHHHHHHHHHh
Confidence            77776655544 33332    24443 3333322 3445555555544

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 ....

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

Probab=96.18  E-value=0.011  Score=47.01  Aligned_cols=49  Identities=18%  Similarity=0.162  Sum_probs=38.5

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      .-.+.+-||||||..-.-.+.    +-+..++++.|.+.|+-|.|.+|++++.
T Consensus        34 ~QtLLGvTGSGKTfT~AnVI~----~~~rPtLV~AhNKTLAaQLy~Efk~fFP   82 (663)
T COG0556          34 HQTLLGVTGSGKTFTMANVIA----KVQRPTLVLAHNKTLAAQLYSEFKEFFP   82 (663)
T ss_pred             eeEEeeeccCCchhHHHHHHH----HhCCCeEEEecchhHHHHHHHHHHHhCc
Confidence            446788999999976422222    2467889999999999999999999864

>PRK14873 primosome assembly protein PriA; Provisional

Probab=96.17  E-value=0.015  Score=47.72  Aligned_cols=45  Identities=9%  Similarity=-0.071  Sum_probs=38.2

Q ss_pred             cCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhh
Q psy2029          83 TSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE  128 (138)
Q Consensus        83 tg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~  128 (138)
                      +|+|||-+++-.+ ......++.+++++|..+|..|..+.|++.|.
T Consensus       169 ~GSGKTevyl~~i-~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~  213 (665)
T PRK14873        169 PGEDWARRLAAAA-AATLRAGRGALVVVPDQRDVDRLEAALRALLG  213 (665)
T ss_pred             CCCcHHHHHHHHH-HHHHHcCCeEEEEecchhhHHHHHHHHHHHcC
Confidence            4999999995544 45555688899999999999999999999985

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=96.10  E-value=0.14  Score=42.78  Aligned_cols=92  Identities=20%  Similarity=0.156  Sum_probs=54.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhhhhHHHhhhhccceEEEee
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIQNKNCVLSIP   82 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~ii~~p   82 (138)
                      .|..+.+.+|.|+|||..+...+.... ..+.+++|+.+--++..+   ..    ...+++.          .++++.-|
T Consensus        59 ~GsiteI~G~~GsGKTtLal~~~~~a~-~~G~~v~yId~E~t~~~~---~A----~~lGvDl----------~~llv~~~  120 (790)
T PRK09519         59 RGRVIEIYGPESSGKTTVALHAVANAQ-AAGGVAAFIDAEHALDPD---YA----KKLGVDT----------DSLLVSQP  120 (790)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH-HcCCcEEEECCccchhHH---HH----HHcCCCh----------hHeEEecC
Confidence            466789999999999999977766544 358899998775554422   11    1112221          22233333


Q ss_pred             cCCCchHhHHHHHHHHHH-hCCCeEEEEccchhHH
Q psy2029          83 TSGGKTLVGEILIMKELK-IKQKSAIFILPYISLV  116 (138)
Q Consensus        83 tg~GKt~~~~~~~l~~~~-~~~~~~~~i~P~~~l~  116 (138)
                      . ++..   .+..+..+. +...+.++|.+..+|.
T Consensus       121 ~-~~E~---~l~~i~~lv~~~~~~LVVIDSI~aL~  151 (790)
T PRK09519        121 D-TGEQ---ALEIADMLIRSGALDIVVIDSVAALV  151 (790)
T ss_pred             C-CHHH---HHHHHHHHhhcCCCeEEEEcchhhhc
Confidence            3 2232   233333333 3457788888877777

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=96.08  E-value=0.008  Score=45.24  Aligned_cols=41  Identities=22%  Similarity=0.141  Sum_probs=27.1

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhh
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISL   45 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL   45 (138)
                      .+.|+++++|||||||...-. ++. .+....+++.+--..+|
T Consensus       159 ~~~nili~G~tgSGKTTll~a-L~~-~ip~~~ri~tiEd~~El  199 (332)
T PRK13900        159 SKKNIIISGGTSTGKTTFTNA-ALR-EIPAIERLITVEDAREI  199 (332)
T ss_pred             cCCcEEEECCCCCCHHHHHHH-HHh-hCCCCCeEEEecCCCcc
Confidence            467999999999999977533 333 33445666665444444

>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=96.03  E-value=0.017  Score=44.33  Aligned_cols=48  Identities=19%  Similarity=0.288  Sum_probs=32.6

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQ   51 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~   51 (138)
                      ...++++.+.||||||.+ +..++..++.++.++++.-|.-++....++
T Consensus        14 e~~~~li~G~~GsGKT~~-i~~ll~~~~~~g~~~iI~D~kg~~~~~f~~   61 (386)
T PF10412_consen   14 ENRHILIIGATGSGKTQA-IRHLLDQIRARGDRAIIYDPKGEFTERFYR   61 (386)
T ss_dssp             GGG-EEEEE-TTSSHHHH-HHHHHHHHHHTT-EEEEEEETTHHHHHH--
T ss_pred             hhCcEEEECCCCCCHHHH-HHHHHHHHHHcCCEEEEEECCchHHHHhcC
Confidence            356899999999999974 455666677778888888888776654444

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.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=96.02  E-value=0.014  Score=40.51  Aligned_cols=33  Identities=15%  Similarity=0.230  Sum_probs=21.3

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhc-CCeEEEE
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIK-QKSAIFI   39 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~-~~~~l~v   39 (138)
                      -+++++|||||||..... ++..+... +++++.+
T Consensus         3 lilI~GptGSGKTTll~~-ll~~~~~~~~~~i~t~   36 (198)
T cd01131           3 LVLVTGPTGSGKSTTLAA-MIDYINKNKTHHILTI   36 (198)
T ss_pred             EEEEECCCCCCHHHHHHH-HHHHhhhcCCcEEEEE
Confidence            478999999999988633 34334332 3455544

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.

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.02  E-value=0.55  Score=36.84  Aligned_cols=35  Identities=20%  Similarity=0.102  Sum_probs=25.8

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      ..+++++|+|+|||..+.-.+. .+.+.+.++.++.
T Consensus        96 ~vI~lvG~~GsGKTTtaakLA~-~L~~~g~kV~lV~  130 (437)
T PRK00771         96 QTIMLVGLQGSGKTTTAAKLAR-YFKKKGLKVGLVA  130 (437)
T ss_pred             eEEEEECCCCCcHHHHHHHHHH-HHHHcCCeEEEec
Confidence            4578999999999988765554 3555667777764

>PLN02199 shikimate kinase

Probab=96.01  E-value=0.16  Score=37.70  Aligned_cols=77  Identities=21%  Similarity=0.273  Sum_probs=43.4

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHH------HHHHHHHHhhhhhhhhHHHhhhhc-
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKY------QSLAKAAEEFKFYLEGKCLEMIQN-   74 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~------~~l~~~~~~~~~~~Q~~~~~~~~~-   74 (138)
                      +.|.++++.++.|||||.++-..+-. +   +.   -++-+-.+.++.+      +-+..+|+......+.+++..+.. 
T Consensus       100 l~~~~I~LIG~~GSGKSTVgr~LA~~-L---g~---~fIDtD~lIe~~~~G~sI~eIf~~~GE~~FR~~E~e~L~~L~~~  172 (303)
T PLN02199        100 LNGRSMYLVGMMGSGKTTVGKLMSKV-L---GY---TFFDCDTLIEQAMNGTSVAEIFVHHGENFFRGKETDALKKLSSR  172 (303)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHHH-h---CC---CEEehHHHHHHHhcCCCHHHHHHHhCHHHHHHHHHHHHHHHHhc
Confidence            56889999999999999998555432 1   11   1222223333321      112223444455556666655554 


Q ss_pred             cceEEEeecCCCc
Q psy2029          75 KNCVLSIPTSGGK   87 (138)
Q Consensus        75 ~~~ii~~ptg~GK   87 (138)
                      .++++  .||+|-
T Consensus       173 ~~~VI--StGGG~  183 (303)
T PLN02199        173 YQVVV--STGGGA  183 (303)
T ss_pred             CCEEE--ECCCcc
Confidence            55554  567775

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.00  E-value=0.011  Score=44.34  Aligned_cols=42  Identities=19%  Similarity=0.211  Sum_probs=27.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHH--hhcCCeEEEEcchhhh
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKEL--KIKQKSAIFILPYISL   45 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~--~~~~~~~l~v~P~~aL   45 (138)
                      .+.|+++++|||||||......+ ..+  .....+++.+-...+|
T Consensus       147 ~~~~ilI~G~tGSGKTTll~aL~-~~~~~~~~~~rivtIEd~~El  190 (319)
T PRK13894        147 AHRNILVIGGTGSGKTTLVNAII-NEMVIQDPTERVFIIEDTGEI  190 (319)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHH-HhhhhcCCCceEEEEcCCCcc
Confidence            56799999999999996653332 222  2234566666655554

>KOG0745|consensus

Probab=95.97  E-value=0.0065  Score=47.16  Aligned_cols=25  Identities=36%  Similarity=0.527  Sum_probs=20.6

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      |+-+|+++.+|||+|||+.+.-.+.
T Consensus       224 LeKSNvLllGPtGsGKTllaqTLAr  248 (564)
T KOG0745|consen  224 LEKSNVLLLGPTGSGKTLLAQTLAR  248 (564)
T ss_pred             eecccEEEECCCCCchhHHHHHHHH
Confidence            4567999999999999999855443

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

Probab=95.97  E-value=0.024  Score=46.23  Aligned_cols=52  Identities=23%  Similarity=0.197  Sum_probs=35.2

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhh--hHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYIS--LVHEKYQSLAKA   56 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~a--L~~q~~~~l~~~   56 (138)
                      ..+++|.+|||+|||..+...+.+. +..+..++++-|--.  |...........
T Consensus       176 ~~H~lv~G~TGsGKT~l~~~l~~q~-i~~g~~viv~DpKgD~~l~~~~~~~~~~~  229 (634)
T TIGR03743       176 VGHTLVLGTTGVGKTRLAELLITQD-IRRGDVVIVIDPKGDADLKRRMRAEAKRA  229 (634)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHH-HHcCCeEEEEeCCCchHHHHHHHHHHHHh
Confidence            3588999999999998876655554 445677777777643  444444444444

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.

>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=95.96  E-value=0.034  Score=40.60  Aligned_cols=56  Identities=14%  Similarity=0.105  Sum_probs=41.6

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhhh
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFY   63 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~   63 (138)
                      -+..+.||-|||+++.+++.-+.+ .|..+-+++...-|...=++.+.++....+..
T Consensus        93 ~laEm~TGEGKTli~~l~a~~~AL-~G~~V~vvT~NdyLA~RD~~~~~~~y~~LGls  148 (266)
T PF07517_consen   93 RLAEMKTGEGKTLIAALPAALNAL-QGKGVHVVTSNDYLAKRDAEEMRPFYEFLGLS  148 (266)
T ss_dssp             SEEEESTTSHHHHHHHHHHHHHHT-TSS-EEEEESSHHHHHHHHHHHHHHHHHTT--
T ss_pred             eeEEecCCCCcHHHHHHHHHHHHH-hcCCcEEEeccHHHhhccHHHHHHHHHHhhhc
Confidence            388999999999999887766555 47888888888888877777777776554443

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 ....

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=95.93  E-value=0.013  Score=43.96  Aligned_cols=42  Identities=19%  Similarity=0.264  Sum_probs=26.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHh--hcCCeEEEEcchhhh
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELK--IKQKSAIFILPYISL   45 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~--~~~~~~l~v~P~~aL   45 (138)
                      .+.|+++++|||||||...-. .+..+.  ..+.+++.+-...+|
T Consensus       143 ~~~nilI~G~tGSGKTTll~a-L~~~i~~~~~~~rivtiEd~~El  186 (323)
T PRK13833        143 SRLNIVISGGTGSGKTTLANA-VIAEIVASAPEDRLVILEDTAEI  186 (323)
T ss_pred             cCCeEEEECCCCCCHHHHHHH-HHHHHhcCCCCceEEEecCCccc
Confidence            467999999999999977633 333332  234466555544444

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=95.92  E-value=0.015  Score=43.96  Aligned_cols=37  Identities=16%  Similarity=0.144  Sum_probs=24.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhc-CCeEEEEc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIK-QKSAIFIL   40 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~-~~~~l~v~   40 (138)
                      .+..+++++|||||||.... ++...+.+. +++++.+-
T Consensus       121 ~~g~ili~G~tGSGKTT~l~-al~~~i~~~~~~~i~tiE  158 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTLA-SMIDYINKNAAGHIITIE  158 (343)
T ss_pred             cCcEEEEECCCCCCHHHHHH-HHHHhhCcCCCCEEEEEc
Confidence            35688999999999998763 334434332 45666554

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.

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=95.92  E-value=0.099  Score=40.31  Aligned_cols=99  Identities=13%  Similarity=0.094  Sum_probs=51.1

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH----H-----------HhhhhhhhhHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA----A-----------EEFKFYLEGKCL   69 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~----~-----------~~~~~~~Q~~~~   69 (138)
                      .|+|+++|.|+|||.+|.+.+-.    .+.....+..+.+=+.++.+.+++.    .           .+.+...|.+.+
T Consensus        49 ~SmIl~GPPG~GKTTlA~liA~~----~~~~f~~~sAv~~gvkdlr~i~e~a~~~~~~gr~tiLflDEIHRfnK~QQD~l  124 (436)
T COG2256          49 HSMILWGPPGTGKTTLARLIAGT----TNAAFEALSAVTSGVKDLREIIEEARKNRLLGRRTILFLDEIHRFNKAQQDAL  124 (436)
T ss_pred             ceeEEECCCCCCHHHHHHHHHHh----hCCceEEeccccccHHHHHHHHHHHHHHHhcCCceEEEEehhhhcChhhhhhh
Confidence            58899999999999998665553    2333344444333222322222222    1           123455666666


Q ss_pred             -hhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccc
Q psy2029          70 -EMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPY  112 (138)
Q Consensus        70 -~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~  112 (138)
                       |.+-+..+++...|-.--++.---+++.     ..+++.+-|+
T Consensus       125 Lp~vE~G~iilIGATTENPsF~ln~ALlS-----R~~vf~lk~L  163 (436)
T COG2256         125 LPHVENGTIILIGATTENPSFELNPALLS-----RARVFELKPL  163 (436)
T ss_pred             hhhhcCCeEEEEeccCCCCCeeecHHHhh-----hhheeeeecC
Confidence             6666655554444433333322222222     3455555554

>PRK06893 DNA replication initiation factor; Validated

Probab=95.91  E-value=0.017  Score=41.05  Aligned_cols=35  Identities=20%  Similarity=0.154  Sum_probs=25.1

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      .+++++|+|+|||..+...+.. +..++.++.|+..
T Consensus        41 ~l~l~G~~G~GKThL~~ai~~~-~~~~~~~~~y~~~   75 (229)
T PRK06893         41 FFYIWGGKSSGKSHLLKAVSNH-YLLNQRTAIYIPL   75 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH-HHHcCCCeEEeeH
Confidence            4689999999999887555544 4445667777543

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=95.87  E-value=0.02  Score=40.15  Aligned_cols=40  Identities=23%  Similarity=0.262  Sum_probs=27.0

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhh
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISL   45 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL   45 (138)
                      +.++++.+|+|+|||..+...+.. +.+.+...+|+ +...+
T Consensus        38 ~~~lll~G~~G~GKT~la~~~~~~-~~~~~~~~~~i-~~~~~   77 (226)
T TIGR03420        38 DRFLYLWGESGSGKSHLLQAACAA-AEERGKSAIYL-PLAEL   77 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH-HHhcCCcEEEE-eHHHH
Confidence            468899999999999998665554 33345555554 43333

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.

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=95.87  E-value=0.014  Score=45.14  Aligned_cols=43  Identities=19%  Similarity=0.181  Sum_probs=30.0

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVH   47 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~   47 (138)
                      .+++++.++||||||... ..++..+..++.+++++-|.-++..
T Consensus        42 ~~h~~i~g~tGsGKt~~i-~~l~~~~~~~~~~~vi~D~kg~~~~   84 (410)
T cd01127          42 EAHTMIIGTTGTGKTTQI-RELLASIRARGDRAIIYDPNGGFVS   84 (410)
T ss_pred             hccEEEEcCCCCCHHHHH-HHHHHHHHhcCCCEEEEeCCcchhH
Confidence            468999999999999863 3334445555677777777665544

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.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=95.86  E-value=0.55  Score=36.70  Aligned_cols=38  Identities=13%  Similarity=0.053  Sum_probs=25.7

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc--chhh
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL--PYIS   44 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~--P~~a   44 (138)
                      -+.+++|+|+|||..+.-.+.. +..++.+++++.  |+++
T Consensus       102 vi~lvG~~GvGKTTtaaKLA~~-l~~~G~kV~lV~~D~~R~  141 (429)
T TIGR01425       102 VIMFVGLQGSGKTTTCTKLAYY-YQRKGFKPCLVCADTFRA  141 (429)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH-HHHCCCCEEEEcCcccch
Confidence            4589999999999776544443 445577777764  4454

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.

>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=95.81  E-value=0.013  Score=43.69  Aligned_cols=49  Identities=22%  Similarity=0.233  Sum_probs=30.5

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAK   55 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~   55 (138)
                      .+|.+||||||+-..=-.+--.+++ ....+++++|.+.+........++
T Consensus        90 ~~VYGPTG~GKSqLlRNLis~~lI~P~PETVfFItP~~~mIpp~E~~aW~  139 (369)
T PF02456_consen   90 GVVYGPTGSGKSQLLRNLISCQLIQPPPETVFFITPQKDMIPPQEITAWE  139 (369)
T ss_pred             EEEECCCCCCHHHHHHHhhhcCcccCCCCceEEECCCCCCCCHHHHHHHH
Confidence            5889999999996531111112333 245889999988776544443333

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

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=95.80  E-value=0.021  Score=47.49  Aligned_cols=46  Identities=17%  Similarity=0.152  Sum_probs=35.3

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcC-CeEEEEcchhhhHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQ-KSAIFILPYISLVHEKY   50 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~-~~~l~v~P~~aL~~q~~   50 (138)
                      -|+.|.|.||+|||.+|+=.|+.--..=| .+-++++|+.|+..-.+
T Consensus        75 lNiDI~METGTGKTy~YlrtmfeLhk~YG~~KFIivVPs~AIkeGv~  121 (985)
T COG3587          75 LNIDILMETGTGKTYTYLRTMFELHKKYGLFKFIIVVPSLAIKEGVF  121 (985)
T ss_pred             ceeeEEEecCCCceeeHHHHHHHHHHHhCceeEEEEeccHHHHhhhH
Confidence            48899999999999999888886333322 37788899999876533

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

Probab=95.80  E-value=0.078  Score=40.17  Aligned_cols=73  Identities=16%  Similarity=0.116  Sum_probs=59.2

Q ss_pred             hhhhhhHHH----hhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCcee
Q psy2029          61 KFYLEGKCL----EMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYL  134 (138)
Q Consensus        61 ~~~~Q~~~~----~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v  134 (138)
                      +.+.|..+-    ..+.+ ++.++-+-||+|||-+- +..++.+.+++.++.+..|-...+-|.+..+++.|.+.++..
T Consensus        98 Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEMi-f~~i~~al~~G~~vciASPRvDVclEl~~Rlk~aF~~~~I~~  175 (441)
T COG4098          98 LSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEMI-FQGIEQALNQGGRVCIASPRVDVCLELYPRLKQAFSNCDIDL  175 (441)
T ss_pred             cChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhhh-HHHHHHHHhcCCeEEEecCcccchHHHHHHHHHhhccCCeee
Confidence            444555444    34445 88999999999999877 667777777899999999999999999999999998777664

>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=95.78  E-value=0.04  Score=40.01  Aligned_cols=52  Identities=27%  Similarity=0.301  Sum_probs=32.9

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhc--C---CeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIK--Q---KSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~--~---~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      .+.++++-..|+|||..+...+. .+.+.  .   +++|+++|. ++..+-.+++.++.
T Consensus        25 ~~g~lL~de~GlGKT~~~i~~~~-~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~~~   81 (299)
T PF00176_consen   25 PRGGLLADEMGLGKTITAIALIS-YLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEKWF   81 (299)
T ss_dssp             T-EEEE---TTSSHHHHHHHHHH-HHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCchhhhhhhhh-hhhhccccccccceeEeecc-chhhhhhhhhcccc
Confidence            45778889999999988866554 23331  1   259999999 66677777777775

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.

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=95.74  E-value=0.36  Score=36.13  Aligned_cols=23  Identities=17%  Similarity=0.265  Sum_probs=16.4

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKEL   29 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~   29 (138)
                      =++|.+|||||||.. +.++..++
T Consensus       127 LILVTGpTGSGKSTT-lAamId~i  149 (353)
T COG2805         127 LILVTGPTGSGKSTT-LAAMIDYI  149 (353)
T ss_pred             eEEEeCCCCCcHHHH-HHHHHHHH
Confidence            468999999999965 24444444

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=95.72  E-value=0.014  Score=43.45  Aligned_cols=38  Identities=29%  Similarity=0.187  Sum_probs=24.7

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcch
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPY   42 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~   42 (138)
                      .|.++++++|||||||...-.. .. ......+++.+-..
T Consensus       143 ~~~~ili~G~tGsGKTTll~al-~~-~~~~~~~iv~ied~  180 (308)
T TIGR02788       143 SRKNIIISGGTGSGKTTFLKSL-VD-EIPKDERIITIEDT  180 (308)
T ss_pred             CCCEEEEECCCCCCHHHHHHHH-Hc-cCCccccEEEEcCc
Confidence            5789999999999999876332 22 23334455555433

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.

>PRK14974 cell division protein FtsY; Provisional

Probab=95.72  E-value=0.63  Score=35.23  Aligned_cols=35  Identities=23%  Similarity=0.038  Sum_probs=24.7

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      -+++.+|+|+|||....-.+. .+.+.+.++.++..
T Consensus       142 vi~~~G~~GvGKTTtiakLA~-~l~~~g~~V~li~~  176 (336)
T PRK14974        142 VIVFVGVNGTGKTTTIAKLAY-YLKKNGFSVVIAAG  176 (336)
T ss_pred             EEEEEcCCCCCHHHHHHHHHH-HHHHcCCeEEEecC
Confidence            468999999999976654443 35556677777653

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=95.70  E-value=0.028  Score=47.25  Aligned_cols=51  Identities=16%  Similarity=0.113  Sum_probs=40.0

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      -+..+.||-|||+++.+|+.-+.+. |+.+.++++..-|+..=.+.+.+...
T Consensus       101 ~IAEM~TGEGKTL~atlpaylnAL~-GkgVhVVTvNdYLA~RDae~m~~vy~  151 (939)
T PRK12902        101 QIAEMKTGEGKTLVATLPSYLNALT-GKGVHVVTVNDYLARRDAEWMGQVHR  151 (939)
T ss_pred             ceeeecCCCChhHHHHHHHHHHhhc-CCCeEEEeCCHHHHHhHHHHHHHHHH
Confidence            4779999999999999988866664 78888888888887766666666543

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=95.69  E-value=0.027  Score=38.35  Aligned_cols=45  Identities=13%  Similarity=0.117  Sum_probs=30.6

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSL   53 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l   53 (138)
                      ..+++.+|+|||||..+...+..    .+.+.+|+.......++..+++
T Consensus         2 ~~ili~G~~~sGKS~~a~~l~~~----~~~~~~~iat~~~~~~e~~~ri   46 (170)
T PRK05800          2 MLILVTGGARSGKSRFAERLAAQ----SGLQVLYIATAQPFDDEMAARI   46 (170)
T ss_pred             CEEEEECCCCccHHHHHHHHHHH----cCCCcEeCcCCCCChHHHHHHH
Confidence            45799999999999998766543    2446677765555444444444

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=95.69  E-value=0.026  Score=39.82  Aligned_cols=37  Identities=11%  Similarity=0.137  Sum_probs=26.2

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      +..+++++|+|+|||..+...... ....+..+.++..
T Consensus        42 ~~~~~l~G~~G~GKT~La~ai~~~-~~~~~~~~~~i~~   78 (227)
T PRK08903         42 DRFFYLWGEAGSGRSHLLQALVAD-ASYGGRNARYLDA   78 (227)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH-HHhCCCcEEEEeh
Confidence            457999999999999887655444 3345666666543

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=95.65  E-value=0.023  Score=38.51  Aligned_cols=48  Identities=15%  Similarity=0.145  Sum_probs=32.8

Q ss_pred             eEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          77 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        77 ~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      +++..|+|+|||..+.-.+...+ ..+.+++|+.. .+..++..+.+..+
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~-~~g~~v~~~s~-e~~~~~~~~~~~~~   49 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGL-ARGEPGLYVTL-EESPEELIENAESL   49 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHH-HCCCcEEEEEC-CCCHHHHHHHHHHc
Confidence            57889999999999966555544 45778888854 44555555555444

A related protein is found in archaea.

>TIGR03744 traC_PFL_4706 conjugative transfer ATPase, PFL_4706 family

Probab=95.65  E-value=0.026  Score=47.80  Aligned_cols=41  Identities=20%  Similarity=0.239  Sum_probs=30.5

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhh
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYIS   44 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~a   44 (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            46899999999999988766666655444677777776444

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.

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=95.64  E-value=0.65  Score=34.80  Aligned_cols=39  Identities=15%  Similarity=0.048  Sum_probs=26.9

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh--c---CCeEEEEcc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI--K---QKSAIFILP   41 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~---~~~~l~v~P   41 (138)
                      .|+-+.+.+|.|+|||..+...+......  .   +++++|+.-
T Consensus        95 ~g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdt  138 (316)
T TIGR02239        95 TGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDT  138 (316)
T ss_pred             CCeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEEC
Confidence            35567899999999999886655433322  2   248888754

This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).

>PRK06321 replicative DNA helicase; Provisional

Probab=95.62  E-value=0.66  Score=36.75  Aligned_cols=128  Identities=10%  Similarity=0.022  Sum_probs=64.2

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhH-HHHHHHHHHHH----Hh-------hhhhhhhHHH--
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLV-HEKYQSLAKAA----EE-------FKFYLEGKCL--   69 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~-~q~~~~l~~~~----~~-------~~~~~Q~~~~--   69 (138)
                      |.=+++-|.+|+|||..+.-.+.......+.+++|+..  ++. .|...++....    ..       ....|+....  
T Consensus       226 G~LiiiaarPgmGKTafal~ia~~~a~~~g~~v~~fSL--EMs~~ql~~Rlla~~s~v~~~~i~~~~l~~~e~~~~~~a~  303 (472)
T PRK06321        226 SNLMILAARPAMGKTALALNIAENFCFQNRLPVGIFSL--EMTVDQLIHRIICSRSEVESKKISVGDLSGRDFQRIVSVV  303 (472)
T ss_pred             CcEEEEEeCCCCChHHHHHHHHHHHHHhcCCeEEEEec--cCCHHHHHHHHHHhhcCCCHHHhhcCCCCHHHHHHHHHHH
Confidence            44458899999999999877555544344667766542  111 23333332210    00       0111221111  


Q ss_pred             hhhhccceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhH---------------HHHHHHHHHHHhhhcCce
Q psy2029          70 EMIQNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISL---------------VHEKYQSLAKAAEEFKFY  133 (138)
Q Consensus        70 ~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l---------------~~q~~~~~~~~~~~~~~~  133 (138)
                      ..+.+.++.+.  ...+-|.--+...++++.. .+.+.++|.....+               +.+..+.++.+++.+++.
T Consensus       304 ~~l~~~~~~id--d~~~~ti~~i~~~~r~~~~~~~~~lvvIDyLql~~~~~~~~~~~~r~~ei~~Isr~LK~lAkel~vp  381 (472)
T PRK06321        304 NEMQEHTLLID--DQPGLKITDLRARARRMKESYDIQFLIIDYLQLLSGSGNLRNSESRQTEISEISRMLKNLARELNIP  381 (472)
T ss_pred             HHHHcCCEEEe--CCCCCCHHHHHHHHHHHHHhcCCCEEEEcchHHcCCCCccCCcchHHHHHHHHHHHHHHHHHHhCCc
Confidence            11222333332  2234455555555555544 34566666554332               223566788888888887


Q ss_pred             ee
Q psy2029         134 LE  135 (138)
Q Consensus       134 v~  135 (138)
                      |.
T Consensus       382 Vi  383 (472)
T PRK06321        382 IL  383 (472)
T ss_pred             EE
Confidence            65

>PRK04296 thymidine kinase; Provisional

Probab=95.60  E-value=0.029  Score=38.71  Aligned_cols=37  Identities=11%  Similarity=-0.003  Sum_probs=27.7

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      |.-.++.+|.|+|||..+.-.+.+ +...+.+++++-|
T Consensus         2 g~i~litG~~GsGKTT~~l~~~~~-~~~~g~~v~i~k~   38 (190)
T PRK04296          2 AKLEFIYGAMNSGKSTELLQRAYN-YEERGMKVLVFKP   38 (190)
T ss_pred             cEEEEEECCCCCHHHHHHHHHHHH-HHHcCCeEEEEec
Confidence            445688999999999887666554 4445788888766

>KOG1803|consensus

Probab=95.59  E-value=0.025  Score=45.40  Aligned_cols=45  Identities=20%  Similarity=0.189  Sum_probs=34.6

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQS   52 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~   52 (138)
                      .++.+|.|+|||..-.-.+.+ +..+++++++..|+..-++.+.++
T Consensus       204 ~~I~GPPGTGKT~TlvEiI~q-lvk~~k~VLVcaPSn~AVdNiver  248 (649)
T KOG1803|consen  204 LIIHGPPGTGKTRTLVEIISQ-LVKQKKRVLVCAPSNVAVDNIVER  248 (649)
T ss_pred             eEeeCCCCCCceeeHHHHHHH-HHHcCCeEEEEcCchHHHHHHHHH
Confidence            589999999999775444444 555789999999998766666664

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=95.57  E-value=0.021  Score=32.30  Aligned_cols=20  Identities=15%  Similarity=0.302  Sum_probs=16.6

Q ss_pred             CccEEEEccCCcchHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~   23 (138)
                      |+..++.+|+|+|||.+...
T Consensus        23 g~~tli~G~nGsGKSTllDA   42 (62)
T PF13555_consen   23 GDVTLITGPNGSGKSTLLDA   42 (62)
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            45789999999999987644

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.57  E-value=0.83  Score=35.60  Aligned_cols=35  Identities=29%  Similarity=0.246  Sum_probs=25.4

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      ..+.+.+|||+|||..+...+.. +..++.++.++.
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~-L~~~GkkVglI~  276 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQ-FHGKKKTVGFIT  276 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHH-HHHcCCcEEEEe
Confidence            46789999999999877555543 445566776654

>PRK13764 ATPase; Provisional

Probab=95.55  E-value=0.028  Score=45.52  Aligned_cols=33  Identities=9%  Similarity=0.063  Sum_probs=21.9

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeE
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSA   36 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~   36 (138)
                      .++++++++|||||||... .++...+..++..+
T Consensus       256 ~~~~ILIsG~TGSGKTTll-~AL~~~i~~~~riV  288 (602)
T PRK13764        256 RAEGILIAGAPGAGKSTFA-QALAEFYADMGKIV  288 (602)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHhhCCCEE
Confidence            3578999999999999776 33334443333333

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=95.53  E-value=0.9  Score=35.74  Aligned_cols=47  Identities=9%  Similarity=-0.008  Sum_probs=29.8

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSL   53 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l   53 (138)
                      +.+++++|+|+|||... .++...+..  .+.+++|+.+ ..+..+....+
T Consensus       142 npl~i~G~~G~GKTHLl-~Ai~~~l~~~~~~~~v~yv~~-~~f~~~~~~~l  190 (450)
T PRK14087        142 NPLFIYGESGMGKTHLL-KAAKNYIESNFSDLKVSYMSG-DEFARKAVDIL  190 (450)
T ss_pred             CceEEECCCCCcHHHHH-HHHHHHHHHhCCCCeEEEEEH-HHHHHHHHHHH
Confidence            34789999999999776 444444443  4568888654 34444444433

>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family

Probab=95.52  E-value=0.05  Score=44.39  Aligned_cols=52  Identities=23%  Similarity=0.307  Sum_probs=36.6

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhh--hHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYIS--LVHEKYQSLAKAA   57 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~a--L~~q~~~~l~~~~   57 (138)
                      .+.+|.+|||+|||......+.+.+ ..+..++++-|...  +....+......+
T Consensus       181 gHtlV~GtTGsGKT~l~~~li~q~i-~~g~~vi~fDpkgD~el~~~~~~~~~~~G  234 (643)
T TIGR03754       181 GHTLVLGTTRVGKTRLAELLITQDI-RRGDVVIVFDPKGDADLLKRMYAEAKRAG  234 (643)
T ss_pred             CceEEECCCCCCHHHHHHHHHHHHH-HcCCeEEEEeCCCCHHHHHHHHHHHHHhC
Confidence            4789999999999999887777644 45778888888664  3344444444443

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.

>PRK10436 hypothetical protein; Provisional

Probab=95.50  E-value=0.026  Score=44.40  Aligned_cols=35  Identities=20%  Similarity=0.202  Sum_probs=23.4

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      +..+++++|||||||... ++++.++.+.+.+++-+
T Consensus       218 ~GliLvtGpTGSGKTTtL-~a~l~~~~~~~~~i~Ti  252 (462)
T PRK10436        218 QGLILVTGPTGSGKTVTL-YSALQTLNTAQINICSV  252 (462)
T ss_pred             CCeEEEECCCCCChHHHH-HHHHHhhCCCCCEEEEe
Confidence            346899999999999875 45565554444444333

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.50  E-value=0.41  Score=37.99  Aligned_cols=36  Identities=19%  Similarity=0.123  Sum_probs=23.2

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCC-eEEEE
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQK-SAIFI   39 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~-~~l~v   39 (138)
                      |.-+.+.+|||+|||......+.......+. ++.++
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~~kV~LI  292 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRHGASKVALL  292 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhcCCCeEEEE
Confidence            5567899999999997765444433333443 55544

>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional

Probab=95.48  E-value=0.016  Score=43.05  Aligned_cols=25  Identities=24%  Similarity=0.090  Sum_probs=19.2

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .+.+-++|.+|||||||..+.-.+.
T Consensus         2 ~~~~ii~I~GpTasGKS~LAl~LA~   26 (300)
T PRK14729          2 KENKIVFIFGPTAVGKSNILFHFPK   26 (300)
T ss_pred             CCCcEEEEECCCccCHHHHHHHHHH
Confidence            3455579999999999988865544

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

Probab=95.47  E-value=0.027  Score=39.69  Aligned_cols=49  Identities=16%  Similarity=0.193  Sum_probs=31.4

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLA  124 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~  124 (138)
                      ..+++..|+|+|||..+.-.+...+.+.+.+++|+.- .+-..+..+.++
T Consensus        20 s~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs~-ee~~~~l~~~~~   68 (226)
T PF06745_consen   20 SVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVSF-EEPPEELIENMK   68 (226)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEES-SS-HHHHHHHHH
T ss_pred             cEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEEe-cCCHHHHHHHHH
Confidence            6677999999999999976666655543777888764 333344444444

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 ....

>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD

Probab=95.46  E-value=0.022  Score=45.85  Aligned_cols=43  Identities=12%  Similarity=0.153  Sum_probs=29.9

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVH   47 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~   47 (138)
                      ..++++.++||||||.+. -.++..++.++.+++++-|.-++..
T Consensus       176 ~~h~li~G~tGsGKs~~i-~~ll~~~~~~g~~~ii~D~~g~~~~  218 (566)
T TIGR02759       176 TQHILIHGTTGSGKSVAI-RKLLRWIRQRGDRAIIYDKGCTFTS  218 (566)
T ss_pred             ccceEEEcCCCCCHHHHH-HHHHHHHHhcCCeEEEEECCCCeeh
Confidence            458999999999999654 3344445556777777777655443

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).

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=95.43  E-value=0.031  Score=40.68  Aligned_cols=36  Identities=25%  Similarity=0.242  Sum_probs=23.4

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      +..+++++|||||||.... +++..+.+.+.+++.+-
T Consensus        80 ~GlilisG~tGSGKTT~l~-all~~i~~~~~~iitiE  115 (264)
T cd01129          80 HGIILVTGPTGSGKTTTLY-SALSELNTPEKNIITVE  115 (264)
T ss_pred             CCEEEEECCCCCcHHHHHH-HHHhhhCCCCCeEEEEC
Confidence            3468999999999998763 34344433344555553

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.

>PRK11054 helD DNA helicase IV; Provisional

Probab=95.39  E-value=0.13  Score=42.48  Aligned_cols=75  Identities=8%  Similarity=-0.077  Sum_probs=52.8

Q ss_pred             hhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHh---CCCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          61 KFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKI---KQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~---~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      +.+-|..+... .+.+.++.+..|+|||.+....+...+..   .+.+++.++.++..+.+..+.+.+.....++.|..
T Consensus       197 L~~~Q~~av~~-~~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~lg~~~v~v~T  274 (684)
T PRK11054        197 LNPSQARAVVN-GEDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRERLGTEDITART  274 (684)
T ss_pred             CCHHHHHHHhC-CCCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHhcCCCCcEEEe
Confidence            44455554421 12677899999999999987666554443   24589999999999999999988776533555554

>KOG4150|consensus

Probab=95.36  E-value=0.034  Score=44.79  Aligned_cols=127  Identities=11%  Similarity=0.104  Sum_probs=71.9

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHH-------HHHH------hhhhhhhhH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLA-------KAAE------EFKFYLEGK   67 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~-------~~~~------~~~~~~Q~~   67 (138)
                      -+|+++++.-.|.+||.+++...+..-+.. .....+|..|++++.++..+.+.       +...      +........
T Consensus       299 ~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~V~~~~I~~~K~A~V~~~D~~sE~~~~  378 (1034)
T KOG4150|consen  299 SEGRADGGNEARQAGKGTCPTSGSRKFQTLCHATNSLLPSEMVEHLRNGSKGQVVHVEVIKARKSAYVEMSDKLSETTKS  378 (1034)
T ss_pred             hhcccccccchhhcCCccCcccchhhhhhcCcccceecchhHHHHhhccCCceEEEEEehhhhhcceeecccCCCchhHH
Confidence            468899999999999999998877654333 45577888888887654432210       0000      000000000


Q ss_pred             HHhhhhc-cceEEEeecC-----CCchHhHHHHHHHHHHh-CCCeEEEEccchhHHHHHHHHHHHHhhhc
Q psy2029          68 CLEMIQN-KNCVLSIPTS-----GGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAAEEF  130 (138)
Q Consensus        68 ~~~~~~~-~~~ii~~ptg-----~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~~q~~~~~~~~~~~~  130 (138)
                      +  ..+. -+.+++.|..     --|.+..-.++.+.+.. -..-.+|.-|+.+++..+.+.+.+++..+
T Consensus       379 A--~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~~~~R~L~~L~~~F  446 (1034)
T KOG4150|consen  379 A--LKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYLFPTKALAQDQLRALSDLIKGF  446 (1034)
T ss_pred             H--HHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeeeecchhhHHHHHHHHHHHHHHHH
Confidence            0  0111 3334333311     11222222333333322 24568999999999999999998887654

>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=95.36  E-value=0.2  Score=35.74  Aligned_cols=69  Identities=17%  Similarity=0.142  Sum_probs=53.0

Q ss_pred             hhhhhhHHHh-hhh--c-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhc
Q psy2029          61 KFYLEGKCLE-MIQ--N-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEF  130 (138)
Q Consensus        61 ~~~~Q~~~~~-~~~--~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~  130 (138)
                      ..+.|.+... ...  . .|.+.-+-.|.|||-+. +|++..+...+.+.+.++=.++|.+|.++.+++.+...
T Consensus        24 iR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsVI-~Pmla~~LAdg~~LvrviVpk~Ll~q~~~~L~~~lg~l   96 (229)
T PF12340_consen   24 IRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSVI-VPMLALALADGSRLVRVIVPKALLEQMRQMLRSRLGGL   96 (229)
T ss_pred             eeHHHHHHHHHHhCCCCCCCeEeeecccCCccchH-HHHHHHHHcCCCcEEEEEcCHHHHHHHHHHHHHHHHHH
Confidence            3455666652 222  2 78899999999999998 77877777777777777777889999999999887664

There are two conserved sequence motifs: LLE and NMG.

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=95.35  E-value=0.029  Score=48.96  Aligned_cols=49  Identities=12%  Similarity=-0.000  Sum_probs=31.0

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcC--CeEEEEcc----hhhhHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQ--KSAIFILP----YISLVHEKYQSLAK   55 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~--~~~l~v~P----~~aL~~q~~~~l~~   55 (138)
                      ..++++++||||||..  +|.+-.-...+  +.+....|    .++|..++.+++..
T Consensus        90 ~VviI~GeTGSGKTTq--lPq~lle~g~g~~g~I~~TQPRRlAArsLA~RVA~El~~  144 (1294)
T PRK11131         90 QVVIVAGETGSGKTTQ--LPKICLELGRGVKGLIGHTQPRRLAARTVANRIAEELET  144 (1294)
T ss_pred             CeEEEECCCCCCHHHH--HHHHHHHcCCCCCCceeeCCCcHHHHHHHHHHHHHHHhh
Confidence            3568889999999994  55332111222  34444556    56788888887765

>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown

Probab=95.34  E-value=0.04  Score=38.86  Aligned_cols=38  Identities=24%  Similarity=0.266  Sum_probs=26.4

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHh-hcCCeEEEEcch
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELK-IKQKSAIFILPY   42 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~-~~~~~~l~v~P~   42 (138)
                      ++++.|.+.||||||...-..+.+ +. ..+.+++++-|.
T Consensus        23 ~~H~~I~G~TGsGKS~~~~~ll~~-l~~~~~~~~ii~D~~   61 (229)
T PF01935_consen   23 NRHIAIFGTTGSGKSNTVKVLLEE-LLKKKGAKVIIFDPH   61 (229)
T ss_pred             cceEEEECCCCCCHHHHHHHHHHH-HHhcCCCCEEEEcCC
Confidence            467899999999999887555444 44 445566655553

It contains several conserved aspartates and histidines that could be metal ligands.

>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=95.33  E-value=0.51  Score=31.68  Aligned_cols=33  Identities=27%  Similarity=0.245  Sum_probs=23.5

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      +++.+|+|+|||..+.-.+. .+.+.+.+++++.
T Consensus         3 ~~~~G~~G~GKTt~~~~la~-~~~~~g~~v~~i~   35 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLAL-YLKKKGKKVLLVA   35 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHH-HHHHCCCcEEEEE
Confidence            57899999999988755444 3445566776653

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.

>PHA02535 P terminase ATPase subunit; Provisional

Probab=95.32  E-value=0.36  Score=39.07  Aligned_cols=85  Identities=14%  Similarity=0.069  Sum_probs=67.3

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSL  123 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~  123 (138)
                      +.++..+.+.+.....++++|..++..-.+ +.-++.-.-..|+|..+...++..+...+...+|+.|+++.+.+-.+.+
T Consensus       123 ~s~~~~~~l~~~~~~~l~~YQ~~W~~~~~~~r~r~ilKSRQiG~T~~fA~EA~~dal~~G~nqiflSas~~QA~~f~~yi  202 (581)
T PHA02535        123 ISDEQTEKLIEAFLDSLFDYQKHWYRAGLHHRTRNILKSRQIGATYYFAREALEDALLTGRNQIFLSASKAQAHVFKQYI  202 (581)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHhCccccceeeEeeecccchHHHHHHHHHHHHHhcCCceEEECCCHHHHHHHHHHH
Confidence            556788888888888999999999854323 4556677788999999988888888877778899999999998766666


Q ss_pred             HHHhhh
Q psy2029         124 AKAAEE  129 (138)
Q Consensus       124 ~~~~~~  129 (138)
                      ..++..
T Consensus       203 ~~~a~~  208 (581)
T PHA02535        203 IAFARE  208 (581)
T ss_pred             HHHHHh
Confidence            666554

>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=95.31  E-value=0.022  Score=36.92  Aligned_cols=22  Identities=27%  Similarity=0.271  Sum_probs=18.3

Q ss_pred             cEEEEccCCcchHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      ++++.+|+|+|||..+...+..
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~   22 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAAL   22 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999988666554

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.

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=95.31  E-value=0.016  Score=45.32  Aligned_cols=48  Identities=23%  Similarity=0.054  Sum_probs=32.5

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ++++.||||||||..+.+|.+   +...+.+++.-|--+|........++.
T Consensus        46 h~lvig~tgSGKt~~~viP~l---l~~~~s~iV~D~KgEl~~~t~~~r~~~   93 (469)
T PF02534_consen   46 HVLVIGPTGSGKTTSFVIPNL---LNYPGSMIVTDPKGELYEKTAGYRKKR   93 (469)
T ss_pred             EEEEEeCCCCCccceeeHhHH---HhccCCEEEEECCCcHHHHHHHHHHHC
Confidence            689999999999998877754   333446666667666655444444433

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

>KOG0953|consensus

Probab=95.31  E-value=0.025  Score=45.20  Aligned_cols=58  Identities=26%  Similarity=0.360  Sum_probs=43.3

Q ss_pred             hhhhc--cceE-EEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCc
Q psy2029          70 EMIQN--KNCV-LSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF  132 (138)
Q Consensus        70 ~~~~~--~~~i-i~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~  132 (138)
                      |..+.  +.++ =+-||-+|||..|    ++++.+ -++.+|--|++.|+.|+++.+.+...+.++
T Consensus       184 P~AR~~~RkIi~H~GPTNSGKTy~A----Lqrl~~-aksGvycGPLrLLA~EV~~r~na~gipCdL  244 (700)
T KOG0953|consen  184 PEARKIRRKIIMHVGPTNSGKTYRA----LQRLKS-AKSGVYCGPLRLLAHEVYDRLNALGIPCDL  244 (700)
T ss_pred             chhHhhhheEEEEeCCCCCchhHHH----HHHHhh-hccceecchHHHHHHHHHHHhhhcCCCccc
Confidence            44554  5555 4669999999666    455544 456799999999999999999998665544

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=95.29  E-value=0.017  Score=39.63  Aligned_cols=20  Identities=35%  Similarity=0.277  Sum_probs=17.5

Q ss_pred             CCCccEEEEccCCcchHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVG   21 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~   21 (138)
                      ..|+++++++|||||||...
T Consensus        23 ~~g~~i~I~G~tGSGKTTll   42 (186)
T cd01130          23 EARKNILISGGTGSGKTTLL   42 (186)
T ss_pred             hCCCEEEEECCCCCCHHHHH
Confidence            35789999999999999775

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.

>PRK08006 replicative DNA helicase; Provisional

Probab=95.24  E-value=1.2  Score=35.31  Aligned_cols=130  Identities=14%  Similarity=0.094  Sum_probs=68.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhH-HHHHHHHHHHH----Hh-----h--hhhhhh--HH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLV-HEKYQSLAKAA----EE-----F--KFYLEG--KC   68 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~-~q~~~~l~~~~----~~-----~--~~~~Q~--~~   68 (138)
                      .|.=+++-|.+|+|||..++-.+.+...+.+.+++|+..  ++. .|...++....    ..     .  .-.|+.  .+
T Consensus       223 ~G~LiiIaarPgmGKTafalnia~~~a~~~g~~V~~fSl--EM~~~ql~~Rlla~~~~v~~~~i~~~~l~~~e~~~~~~a  300 (471)
T PRK08006        223 PSDLIIVAARPSMGKTTFAMNLCENAAMLQDKPVLIFSL--EMPGEQIMMRMLASLSRVDQTRIRTGQLDDEDWARISGT  300 (471)
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHhcCCeEEEEec--cCCHHHHHHHHHHHhcCCCHHHhhcCCCCHHHHHHHHHH
Confidence            345568899999999999877776654445667776642  111 23333332210    00     0  011111  11


Q ss_pred             Hhhh-hccceEEEeecCCCchHhHHHHHHHHHHh-C-CCeEEEEccchhH------------HHHHHHHHHHHhhhcCce
Q psy2029          69 LEMI-QNKNCVLSIPTSGGKTLVGEILIMKELKI-K-QKSAIFILPYISL------------VHEKYQSLAKAAEEFKFY  133 (138)
Q Consensus        69 ~~~~-~~~~~ii~~ptg~GKt~~~~~~~l~~~~~-~-~~~~~~i~P~~~l------------~~q~~~~~~~~~~~~~~~  133 (138)
                      ...+ .+.++.+.  ..++-|..-+....+++.. + +.+.++|.....+            +.+..+.++.+++.+++.
T Consensus       301 ~~~~~~~~~l~I~--d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDYLqli~~~~~~~~r~~ei~~isr~LK~lAkel~ip  378 (471)
T PRK08006        301 MGILLEKRNMYID--DSSGLTPTEVRSRARRIFREHGGLSLIMIDYLQLMRVPSLSDNRTLEIAEISRSLKALAKELQVP  378 (471)
T ss_pred             HHHHHhcCCEEEE--CCCCCCHHHHHHHHHHHHHhcCCCCEEEEccHHHccCCCCCCCcHHHHHHHHHHHHHHHHHhCCe
Confidence            1122 22443332  3345566665556655543 2 3566666553222            345667888888888887


Q ss_pred             eee
Q psy2029         134 LEV  136 (138)
Q Consensus       134 v~~  136 (138)
                      |.-
T Consensus       379 Vi~  381 (471)
T PRK08006        379 VVA  381 (471)
T ss_pred             EEE
Confidence            653

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=95.23  E-value=0.046  Score=39.02  Aligned_cols=53  Identities=15%  Similarity=0.206  Sum_probs=37.8

Q ss_pred             hhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          72 IQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        72 ~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      +.. ..+++..|+|+|||..+.-.+...+ ..+.+++|+. +.+...|..+++.++
T Consensus        18 ~~~gs~~lI~G~pGsGKT~la~~~l~~~~-~~ge~~lyvs-~ee~~~~i~~~~~~~   71 (237)
T TIGR03877        18 IPERNVVLLSGGPGTGKSIFSQQFLWNGL-QMGEPGIYVA-LEEHPVQVRRNMAQF   71 (237)
T ss_pred             CcCCeEEEEEcCCCCCHHHHHHHHHHHHH-HcCCcEEEEE-eeCCHHHHHHHHHHh
Confidence            444 6778999999999999976666555 4577888887 445666666655543

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.

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.20  E-value=0.54  Score=36.66  Aligned_cols=23  Identities=35%  Similarity=0.224  Sum_probs=17.7

Q ss_pred             CCccEEEEccCCcchHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      +|+.+.+.+|||+|||......+
T Consensus       190 ~g~vi~lvGpnG~GKTTtlakLA  212 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTAKLA  212 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHH
Confidence            46678999999999996654433

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

Probab=95.19  E-value=0.088  Score=45.07  Aligned_cols=56  Identities=18%  Similarity=0.110  Sum_probs=45.0

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHHHhh
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAEEF   60 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~~~~   60 (138)
                      ++..+||=-||||||+.-...+.. +++  ...++++|+--+.|-.|..++|..++...
T Consensus       273 ~~~G~IWHtqGSGKTlTm~~~A~~-l~~~~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~  330 (962)
T COG0610         273 GKGGYIWHTQGSGKTLTMFKLARL-LLELPKNPKVLFVVDRKDLDDQTSDEFQSFGKVA  330 (962)
T ss_pred             CCceEEEeecCCchHHHHHHHHHH-HHhccCCCeEEEEechHHHHHHHHHHHHHHHHhh
Confidence            467899999999999987666554 333  46699999999999999999999986544

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=95.19  E-value=0.034  Score=44.77  Aligned_cols=31  Identities=19%  Similarity=0.222  Sum_probs=21.1

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeE
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSA   36 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~   36 (138)
                      ..+++++|||||||... ++++..+.+...++
T Consensus       317 Glilv~G~tGSGKTTtl-~a~l~~~~~~~~~i  347 (564)
T TIGR02538       317 GMVLVTGPTGSGKTVSL-YTALNILNTEEVNI  347 (564)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHhhCCCCceE
Confidence            46799999999999775 55555553333333

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.

>KOG1131|consensus

Probab=95.16  E-value=0.09  Score=41.95  Aligned_cols=53  Identities=19%  Similarity=0.347  Sum_probs=34.0

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh---cCCeEEEEcchhhhHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI---KQKSAIFILPYISLVHEKYQSLAK   55 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~---~~~~~l~v~P~~aL~~q~~~~l~~   55 (138)
                      .+.++++.+|+|+|||..-+..+....+.   .-.|.+|..-+..-.+....+++.
T Consensus        34 akGh~llEMPSGTGKTvsLLSli~aYq~~~p~~~~KliYCSRTvpEieK~l~El~~   89 (755)
T KOG1131|consen   34 AKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEIEKALEELKR   89 (755)
T ss_pred             cCCcEEEECCCCCCcchHHHHHHHHHHHhCCcccceEEEecCcchHHHHHHHHHHH
Confidence            35689999999999998776655544444   234778876655433333444433

>KOG1802|consensus

Probab=95.15  E-value=0.044  Score=44.78  Aligned_cols=54  Identities=19%  Similarity=0.220  Sum_probs=39.1

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +..-.++.+|.|+|||..... +.+|+.+ ..+++|++.|..--++|+.+.+.+.+
T Consensus       424 ~rplsLIQGPPGTGKTvtsa~-IVyhl~~~~~~~VLvcApSNiAVDqLaeKIh~tg  478 (935)
T KOG1802|consen  424 QRPLSLIQGPPGTGKTVTSAT-IVYHLARQHAGPVLVCAPSNIAVDQLAEKIHKTG  478 (935)
T ss_pred             cCCceeeecCCCCCceehhHH-HHHHHHHhcCCceEEEcccchhHHHHHHHHHhcC
Confidence            334458999999999988744 4445555 57799999998776777776665543

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

Probab=95.14  E-value=0.14  Score=35.50  Aligned_cols=59  Identities=20%  Similarity=0.182  Sum_probs=39.7

Q ss_pred             hhhhHHHhhhh-c--cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHH
Q psy2029          63 YLEGKCLEMIQ-N--KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQS  122 (138)
Q Consensus        63 ~~Q~~~~~~~~-~--~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~  122 (138)
                      +-|..++..+. .  +-.++..|.|+|||... -.+.+.+...+.++++++|+..-+.+..+.
T Consensus         4 ~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l-~~~~~~~~~~g~~v~~~apT~~Aa~~L~~~   65 (196)
T PF13604_consen    4 EEQREAVRAILTSGDRVSVLQGPAGTGKTTLL-KALAEALEAAGKRVIGLAPTNKAAKELREK   65 (196)
T ss_dssp             HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHH-HHHHHHHHHTT--EEEEESSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCeEEEEEECCCCCHHHHH-HHHHHHHHhCCCeEEEECCcHHHHHHHHHh
Confidence            44666665453 3  34568899999999764 445555555678999999998877665544

>PRK00131 aroK shikimate kinase; Reviewed

Probab=95.11  E-value=0.028  Score=37.58  Aligned_cols=26  Identities=31%  Similarity=0.416  Sum_probs=21.4

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHH
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      |.++.++++++|.|||||.++...+-
T Consensus         1 ~~~~~~i~l~G~~GsGKstla~~La~   26 (175)
T PRK00131          1 MLKGPNIVLIGFMGAGKSTIGRLLAK   26 (175)
T ss_pred             CCCCCeEEEEcCCCCCHHHHHHHHHH
Confidence            56788999999999999999855444

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=95.09  E-value=0.072  Score=41.74  Aligned_cols=36  Identities=17%  Similarity=0.222  Sum_probs=26.8

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      +.+++++|+|+|||..+- ++...+...+.+++|+..
T Consensus       142 npl~L~G~~G~GKTHLl~-Ai~~~l~~~~~~v~yi~~  177 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQ-AAVHALRESGGKILYVRS  177 (445)
T ss_pred             ceEEEEcCCCCCHHHHHH-HHHHHHHHcCCCEEEeeH
Confidence            358999999999998874 444445556788888754

>PRK06749 replicative DNA helicase; Provisional

Probab=95.08  E-value=0.97  Score=35.33  Aligned_cols=131  Identities=15%  Similarity=0.084  Sum_probs=65.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhH-HHHHHHHHHHH----Hhhhhh----h-hhHH--H-
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLV-HEKYQSLAKAA----EEFKFY----L-EGKC--L-   69 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~-~q~~~~l~~~~----~~~~~~----~-Q~~~--~-   69 (138)
                      .|.=+++-|.+|+|||..+.-.+.... ..+.+++++..  ++. .|...++....    ......    . +.++  + 
T Consensus       185 ~G~LiiIaarPgmGKTafal~ia~~~a-~~g~~v~~fSl--EMs~~ql~~R~ls~~~~i~~~~l~~~~~~l~~~e~~~~~  261 (428)
T PRK06749        185 EGDFVVLGARPSMGKTAFALNVGLHAA-KSGAAVGLFSL--EMSSKQLLKRMASCVGEVSGGRLKNPKHRFAMEDWEKVS  261 (428)
T ss_pred             CCcEEEEEeCCCCCchHHHHHHHHHHH-hcCCCEEEEEe--eCCHHHHHHHHHHhccCCCHHHHhcCcccCCHHHHHHHH
Confidence            355578899999999999876666544 34666666542  111 23333322210    000000    0 1111  1 


Q ss_pred             hhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC-CC-e-EEEEccchhH-------------HHHHHHHHHHHhhhcCc
Q psy2029          70 EMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK-QK-S-AIFILPYISL-------------VHEKYQSLAKAAEEFKF  132 (138)
Q Consensus        70 ~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~-~~-~-~~~i~P~~~l-------------~~q~~~~~~~~~~~~~~  132 (138)
                      ..... .+.-+.....++-|+.-+...++++... +. . .++|....-+             +.++.+.++.+++++++
T Consensus       262 ~a~~~l~~~~i~i~d~~~~t~~~I~~~~r~~~~~~~~~~~lvvIDyLqli~~~~~~~~~r~~ei~~isr~LK~lAkel~v  341 (428)
T PRK06749        262 KAFAEIGELPLEIYDNAGVTVQDIWMQTRKLKRKHGDKKILIIVDYLQLITGDPKHKGNRFQEISEISRKLKLLARELNV  341 (428)
T ss_pred             HHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCcEEEEeChhhcCCCCCCCCCHHHHHHHHHHHHHHHHHHhCC
Confidence            11111 2222333445666666666666666542 32 2 4444332211             23467778888888888


Q ss_pred             eeee
Q psy2029         133 YLEV  136 (138)
Q Consensus       133 ~v~~  136 (138)
                      .|.-
T Consensus       342 pVi~  345 (428)
T PRK06749        342 CVVA  345 (428)
T ss_pred             eEEE
Confidence            7653

>PRK10536 hypothetical protein; Provisional

Probab=95.08  E-value=0.041  Score=40.04  Aligned_cols=53  Identities=17%  Similarity=0.154  Sum_probs=37.5

Q ss_pred             hhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCC-CeEEEEccchh
Q psy2029          62 FYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQ-KSAIFILPYIS  114 (138)
Q Consensus        62 ~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~-~~~~~i~P~~~  114 (138)
                      ...|......+.+ ..+++..|.|+|||+.+....++.+.++. .++++.-|..+
T Consensus        61 n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI~RP~v~  115 (262)
T PRK10536         61 NEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRPVLQ  115 (262)
T ss_pred             CHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEEeCCCCC
Confidence            3446655565666 77789999999999999888887775533 45666656543

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=95.05  E-value=0.012  Score=44.89  Aligned_cols=47  Identities=15%  Similarity=0.020  Sum_probs=32.5

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK   55 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~   55 (138)
                      ++++.||||||||..+.+|.+   ++..+.++++-|.-++........++
T Consensus         1 H~lv~g~tGsGKt~~~viP~l---l~~~~s~vv~D~Kge~~~~t~~~r~~   47 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNL---LTWPGSVVVLDPKGENFELTSEHRRA   47 (384)
T ss_pred             CeeEecCCCCCCccEEEccch---hcCCCCEEEEccchhHHHHHHHHHHH
Confidence            478999999999988766643   23456777777877776554444333

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.

>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=95.00  E-value=0.025  Score=38.48  Aligned_cols=39  Identities=21%  Similarity=0.249  Sum_probs=24.1

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhh
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYIS   44 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~a   44 (138)
                      .++++.+|||+|||..+...+-. +--.+.+.+...-...
T Consensus         4 ~~~ll~GpsGvGKT~la~~la~~-l~~~~~~~~~~~d~s~   42 (171)
T PF07724_consen    4 SNFLLAGPSGVGKTELAKALAEL-LFVGSERPLIRIDMSE   42 (171)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHH-HT-SSCCEEEEEEGGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH-hccCCccchHHHhhhc
Confidence            47899999999999887554443 2202334454444333

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 ....

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=94.99  E-value=0.17  Score=43.18  Aligned_cols=61  Identities=15%  Similarity=0.103  Sum_probs=49.9

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      ..-+..+.||.|||+++.+|+.-.++. ++.+=+|...--|+.--++....++..+|+.|+.
T Consensus       152 ~G~IAEM~TGEGKTLvatlp~yLnAL~-G~gVHvVTvNDYLA~RDaewm~p~y~flGLtVg~  212 (1025)
T PRK12900        152 SGKISEMATGEGKTLVSTLPTFLNALT-GRGVHVVTVNDYLAQRDKEWMNPVFEFHGLSVGV  212 (1025)
T ss_pred             cCCccccCCCCCcchHhHHHHHHHHHc-CCCcEEEeechHhhhhhHHHHHHHHHHhCCeeee
Confidence            444678999999999999999777765 4555566677779999999999999999998864

>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=94.95  E-value=0.028  Score=35.38  Aligned_cols=20  Identities=25%  Similarity=0.385  Sum_probs=16.5

Q ss_pred             EEEEccCCcchHHHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ++|.+|+|||||.++-..+-
T Consensus         2 I~I~G~~gsGKST~a~~La~   21 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAE   21 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57999999999999855544

...

>KOG0953|consensus

Probab=94.93  E-value=0.04  Score=44.06  Aligned_cols=51  Identities=31%  Similarity=0.377  Sum_probs=40.2

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      .+-++=++||-||||.-|    ++++.+ -++.+|.-|++-|..+.++.+...+..
T Consensus       191 RkIi~H~GPTNSGKTy~A----Lqrl~~-aksGvycGPLrLLA~EV~~r~na~gip  241 (700)
T KOG0953|consen  191 RKIIMHVGPTNSGKTYRA----LQRLKS-AKSGVYCGPLRLLAHEVYDRLNALGIP  241 (700)
T ss_pred             heEEEEeCCCCCchhHHH----HHHHhh-hccceecchHHHHHHHHHHHhhhcCCC
Confidence            445667899999999876    445543 567799999999999999998887653

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=94.89  E-value=0.067  Score=38.79  Aligned_cols=50  Identities=16%  Similarity=0.077  Sum_probs=34.9

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhh-----cCCeEEEEcchhhhHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKI-----KQKSAIFILPYISLVHEKYQSLAK   55 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~-----~~~~~l~v~P~~aL~~q~~~~l~~   55 (138)
                      -.=+++|.|+|||-.++..+...++.     .+++++|+--...+..+...++.+
T Consensus        40 itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~~i~~   94 (256)
T PF08423_consen   40 ITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQQIAE   94 (256)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHHHHHH
T ss_pred             EEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHHHHhh
Confidence            34589999999999987776665544     256999997655566665555544

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 ....

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=94.87  E-value=0.21  Score=35.67  Aligned_cols=23  Identities=22%  Similarity=0.300  Sum_probs=18.8

Q ss_pred             ccEEEEccCCcchHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      .++++++|.|.|||..|.+.+-+
T Consensus        51 ~h~lf~GPPG~GKTTLA~IIA~e   73 (233)
T PF05496_consen   51 DHMLFYGPPGLGKTTLARIIANE   73 (233)
T ss_dssp             -EEEEESSTTSSHHHHHHHHHHH
T ss_pred             ceEEEECCCccchhHHHHHHHhc
Confidence            37899999999999998766554

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=94.87  E-value=0.023  Score=41.24  Aligned_cols=25  Identities=20%  Similarity=0.124  Sum_probs=20.8

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ..|.++++.+|+|+|||.++...+.
T Consensus        19 ~~g~~vLL~G~~GtGKT~lA~~la~   43 (262)
T TIGR02640        19 KSGYPVHLRGPAGTGKTTLAMHVAR   43 (262)
T ss_pred             hcCCeEEEEcCCCCCHHHHHHHHHH
Confidence            3577999999999999999866554

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).

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=94.86  E-value=0.11  Score=40.58  Aligned_cols=42  Identities=10%  Similarity=0.051  Sum_probs=27.7

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhc--CCeEEEEcchhhhHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHE   48 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~--~~~~l~v~P~~aL~~q   48 (138)
                      ..+++++|+|+|||..+...... +..+  +.+++|+.. ..+.++
T Consensus       149 ~~l~l~G~~G~GKThL~~ai~~~-~~~~~~~~~v~yi~~-~~~~~~  192 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLHAIGNY-ILEKNPNAKVVYVTS-EKFTND  192 (450)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH-HHHhCCCCeEEEEEH-HHHHHH
Confidence            45899999999999887554443 4443  567777643 334333

>PRK11054 helD DNA helicase IV; Provisional

Probab=94.85  E-value=0.082  Score=43.62  Aligned_cols=53  Identities=11%  Similarity=-0.013  Sum_probs=39.2

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhh---cCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKI---KQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~---~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ..+++|.|..|||||.+...-+...+..   ...+++.++.++...++..+++.+.
T Consensus       209 ~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~  264 (684)
T PRK11054        209 EDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRER  264 (684)
T ss_pred             CCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHh
Confidence            4578999999999998876555443322   2348999999998888777777653

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

Probab=94.83  E-value=0.087  Score=39.86  Aligned_cols=50  Identities=22%  Similarity=0.250  Sum_probs=38.8

Q ss_pred             eEEEeecCCCchHhHHHHHHHHH--HhCCCeEEEEccchhHHHHHHHHHHHHh
Q psy2029          77 CVLSIPTSGGKTLVGEILIMKEL--KIKQKSAIFILPYISLVHEKYQSLAKAA  127 (138)
Q Consensus        77 ~ii~~ptg~GKt~~~~~~~l~~~--~~~~~~~~~i~P~~~l~~q~~~~~~~~~  127 (138)
                      ++|.-..|+|||+++.. .+.++  ...+.+++|+++..+|.....+.+.+..
T Consensus         4 ~~I~G~aGTGKTvla~~-l~~~l~~~~~~~~~~~l~~n~~l~~~l~~~l~~~~   55 (352)
T PF09848_consen    4 ILITGGAGTGKTVLALN-LAKELQNSEEGKKVLYLCGNHPLRNKLREQLAKKY   55 (352)
T ss_pred             EEEEecCCcCHHHHHHH-HHHHhhccccCCceEEEEecchHHHHHHHHHhhhc
Confidence            46778899999999954 44556  4457889999999999987777776553

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

>TIGR02746 TraC-F-type type-IV secretion system protein TraC

Probab=94.79  E-value=0.061  Score=44.88  Aligned_cols=37  Identities=19%  Similarity=0.101  Sum_probs=26.0

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      +.|++|.++||||||......+.. ++..+.+++++-|
T Consensus       430 n~n~~I~G~tGsGKS~~~~~l~~~-~~~~g~~v~iiD~  466 (797)
T TIGR02746       430 NYNIAVVGGSGAGKSFFMQELIVD-NLSRGGKVWVIDV  466 (797)
T ss_pred             ccceEEEcCCCCCHHHHHHHHHHH-HHhCCCEEEEEeC
Confidence            358999999999999887655544 3334556666554

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.

>KOG1123|consensus

Probab=94.78  E-value=0.023  Score=45.04  Aligned_cols=64  Identities=22%  Similarity=0.250  Sum_probs=49.3

Q ss_pred             hhhhhhHHHhhhh-c---cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhh
Q psy2029          61 KFYLEGKCLEMIQ-N---KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE  128 (138)
Q Consensus        61 ~~~~Q~~~~~~~~-~---~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~  128 (138)
                      ..|.|..++.... +   ++.++..|-|+|||++..-++..    -++++++++...-.|+|...+|..|..
T Consensus       303 iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~t----ikK~clvLcts~VSVeQWkqQfk~wst  370 (776)
T KOG1123|consen  303 IRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAACT----IKKSCLVLCTSAVSVEQWKQQFKQWST  370 (776)
T ss_pred             cCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeeee----ecccEEEEecCccCHHHHHHHHHhhcc
Confidence            4667888884332 2   88899999999999999654432    256778888888888999999999863

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=94.77  E-value=0.086  Score=46.27  Aligned_cols=54  Identities=19%  Similarity=0.164  Sum_probs=38.8

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhc--CCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~--~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .|+|++|+|..|||||.+..--+...+.+.  -.++++++-|++-..+.-.++.+.
T Consensus        13 ~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~~~~~il~~tFt~~aa~e~~~ri~~~   68 (1232)
T TIGR02785        13 RGQNILVSASAGSGKTAVLVERIIKKILRGVDIDRLLVVTFTNAAAREMKERIEEA   68 (1232)
T ss_pred             CCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCHhhEEEEeccHHHHHHHHHHHHHH
Confidence            477999999999999998766555544432  236888888887776665555543

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.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.76  E-value=0.13  Score=39.70  Aligned_cols=37  Identities=24%  Similarity=0.100  Sum_probs=26.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      .++.+.+.+|+|+|||..+.-.+.. +..++.++.++.
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~-l~~~g~~V~lIt  241 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQ-LLKQNRTVGFIT  241 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH-HHHcCCeEEEEe
Confidence            3567899999999999777555544 444566776654

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=94.76  E-value=0.078  Score=45.35  Aligned_cols=61  Identities=13%  Similarity=0.112  Sum_probs=50.3

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      ..-+..+.||.|||++|.+|+.-.++. ++.+-+|...--||.--++....++..+|+.|+-
T Consensus       183 ~G~IAEM~TGEGKTLvAtlp~yLnAL~-GkgVHvVTVNDYLA~RDaewmgply~fLGLsvg~  243 (1112)
T PRK12901        183 QGKIAEMATGEGKTLVATLPVYLNALT-GNGVHVVTVNDYLAKRDSEWMGPLYEFHGLSVDC  243 (1112)
T ss_pred             CCceeeecCCCCchhHHHHHHHHHHHc-CCCcEEEEechhhhhccHHHHHHHHHHhCCceee
Confidence            555789999999999999999877775 4455666777789999999999999999998764

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=94.76  E-value=0.12  Score=42.60  Aligned_cols=53  Identities=15%  Similarity=0.084  Sum_probs=39.0

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhc---CCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIK---QKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~---~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +..++|.|..|||||.+...-+...+.+.   ..+++.++.++.-..+..+++...
T Consensus        15 ~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v~p~~IL~lTFT~kAA~em~~Rl~~~   70 (672)
T PRK10919         15 TGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQT   70 (672)
T ss_pred             CCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHH
Confidence            45789999999999988755555433222   248899999998888777776654

>COG3451 VirB4 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]

Probab=94.71  E-value=0.057  Score=45.25  Aligned_cols=25  Identities=28%  Similarity=0.444  Sum_probs=19.9

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKEL   29 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~   29 (138)
                      +|.+|++|||+|||..-...+.+..
T Consensus       437 ghT~I~G~tGaGKTvLl~~llaq~~  461 (796)
T COG3451         437 GHTLIIGPTGAGKTVLLSFLLAQAL  461 (796)
T ss_pred             CCeEEECCCCCCHHHHHHHHHHHHH
Confidence            4899999999999987766655543

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=94.70  E-value=0.087  Score=44.10  Aligned_cols=60  Identities=18%  Similarity=0.179  Sum_probs=41.6

Q ss_pred             hhhhhhHHH-h---h-hhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHH
Q psy2029          61 KFYLEGKCL-E---M-IQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        61 ~~~~Q~~~~-~---~-~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~  121 (138)
                      ...+|..+. +   . ..+ -|+.+.+-||+|||.+++-.++ ++..  +-.|.++++|+.|.-+-++.
T Consensus        55 i~n~qs~n~I~~~~~~~~~~lNiDI~METGTGKTy~Ylrtmf-eLhk~YG~~KFIivVPs~AIkeGv~~  122 (985)
T COG3587          55 INNIQSKNGITQGSVRIDDKLNIDILMETGTGKTYTYLRTMF-ELHKKYGLFKFIIVVPSLAIKEGVFL  122 (985)
T ss_pred             HHHHHhccCCCcccccCCCcceeeEEEecCCCceeeHHHHHH-HHHHHhCceeEEEEeccHHHHhhhHH
Confidence            344566665 2   2 223 7888999999999999955444 5654  23689999999988765443

>PLN02165 adenylate isopentenyltransferase

Probab=94.69  E-value=0.034  Score=41.84  Aligned_cols=22  Identities=27%  Similarity=0.277  Sum_probs=18.1

Q ss_pred             CCccEEEEccCCcchHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      .|+.+++.+|||||||..+...
T Consensus        42 ~g~iivIiGPTGSGKStLA~~L   63 (334)
T PLN02165         42 KDKVVVIMGATGSGKSRLSVDL   63 (334)
T ss_pred             CCCEEEEECCCCCcHHHHHHHH
Confidence            4567899999999999888553

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=94.68  E-value=0.16  Score=41.80  Aligned_cols=66  Identities=14%  Similarity=0.067  Sum_probs=50.0

Q ss_pred             hhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHh---CCCeEEEEccchhHHHHHHHHHHHHhh
Q psy2029          62 FYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKI---KQKSAIFILPYISLVHEKYQSLAKAAE  128 (138)
Q Consensus        62 ~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~---~~~~~~~i~P~~~l~~q~~~~~~~~~~  128 (138)
                      .+-|.+++.. .+.++++.+..|+|||.+....+.+.+..   .+.+++.++-|+.-+.+.-+.+.+...
T Consensus         4 n~~Q~~av~~-~~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v~p~~IL~lTFT~kAA~em~~Rl~~~l~   72 (672)
T PRK10919          4 NPGQQQAVEF-VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQTLG   72 (672)
T ss_pred             CHHHHHHHhC-CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHHhC
Confidence            3446555432 23778899999999999987777765543   245799999999999999999988754

>KOG0390|consensus

Probab=94.68  E-value=0.14  Score=42.64  Aligned_cols=68  Identities=19%  Similarity=0.190  Sum_probs=48.3

Q ss_pred             hhhhhhhHHHhhhh----------c-cceEEEeecCCCchHhHHHHHHHHHHh--CC-----CeEEEEccchhHHHHHHH
Q psy2029          60 FKFYLEGKCLEMIQ----------N-KNCVLSIPTSGGKTLVGEILIMKELKI--KQ-----KSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~----------~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~-----~~~~~i~P~~~l~~q~~~  121 (138)
                      .+.|+|.+.+..++          + .-++++-..|.|||+... ..++.++.  +.     .+.++|+|.. |+.-..+
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~I-sflwtlLrq~P~~~~~~~k~lVV~P~s-Lv~nWkk  315 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCI-SFIWTLLRQFPQAKPLINKPLVVAPSS-LVNNWKK  315 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHHH-HHHHHHHHhCcCccccccccEEEccHH-HHHHHHH
Confidence            35566666664333          3 345677778999999994 44555554  34     6899999975 8889999


Q ss_pred             HHHHHhhh
Q psy2029         122 SLAKAAEE  129 (138)
Q Consensus       122 ~~~~~~~~  129 (138)
                      +|.+|...
T Consensus       316 EF~KWl~~  323 (776)
T KOG0390|consen  316 EFGKWLGN  323 (776)
T ss_pred             HHHHhccc
Confidence            99999765

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=94.66  E-value=0.17  Score=41.60  Aligned_cols=50  Identities=18%  Similarity=0.207  Sum_probs=40.2

Q ss_pred             ceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhh
Q psy2029          76 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEE  129 (138)
Q Consensus        76 ~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~  129 (138)
                      +.++..-||+|||+.... +++.   .++++++|+|...++.|.+.+|+.++.+
T Consensus        31 ~~~l~Gvtgs~kt~~~a~-~~~~---~~~p~Lvi~~n~~~A~ql~~el~~f~p~   80 (655)
T TIGR00631        31 HQTLLGVTGSGKTFTMAN-VIAQ---VNRPTLVIAHNKTLAAQLYNEFKEFFPE   80 (655)
T ss_pred             cEEEECCCCcHHHHHHHH-HHHH---hCCCEEEEECCHHHHHHHHHHHHHhCCC
Confidence            556888899999987643 2222   3567999999999999999999999754

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

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=94.65  E-value=0.22  Score=42.98  Aligned_cols=67  Identities=16%  Similarity=0.091  Sum_probs=47.7

Q ss_pred             hhhhhhHHHhhh----hc-cceEEEeecCCCchHhHHHHHHHHHHh---CCCeEEEEccchhHHHHHHHHHHHHhhh
Q psy2029          61 KFYLEGKCLEMI----QN-KNCVLSIPTSGGKTLVGEILIMKELKI---KQKSAIFILPYISLVHEKYQSLAKAAEE  129 (138)
Q Consensus        61 ~~~~Q~~~~~~~----~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~---~~~~~~~i~P~~~l~~q~~~~~~~~~~~  129 (138)
                      +.++|...+..+    .. .+.+++-..|-|||+.++ .++..+..   ..++.|+|+|. +++.+..+++.+|+..
T Consensus       170 Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQaI-alL~~L~~~~~~~gp~LIVvP~-SlL~nW~~Ei~kw~p~  244 (1033)
T PLN03142        170 MRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTI-SLLGYLHEYRGITGPHMVVAPK-STLGNWMNEIRRFCPV  244 (1033)
T ss_pred             hHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHHH-HHHHHHHHhcCCCCCEEEEeCh-HHHHHHHHHHHHHCCC
Confidence            566777776322    23 688999999999999874 34444433   23578999996 5677899999998643

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.65  E-value=0.39  Score=36.84  Aligned_cols=60  Identities=15%  Similarity=-0.019  Sum_probs=34.8

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCC-CeEEEEccchhHHHHHHHHHHHHhhhcCceee
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQ-KSAIFILPYISLVHEKYQSLAKAAEEFKFYLE  135 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~-~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~  135 (138)
                      ..+.+.-|+|.|||......+.+.....+ .++.++. +...----.++++.|++..|+.+.
T Consensus       138 ~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit-~D~~R~ga~EqL~~~a~~~gv~~~  198 (374)
T PRK14722        138 GVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLT-TDSYRIGGHEQLRIFGKILGVPVH  198 (374)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEe-cccccccHHHHHHHHHHHcCCceE
Confidence            56679999999999988766655444434 3544443 222211123455555555666554

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=94.64  E-value=1.2  Score=32.56  Aligned_cols=35  Identities=26%  Similarity=0.136  Sum_probs=25.0

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      +-+.+++|+|+|||..+.-.+.. +.+.+.+++++.
T Consensus        73 ~vi~l~G~~G~GKTTt~akLA~~-l~~~g~~V~li~  107 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIAKLANK-LKKQGKSVLLAA  107 (272)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHH-HHhcCCEEEEEe
Confidence            45678899999999776555543 445577887764

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.

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=94.58  E-value=0.033  Score=40.29  Aligned_cols=22  Identities=27%  Similarity=0.226  Sum_probs=18.6

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .++++.+|+|+|||.++-..+.
T Consensus        43 ~~vll~GppGtGKTtlA~~ia~   64 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVARILGK   64 (261)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHH
Confidence            4789999999999999866544

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=94.57  E-value=0.038  Score=40.47  Aligned_cols=22  Identities=23%  Similarity=0.305  Sum_probs=18.6

Q ss_pred             CCccEEEEccCCcchHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      .++.+++++|+|+|||......
T Consensus        32 ~~~pvLl~G~~GtGKT~li~~~   53 (272)
T PF12775_consen   32 NGRPVLLVGPSGTGKTSLIQNF   53 (272)
T ss_dssp             CTEEEEEESSTTSSHHHHHHHH
T ss_pred             cCCcEEEECCCCCchhHHHHhh
Confidence            5779999999999999876544

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=94.55  E-value=0.038  Score=42.83  Aligned_cols=23  Identities=39%  Similarity=0.511  Sum_probs=19.2

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ..++++.+|||+|||.++-..+.
T Consensus       108 ~~~iLl~Gp~GtGKT~lAr~lA~  130 (412)
T PRK05342        108 KSNILLIGPTGSGKTLLAQTLAR  130 (412)
T ss_pred             CceEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999866543

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=94.55  E-value=0.038  Score=42.09  Aligned_cols=26  Identities=27%  Similarity=0.327  Sum_probs=19.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKEL   29 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~   29 (138)
                      .+..+++++|||||||... .+++..+
T Consensus       133 ~~glilI~GpTGSGKTTtL-~aLl~~i  158 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLL-AAIIREL  158 (358)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHH
Confidence            4568999999999999775 4444444

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.

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=94.55  E-value=0.076  Score=40.65  Aligned_cols=35  Identities=11%  Similarity=0.087  Sum_probs=22.8

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEE
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFI   39 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v   39 (138)
                      +..+++++|||||||... .+++.++.+  .+.+++-+
T Consensus       149 ~GlilI~G~TGSGKTT~l-~al~~~i~~~~~~~~Ivti  185 (372)
T TIGR02525       149 AGLGLICGETGSGKSTLA-ASIYQHCGETYPDRKIVTY  185 (372)
T ss_pred             CCEEEEECCCCCCHHHHH-HHHHHHHHhcCCCceEEEE
Confidence            447899999999999775 444444433  23455544

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).

>PF12846 AAA_10: AAA-like domain

Probab=94.54  E-value=0.13  Score=37.26  Aligned_cols=41  Identities=15%  Similarity=0.148  Sum_probs=31.8

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLV  116 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~  116 (138)
                      .++++..+||+|||.... .++..+...+..++++.|..+..
T Consensus         2 ~h~~i~G~tGsGKT~~~~-~l~~~~~~~g~~~~i~D~~g~~~   42 (304)
T PF12846_consen    2 PHTLILGKTGSGKTTLLK-NLLEQLIRRGPRVVIFDPKGDYS   42 (304)
T ss_pred             CeEEEECCCCCcHHHHHH-HHHHHHHHcCCCEEEEcCCchHH
Confidence            578899999999998886 55566666688888888875444

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

Probab=94.54  E-value=0.11  Score=43.30  Aligned_cols=51  Identities=25%  Similarity=0.190  Sum_probs=40.5

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      -.++.+|.|+|||..-.-+....+.+...+++++.--++|..+..+.+...
T Consensus        51 V~vVRSpMGTGKTtaLi~wLk~~l~~~~~~VLvVShRrSL~~sL~~rf~~~  101 (824)
T PF02399_consen   51 VLVVRSPMGTGKTTALIRWLKDALKNPDKSVLVVSHRRSLTKSLAERFKKA  101 (824)
T ss_pred             eEEEECCCCCCcHHHHHHHHHHhccCCCCeEEEEEhHHHHHHHHHHHHhhc
Confidence            458999999999987655555444456789999999999999999888765

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

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=94.53  E-value=0.091  Score=38.10  Aligned_cols=56  Identities=18%  Similarity=0.218  Sum_probs=36.3

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCc
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF  132 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~  132 (138)
                      .-+++..|+|+|||..+.-.+.+.+. .+.+++|+.-- +-.++..+++.+.+..+|+
T Consensus        37 s~~lI~G~pGtGKT~l~~qf~~~~a~-~Ge~vlyis~E-e~~~~~~~~l~~~a~~~g~   92 (259)
T TIGR03878        37 SVINITGVSDTGKSLMVEQFAVTQAS-RGNPVLFVTVE-SPANFVYTSLKERAKAMGV   92 (259)
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHHHh-CCCcEEEEEec-CCchHHHHHHHHHHHHcCC
Confidence            55578999999999999766665544 47788888743 3334444445444444444

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

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=94.51  E-value=0.05  Score=34.46  Aligned_cols=31  Identities=29%  Similarity=0.177  Sum_probs=21.4

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      +++.+|.|+|||..+...+.. +   +...+.+..
T Consensus         1 ill~G~~G~GKT~l~~~la~~-l---~~~~~~i~~   31 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQY-L---GFPFIEIDG   31 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHH-T---TSEEEEEET
T ss_pred             CEEECcCCCCeeHHHHHHHhh-c---ccccccccc
Confidence            578999999999998665554 2   344555443

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 ....

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=94.51  E-value=0.14  Score=39.38  Aligned_cols=36  Identities=14%  Similarity=0.099  Sum_probs=25.2

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhc--CCeEEEEcc
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILP   41 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~--~~~~l~v~P   41 (138)
                      ..+++++|+|+|||..+.. +...+.++  +.+++|+..
T Consensus       137 n~l~l~G~~G~GKThL~~a-i~~~l~~~~~~~~v~yi~~  174 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLLHA-IGNEILENNPNAKVVYVSS  174 (405)
T ss_pred             CeEEEECCCCCcHHHHHHH-HHHHHHHhCCCCcEEEEEH
Confidence            3578999999999988744 44444443  567888643

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).

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=94.48  E-value=0.093  Score=39.32  Aligned_cols=36  Identities=19%  Similarity=0.041  Sum_probs=25.1

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      ++-+.+.+|+|+|||..+.-.+.. +...+++++++.
T Consensus       114 ~~vi~lvGpnGsGKTTt~~kLA~~-l~~~g~~V~Li~  149 (318)
T PRK10416        114 PFVILVVGVNGVGKTTTIGKLAHK-YKAQGKKVLLAA  149 (318)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHH-HHhcCCeEEEEe
Confidence            456788999999999776444433 344567777764

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=94.46  E-value=0.15  Score=39.88  Aligned_cols=36  Identities=11%  Similarity=0.006  Sum_probs=25.3

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcc
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILP   41 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P   41 (138)
                      ..+++++|+|+|||..+-... ..+.+  .+.+++|+..
T Consensus       131 n~l~lyG~~G~GKTHLl~ai~-~~l~~~~~~~~v~yi~~  168 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLLQSIG-NYVVQNEPDLRVMYITS  168 (440)
T ss_pred             CeEEEEcCCCCcHHHHHHHHH-HHHHHhCCCCeEEEEEH
Confidence            368999999999998874433 34444  2458888654

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=94.45  E-value=0.046  Score=40.21  Aligned_cols=22  Identities=18%  Similarity=0.107  Sum_probs=17.9

Q ss_pred             CccEEEEccCCcchHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      +.++++.+|+|+|||.+|...+
T Consensus        58 ~~~vll~G~pGTGKT~lA~~ia   79 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVALRMA   79 (284)
T ss_pred             CceEEEEcCCCCCHHHHHHHHH
Confidence            3579999999999999885443

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.

>PRK13700 conjugal transfer protein TraD; Provisional

Probab=94.45  E-value=0.072  Score=43.99  Aligned_cols=48  Identities=15%  Similarity=0.088  Sum_probs=36.9

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQ   51 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~   51 (138)
                      +..++++.+.||+|||.+. .-++..++.++.++++.-|.-++....|+
T Consensus       184 E~~H~li~GttGSGKS~~i-~~LL~~ir~RGdrAIIyD~~GeFv~~FY~  231 (732)
T PRK13700        184 EIQNFCLHGTVGAGKSEVI-RRLANYARQRGDMVVIYDRSGEFVKSYYD  231 (732)
T ss_pred             hhcceEEeCCCCCCHHHHH-HHHHHHHHHcCCeEEEEeCCCchHHHhcC
Confidence            3468899999999999965 44555566788899998888877765543

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=94.44  E-value=0.15  Score=39.46  Aligned_cols=35  Identities=9%  Similarity=0.003  Sum_probs=24.2

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcc
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILP   41 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P   41 (138)
                      -+++++|+|+|||...-..-.. ...  .+.+++|+..
T Consensus       115 plfi~G~~GlGKTHLl~Aign~-~~~~~~~a~v~y~~s  151 (408)
T COG0593         115 PLFIYGGVGLGKTHLLQAIGNE-ALANGPNARVVYLTS  151 (408)
T ss_pred             cEEEECCCCCCHHHHHHHHHHH-HHhhCCCceEEeccH
Confidence            4689999999999876443333 333  3458888775

>CHL00181 cbbX CbbX; Provisional

Probab=94.43  E-value=0.042  Score=40.52  Aligned_cols=24  Identities=17%  Similarity=0.048  Sum_probs=19.8

Q ss_pred             CccEEEEccCCcchHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      |.++++.+|+|+|||.+|-..+..
T Consensus        59 ~~~ill~G~pGtGKT~lAr~la~~   82 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVALKMADI   82 (287)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHH
Confidence            557899999999999999666543

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=94.42  E-value=0.077  Score=41.53  Aligned_cols=56  Identities=23%  Similarity=0.097  Sum_probs=40.5

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeeec
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEVL  137 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~~  137 (138)
                      .++++..|||+|||....+|.+-   ..+..+++..|--+|....+...++.    |-+|..+
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll---~~~~s~iV~D~KgEl~~~t~~~r~~~----G~~V~vl  100 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLL---NYPGSMIVTDPKGELYEKTAGYRKKR----GYKVYVL  100 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHH---hccCCEEEEECCCcHHHHHHHHHHHC----CCEEEEe
Confidence            36899999999999998877653   33457888889888876666555554    4455444

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

>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=94.40  E-value=0.055  Score=34.13  Aligned_cols=21  Identities=24%  Similarity=0.183  Sum_probs=17.0

Q ss_pred             EEEEccCCcchHHHHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      +++.+++|+|||.++......
T Consensus         1 I~i~G~~GsGKtTia~~L~~~   21 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAER   21 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHH
Confidence            478999999999998665554

...

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=94.38  E-value=0.043  Score=42.53  Aligned_cols=22  Identities=41%  Similarity=0.560  Sum_probs=18.7

Q ss_pred             CccEEEEccCCcchHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      ..++++.+|||+|||..+-..+
T Consensus       116 ~~~iLL~GP~GsGKT~lAraLA  137 (413)
T TIGR00382       116 KSNILLIGPTGSGKTLLAQTLA  137 (413)
T ss_pred             CceEEEECCCCcCHHHHHHHHH
Confidence            4689999999999999986554

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.

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=94.38  E-value=0.039  Score=45.32  Aligned_cols=50  Identities=18%  Similarity=0.073  Sum_probs=0.0

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      .++++.||||||||..+.+|   ++++..+.++++-|.-++-.......+..|
T Consensus       140 ~hvlviApTgSGKgvg~VIP---nLL~~~gS~VV~DpKGE~~~~Ta~~R~~~G  189 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIP---TLLTFKGSVIALDVKGELFELTSRARKASG  189 (670)
T ss_pred             ceEEEEecCCCCceeeehHh---HHhcCCCCEEEEeCCchHHHHHHHHHHhCC

>PRK00300 gmk guanylate kinase; Provisional

Probab=94.37  E-value=0.053  Score=37.51  Aligned_cols=23  Identities=30%  Similarity=0.316  Sum_probs=18.6

Q ss_pred             CCCccEEEEccCCcchHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      -.|.-+++.+|+|||||..+...
T Consensus         3 ~~g~~i~i~G~sGsGKstl~~~l   25 (205)
T PRK00300          3 RRGLLIVLSGPSGAGKSTLVKAL   25 (205)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHH
Confidence            46778899999999999776443

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=94.34  E-value=0.059  Score=42.67  Aligned_cols=33  Identities=18%  Similarity=0.270  Sum_probs=21.4

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      -+++++|||||||... .+++..+...+.+++.+
T Consensus       244 lilitGptGSGKTTtL-~a~L~~l~~~~~~iiTi  276 (486)
T TIGR02533       244 IILVTGPTGSGKTTTL-YAALSRLNTPERNILTV  276 (486)
T ss_pred             EEEEEcCCCCCHHHHH-HHHHhccCCCCCcEEEE
Confidence            4789999999999875 44455443333344443

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.

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=94.28  E-value=0.037  Score=44.95  Aligned_cols=23  Identities=26%  Similarity=0.234  Sum_probs=19.5

Q ss_pred             ccEEEEccCCcchHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      .++++.||||||||..+.+|.+-
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL  181 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLL  181 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHH
Confidence            47899999999999988777554

>PRK13891 conjugal transfer protein TrbE; Provisional

Probab=94.28  E-value=0.092  Score=44.38  Aligned_cols=36  Identities=17%  Similarity=0.052  Sum_probs=22.8

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      .|.+|.+|||+|||......+.+...-.+.+++++-
T Consensus       489 gh~~I~G~tGsGKS~l~~~L~~~~~k~~~~~v~i~D  524 (852)
T PRK13891        489 GHTFMFGPTGAGKSTHLGIIAAQLRRYAGMSIYAFD  524 (852)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhcCCCEEEEEc
Confidence            368999999999998876555543321233444333

>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=94.26  E-value=0.21  Score=35.32  Aligned_cols=35  Identities=23%  Similarity=0.208  Sum_probs=23.6

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcc
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILP   41 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P   41 (138)
                      .+.+++|+|+|||... .++...+.+  ++.+++|+..
T Consensus        36 ~l~l~G~~G~GKTHLL-~Ai~~~~~~~~~~~~v~y~~~   72 (219)
T PF00308_consen   36 PLFLYGPSGLGKTHLL-QAIANEAQKQHPGKRVVYLSA   72 (219)
T ss_dssp             EEEEEESTTSSHHHHH-HHHHHHHHHHCTTS-EEEEEH
T ss_pred             ceEEECCCCCCHHHHH-HHHHHHHHhccccccceeecH
Confidence            4799999999999864 344444443  4678888653

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.

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=94.25  E-value=0.08  Score=46.41  Aligned_cols=41  Identities=15%  Similarity=-0.002  Sum_probs=24.0

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhh
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYIS   44 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~a   44 (138)
                      +..++++|+||||||..-....+..-....++++...|-+-
T Consensus        82 ~~vvii~g~TGSGKTTqlPq~lle~~~~~~~~I~~tQPRRl  122 (1283)
T TIGR01967        82 NQVVIIAGETGSGKTTQLPKICLELGRGSHGLIGHTQPRRL  122 (1283)
T ss_pred             CceEEEeCCCCCCcHHHHHHHHHHcCCCCCceEecCCccHH
Confidence            34668999999999986443333321112235555566443

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.

>KOG2028|consensus

Probab=94.21  E-value=0.62  Score=35.99  Aligned_cols=19  Identities=26%  Similarity=0.450  Sum_probs=16.2

Q ss_pred             cEEEEccCCcchHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~   24 (138)
                      ++|+|+|.|+|||..|-+.
T Consensus       164 SmIlWGppG~GKTtlArli  182 (554)
T KOG2028|consen  164 SMILWGPPGTGKTTLARLI  182 (554)
T ss_pred             ceEEecCCCCchHHHHHHH
Confidence            6899999999999887443

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

Probab=94.15  E-value=0.14  Score=37.07  Aligned_cols=49  Identities=27%  Similarity=0.299  Sum_probs=38.1

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK  125 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~  125 (138)
                      .|+++.-|.|.|||-.+ .++..++. ..+..++.+++.+++.+....+..
T Consensus       106 ~nl~l~G~~G~GKThLa-~Ai~~~l~-~~g~sv~f~~~~el~~~Lk~~~~~  154 (254)
T COG1484         106 ENLVLLGPPGVGKTHLA-IAIGNELL-KAGISVLFITAPDLLSKLKAAFDE  154 (254)
T ss_pred             CcEEEECCCCCcHHHHH-HHHHHHHH-HcCCeEEEEEHHHHHHHHHHHHhc
Confidence            79999999999999999 44555666 455567778999999887776653

>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=94.15  E-value=0.039  Score=35.70  Aligned_cols=18  Identities=28%  Similarity=0.468  Sum_probs=15.0

Q ss_pred             EEEEccCCcchHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~   24 (138)
                      +++++|.|||||..+...
T Consensus         2 ii~~G~pgsGKSt~a~~l   19 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRL   19 (143)
T ss_dssp             EEEEESTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            589999999999887443

...

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=94.14  E-value=0.059  Score=41.17  Aligned_cols=47  Identities=15%  Similarity=0.020  Sum_probs=35.5

Q ss_pred             ceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHH
Q psy2029          76 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK  125 (138)
Q Consensus        76 ~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~  125 (138)
                      ++++..|||+|||....+|-+-   ..+..++++.|--++.+..+...++
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll---~~~~s~vv~D~Kge~~~~t~~~r~~   47 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLL---TWPGSVVVLDPKGENFELTSEHRRA   47 (384)
T ss_pred             CeeEecCCCCCCccEEEccchh---cCCCCEEEEccchhHHHHHHHHHHH
Confidence            4688999999999888776554   2457889999998888666555543

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.

>PHA00729 NTP-binding motif containing protein

Probab=94.14  E-value=0.18  Score=35.96  Aligned_cols=22  Identities=18%  Similarity=0.057  Sum_probs=18.0

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .|+++.+|+|+|||..|...+.
T Consensus        18 ~nIlItG~pGvGKT~LA~aLa~   39 (226)
T PHA00729         18 VSAVIFGKQGSGKTTYALKVAR   39 (226)
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            4789999999999988855444

>PHA02244 ATPase-like protein

Probab=94.11  E-value=0.055  Score=41.42  Aligned_cols=24  Identities=21%  Similarity=0.194  Sum_probs=19.8

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .+.++++.+|||+|||.++...+.
T Consensus       118 ~~~PVLL~GppGtGKTtLA~aLA~  141 (383)
T PHA02244        118 ANIPVFLKGGAGSGKNHIAEQIAE  141 (383)
T ss_pred             cCCCEEEECCCCCCHHHHHHHHHH
Confidence            467899999999999988866544

>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=94.09  E-value=0.084  Score=39.43  Aligned_cols=37  Identities=16%  Similarity=0.169  Sum_probs=23.9

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      .+++++++++|||||||..- .+++ .++....|.+.+-
T Consensus       141 e~~~siii~G~t~sGKTt~l-nall-~~Ip~~~rivtIE  177 (312)
T COG0630         141 EARKSIIICGGTASGKTTLL-NALL-DFIPPEERIVTIE  177 (312)
T ss_pred             HcCCcEEEECCCCCCHHHHH-HHHH-HhCCchhcEEEEe
Confidence            35789999999999999663 2222 2334444555543

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=94.08  E-value=0.18  Score=41.50  Aligned_cols=48  Identities=19%  Similarity=0.171  Sum_probs=38.1

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +-++.+-||||||+...-.+ .   +.++.+++++|.+.+..|.+++++.++
T Consensus        31 ~~~l~Gvtgs~kt~~~a~~~-~---~~~~p~Lvi~~n~~~A~ql~~el~~f~   78 (655)
T TIGR00631        31 HQTLLGVTGSGKTFTMANVI-A---QVNRPTLVIAHNKTLAAQLYNEFKEFF   78 (655)
T ss_pred             cEEEECCCCcHHHHHHHHHH-H---HhCCCEEEEECCHHHHHHHHHHHHHhC
Confidence            45689999999998753322 2   236788999999999999999998874

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

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=94.07  E-value=0.17  Score=41.41  Aligned_cols=53  Identities=17%  Similarity=0.088  Sum_probs=38.3

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhc---CCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIK---QKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~---~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +.+++|.|..|||||.+...-+...+.+.   ..+++.++.++.-..+..+++.+.
T Consensus        14 ~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~~p~~IL~vTFt~~Aa~em~~Rl~~~   69 (664)
T TIGR01074        14 TGPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKT   69 (664)
T ss_pred             CCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHH
Confidence            45899999999999988766565544332   247788888887777777776653

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

>KOG1803|consensus

Probab=94.05  E-value=0.2  Score=40.48  Aligned_cols=64  Identities=19%  Similarity=0.159  Sum_probs=46.8

Q ss_pred             hhhhhhhHHHhhhhc-cc-eEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHH
Q psy2029          60 FKFYLEGKCLEMIQN-KN-CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLA  124 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~-~~-~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~  124 (138)
                      .+.+.|..+.....+ ++ .++--|.|+|||..-...+ .++..++.++++.+|+..-++-+.+.+.
T Consensus       185 ~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI-~qlvk~~k~VLVcaPSn~AVdNiverl~  250 (649)
T KOG1803|consen  185 NLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEII-SQLVKQKKRVLVCAPSNVAVDNIVERLT  250 (649)
T ss_pred             cccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHH-HHHHHcCCeEEEEcCchHHHHHHHHHhc
Confidence            345567777765555 33 4688999999998875544 4555568999999999988877777544

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=94.04  E-value=0.21  Score=41.42  Aligned_cols=52  Identities=17%  Similarity=-0.003  Sum_probs=39.2

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhh-c---CCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKI-K---QKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~-~---~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ..+++|.|..|||||.+...=+.. +++ .   ..+++.++.++.-..+..+++.+.
T Consensus        22 ~g~~lV~AgaGSGKT~vl~~Ria~-Li~~~~v~p~~IL~lTFT~kAA~Em~~Rl~~~   77 (721)
T PRK11773         22 LGNMLVLAGAGSGKTRVLVHRIAW-LMQVENASPYSIMAVTFTNKAAAEMRHRIEQL   77 (721)
T ss_pred             CCCEEEEecCCCCHHHHHHHHHHH-HHHcCCCChhHeEeeeccHHHHHHHHHHHHHH
Confidence            358899999999999887555554 443 2   348899999998888877777664

>PRK13873 conjugal transfer ATPase TrbE; Provisional

Probab=94.04  E-value=0.096  Score=44.00  Aligned_cols=22  Identities=18%  Similarity=0.446  Sum_probs=17.8

Q ss_pred             cEEEEccCCcchHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      |.+|.+|||||||......+.+
T Consensus       443 n~~I~G~tGsGKS~l~~~l~~~  464 (811)
T PRK13873        443 HTLVVGPTGAGKSVLLALMALQ  464 (811)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            8899999999999877554443

>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=94.04  E-value=0.11  Score=37.34  Aligned_cols=36  Identities=25%  Similarity=0.236  Sum_probs=23.9

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      -+++|.+|+|||||...... +.++...-..+++++|
T Consensus        14 fr~viIG~sGSGKT~li~~l-L~~~~~~f~~I~l~t~   49 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTTLIKSL-LYYLRHKFDHIFLITP   49 (241)
T ss_pred             ceEEEECCCCCCHHHHHHHH-HHhhcccCCEEEEEec
Confidence            37899999999999876443 3444433345555566

This is thought to be an ATPase involved in viral DNA packaging [].

>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=93.99  E-value=0.22  Score=35.64  Aligned_cols=53  Identities=19%  Similarity=0.190  Sum_probs=38.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +|+|.+..+-.|.|||-+- .|++...+.++.+.+.++=.++|.+|..+.+...
T Consensus        40 ~~~n~v~QlnMGeGKTsVI-~Pmla~~LAdg~~LvrviVpk~Ll~q~~~~L~~~   92 (229)
T PF12340_consen   40 SGKNSVMQLNMGEGKTSVI-VPMLALALADGSRLVRVIVPKALLEQMRQMLRSR   92 (229)
T ss_pred             CCCCeEeeecccCCccchH-HHHHHHHHcCCCcEEEEEcCHHHHHHHHHHHHHH
Confidence            4789999999999999774 5555445555666655555567888887777665

There are two conserved sequence motifs: LLE and NMG.

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=93.99  E-value=0.24  Score=40.35  Aligned_cols=43  Identities=9%  Similarity=-0.052  Sum_probs=27.5

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKY   50 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~   50 (138)
                      .+++++++|+|||..+-..... +..  .+.+++|+. ...+.++..
T Consensus       316 pL~LyG~sGsGKTHLL~AIa~~-a~~~~~g~~V~Yit-aeef~~el~  360 (617)
T PRK14086        316 PLFIYGESGLGKTHLLHAIGHY-ARRLYPGTRVRYVS-SEEFTNEFI  360 (617)
T ss_pred             cEEEECCCCCCHHHHHHHHHHH-HHHhCCCCeEEEee-HHHHHHHHH
Confidence            4899999999999886444333 332  366888854 344444433

>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=93.98  E-value=0.075  Score=37.69  Aligned_cols=22  Identities=32%  Similarity=0.353  Sum_probs=17.0

Q ss_pred             EEEEccCCcchHHHHHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKE   28 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~   28 (138)
                      .++.+|||+|||..+...+.+.
T Consensus         4 ~~i~GpT~tGKt~~ai~lA~~~   25 (233)
T PF01745_consen    4 YLIVGPTGTGKTALAIALAQKT   25 (233)
T ss_dssp             EEEE-STTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCChhHHHHHHHHHh
Confidence            4789999999999987766653

; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.

>PRK00091 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed

Probab=93.94  E-value=0.054  Score=40.41  Aligned_cols=22  Identities=36%  Similarity=0.335  Sum_probs=17.4

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .-+++++|||||||.++.-.+-
T Consensus         5 ~~i~i~GptgsGKt~la~~la~   26 (307)
T PRK00091          5 KVIVIVGPTASGKTALAIELAK   26 (307)
T ss_pred             eEEEEECCCCcCHHHHHHHHHH
Confidence            3468999999999998865443

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=93.94  E-value=0.29  Score=31.77  Aligned_cols=20  Identities=20%  Similarity=0.218  Sum_probs=16.6

Q ss_pred             EEEccCCcchHHHHHHHHHH
Q psy2029           8 VLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~~~~~   27 (138)
                      .+.+|||+|||.++-+.+..
T Consensus        57 SfHG~tGtGKn~v~~liA~~   76 (127)
T PF06309_consen   57 SFHGWTGTGKNFVSRLIAEH   76 (127)
T ss_pred             EeecCCCCcHHHHHHHHHHH
Confidence            47899999999999776654

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

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=93.94  E-value=0.075  Score=40.60  Aligned_cols=40  Identities=18%  Similarity=0.213  Sum_probs=30.6

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcC--CeEEEEcchhhhH
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQ--KSAIFILPYISLV   46 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~--~~~l~v~P~~aL~   46 (138)
                      +.+.++.|+|||+.|+.+.+....+++  .|+++.=|+..+-
T Consensus       248 V~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG  289 (436)
T COG1875         248 VSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVG  289 (436)
T ss_pred             EEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCcc
Confidence            567899999999999999887776643  3666666766654

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

Probab=93.92  E-value=0.17  Score=34.69  Aligned_cols=44  Identities=30%  Similarity=0.308  Sum_probs=29.8

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKY  120 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~  120 (138)
                      .++++.-|+|.|||..+.. +..++...+.+++| ++...|+++..
T Consensus        48 ~~l~l~G~~G~GKThLa~a-i~~~~~~~g~~v~f-~~~~~L~~~l~   91 (178)
T PF01695_consen   48 ENLILYGPPGTGKTHLAVA-IANEAIRKGYSVLF-ITASDLLDELK   91 (178)
T ss_dssp             -EEEEEESTTSSHHHHHHH-HHHHHHHTT--EEE-EEHHHHHHHHH
T ss_pred             eEEEEEhhHhHHHHHHHHH-HHHHhccCCcceeE-eecCceecccc
Confidence            8899999999999999844 45556655555555 56777775543

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.

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=93.92  E-value=0.16  Score=44.29  Aligned_cols=54  Identities=11%  Similarity=0.107  Sum_probs=39.6

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcC----CeEEEEcchhhhHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQ----KSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~----~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .+.+++|.|-.|||||.+-..-++.-++..+    .++++++.|++=..+...++.+.
T Consensus        15 ~~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~~v~~ILvvTFT~aAa~Emk~RI~~~   72 (1139)
T COG1074          15 PGQSVLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRDR   72 (1139)
T ss_pred             CCCcEEEEEcCCCCchhHHHHHHHHHHhhcCCCChhHeeeeeccHHHHHHHHHHHHHH
Confidence            3568999999999999887666676666643    37899998887666555554443

>TIGR01075 uvrD DNA helicase II

Probab=93.91  E-value=0.22  Score=41.30  Aligned_cols=54  Identities=17%  Similarity=0.046  Sum_probs=0.0

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCC---eEEEEcchhhhHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQK---SAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~---~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .+.+++|.|..|||||.+...=+..-+.+.+.   +++.++.++.-..+..+++...
T Consensus        16 ~~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v~p~~IL~lTFTnkAA~em~~Rl~~~   72 (715)
T TIGR01075        16 PPGNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKAAAEMRHRIGAL   72 (715)
T ss_pred             CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCCCHHHeEeeeccHHHHHHHHHHHHHH

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

>PF13173 AAA_14: AAA domain

Probab=93.88  E-value=0.12  Score=33.08  Aligned_cols=35  Identities=26%  Similarity=0.311  Sum_probs=25.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      +++-+++.+|.|+|||......+....  ...+++|+
T Consensus         1 n~~~~~l~G~R~vGKTtll~~~~~~~~--~~~~~~yi   35 (128)
T PF13173_consen    1 NRKIIILTGPRGVGKTTLLKQLAKDLL--PPENILYI   35 (128)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHhc--ccccceee
Confidence            456789999999999988766555432  34566775

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=93.88  E-value=0.16  Score=33.92  Aligned_cols=34  Identities=26%  Similarity=0.219  Sum_probs=23.0

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      +.+++++|+|||.+....+. .+.+++.++-++-+
T Consensus         2 i~i~G~~gsGKTtl~~~l~~-~l~~~G~~V~viK~   35 (155)
T TIGR00176         2 LQIVGPKNSGKTTLIERLVK-ALKARGYRVATIKH   35 (155)
T ss_pred             EEEECCCCCCHHHHHHHHHH-HHHhcCCeEEEEec
Confidence            46789999999988654444 34455657766543

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.

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

Probab=93.75  E-value=0.13  Score=39.12  Aligned_cols=41  Identities=20%  Similarity=0.289  Sum_probs=29.5

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYI   43 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~   43 (138)
                      .++.++.+.+|-|+|||.+.-... ..+...+..++.++|+-
T Consensus        20 ~~~~~~fv~G~~GtGKs~l~~~i~-~~~~~~~~~~~~~a~tg   60 (364)
T PF05970_consen   20 EEGLNFFVTGPAGTGKSFLIKAII-DYLRSRGKKVLVTAPTG   60 (364)
T ss_pred             cCCcEEEEEcCCCCChhHHHHHHH-HHhccccceEEEecchH
Confidence            357789999999999998864332 23444566778888865

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

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=93.71  E-value=0.2  Score=44.07  Aligned_cols=63  Identities=13%  Similarity=0.069  Sum_probs=38.8

Q ss_pred             hhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCC--CeEEEEcc----chhHHHHHHHHHHH-HhhhcCcee
Q psy2029          70 EMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQ--KSAIFILP----YISLVHEKYQSLAK-AAEEFKFYL  134 (138)
Q Consensus        70 ~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~--~~~~~i~P----~~~l~~q~~~~~~~-~~~~~~~~v  134 (138)
                      +.+.+ ..++++.+||||||.  .+|.+-.-...+  .+++..-|    .++|+.++++++.. ++...|..|
T Consensus        84 ~ai~~~~VviI~GeTGSGKTT--qlPq~lle~g~g~~g~I~~TQPRRlAArsLA~RVA~El~~~lG~~VGY~v  154 (1294)
T PRK11131         84 EAIRDHQVVIVAGETGSGKTT--QLPKICLELGRGVKGLIGHTQPRRLAARTVANRIAEELETELGGCVGYKV  154 (1294)
T ss_pred             HHHHhCCeEEEECCCCCCHHH--HHHHHHHHcCCCCCCceeeCCCcHHHHHHHHHHHHHHHhhhhcceeceee
Confidence            44555 556788999999998  366432211112  23444446    57888888888875 444456654

>PF09439 SRPRB: Signal recognition particle receptor beta subunit; InterPro: IPR019009 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=93.70  E-value=0.072  Score=36.69  Aligned_cols=25  Identities=24%  Similarity=0.291  Sum_probs=17.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      +...+++.+|.|||||..+......
T Consensus         2 k~~~vlL~Gps~SGKTaLf~~L~~~   26 (181)
T PF09439_consen    2 KRPTVLLVGPSGSGKTALFSQLVNG   26 (181)
T ss_dssp             ---EEEEE-STTSSHHHHHHHHHHS
T ss_pred             CCceEEEEcCCCCCHHHHHHHHhcC
Confidence            3567899999999999888655543

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase, which anchors the alpha subunit to the endoplasmic reticulum membrane []. ; PDB: 2GED_B 1NRJ_B 2GO5_2 2FH5_B.

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=93.68  E-value=0.21  Score=40.61  Aligned_cols=56  Identities=20%  Similarity=0.148  Sum_probs=0.0

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh-----cCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI-----KQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-----~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      +++-++|.+-.|||||.+|+.=+..-+-.     ..+.++++.|.+-+..=+.+.+-+.|.
T Consensus       225 k~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~vFleYis~VLPeLGe  285 (747)
T COG3973         225 KNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNRVFLEYISRVLPELGE  285 (747)
T ss_pred             CCCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEEEcCcHHHHHHHHHhchhhcc

>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=93.67  E-value=0.17  Score=35.11  Aligned_cols=28  Identities=18%  Similarity=0.240  Sum_probs=18.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHh
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELK   30 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~   30 (138)
                      +..++++.++||||||......+..-+.
T Consensus        37 ~~~h~li~G~tgsGKS~~l~~ll~~l~~   64 (205)
T PF01580_consen   37 KNPHLLIAGATGSGKSTLLRTLLLSLAL   64 (205)
T ss_dssp             GS-SEEEE--TTSSHHHHHHHHHHHHHT
T ss_pred             CCceEEEEcCCCCCccHHHHHHHHHHHH
Confidence            3458999999999999887655554333

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.

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=93.67  E-value=1.2  Score=37.07  Aligned_cols=57  Identities=11%  Similarity=0.211  Sum_probs=46.8

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcC
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFK  131 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~  131 (138)
                      +-.++.+|-|.|||-+..+.+...+...+.+++|.+|....+.+.++.++..++..|
T Consensus       188 ~~tV~taPRqrGKS~iVgi~l~~La~f~Gi~IlvTAH~~~ts~evF~rv~~~le~lg  244 (752)
T PHA03333        188 CYTAATVPRRCGKTTIMAIILAAMISFLEIDIVVQAQRKTMCLTLYNRVETVVHAYQ  244 (752)
T ss_pred             cceEEEeccCCCcHHHHHHHHHHHHHhcCCeEEEECCChhhHHHHHHHHHHHHHHhc
Confidence            566889999999998887666654442578999999999999999999998887543

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=93.67  E-value=1.9  Score=30.92  Aligned_cols=32  Identities=22%  Similarity=0.226  Sum_probs=21.4

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      ++++++.|||||..+...+- ++...+.++.++
T Consensus         2 Ivl~G~pGSGKST~a~~La~-~l~~~~~~v~~i   33 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAK-KLSEKNIDVIIL   33 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHH-HHHHcCCceEEE
Confidence            57899999999998855443 233334455554

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.

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=93.62  E-value=0.077  Score=36.35  Aligned_cols=21  Identities=29%  Similarity=0.211  Sum_probs=17.8

Q ss_pred             CccEEEEccCCcchHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      |..+++.+|.|||||.++-..
T Consensus         2 g~~i~l~G~sGsGKsTl~~~l   22 (186)
T PRK10078          2 GKLIWLMGPSGSGKDSLLAAL   22 (186)
T ss_pred             CcEEEEECCCCCCHHHHHHHH
Confidence            678899999999999887444

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=93.61  E-value=0.091  Score=39.73  Aligned_cols=41  Identities=20%  Similarity=0.189  Sum_probs=26.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhh
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISL   45 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL   45 (138)
                      .+.|+++++|||+|||...... .. ++....+.+.+-...+|
T Consensus       177 ~~~~ili~G~tGsGKTTll~al-~~-~i~~~~riv~iEd~~El  217 (340)
T TIGR03819       177 ARLAFLISGGTGSGKTTLLSAL-LA-LVAPDERIVLVEDAAEL  217 (340)
T ss_pred             CCCeEEEECCCCCCHHHHHHHH-Hc-cCCCCCcEEEECCccee
Confidence            4679999999999999765332 22 33344566665544444

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.

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=93.60  E-value=0.14  Score=41.76  Aligned_cols=56  Identities=16%  Similarity=-0.048  Sum_probs=43.0

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeeec
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEVL  137 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~~  137 (138)
                      .++++.+|||+|||....+|-+-.   -+..+|++.|--++....+...++.    |..|..+
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~---~~~S~VV~DpKGEl~~~Ta~~R~~~----G~~V~vf  214 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLF---WEDSVVVHDIKLENYELTSGWREKQ----GQKVFVW  214 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHh---CCCCEEEEeCcHHHHHHHHHHHHHC----CCeEEEE
Confidence            678999999999999998888754   3567889999998887777666554    5555444

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	138
2zj2_A	720	Archaeal Dna Helicase Hjm Apo State In Form 1 Lengt		9e-06
2p6r_A	702	Crystal Structure Of Superfamily 2 Helicase Hel308		3e-05

>pdb|2ZJ2|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 1 Length = 720

Iteration: 1
 Score = 45.4 bits (106), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 19/53 (35%), Positives = 35/53 (66%)
Query: 71  MIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSL 123
           +++ KN ++SIPT+ GKTL+ EI ++  +  +   A++I+P  +L  EK+Q  
Sbjct: 36  ILEGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPLKALAEEKFQEF 88

>pdb|2P6R|A Chain A, Crystal Structure Of Superfamily 2 Helicase Hel308 In Complex With Unwound Dna Length = 702

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 20/56 (35%), Positives = 38/56 (67%), Gaps = 1/56 (1%)
Query: 70  EMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK 125
           ++   KN +L++PT+ GKTL+ E+ +++E  IK   +++++P  +L  EKY+S  K
Sbjct: 36  KVFSGKNLLLAMPTAAGKTLLAEMAMVRE-AIKGGKSLYVVPLRALAGEKYESFKK 90

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	138
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	3e-16
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	5e-16
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	5e-12
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	7e-12
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	6e-12
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	6e-12
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	9e-07
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	7e-06
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	2e-06
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	9e-06
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	2e-05
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	4e-05
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	3e-05
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	6e-04
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	9e-05
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	2e-04
3b6e_A	216	Interferon-induced helicase C domain-containing P;	2e-04
3b6e_A	216	Interferon-induced helicase C domain-containing P;	3e-04

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 73.2 bits (180), Expect = 3e-16
 Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 2/64 (3%)

Query: 67  KCLEMI--QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLA 124
           + ++    +    +L+ PT  GKTL+ E+ I+  L      AI++ P  +L +EKY +  
Sbjct: 37  EAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAIYVTPLRALTNEKYLTFK 96

Query: 125 KAAE 128
               
Sbjct: 97  DWEL 100

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 72.1 bits (177), Expect = 5e-16
 Identities = 17/56 (30%), Positives = 28/56 (50%)

Query: 3   QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE 58
           +    +L+ PT  GKTL+ E+ I+  L      AI++ P  +L +EKY +      
Sbjct: 45  EGNRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAIYVTPLRALTNEKYLTFKDWEL 100

>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 = 61.0 bits (148), Expect = 5e-12
 Identities = 20/60 (33%), Positives = 39/60 (65%), Gaps = 2/60 (3%)

Query: 67  KCLEMI-QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK 125
           + +E +   KN +L++PT+ GKTL+ E+ +++E     K +++++P  +L  EKY+S  K
Sbjct: 32  EAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGK-SLYVVPLRALAGEKYESFKK 90

>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 = 60.6 bits (147), Expect = 7e-12
 Identities = 19/55 (34%), Positives = 36/55 (65%), Gaps = 1/55 (1%)

Query: 1  MVQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK 55
          +   KN +L++PT+ GKTL+ E+ +++E     K +++++P  +L  EKY+S  K
Sbjct: 37 VFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGK-SLYVVPLRALAGEKYESFKK 90

>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 = 60.6 bits (147), Expect = 6e-12
 Identities = 19/53 (35%), Positives = 33/53 (62%)

Query: 3  QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK 55
          + KN ++SIPT+ GKTL+ EI ++  +  +   A++I+P  +L  EK+Q    
Sbjct: 38 EGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPLKALAEEKFQEFQD 90

>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 = 60.6 bits (147), Expect = 6e-12
 Identities = 19/53 (35%), Positives = 33/53 (62%)

Query: 73  QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK 125
           + KN ++SIPT+ GKTL+ EI ++  +  +   A++I+P  +L  EK+Q    
Sbjct: 38  EGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPLKALAEEKFQEFQD 90

>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 = 46.0 bits (108), Expect = 9e-07
 Identities = 28/120 (23%), Positives = 50/120 (41%), Gaps = 5/120 (4%)

Query: 10  SIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYL----E 65
           S   +  +TL  E      L  + +  + + P               A  + F L    +
Sbjct: 131 SKGLTNSETLQVEQDGKVRLSHQVRHQVALPPNYDYTPIAEHKRVNEARTYPFTLDPFQD 190

Query: 66  GKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK 125
                + + ++ ++S  TS GKT+V E  I + LK KQ+  I+  P  +L ++KY+ L  
Sbjct: 191 TAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQR-VIYTSPIKALSNQKYRELLA 249

>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 = 43.3 bits (101), Expect = 7e-06
 Identities = 19/53 (35%), Positives = 32/53 (60%), Gaps = 1/53 (1%)

Query: 3   QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK 55
           + ++ ++S  TS GKT+V E  I + LK KQ+  I+  P  +L ++KY+ L  
Sbjct: 198 RGESVLVSAHTSAGKTVVAEYAIAQSLKNKQR-VIYTSPIKALSNQKYRELLA 249

>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 = 45.2 bits (106), Expect = 2e-06
 Identities = 31/120 (25%), Positives = 48/120 (40%), Gaps = 5/120 (4%)

Query: 10  SIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEG--- 66
           S   +  +TL  E      L  + +  + + P               A  + F L+    
Sbjct: 33  SKGLTNSETLQVEQDGKVRLSHQVRHQVALPPNYDYTPIAEHKRVNEARTYPFTLDPFQD 92

Query: 67  KCLEMIQNKNCVL-SIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK 125
             +  I     VL S  TS GKT+V E  I + LK KQ+  I+  P  +L ++KY+ L  
Sbjct: 93  TAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQR-VIYTSPIKALSNQKYRELLA 151

>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 = 42.9 bits (100), Expect = 9e-06
 Identities = 19/53 (35%), Positives = 32/53 (60%), Gaps = 1/53 (1%)

Query: 3   QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK 55
           + ++ ++S  TS GKT+V E  I + LK KQ+  I+  P  +L ++KY+ L  
Sbjct: 100 RGESVLVSAHTSAGKTVVAEYAIAQSLKNKQR-VIYTSPIKALSNQKYRELLA 151

>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* Length = 472

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 11/48 (22%), Positives = 22/48 (45%), Gaps = 4/48 (8%)

Query: 70  EMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVH 117
             + +K   + +PT  GKT V  +  + EL       + ++P ++L  
Sbjct: 104 RWLVDKRGCIVLPTGSGKTHVA-MAAINELS---TPTLIVVPTLALAE 147

>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* Length = 472

 Score = 41.0 bits (96), Expect = 4e-05
 Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 4/47 (8%)

Query: 1   MVQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVH 47
            + +K   + +PT  GKT V  +  + EL       + ++P ++L  
Sbjct: 105 WLVDKRGCIVLPTGSGKTHVA-MAAINELS---TPTLIVVPTLALAE 147

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A Length = 997

 Score = 41.8 bits (97), Expect = 3e-05
 Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 5/80 (6%)

Query: 50  YQSLAKAAEEFKFYL----EGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKS 105
            + +   A  + F L    +     + Q  +  ++  TS GKT+V E  I    +   K 
Sbjct: 26  DELIPNPARSWPFELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRNMTK- 84

Query: 106 AIFILPYISLVHEKYQSLAK 125
            I+  P  +L ++K++   +
Sbjct: 85  TIYTSPIKALSNQKFRDFKE 104

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A Length = 997

 Score = 37.9 bits (87), Expect = 6e-04
 Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 1   MVQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK 55
           + Q  +  ++  TS GKT+V E  I    +   K  I+  P  +L ++K++   +
Sbjct: 51  LEQGDSVFVAAHTSAGKTVVAEYAIAMAHRNMTK-TIYTSPIKALSNQKFRDFKE 104

>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 Length = 237

 Score = 39.7 bits (93), Expect = 9e-05
 Identities = 11/48 (22%), Positives = 22/48 (45%), Gaps = 4/48 (8%)

Query: 70  EMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVH 117
             + +K   + +PT  GKT V  +  + EL       + ++P ++L  
Sbjct: 104 RWLVDKRGCIVLPTGSGKTHVA-MAAINELS---TPTLIVVPTLALAE 147

>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 Length = 237

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 4/47 (8%)

Query: 1   MVQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVH 47
            + +K   + +PT  GKT V  +  + EL       + ++P ++L  
Sbjct: 105 WLVDKRGCIVLPTGSGKTHVA-MAAINELS---TPTLIVVPTLALAE 147

>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 = 39.0 bits (91), Expect = 2e-04
 Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 5/59 (8%)

Query: 72  IQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKS-----AIFILPYISLVHEKYQSLAK 125
           ++ KN ++ +PT  GKT V   +    L  K+K+      I ++  + LV + ++   +
Sbjct: 46  LEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQ 104

>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 = 38.3 bits (89), Expect = 3e-04
 Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 5/59 (8%)

Query: 2   VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKS-----AIFILPYISLVHEKYQSLAK 55
           ++ KN ++ +PT  GKT V   +    L  K+K+      I ++  + LV + ++   +
Sbjct: 46  LEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQ 104

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	138
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.64
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.63
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.63
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.6
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.59
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.59
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.59
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.58
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.58
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.58
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.56
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.56
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.55
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.55
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.55
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.54
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.53
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.52
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.5
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.49
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.49
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.48
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.47
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.46
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.46
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.45
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.44
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.44
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.43
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.43
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.43
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.41
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.41
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.39
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.39
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.38
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.38
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.38
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.37
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.35
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.35
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.35
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.34
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.33
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.31
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.29
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.29
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.28
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.28
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.28
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.27
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.27
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.27
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.26
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.25
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.25
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.25
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.24
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.24
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.23
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.23
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.22
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.21
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.21
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.21
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.2
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.19
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.19
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.19
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.19
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.17
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.17
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.17
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.16
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.15
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.14
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.14
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.13
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.13
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.12
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.12
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.12
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.11
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.11
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.11
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.1
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.1
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.1
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.1
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.1
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.09
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.09
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.09
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.08
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.08
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.07
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.07
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.07
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.06
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.06
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.05
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.05
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.04
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.04
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.03
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.03
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.02
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.01
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.0
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.0
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	98.99
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	98.99
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	98.99
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	98.98
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	98.97
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	98.96
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	98.95
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	98.94
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	98.94
4gl2_A	699	Interferon-induced helicase C domain-containing P;	98.94
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	98.94
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	98.93
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	98.92
1yks_A	440	Genome polyprotein [contains: flavivirin protease	98.92
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	98.91
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	98.88
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	98.87
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	98.84
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	98.83
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	98.79
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	98.78
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	98.77
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	98.76
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	98.73
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.72
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	98.72
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	98.71
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	98.7
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	98.66
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.65
3h1t_A	590	Type I site-specific restriction-modification syst	98.62
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	98.59
3h1t_A	590	Type I site-specific restriction-modification syst	98.54
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	98.51
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	98.43
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	98.39
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	98.39
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	98.36
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	98.35
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	98.35
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	98.32
3jux_A	822	Protein translocase subunit SECA; protein transloc	98.23
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	98.18
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	98.12
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	98.03
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	97.91
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	97.81
3jux_A	822	Protein translocase subunit SECA; protein transloc	97.58
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	97.55
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	97.49
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	97.45
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	97.35
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	97.23
2z43_A	324	DNA repair and recombination protein RADA; archaea	97.19
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	97.18
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	97.04
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	96.92
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	96.92
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	96.86
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	96.85
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	96.81
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	96.8
2r6a_A	454	DNAB helicase, replicative helicase; replication,	96.76
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	96.75
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	96.74
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	96.73
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.73
2cvh_A	220	DNA repair and recombination protein RADB; filamen	96.73
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	96.62
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	96.62
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	96.6
3io5_A	333	Recombination and repair protein; storage dimer, i	96.58
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	96.56
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	96.56
2qgz_A	308	Helicase loader, putative primosome component; str	96.52
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	96.48
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	96.44
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	96.31
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	96.3
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.25
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	96.17
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	96.14
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	96.11
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	96.11
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	96.08
4a74_A	231	DNA repair and recombination protein RADA; hydrola	96.08
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	96.01
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	95.98
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	95.98
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	95.98
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	95.93
3bos_A	242	Putative DNA replication factor; P-loop containing	95.93
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	95.93
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	95.91
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	95.85
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	95.83
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	95.83
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	95.8
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	95.8
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	95.77
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	95.74
3co5_A	143	Putative two-component system transcriptional RES	95.7
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	95.64
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	95.6
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	95.59
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	95.54
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	95.53
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	95.45
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	95.35
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	95.27
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	95.22
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	95.22
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	95.21
2eyu_A	261	Twitching motility protein PILT; pilus retraction	95.12
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	95.12
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	95.02
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	95.01
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	95.0
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	94.99
1p9r_A	418	General secretion pathway protein E; bacterial typ	94.9
1u94_A	356	RECA protein, recombinase A; homologous recombinat	94.88
2ewv_A	372	Twitching motility protein PILT; pilus retraction	94.86
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	94.85
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	94.82
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	94.77
3bs4_A	260	Uncharacterized protein PH0321; structural genomic	94.77
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	94.72
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	94.67
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	94.65
1xp8_A	366	RECA protein, recombinase A; recombination, radior	94.64
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	94.51
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	94.49
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	94.43
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	94.42
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	94.42
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	94.41
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	94.37
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	94.31
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	94.3
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	94.3
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	94.28
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	94.27
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	94.26
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	94.24
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	94.19
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	94.17
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	94.17
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	94.15
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	94.14
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	94.11
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	94.06
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	94.04
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	94.03
2xxa_A	433	Signal recognition particle protein; protein trans	94.03
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	93.99
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	93.98
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	93.87
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	93.81
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	93.79
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	93.77
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	93.71
2chg_A	226	Replication factor C small subunit; DNA-binding pr	93.71
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	93.69
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	93.69
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	93.66
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	93.64
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	93.59
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	93.55
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	93.47
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	93.47
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	93.43
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	93.35
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	93.35
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	93.34
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	93.34
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	93.34
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	93.31
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	93.3
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	93.26
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	93.26
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	93.22
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	93.21
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	93.17
2r44_A	331	Uncharacterized protein; putative ATPase, structur	93.1
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	93.07
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	93.07
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	93.07
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	93.04
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	93.03
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	93.02
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	93.01
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	93.01
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	92.99
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	92.99
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	92.95
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	92.93
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	92.9
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	92.9
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	92.9
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	92.88
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	92.86
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	92.85
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	92.8
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	92.77
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	92.74
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	92.7
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	92.63
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	92.61
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	92.6
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	92.56
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	92.54
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	92.51
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	92.49
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	92.46
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	92.39
3pvs_A	447	Replication-associated recombination protein A; ma	92.36
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	92.34
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	92.26
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	92.24
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	92.19
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	92.18
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	92.14
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	92.14
1tue_A	212	Replication protein E1; helicase, replication, E1E	92.13
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	92.12
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	92.12
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	92.12
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	92.09
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	92.0
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	91.99
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	91.9
2og2_A	359	Putative signal recognition particle receptor; nuc	91.9
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	91.89
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	91.87
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	91.77
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	91.76
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	91.76
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	91.73
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	91.68
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	91.67
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	91.6
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	91.59
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	91.56
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	91.42
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	91.4
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	91.34
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	91.29
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	91.28
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	91.27
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	91.23
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	91.23
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	91.19
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	91.12
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	91.11
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	91.1
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	91.08
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	91.08
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	91.01
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	90.96
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	90.91
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	90.9
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	90.81
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	90.79
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	90.79
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	90.74
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	90.71
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	90.71
3of5_A	228	Dethiobiotin synthetase; structural genomics, cent	90.71
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	90.71
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	90.68
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	90.66
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	90.61
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	90.57
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	90.56
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	90.54
3kta_A	182	Chromosome segregation protein SMC; structural mai	90.52
3qf7_A	365	RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.	90.5
1via_A	175	Shikimate kinase; structural genomics, transferase	90.44
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	90.35
3auy_A	371	DNA double-strand break repair RAD50 ATPase; DNA r	90.2
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	90.18
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	90.15
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	90.14
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	90.08
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	89.84
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	89.74
1byi_A	224	Dethiobiotin synthase; biotin synthesis, cyclo-lig	89.72
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	89.71
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	89.7
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	89.68
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	89.62
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	89.59
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	89.49
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	89.43
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	89.43
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	89.37
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	89.3
2chq_A	319	Replication factor C small subunit; DNA-binding pr	89.28
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	89.24
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	89.2
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	89.2
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	89.2
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	89.17
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	89.12
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	89.12
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	89.05
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	89.04
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	89.01
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	88.95
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	88.94
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	88.88
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	88.82
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	88.81
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	88.74
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	88.68
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	88.62
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	88.62
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	88.61
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	88.53
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	88.44
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	88.43
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	88.4
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	88.39
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	88.35
2qgz_A	308	Helicase loader, putative primosome component; str	88.33
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	88.22
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	88.18
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	88.16
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	88.15
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	88.13
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	88.12
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	88.11
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	88.09
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	88.08
3qks_A	203	DNA double-strand break repair RAD50 ATPase; RECA-	88.0
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	87.93
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	87.92
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	87.91
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	87.85
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	87.81
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	87.81
2vli_A	183	Antibiotic resistance protein; transferase, tunica	87.79
3zq6_A	324	Putative arsenical pump-driving ATPase; tail-ancho	87.69
3qkt_A	339	DNA double-strand break repair RAD50 ATPase; RECA-	87.68
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	87.66
2r6a_A	454	DNAB helicase, replicative helicase; replication,	87.63
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	87.62
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	87.61
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	87.6
2ghi_A	260	Transport protein; multidrug resistance protein, M	87.55
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	87.53
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	87.5
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	87.42
1ihu_A	589	Arsenical pump-driving ATPase; aluminum fluoride,	87.42
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	87.36
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	87.35
1g3q_A	237	MIND ATPase, cell division inhibitor; alpha-beta-a	87.34
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	87.32
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	87.27
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	87.25
1g6h_A	257	High-affinity branched-chain amino acid transport	87.2
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	87.18
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	87.18
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	87.17
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	87.16
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	87.03
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	87.01
2woo_A	329	ATPase GET3; tail-anchored, membrane protein, targ	86.98
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	86.98
1sgw_A	214	Putative ABC transporter; structural genomics, P p	86.97
3bos_A	242	Putative DNA replication factor; P-loop containing	86.97
1ji0_A	240	ABC transporter; ATP binding protein, structural g	86.97
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	86.92
1hyq_A	263	MIND, cell division inhibitor (MIND-1); MINC, FTSZ	86.88
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	86.77
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	86.75
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	86.73
3nwn_A	359	Kinesin-like protein KIF9; motor domain, ADP, stru	86.71
3t0q_A	349	AGR253WP; kinesin, alpha and beta proteins, P-loop	86.64
1b0u_A	262	Histidine permease; ABC transporter, transport pro	86.6
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	86.53
1f9v_A	347	Kinesin-like protein KAR3; kinesin-related protein	86.36
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	86.3
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	86.26
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	86.15
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	86.14
3ug7_A	349	Arsenical pump-driving ATPase; tail-anchored, memb	85.98
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	85.96
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	85.92
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	85.91

>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=99.64  E-value=7.1e-16  Score=108.77  Aligned_cols=92  Identities=24%  Similarity=0.291  Sum_probs=79.3

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh---CCCeEEEEccchhHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI---KQKSAIFILPYISLVHEKY  120 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~---~~~~~~~i~P~~~l~~q~~  120 (138)
                      |.....+.+.+.++..++++|.++++.+.+ +++++.+|||+|||+++.+++++.+..   .+.+++|++|+++|+.|++
T Consensus        36 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~lil~Pt~~L~~q~~  115 (245)
T 3dkp_A           36 INSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIH  115 (245)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHCSCCSSSCCEEEECSSHHHHHHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHhhcccCCceEEEEeCCHHHHHHHH
Confidence            345566777777788899999999988887 999999999999999999999998864   3568999999999999999


Q ss_pred             HHHHHHhhhcCceeee
Q psy2029         121 QSLAKAAEEFKFYLEV  136 (138)
Q Consensus       121 ~~~~~~~~~~~~~v~~  136 (138)
                      +++++++...++.+..
T Consensus       116 ~~~~~~~~~~~~~~~~  131 (245)
T 3dkp_A          116 RELIKISEGTGFRIHM  131 (245)
T ss_dssp             HHHHHHTTTSCCCEEC
T ss_pred             HHHHHHhcccCceEEE
Confidence            9999998887776643

>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=99.63  E-value=6.5e-16  Score=110.44  Aligned_cols=92  Identities=11%  Similarity=0.128  Sum_probs=80.8

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh------CCCeEEEEccchhHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI------KQKSAIFILPYISLVH  117 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~------~~~~~~~i~P~~~l~~  117 (138)
                      |..+..+.+.+.++..++++|.++++.+.. +++++.+|||+|||+++.+++++.+..      .+.+++|++|+++|+.
T Consensus        61 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~lil~Pt~~La~  140 (262)
T 3ly5_A           61 VNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAM  140 (262)
T ss_dssp             CCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHH
T ss_pred             cCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceEEEEeCCHHHHH
Confidence            456777888888888899999999988777 999999999999999999999998875      4678999999999999


Q ss_pred             HHHHHHHHHhhhcCceeee
Q psy2029         118 EKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus       118 q~~~~~~~~~~~~~~~v~~  136 (138)
                      |+++.+++++...+..+..
T Consensus       141 q~~~~~~~~~~~~~~~~~~  159 (262)
T 3ly5_A          141 QTFGVLKELMTHHVHTYGL  159 (262)
T ss_dssp             HHHHHHHHHTTTCCSCEEE
T ss_pred             HHHHHHHHHHhhcCceEEE
Confidence            9999999998887766543

>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=99.63  E-value=1e-15  Score=107.95  Aligned_cols=92  Identities=12%  Similarity=0.068  Sum_probs=81.0

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh-------CCCeEEEEccchhHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI-------KQKSAIFILPYISLV  116 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~-------~~~~~~~i~P~~~l~  116 (138)
                      |..+..+.+.+.++..++++|.++++.+.+ +++++.+|||+|||+++.+++++.+..       .+.+++|++|+++|+
T Consensus        36 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~~~~~~lil~Pt~~L~  115 (242)
T 3fe2_A           36 FPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELA  115 (242)
T ss_dssp             CCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCCCCTTCCCSEEEECSSHHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhccccccCCCCEEEEEeCcHHHH
Confidence            567778888888888899999999988877 999999999999999999999998874       356899999999999


Q ss_pred             HHHHHHHHHHhhhcCceeee
Q psy2029         117 HEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus       117 ~q~~~~~~~~~~~~~~~v~~  136 (138)
                      .|+++.++++....++.+..
T Consensus       116 ~Q~~~~~~~~~~~~~~~~~~  135 (242)
T 3fe2_A          116 QQVQQVAAEYCRACRLKSTC  135 (242)
T ss_dssp             HHHHHHHHHHHHHTTCCEEE
T ss_pred             HHHHHHHHHHHhhcCceEEE
Confidence            99999999998887776653

>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=99.60  E-value=3.9e-15  Score=105.66  Aligned_cols=92  Identities=11%  Similarity=0.060  Sum_probs=80.2

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC--CCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~--~~~~~~i~P~~~l~~q~~~  121 (138)
                      |..+..+.+.+.++..++++|.++++.+.+ +++++.+|||+|||+++.+++++.+...  +.+++|++|+++|+.|+++
T Consensus        50 l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~~~~~~lil~Ptr~L~~q~~~  129 (249)
T 3ber_A           50 VTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTPTRELAFQISE  129 (249)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCCSSCEEEECSSHHHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCCCCceEEEEeCCHHHHHHHHH
Confidence            456777788888888899999999988887 9999999999999999999999988763  4579999999999999999


Q ss_pred             HHHHHhhhcCceeee
Q psy2029         122 SLAKAAEEFKFYLEV  136 (138)
Q Consensus       122 ~~~~~~~~~~~~v~~  136 (138)
                      .++++....++++..
T Consensus       130 ~~~~~~~~~~~~~~~  144 (249)
T 3ber_A          130 QFEALGSSIGVQSAV  144 (249)
T ss_dssp             HHHHHHGGGTCCEEE
T ss_pred             HHHHHhccCCeeEEE
Confidence            999998877776543

>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=4e-15  Score=104.37  Aligned_cols=92  Identities=17%  Similarity=0.246  Sum_probs=80.0

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh------CCCeEEEEccchhHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI------KQKSAIFILPYISLVH  117 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~------~~~~~~~i~P~~~l~~  117 (138)
                      |.....+.+.+.++..++++|.++++.+.+ +++++.+|||+|||+++.+++++.+..      .+.+++|++|+++|+.
T Consensus        32 l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~lil~Pt~~L~~  111 (236)
T 2pl3_A           32 LSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELAY  111 (236)
T ss_dssp             CCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceEEEEeCCHHHHH
Confidence            456778888888888899999999988877 999999999999999999999988753      3578999999999999


Q ss_pred             HHHHHHHHHhhhcCceeee
Q psy2029         118 EKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus       118 q~~~~~~~~~~~~~~~v~~  136 (138)
                      |+++.+++++...++.+..
T Consensus       112 q~~~~~~~~~~~~~~~~~~  130 (236)
T 2pl3_A          112 QTFEVLRKVGKNHDFSAGL  130 (236)
T ss_dssp             HHHHHHHHHTTTSSCCEEE
T ss_pred             HHHHHHHHHhCCCCeeEEE
Confidence            9999999998776666543

>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=99.59  E-value=3.7e-15  Score=103.60  Aligned_cols=93  Identities=13%  Similarity=0.109  Sum_probs=80.6

Q ss_pred             hhHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHH
Q psy2029          44 SLVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKY  120 (138)
Q Consensus        44 aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~  120 (138)
                      .|.....+.+.+.++..++++|.++++.+.+ +++++.+|||+|||+++.+++++.+..  .+.++++++|+++|+.|.+
T Consensus        20 ~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~   99 (224)
T 1qde_A           20 ELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQ   99 (224)
T ss_dssp             TCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHH
T ss_pred             CCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccCCCceEEEEECCHHHHHHHH
Confidence            3557778888888888899999999988877 999999999999999999999988764  3468999999999999999


Q ss_pred             HHHHHHhhhcCceeee
Q psy2029         121 QSLAKAAEEFKFYLEV  136 (138)
Q Consensus       121 ~~~~~~~~~~~~~v~~  136 (138)
                      +.+++++...++.+..
T Consensus       100 ~~~~~~~~~~~~~~~~  115 (224)
T 1qde_A          100 KVVMALAFHMDIKVHA  115 (224)
T ss_dssp             HHHHHHTTTSCCCEEE
T ss_pred             HHHHHHhcccCceEEE
Confidence            9999998777766543

>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=99.59  E-value=1.8e-15  Score=130.18  Aligned_cols=98  Identities=21%  Similarity=0.353  Sum_probs=84.9

Q ss_pred             cchhhhHHHHHHHHHHHHHhhhhhhhhHHHhhhhc--cceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHH
Q psy2029          40 LPYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIQN--KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLV  116 (138)
Q Consensus        40 ~P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~--~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~  116 (138)
                      .|..+|.+..++.+....+..+.++|.++++.+.+  +|+++++|||+|||+++++++++.+.. .+.+++|++|++||+
T Consensus       906 lp~s~L~~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~~~~kavyi~P~raLa  985 (1724)
T 4f92_B          906 LPVSALRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITPMEALA  985 (1724)
T ss_dssp             CBGGGSCCHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHCTTCCEEEECSCHHHH
T ss_pred             CCcccccCHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhCCCCEEEEEcChHHHH
Confidence            47778888888888776677899999999987754  899999999999999999999999886 467999999999999


Q ss_pred             HHHHHHHHHHhh-hcCceeeec
Q psy2029         117 HEKYQSLAKAAE-EFKFYLEVL  137 (138)
Q Consensus       117 ~q~~~~~~~~~~-~~~~~v~~~  137 (138)
                      +|+++++++.+. ..|++|..+
T Consensus       986 ~q~~~~~~~~f~~~~g~~V~~l 1007 (1724)
T 4f92_B          986 EQVYMDWYEKFQDRLNKKVVLL 1007 (1724)
T ss_dssp             HHHHHHHHHHHTTTSCCCEEEC
T ss_pred             HHHHHHHHHHhchhcCCEEEEE
Confidence            999999988665 468888765

>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=99.58  E-value=3.9e-15  Score=102.18  Aligned_cols=91  Identities=13%  Similarity=0.130  Sum_probs=78.1

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~  121 (138)
                      |.++..+.+.+.++..++++|.++++.+.+ +++++.+|||+|||+++.+++++.+..  .+.+++|++|+++|++|.++
T Consensus        10 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~   89 (206)
T 1vec_A           10 LKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQ   89 (206)
T ss_dssp             CCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHHHHHHHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhcccCCCeeEEEEeCcHHHHHHHHH
Confidence            456777888888888899999999988887 999999999999999999999987654  34689999999999999999


Q ss_pred             HHHHHhhhc-Cceee
Q psy2029         122 SLAKAAEEF-KFYLE  135 (138)
Q Consensus       122 ~~~~~~~~~-~~~v~  135 (138)
                      .++++.... ++.+.
T Consensus        90 ~~~~~~~~~~~~~~~  104 (206)
T 1vec_A           90 ICIQVSKHMGGAKVM  104 (206)
T ss_dssp             HHHHHTTTSSSCCEE
T ss_pred             HHHHHHhhcCCceEE
Confidence            999998766 55543

>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=99.58  E-value=6.6e-15  Score=102.76  Aligned_cols=83  Identities=13%  Similarity=0.079  Sum_probs=72.9

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--------CCCeEEEEccchhH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--------KQKSAIFILPYISL  115 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--------~~~~~~~i~P~~~l  115 (138)
                      +..+..+.+.+.++..++++|.++++.+.+ +++++.+|||+|||+++.++++..+..        .+.+++|++|+++|
T Consensus        27 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~~~~~lil~Pt~~L  106 (228)
T 3iuy_A           27 QYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTREL  106 (228)
T ss_dssp             TCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC---------CCCSEEEECSSHHH
T ss_pred             cCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchhhccCCCcEEEEeCCHHH
Confidence            445677888888888899999999988877 999999999999999999999987753        45789999999999


Q ss_pred             HHHHHHHHHHHh
Q psy2029         116 VHEKYQSLAKAA  127 (138)
Q Consensus       116 ~~q~~~~~~~~~  127 (138)
                      +.|+++.++++.
T Consensus       107 ~~q~~~~~~~~~  118 (228)
T 3iuy_A          107 ALHVEAECSKYS  118 (228)
T ss_dssp             HHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhc
Confidence            999999999975

>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=99.58  E-value=4.8e-15  Score=103.82  Aligned_cols=91  Identities=12%  Similarity=0.107  Sum_probs=78.6

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~  121 (138)
                      |.....+.+.+.++..++++|.++++.+.+ +++++.+|||+|||+++.+++++.+..  .+.+++|++|+++|++|+++
T Consensus        31 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~  110 (230)
T 2oxc_A           31 LSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHS  110 (230)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEeCCHHHHHHHHH
Confidence            456778888888888899999999988887 999999999999999999999988754  35789999999999999999


Q ss_pred             HHHHHhhhc-Cceee
Q psy2029         122 SLAKAAEEF-KFYLE  135 (138)
Q Consensus       122 ~~~~~~~~~-~~~v~  135 (138)
                      .++++.... ++++.
T Consensus       111 ~~~~~~~~~~~~~~~  125 (230)
T 2oxc_A          111 VITAIGIKMEGLECH  125 (230)
T ss_dssp             HHHHHTTTSTTCCEE
T ss_pred             HHHHHhcccCCceEE
Confidence            999997655 55554

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.56  E-value=4.5e-15  Score=103.07  Aligned_cols=86  Identities=15%  Similarity=0.075  Sum_probs=75.7

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~  121 (138)
                      |.....+.+.+.+...++++|.++++.+.+ +++++.+|||+|||+++.+++++.+..  .+.+++|++|+++|++|+++
T Consensus        11 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~   90 (219)
T 1q0u_A           11 FQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQIYH   90 (219)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhCcCCceEEEEcCcHHHHHHHHH
Confidence            456777888888888899999999988877 999999999999999999999988764  34689999999999999999


Q ss_pred             HHHHHhhhc
Q psy2029         122 SLAKAAEEF  130 (138)
Q Consensus       122 ~~~~~~~~~  130 (138)
                      .++++....
T Consensus        91 ~~~~~~~~~   99 (219)
T 1q0u_A           91 ETLKITKFC   99 (219)
T ss_dssp             HHHHHHTTS
T ss_pred             HHHHHhhhc
Confidence            999998765

>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=99.56  E-value=8.9e-15  Score=101.51  Aligned_cols=91  Identities=13%  Similarity=0.130  Sum_probs=78.0

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC--CCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~--~~~~~~i~P~~~l~~q~~~  121 (138)
                      |.++..+.+.+.++..++++|.++++.+.+ +++++.+|||+|||+++.+++++.+...  +.+++|++|+++|+.|.++
T Consensus        21 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~  100 (220)
T 1t6n_A           21 LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISK  100 (220)
T ss_dssp             CCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEeCCHHHHHHHHH
Confidence            557778888888888899999999988877 9999999999999999999999876542  3589999999999999999


Q ss_pred             HHHHHhhhc-Cceee
Q psy2029         122 SLAKAAEEF-KFYLE  135 (138)
Q Consensus       122 ~~~~~~~~~-~~~v~  135 (138)
                      +++++.... ++++.
T Consensus       101 ~~~~~~~~~~~~~v~  115 (220)
T 1t6n_A          101 EYERFSKYMPNVKVA  115 (220)
T ss_dssp             HHHHHTTTSTTCCEE
T ss_pred             HHHHHHhhCCCceEE
Confidence            999997665 55554

>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=99.55  E-value=5.4e-15  Score=104.02  Aligned_cols=91  Identities=14%  Similarity=0.142  Sum_probs=78.9

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~  121 (138)
                      |.....+.+.+.++..++++|.++++.+.+ +++++.+|||+|||+++.+++++.+..  .+.+++|++|+++|+.|+++
T Consensus        37 l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~  116 (237)
T 3bor_A           37 LKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQK  116 (237)
T ss_dssp             CCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEECcHHHHHHHHH
Confidence            556778888888888899999999988877 899999999999999999999987754  35689999999999999999


Q ss_pred             HHHHHhhhcCceee
Q psy2029         122 SLAKAAEEFKFYLE  135 (138)
Q Consensus       122 ~~~~~~~~~~~~v~  135 (138)
                      .+++++...++.+.
T Consensus       117 ~~~~~~~~~~~~~~  130 (237)
T 3bor_A          117 VILALGDYMGATCH  130 (237)
T ss_dssp             HHHHHTTTTTCCEE
T ss_pred             HHHHHhhhcCceEE
Confidence            99999876665543

>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=99.55  E-value=1.1e-14  Score=110.71  Aligned_cols=91  Identities=15%  Similarity=0.154  Sum_probs=80.5

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC-------CCeEEEEccchhHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK-------QKSAIFILPYISLV  116 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~-------~~~~~~i~P~~~l~  116 (138)
                      |.....+.+.+.++..++++|.++++.+.+ +++++.+|||+|||+++++++++.+...       +.++++++|+++|+
T Consensus        63 l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~~~~lil~PtreLa  142 (434)
T 2db3_A           63 LRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELA  142 (434)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTCCSEEEECSSHHHH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccccccCCccEEEEecCHHHH
Confidence            566788888888888999999999998887 9999999999999999999999988753       45899999999999


Q ss_pred             HHHHHHHHHHhhhcCceee
Q psy2029         117 HEKYQSLAKAAEEFKFYLE  135 (138)
Q Consensus       117 ~q~~~~~~~~~~~~~~~v~  135 (138)
                      .|+++++++++...++++.
T Consensus       143 ~Q~~~~~~~~~~~~~~~~~  161 (434)
T 2db3_A          143 IQIFNEARKFAFESYLKIG  161 (434)
T ss_dssp             HHHHHHHHHHTTTSSCCCC
T ss_pred             HHHHHHHHHHhccCCcEEE
Confidence            9999999999877666543

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.55  E-value=1.5e-14  Score=108.40  Aligned_cols=91  Identities=11%  Similarity=0.090  Sum_probs=79.4

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCC--------------------
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQ--------------------  103 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~--------------------  103 (138)
                      |...+.+.+...++..++++|.++++.+.+ +++++.+|||+|||+++.+++++.+...+                    
T Consensus        22 l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (417)
T 2i4i_A           22 MGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQY  101 (417)
T ss_dssp             CCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHHHCBTTBSCSBC
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhccccccccccccCC
Confidence            557788888888888999999999998887 99999999999999999999998876422                    


Q ss_pred             CeEEEEccchhHHHHHHHHHHHHhhhcCceee
Q psy2029         104 KSAIFILPYISLVHEKYQSLAKAAEEFKFYLE  135 (138)
Q Consensus       104 ~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~  135 (138)
                      .++++++|+++|+.|+++.++++....++++.
T Consensus       102 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~  133 (417)
T 2i4i_A          102 PISLVLAPTRELAVQIYEEARKFSYRSRVRPC  133 (417)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHTTSSCCEE
T ss_pred             ccEEEECCcHHHHHHHHHHHHHHhCcCCceEE
Confidence            57999999999999999999999877766554

>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=99.54  E-value=1.2e-14  Score=125.14  Aligned_cols=81  Identities=25%  Similarity=0.305  Sum_probs=72.2

Q ss_pred             HHhhhhhhhhHHHhhhhc--cceEEEeecCCCchHhHHHHHHHHHHh----------CCCeEEEEccchhHHHHHHHHHH
Q psy2029          57 AEEFKFYLEGKCLEMIQN--KNCVLSIPTSGGKTLVGEILIMKELKI----------KQKSAIFILPYISLVHEKYQSLA  124 (138)
Q Consensus        57 ~~~~~~~~Q~~~~~~~~~--~~~ii~~ptg~GKt~~~~~~~l~~~~~----------~~~~~~~i~P~~~l~~q~~~~~~  124 (138)
                      +++.+.++|.++++.+.+  +|+++++|||+|||++|++++++.+..          .+.+++|++|++||++|++++|+
T Consensus        76 g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~kALa~e~~~~l~  155 (1724)
T 4f92_B           76 GFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFG  155 (1724)
T ss_dssp             TCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSSHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCHHHHHHHHHHHHH
Confidence            355688999999987654  999999999999999999999999864          24689999999999999999999


Q ss_pred             HHhhhcCceeeec
Q psy2029         125 KAAEEFKFYLEVL  137 (138)
Q Consensus       125 ~~~~~~~~~v~~~  137 (138)
                      +.+.+.|++|.++
T Consensus       156 ~~~~~~gi~V~~~  168 (1724)
T 4f92_B          156 KRLATYGITVAEL  168 (1724)
T ss_dssp             HHHTTTTCCEEEC
T ss_pred             HHHhhCCCEEEEE
Confidence            9999999998875

>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=99.53  E-value=2.1e-14  Score=104.55  Aligned_cols=86  Identities=10%  Similarity=0.133  Sum_probs=75.7

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc---cceEEEeecCCCchHhHHHHHHHHHHhC--CCeEEEEccchhHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN---KNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEK  119 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~---~~~ii~~ptg~GKt~~~~~~~l~~~~~~--~~~~~~i~P~~~l~~q~  119 (138)
                      |.....+.+...++..++++|..+++.+..   +++++.+|||+|||+++.+++++.+...  +.+++|++|+++|+.|+
T Consensus        99 l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~lil~PtreLa~Q~  178 (300)
T 3fmo_B           99 LKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQT  178 (300)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccCCCceEEEEcCcHHHHHHH
Confidence            567788888888888999999999987764   7999999999999999999999988653  35899999999999999


Q ss_pred             HHHHHHHhhhc
Q psy2029         120 YQSLAKAAEEF  130 (138)
Q Consensus       120 ~~~~~~~~~~~  130 (138)
                      ++.++++....
T Consensus       179 ~~~~~~l~~~~  189 (300)
T 3fmo_B          179 GKVIEQMGKFY  189 (300)
T ss_dssp             HHHHHHHTTTS
T ss_pred             HHHHHHHHhhC
Confidence            99999987654

>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=99.52  E-value=5.7e-15  Score=104.65  Aligned_cols=88  Identities=14%  Similarity=0.083  Sum_probs=74.3

Q ss_pred             HHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC-----------CCeEEEEccchhH
Q psy2029          48 EKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK-----------QKSAIFILPYISL  115 (138)
Q Consensus        48 q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~-----------~~~~~~i~P~~~l  115 (138)
                      ...+.+.+.++..++++|.++++.+.+ +++++.+|||+|||+++.+++++.+...           +.+++|++|+++|
T Consensus        33 ~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~~~~lil~Pt~~L  112 (253)
T 1wrb_A           33 TIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTREL  112 (253)
T ss_dssp             STTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHH
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccCCceEEEEECCHHH
Confidence            444556666777889999999988887 9999999999999999999999988642           2589999999999


Q ss_pred             HHHHHHHHHHHhhhcCceee
Q psy2029         116 VHEKYQSLAKAAEEFKFYLE  135 (138)
Q Consensus       116 ~~q~~~~~~~~~~~~~~~v~  135 (138)
                      +.|+++.++++....++.+.
T Consensus       113 ~~q~~~~~~~~~~~~~~~~~  132 (253)
T 1wrb_A          113 AIQILSESQKFSLNTPLRSC  132 (253)
T ss_dssp             HHHHHHHHHHHHTTSSCCEE
T ss_pred             HHHHHHHHHHHhccCCceEE
Confidence            99999999999877666543

>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=99.50  E-value=4.2e-14  Score=96.97  Aligned_cols=85  Identities=20%  Similarity=0.189  Sum_probs=74.5

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh-----CCCeEEEEccchhHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI-----KQKSAIFILPYISLVHE  118 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~-----~~~~~~~i~P~~~l~~q  118 (138)
                      |.+...+.+.+.+...++++|.++++.+.+ +++++.+|||+|||+++.+++++.+..     .+.+++|++|+++|+.|
T Consensus         8 l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~~~L~~q   87 (207)
T 2gxq_A            8 LKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQ   87 (207)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSSHHHHHH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEECCHHHHHH
Confidence            446677888888888899999999988887 999999999999999999999988753     35789999999999999


Q ss_pred             HHHHHHHHhhh
Q psy2029         119 KYQSLAKAAEE  129 (138)
Q Consensus       119 ~~~~~~~~~~~  129 (138)
                      .++.++++...
T Consensus        88 ~~~~~~~~~~~   98 (207)
T 2gxq_A           88 VASELTAVAPH   98 (207)
T ss_dssp             HHHHHHHHCTT
T ss_pred             HHHHHHHHhhc
Confidence            99999998754

>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=99.49  E-value=7.4e-14  Score=101.69  Aligned_cols=86  Identities=15%  Similarity=0.150  Sum_probs=75.5

Q ss_pred             HHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHH
Q psy2029          47 HEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK  125 (138)
Q Consensus        47 ~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~  125 (138)
                      +++.+.+.+.++..++++|.++++.+.+ +++++.+|||+|||+++.+++++.    +.++++++|+++|+.|.++.+++
T Consensus         3 ~~i~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~----~~~~liv~P~~~L~~q~~~~~~~   78 (337)
T 2z0m_A            3 EKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL----GMKSLVVTPTRELTRQVASHIRD   78 (337)
T ss_dssp             HHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH----TCCEEEECSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhh----cCCEEEEeCCHHHHHHHHHHHHH
Confidence            5667788888888899999999988877 999999999999999998888763    77899999999999999999999


Q ss_pred             HhhhcCceeee
Q psy2029         126 AAEEFKFYLEV  136 (138)
Q Consensus       126 ~~~~~~~~v~~  136 (138)
                      +....+..+..
T Consensus        79 ~~~~~~~~~~~   89 (337)
T 2z0m_A           79 IGRYMDTKVAE   89 (337)
T ss_dssp             HTTTSCCCEEE
T ss_pred             HhhhcCCcEEE
Confidence            98777766543

>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=99.49  E-value=5e-14  Score=105.59  Aligned_cols=92  Identities=14%  Similarity=0.194  Sum_probs=80.6

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~  121 (138)
                      |..+..+.+.+.++..++++|.++++.+.+ +++++.+|||+|||+++.+++++.+..  .+.++++++|+++|+.|+++
T Consensus        44 l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~Pt~~L~~q~~~  123 (410)
T 2j0s_A           44 LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQK  123 (410)
T ss_dssp             CCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhccCCceEEEEcCcHHHHHHHHH
Confidence            557888888888888899999999988887 999999999999999999999987653  45799999999999999999


Q ss_pred             HHHHHhhhcCceeee
Q psy2029         122 SLAKAAEEFKFYLEV  136 (138)
Q Consensus       122 ~~~~~~~~~~~~v~~  136 (138)
                      .++++....++.+..
T Consensus       124 ~~~~~~~~~~~~~~~  138 (410)
T 2j0s_A          124 GLLALGDYMNVQCHA  138 (410)
T ss_dssp             HHHHHTTTTTCCEEE
T ss_pred             HHHHHhccCCeEEEE
Confidence            999998777766543

>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=99.48  E-value=7.4e-14  Score=104.24  Aligned_cols=93  Identities=15%  Similarity=0.133  Sum_probs=80.5

Q ss_pred             hhHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHH
Q psy2029          44 SLVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKY  120 (138)
Q Consensus        44 aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~  120 (138)
                      .|..+..+.+.+.++..++++|.++++.+.+ +++++.+|||+|||+++.+++++.+..  .+.++++++|+++|+.|.+
T Consensus        27 ~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~  106 (400)
T 1s2m_A           27 YLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTS  106 (400)
T ss_dssp             CCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcCCHHHHHHHH
Confidence            3557788888888888899999999988877 899999999999999999999987654  3568999999999999999


Q ss_pred             HHHHHHhhhcCceeee
Q psy2029         121 QSLAKAAEEFKFYLEV  136 (138)
Q Consensus       121 ~~~~~~~~~~~~~v~~  136 (138)
                      +.+++++...++.+..
T Consensus       107 ~~~~~~~~~~~~~~~~  122 (400)
T 1s2m_A          107 QVVRTLGKHCGISCMV  122 (400)
T ss_dssp             HHHHHHTTTTTCCEEE
T ss_pred             HHHHHHhcccCceEEE
Confidence            9999998877776543

>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=99.47  E-value=5.2e-14  Score=104.62  Aligned_cols=93  Identities=13%  Similarity=0.109  Sum_probs=81.4

Q ss_pred             hhHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHH
Q psy2029          44 SLVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKY  120 (138)
Q Consensus        44 aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~  120 (138)
                      .|..++.+.+...++..++++|.++++.+.+ +++++.+|||+|||+++.+++++.+..  .+.++++++|+++|+.|.+
T Consensus        27 ~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L~~q~~  106 (394)
T 1fuu_A           27 ELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQ  106 (394)
T ss_dssp             CCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHH
T ss_pred             CCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEEcCCHHHHHHHH
Confidence            4567888888888888899999999988877 999999999999999999999987764  3569999999999999999


Q ss_pred             HHHHHHhhhcCceeee
Q psy2029         121 QSLAKAAEEFKFYLEV  136 (138)
Q Consensus       121 ~~~~~~~~~~~~~v~~  136 (138)
                      +.+++++...++.+..
T Consensus       107 ~~~~~~~~~~~~~~~~  122 (394)
T 1fuu_A          107 KVVMALAFHMDIKVHA  122 (394)
T ss_dssp             HHHHHHTTTSCCCEEE
T ss_pred             HHHHHHhccCCeeEEE
Confidence            9999998877776653

>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=99.46  E-value=1.3e-13  Score=102.43  Aligned_cols=91  Identities=13%  Similarity=0.132  Sum_probs=77.8

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~  121 (138)
                      |..+..+.+.+.++..++++|.++++.+.+ +++++.+|||+|||+++.+++++.+..  .+.++++++|+++|++|.++
T Consensus        15 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L~~q~~~   94 (391)
T 1xti_A           15 LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISK   94 (391)
T ss_dssp             CCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCCHHHHHHHHH
Confidence            456777888888888899999999988877 999999999999999999999887654  34689999999999999999


Q ss_pred             HHHHHhhhc-Cceee
Q psy2029         122 SLAKAAEEF-KFYLE  135 (138)
Q Consensus       122 ~~~~~~~~~-~~~v~  135 (138)
                      .++++.... ++++.
T Consensus        95 ~~~~~~~~~~~~~~~  109 (391)
T 1xti_A           95 EYERFSKYMPNVKVA  109 (391)
T ss_dssp             HHHHHTTTCTTCCEE
T ss_pred             HHHHHHhhCCCeEEE
Confidence            999997665 55554

>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=99.46  E-value=1.4e-13  Score=103.05  Aligned_cols=93  Identities=12%  Similarity=0.128  Sum_probs=80.5

Q ss_pred             hhHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHH
Q psy2029          44 SLVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKY  120 (138)
Q Consensus        44 aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~  120 (138)
                      .+.....+.+.+.+...++++|.++++.+.+ +++++.+|||+|||+++.+++++.+..  .+.++++++|+++|+.|.+
T Consensus        46 ~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~  125 (414)
T 3eiq_A           46 NLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQ  125 (414)
T ss_dssp             CCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHH
T ss_pred             CCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcCCceeEEEEeChHHHHHHHH
Confidence            3556777888888888899999999988877 899999999999999999999987765  4578999999999999999


Q ss_pred             HHHHHHhhhcCceeee
Q psy2029         121 QSLAKAAEEFKFYLEV  136 (138)
Q Consensus       121 ~~~~~~~~~~~~~v~~  136 (138)
                      +.+++++...+..+..
T Consensus       126 ~~~~~~~~~~~~~~~~  141 (414)
T 3eiq_A          126 KVVMALGDYMGASCHA  141 (414)
T ss_dssp             HHHHHHGGGSCCCEEE
T ss_pred             HHHHHHhcccCceEEE
Confidence            9999998777766543

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.45  E-value=2.2e-13  Score=102.48  Aligned_cols=84  Identities=21%  Similarity=0.188  Sum_probs=68.4

Q ss_pred             HHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhc
Q psy2029          52 SLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEF  130 (138)
Q Consensus        52 ~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~  130 (138)
                      .+.+.....++++|.++++.+.+ +++++.+|||+|||+++++++++.+ ..+.+++|++|+++|+.|+++.+++++. .
T Consensus        13 ~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~-~   90 (414)
T 3oiy_A           13 FFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA-RKGKKSALVFPTVTLVKQTLERLQKLAD-E   90 (414)
T ss_dssp             HHHHHHSSCCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHH-TTTCCEEEEESSHHHHHHHHHHHHHHCC-S
T ss_pred             HHHHhcCCCCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHh-cCCCEEEEEECCHHHHHHHHHHHHHHcc-C
Confidence            33333333578999999988887 9999999999999998888777654 4578999999999999999999999876 6


Q ss_pred             Cceeeec
Q psy2029         131 KFYLEVL  137 (138)
Q Consensus       131 ~~~v~~~  137 (138)
                      |+++..+
T Consensus        91 ~~~v~~~   97 (414)
T 3oiy_A           91 KVKIFGF   97 (414)
T ss_dssp             SCCEEEC
T ss_pred             CceEEEE
Confidence            6666543

>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=99.44  E-value=2.1e-13  Score=101.18  Aligned_cols=91  Identities=13%  Similarity=0.174  Sum_probs=77.7

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc---cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN---KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEK  119 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~---~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~  119 (138)
                      |.....+.+.+.++..++++|.++++.+.+   +++++.+|||+|||+++.+++++.+..  .+.++++++|+++|+.|.
T Consensus        12 l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~   91 (395)
T 3pey_A           12 LAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELARQT   91 (395)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEECCCHHHHHHH
Confidence            456778888888888999999999977654   789999999999999999999987764  356899999999999999


Q ss_pred             HHHHHHHhhhcCceee
Q psy2029         120 YQSLAKAAEEFKFYLE  135 (138)
Q Consensus       120 ~~~~~~~~~~~~~~v~  135 (138)
                      ++.++++....++.+.
T Consensus        92 ~~~~~~~~~~~~~~~~  107 (395)
T 3pey_A           92 LEVVQEMGKFTKITSQ  107 (395)
T ss_dssp             HHHHHHHTTTSCCCEE
T ss_pred             HHHHHHHhcccCeeEE
Confidence            9999998876665543

>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=99.44  E-value=1.6e-13  Score=110.02  Aligned_cols=92  Identities=26%  Similarity=0.423  Sum_probs=76.9

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhh-hhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEM-IQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQS  122 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~-~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~  122 (138)
                      |.....+.+.+.++..++++|.++++. +.+ +++++++|||+|||+++.+++++.+...+.+++|++|+++|+.|++++
T Consensus         8 l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~~l~i~P~raLa~q~~~~   87 (720)
T 2zj8_A            8 VDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPLKALAEEKFQE   87 (720)
T ss_dssp             SCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHHCSEEEEECSSGGGHHHHHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhCCCEEEEEcCcHHHHHHHHHH
Confidence            345566677777777899999999976 666 999999999999999999999988876688999999999999999999


Q ss_pred             HHHHhhhcCceeeec
Q psy2029         123 LAKAAEEFKFYLEVL  137 (138)
Q Consensus       123 ~~~~~~~~~~~v~~~  137 (138)
                      ++++ .+.|++|..+
T Consensus        88 ~~~l-~~~g~~v~~~  101 (720)
T 2zj8_A           88 FQDW-EKIGLRVAMA  101 (720)
T ss_dssp             TGGG-GGGTCCEEEE
T ss_pred             HHHH-HhcCCEEEEe
Confidence            9644 4557776553

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.43  E-value=2.7e-13  Score=108.61  Aligned_cols=92  Identities=23%  Similarity=0.292  Sum_probs=76.9

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhh-hhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEM-IQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQS  122 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~-~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~  122 (138)
                      |.....+.+.+.++..++++|.++++. +.+ +++++++|||+|||+++.+++++.+...+.+++|++|+++|+.|++++
T Consensus        15 l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~il~i~P~r~La~q~~~~   94 (715)
T 2va8_A           15 LPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAIYVTPLRALTNEKYLT   94 (715)
T ss_dssp             SCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCSEEEEECSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHCCCeEEEEeCcHHHHHHHHHH
Confidence            345666667777777899999999977 555 999999999999999999999998876688999999999999999999


Q ss_pred             HHHHhhhcCceeeec
Q psy2029         123 LAKAAEEFKFYLEVL  137 (138)
Q Consensus       123 ~~~~~~~~~~~v~~~  137 (138)
                      ++ .+...|++|..+
T Consensus        95 ~~-~~~~~g~~v~~~  108 (715)
T 2va8_A           95 FK-DWELIGFKVAMT  108 (715)
T ss_dssp             HG-GGGGGTCCEEEC
T ss_pred             HH-HhhcCCCEEEEE
Confidence            95 445567776543

>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=99.43  E-value=2.8e-13  Score=99.58  Aligned_cols=91  Identities=16%  Similarity=0.141  Sum_probs=78.0

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc--cceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN--KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~--~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~~q~~~  121 (138)
                      |.++..+.+.+.+...+.++|.++++.+.+  +++++.+|||+|||+++.+++++.+.. .+.++++++|+++|+.|.++
T Consensus        13 l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~   92 (367)
T 1hv8_A           13 LSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQVAD   92 (367)
T ss_dssp             CCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHHHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhcccCCCcEEEEcCCHHHHHHHHH
Confidence            557788888888888899999999977654  689999999999999999998887654 45789999999999999999


Q ss_pred             HHHHHhhhcCceee
Q psy2029         122 SLAKAAEEFKFYLE  135 (138)
Q Consensus       122 ~~~~~~~~~~~~v~  135 (138)
                      .+++++...++.+.
T Consensus        93 ~~~~~~~~~~~~v~  106 (367)
T 1hv8_A           93 EIESLKGNKNLKIA  106 (367)
T ss_dssp             HHHHHHCSSCCCEE
T ss_pred             HHHHHhCCCCceEE
Confidence            99999877666554

>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=99.43  E-value=2.3e-13  Score=106.03  Aligned_cols=84  Identities=18%  Similarity=0.156  Sum_probs=72.1

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhh--c-cceEEEeecCCCchHhHHHHHHHHHHhCC------CeEEEEccchhH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQ--N-KNCVLSIPTSGGKTLVGEILIMKELKIKQ------KSAIFILPYISL  115 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~--~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~------~~~~~i~P~~~l  115 (138)
                      |.....+.+.+.++..++++|.++++.+.  + +++++.+|||+|||+++++++++.+...+      .+++|++|+++|
T Consensus        79 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lil~Ptr~L  158 (563)
T 3i5x_A           79 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDL  158 (563)
T ss_dssp             SCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccccccCCeeEEEEcCcHHH
Confidence            44566677777777789999999997776  4 89999999999999999999999987632      489999999999


Q ss_pred             HHHHHHHHHHHhh
Q psy2029         116 VHEKYQSLAKAAE  128 (138)
Q Consensus       116 ~~q~~~~~~~~~~  128 (138)
                      +.|+++.++++..
T Consensus       159 a~Q~~~~~~~~~~  171 (563)
T 3i5x_A          159 ALQIEAEVKKIHD  171 (563)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999999764

>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=99.41  E-value=1.9e-13  Score=96.35  Aligned_cols=58  Identities=17%  Similarity=0.144  Sum_probs=50.8

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh-------cCCeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI-------KQKSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-------~~~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      ++|+|++++||||+|||++|.++++.++..       .+.++++++|+++|..|.++.+.++...
T Consensus        64 ~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~  128 (242)
T 3fe2_A           64 LSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRA  128 (242)
T ss_dssp             HHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHHHH
T ss_pred             hCCCCEEEECCCcCHHHHHHHHHHHHHHHhccccccCCCCEEEEEeCcHHHHHHHHHHHHHHHhh
Confidence            468899999999999999999999987763       3568999999999999999999887544

>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=99.41  E-value=4.9e-13  Score=99.84  Aligned_cols=87  Identities=11%  Similarity=0.145  Sum_probs=75.3

Q ss_pred             hhHHHHHHHHHHHHHhhhhhhhhHHHhhhhc---cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHH
Q psy2029          44 SLVHEKYQSLAKAAEEFKFYLEGKCLEMIQN---KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHE  118 (138)
Q Consensus        44 aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~---~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q  118 (138)
                      .|..+..+.+.+.++..++++|.++++.+.+   +++++.+|||+|||+++.+++++.+..  .+.+++|++|+++|+.|
T Consensus        31 ~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q  110 (412)
T 3fht_A           31 RLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQ  110 (412)
T ss_dssp             TCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHH
T ss_pred             CCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhcCCCCCEEEECCCHHHHHH
Confidence            4567888888888888999999999977654   789999999999999999999988765  33589999999999999


Q ss_pred             HHHHHHHHhhhc
Q psy2029         119 KYQSLAKAAEEF  130 (138)
Q Consensus       119 ~~~~~~~~~~~~  130 (138)
                      +++.++++....
T Consensus       111 ~~~~~~~~~~~~  122 (412)
T 3fht_A          111 TGKVIEQMGKFY  122 (412)
T ss_dssp             HHHHHHHHTTTS
T ss_pred             HHHHHHHHHhhc
Confidence            999999987653

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.39  E-value=5.8e-13  Score=104.45  Aligned_cols=84  Identities=18%  Similarity=0.146  Sum_probs=72.8

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhh--c-cceEEEeecCCCchHhHHHHHHHHHHhC------CCeEEEEccchhH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQ--N-KNCVLSIPTSGGKTLVGEILIMKELKIK------QKSAIFILPYISL  115 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~--~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~------~~~~~~i~P~~~l  115 (138)
                      |..++.+.+.+.++..+.++|.++++.+.  + +++++.+|||+|||+++.+++++.+...      +.+++|++|+++|
T Consensus        28 l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lvl~Ptr~L  107 (579)
T 3sqw_A           28 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDL  107 (579)
T ss_dssp             SCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccccccCCCeEEEEcchHHH
Confidence            34566777777888889999999998776  5 8999999999999999999999988763      3489999999999


Q ss_pred             HHHHHHHHHHHhh
Q psy2029         116 VHEKYQSLAKAAE  128 (138)
Q Consensus       116 ~~q~~~~~~~~~~  128 (138)
                      +.|+++.+++++.
T Consensus       108 a~Q~~~~~~~~~~  120 (579)
T 3sqw_A          108 ALQIEAEVKKIHD  120 (579)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999999864

>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=99.39  E-value=2.8e-13  Score=108.41  Aligned_cols=91  Identities=24%  Similarity=0.388  Sum_probs=72.8

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSL  123 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~  123 (138)
                      |.....+.+.+.++..++++|.++++.+.+ +++++++|||+|||+++.+++++.+.. +.+++|++|+++|+.|+++++
T Consensus        10 l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~-~~~~l~i~P~r~La~q~~~~~   88 (702)
T 2p6r_A           10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK-GGKSLYVVPLRALAGEKYESF   88 (702)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT-TCCEEEEESSHHHHHHHHHHH
T ss_pred             cCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHh-CCcEEEEeCcHHHHHHHHHHH
Confidence            444555666666777899999999988777 999999999999999999999988764 789999999999999999999


Q ss_pred             HHHhhhcCceeeec
Q psy2029         124 AKAAEEFKFYLEVL  137 (138)
Q Consensus       124 ~~~~~~~~~~v~~~  137 (138)
                      + .+.+.|+++..+
T Consensus        89 ~-~~~~~g~~v~~~  101 (702)
T 2p6r_A           89 K-KWEKIGLRIGIS  101 (702)
T ss_dssp             T-TTTTTTCCEEEE
T ss_pred             H-HHHhcCCEEEEE
Confidence            5 445557766543

>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=99.38  E-value=1.6e-13  Score=97.98  Aligned_cols=57  Identities=16%  Similarity=0.225  Sum_probs=50.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh------cCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI------KQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~------~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|++++||||+|||++|.++++..+.+      .+.++++++|+++|+.|+++.+.+++.
T Consensus        89 ~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~~~~  151 (262)
T 3ly5_A           89 LEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMT  151 (262)
T ss_dssp             HHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             hCCCcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceEEEEeCCHHHHHHHHHHHHHHHh
Confidence            467899999999999999999999987764      467899999999999999999998754

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.38  E-value=1.6e-12  Score=100.35  Aligned_cols=78  Identities=17%  Similarity=0.225  Sum_probs=69.3

Q ss_pred             hhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC----CCeEEEEccchhHHHHHHHHHHHHhhhcCcee
Q psy2029          60 FKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK----QKSAIFILPYISLVHEKYQSLAKAAEEFKFYL  134 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~----~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v  134 (138)
                      .++++|.++++.+.+ +++++.+|||+|||+++.+++++.+...    +.++++++|+++|+.|+++.+++++...++++
T Consensus         4 ~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~   83 (555)
T 3tbk_A            4 KPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFERLGYNI   83 (555)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTTTCCE
T ss_pred             CCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhccCCcEE
Confidence            367899999988877 9999999999999999999999888763    67899999999999999999999998887776


Q ss_pred             eec
Q psy2029         135 EVL  137 (138)
Q Consensus       135 ~~~  137 (138)
                      ..+
T Consensus        84 ~~~   86 (555)
T 3tbk_A           84 ASI   86 (555)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            654

>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=99.38  E-value=7.3e-13  Score=101.49  Aligned_cols=86  Identities=10%  Similarity=0.113  Sum_probs=74.9

Q ss_pred             hhHHHHHHHHHHHHHhhhhhhhhHHHhhhhc---cceEEEeecCCCchHhHHHHHHHHHHhC--CCeEEEEccchhHHHH
Q psy2029          44 SLVHEKYQSLAKAAEEFKFYLEGKCLEMIQN---KNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHE  118 (138)
Q Consensus        44 aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~---~~~ii~~ptg~GKt~~~~~~~l~~~~~~--~~~~~~i~P~~~l~~q  118 (138)
                      .|..+..+.+.+.++..++++|.++++.+..   +++++.+|||+|||+++.+++++.+...  +.+++|++|+++|+.|
T Consensus        98 ~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q  177 (479)
T 3fmp_B           98 RLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQ  177 (479)
T ss_dssp             TCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTTSCSCCEEEECSSHHHHHH
T ss_pred             CCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhcCCCCcEEEEeChHHHHHH
Confidence            4667888899988899999999999977764   7899999999999999999999877652  3489999999999999


Q ss_pred             HHHHHHHHhhh
Q psy2029         119 KYQSLAKAAEE  129 (138)
Q Consensus       119 ~~~~~~~~~~~  129 (138)
                      +++.++++...
T Consensus       178 ~~~~~~~~~~~  188 (479)
T 3fmp_B          178 TGKVIEQMGKF  188 (479)
T ss_dssp             HHHHHHHHHTT
T ss_pred             HHHHHHHHHhh
Confidence            99999988764

>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=99.37  E-value=2e-12  Score=100.02  Aligned_cols=79  Identities=14%  Similarity=0.217  Sum_probs=69.1

Q ss_pred             hhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC----CCeEEEEccchhHHHHHHHHHHHHhhhcCce
Q psy2029          59 EFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK----QKSAIFILPYISLVHEKYQSLAKAAEEFKFY  133 (138)
Q Consensus        59 ~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~----~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~  133 (138)
                      ..+.++|.++++.+.+ +++++.+|||+|||+++.+++++.+...    +.++++++|+++|+.|+++.+++++...+++
T Consensus         6 ~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~   85 (556)
T 4a2p_A            6 KKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYS   85 (556)
T ss_dssp             --CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGGTCC
T ss_pred             CCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhcccCce
Confidence            3578899999988876 9999999999999999999999888763    6789999999999999999999999888777


Q ss_pred             eeec
Q psy2029         134 LEVL  137 (138)
Q Consensus       134 v~~~  137 (138)
                      +..+
T Consensus        86 ~~~~   89 (556)
T 4a2p_A           86 VQGI   89 (556)
T ss_dssp             EEEC
T ss_pred             EEEE
Confidence            7654

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.35  E-value=1.4e-12  Score=103.81  Aligned_cols=85  Identities=16%  Similarity=0.132  Sum_probs=71.2

Q ss_pred             HHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCC----CeEEEEccchhHHHHHHHHHHHHh
Q psy2029          53 LAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQ----KSAIFILPYISLVHEKYQSLAKAA  127 (138)
Q Consensus        53 l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~----~~~~~i~P~~~l~~q~~~~~~~~~  127 (138)
                      +..+++..+.++|.++++.+.+ +++++.+|||+|||+++.+++++.+....    .++++++|+++|+.|+.+.+++++
T Consensus         6 l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L~~Q~~~~~~~~~   85 (696)
T 2ykg_A            6 TNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVFSKYF   85 (696)
T ss_dssp             -CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHHHHHHHHHHHHHT
T ss_pred             ccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHHHHHHHHHHHHHh
Confidence            3445667789999999988876 99999999999999999999998877633    789999999999999999999998


Q ss_pred             hhcCceeeec
Q psy2029         128 EEFKFYLEVL  137 (138)
Q Consensus       128 ~~~~~~v~~~  137 (138)
                      ...++++..+
T Consensus        86 ~~~~~~v~~~   95 (696)
T 2ykg_A           86 ERHGYRVTGI   95 (696)
T ss_dssp             TTTTCCEEEE
T ss_pred             ccCCceEEEE
Confidence            8777776543

>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=99.35  E-value=1.2e-12  Score=92.83  Aligned_cols=58  Identities=17%  Similarity=0.170  Sum_probs=50.9

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhc--CCeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~--~~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      ++|+|+++++|||+|||+++.++++..+...  +.++++++|+++|..|.++.+.+++..
T Consensus        78 ~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~~~~~~lil~Ptr~L~~q~~~~~~~~~~~  137 (249)
T 3ber_A           78 LQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTPTRELAFQISEQFEALGSS  137 (249)
T ss_dssp             HTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCCSSCEEEECSSHHHHHHHHHHHHHHHGG
T ss_pred             hCCCCEEEEcCCCCCchhHhHHHHHHHHhcCCCCceEEEEeCCHHHHHHHHHHHHHHhcc
Confidence            5789999999999999999999999877663  457999999999999999999887543

>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=99.35  E-value=1.3e-12  Score=91.13  Aligned_cols=56  Identities=18%  Similarity=0.131  Sum_probs=49.1

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh--------cCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI--------KQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--------~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|+|+++++|||+|||+++.++++..+..        .+.++++++|+++|++|..+++.++.
T Consensus        55 ~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  118 (228)
T 3iuy_A           55 LQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYS  118 (228)
T ss_dssp             HTTCCEEEECCTTSCHHHHHHHHHHHHHC---------CCCSEEEECSSHHHHHHHHHHHHHHC
T ss_pred             hCCCCEEEECCCCChHHHHHHHHHHHHHHhccchhhccCCCcEEEEeCCHHHHHHHHHHHHHhc
Confidence            578999999999999999999999887653        46689999999999999999998873

>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=99.34  E-value=9.5e-13  Score=93.14  Aligned_cols=58  Identities=17%  Similarity=0.194  Sum_probs=50.3

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhc-----------CCeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIK-----------QKSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~-----------~~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      ++|+|+++++|||+|||+++.++++.++...           +.++++++|+++|..|.++++.+++..
T Consensus        58 ~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  126 (253)
T 1wrb_A           58 LEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLN  126 (253)
T ss_dssp             HTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTT
T ss_pred             hCCCCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccCCceEEEEECCHHHHHHHHHHHHHHhcc
Confidence            5688999999999999999999999877542           358999999999999999999887543

>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=99.33  E-value=1.7e-12  Score=91.32  Aligned_cols=58  Identities=33%  Similarity=0.385  Sum_probs=51.1

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh---cCCeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI---KQKSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~---~~~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      ++|+|++++||||+|||++|.++++..+.+   ++.++++++|+++|..|.++++.+++..
T Consensus        64 ~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  124 (245)
T 3dkp_A           64 LHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEG  124 (245)
T ss_dssp             HTTCCEEEECCTTSCHHHHHHHHHHHHHCSCCSSSCCEEEECSSHHHHHHHHHHHHHHTTT
T ss_pred             hCCCCEEEECCCCCcHHHHHHHHHHHHHhhcccCCceEEEEeCCHHHHHHHHHHHHHHhcc
Confidence            578899999999999999999999987764   4558999999999999999999887543

>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=99.31  E-value=6.8e-12  Score=101.71  Aligned_cols=80  Identities=14%  Similarity=0.214  Sum_probs=69.9

Q ss_pred             HhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC----CCeEEEEccchhHHHHHHHHHHHHhhhcCc
Q psy2029          58 EEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK----QKSAIFILPYISLVHEKYQSLAKAAEEFKF  132 (138)
Q Consensus        58 ~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~----~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~  132 (138)
                      ...+.++|.++++.+.+ +++++.+|||+|||+++.+++++.+...    +.++++++|+++|+.|+++.+++++...++
T Consensus       246 ~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~Pt~~L~~Q~~~~~~~~~~~~~~  325 (797)
T 4a2q_A          246 TKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGY  325 (797)
T ss_dssp             --CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGGTC
T ss_pred             CCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHhcccCCc
Confidence            45688999999988877 9999999999999999999999888763    678999999999999999999999988777


Q ss_pred             eeeec
Q psy2029         133 YLEVL  137 (138)
Q Consensus       133 ~v~~~  137 (138)
                      ++..+
T Consensus       326 ~v~~~  330 (797)
T 4a2q_A          326 SVQGI  330 (797)
T ss_dssp             CEEEE
T ss_pred             eEEEE
Confidence            77654

>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=99.29  E-value=2.1e-12  Score=98.11  Aligned_cols=57  Identities=18%  Similarity=0.190  Sum_probs=50.9

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhc-------CCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIK-------QKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~-------~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|++++||||||||+++.++++.++.+.       +.++++++|+++|+.|+++++.+++.
T Consensus        91 ~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~  154 (434)
T 2db3_A           91 SSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAF  154 (434)
T ss_dssp             HTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTCCSEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             hcCCCEEEECCCCCCchHHHHHHHHHHHHhcccccccCCccEEEEecCHHHHHHHHHHHHHHhc
Confidence            5789999999999999999999999887653       45899999999999999999998754

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.29  E-value=4.7e-12  Score=88.61  Aligned_cols=57  Identities=23%  Similarity=0.303  Sum_probs=50.3

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh------cCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI------KQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~------~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|+++++|||+|||+++.++++..+.+      .+.++++++|+++|..|..+.+.+++.
T Consensus        60 ~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  122 (236)
T 2pl3_A           60 LQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGK  122 (236)
T ss_dssp             HTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             hCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceEEEEeCCHHHHHHHHHHHHHHhC
Confidence            578999999999999999999999987643      467899999999999999999988754

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.28  E-value=3.2e-12  Score=88.61  Aligned_cols=57  Identities=23%  Similarity=0.262  Sum_probs=50.0

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|+++++|||+|||+++.++++..+..  .+.++++++|+++|.+|.++++.++..
T Consensus        39 ~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~   97 (219)
T 1q0u_A           39 LRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQIYHETLKITK   97 (219)
T ss_dssp             HHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHHT
T ss_pred             hCCCCEEEECCCCChHHHHHHHHHHHHHHhCcCCceEEEEcCcHHHHHHHHHHHHHHhh
Confidence            467899999999999999999999987654  356899999999999999999988754

>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=99.28  E-value=5e-12  Score=91.98  Aligned_cols=57  Identities=11%  Similarity=0.190  Sum_probs=49.5

Q ss_pred             CCC--ccEEEEccCCcchHHHHHHHHHHHHhhc--CCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQN--KNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~--~~~~~~~ptg~GKt~~~~~~~~~~~~~~--~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|  +|++++||||||||++|.++++.++...  +.++++++|+++|+.|+++.+..++.
T Consensus       127 l~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~lil~PtreLa~Q~~~~~~~l~~  187 (300)
T 3fmo_B          127 LAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGK  187 (300)
T ss_dssp             TSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             HcCCCCeEEEECCCCCCccHHHHHHHHHhhhccCCCceEEEEcCcHHHHHHHHHHHHHHHh
Confidence            455  8999999999999999999999887653  34899999999999999999888753

>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=99.28  E-value=9.5e-12  Score=98.07  Aligned_cols=78  Identities=22%  Similarity=0.246  Sum_probs=68.4

Q ss_pred             hHHHHHHHHHH-HHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHH
Q psy2029          45 LVHEKYQSLAK-AAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQS  122 (138)
Q Consensus        45 L~~q~~~~l~~-~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~  122 (138)
                      +..+..+.+.+ +++..+.++|.++++.+.+ +++++.+|||+|||+++.++++.    .++++++++|+++|+.|+++.
T Consensus        28 l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~----~~g~~lVisP~~~L~~q~~~~  103 (591)
T 2v1x_A           28 WSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALC----SDGFTLVICPLISLMEDQLMV  103 (591)
T ss_dssp             THHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHT----SSSEEEEECSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHH----cCCcEEEEeCHHHHHHHHHHH
Confidence            44566677777 4777889999999988887 99999999999999999999875    367999999999999999999


Q ss_pred             HHHH
Q psy2029         123 LAKA  126 (138)
Q Consensus       123 ~~~~  126 (138)
                      ++++
T Consensus       104 l~~~  107 (591)
T 2v1x_A          104 LKQL  107 (591)
T ss_dssp             HHHH
T ss_pred             HHhc
Confidence            9987

>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=99.27  E-value=5.2e-12  Score=88.28  Aligned_cols=57  Identities=11%  Similarity=0.132  Sum_probs=50.1

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|+++++|||+|||+++.++++..+..  .+.++++++|+++|.+|.++++.+++.
T Consensus        59 ~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  117 (230)
T 2oxc_A           59 RCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGI  117 (230)
T ss_dssp             HTTCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             hCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEeCCHHHHHHHHHHHHHHhc
Confidence            568899999999999999999999887654  356999999999999999999988753

>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=99.27  E-value=5.9e-12  Score=86.20  Aligned_cols=57  Identities=16%  Similarity=0.223  Sum_probs=49.4

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|+++++|||+|||+++.++++..+..  .+.++++++|+++|.+|.++.+.++..
T Consensus        38 ~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~   96 (206)
T 1vec_A           38 LSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSK   96 (206)
T ss_dssp             HTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHHHHHHHHHHHHHHTT
T ss_pred             ccCCCEEEECCCCCchHHHHHHHHHHHhcccCCCeeEEEEeCcHHHHHHHHHHHHHHHh
Confidence            468899999999999999999999987644  355899999999999999999988743

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.26  E-value=1e-11  Score=93.01  Aligned_cols=57  Identities=16%  Similarity=0.197  Sum_probs=49.6

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcC--------------------CeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQ--------------------KSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~--------------------~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|++++||||+|||+++.++++..+...+                    .++++++|+++|+.|.++.+.+++.
T Consensus        50 ~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  126 (417)
T 2i4i_A           50 KEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSY  126 (417)
T ss_dssp             HTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHHHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHT
T ss_pred             ccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhccccccccccccCCccEEEECCcHHHHHHHHHHHHHHhC
Confidence            57899999999999999999999998765422                    4799999999999999999988754

>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=99.25  E-value=7.9e-12  Score=86.68  Aligned_cols=57  Identities=16%  Similarity=0.201  Sum_probs=49.9

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|+++++|||+|||+++.++++..+..  ++.++++++|+++|.+|.++.+.+++.
T Consensus        49 ~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (224)
T 1qde_A           49 IEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAF  107 (224)
T ss_dssp             HTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             hcCCCEEEECCCCCcHHHHHHHHHHHHHhccCCCceEEEEECCHHHHHHHHHHHHHHhc
Confidence            568899999999999999999999987654  356999999999999999999988753

>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=99.25  E-value=8.4e-12  Score=85.40  Aligned_cols=56  Identities=23%  Similarity=0.271  Sum_probs=49.6

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh-----cCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI-----KQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-----~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|+|+++++|||+|||+++.++++..+.+     ++.++++++|+++|..|..+++.++.
T Consensus        36 ~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~   96 (207)
T 2gxq_A           36 LEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVA   96 (207)
T ss_dssp             HTTCCEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHC
T ss_pred             cCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEECCHHHHHHHHHHHHHHh
Confidence            468899999999999999999999987753     46689999999999999999998874

>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=99.25  E-value=5.3e-12  Score=88.67  Aligned_cols=57  Identities=19%  Similarity=0.332  Sum_probs=50.3

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|+++++|||+|||+++.++++..+..  .+.++++++|+++|..|.++.+.+++.
T Consensus        65 ~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  123 (237)
T 3bor_A           65 IKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGD  123 (237)
T ss_dssp             HTTCCEEECCCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             hCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEECcHHHHHHHHHHHHHHhh
Confidence            578899999999999999999999987654  356999999999999999999988754

>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=99.24  E-value=1.9e-11  Score=87.87  Aligned_cols=70  Identities=16%  Similarity=0.201  Sum_probs=60.3

Q ss_pred             hhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhh
Q psy2029          60 FKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEE  129 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~  129 (138)
                      .+.++|.++++.+.+ .+.++++|||+|||+++..++...+...+.++++++|+++|++|..++++++...
T Consensus       113 ~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~l~~~~~~  183 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLF  183 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECSSHHHHHHHHHHHHHHTSC
T ss_pred             CccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHHHHHhccc
Confidence            478889999987666 7889999999999999988877766555569999999999999999999998654

>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=99.24  E-value=2e-11  Score=101.63  Aligned_cols=73  Identities=23%  Similarity=0.225  Sum_probs=66.0

Q ss_pred             HHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCc
Q psy2029          57 AEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF  132 (138)
Q Consensus        57 ~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~  132 (138)
                      ++. + ++|.++++.+.+ +++++.+|||+|||+ +.++++..+...+.++++++|+++|+.|+++.+++++...++
T Consensus        55 g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~~~~~~lil~PtreLa~Q~~~~l~~l~~~~~i  128 (1054)
T 1gku_B           55 GEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGV  128 (1054)
T ss_dssp             CSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHTTSCCEEEEESCHHHHHHHHHHHHHHHTTTCC
T ss_pred             CCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhhcCCeEEEEeccHHHHHHHHHHHHHHHhhcCC
Confidence            455 7 999999988888 999999999999998 778888888777889999999999999999999999988777

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.23  E-value=2.8e-11  Score=101.14  Aligned_cols=75  Identities=23%  Similarity=0.202  Sum_probs=64.4

Q ss_pred             hhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          60 FKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      .++++|.++++.+.+ +++++.+|||+|||++++.++++.+ ..+.++++++|+++|+.|+++.++++. ..++++..
T Consensus        78 ~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~-~~~~~~Lil~PtreLa~Q~~~~l~~l~-~~~i~v~~  153 (1104)
T 4ddu_A           78 DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA-RKGKKSALVFPTVTLVKQTLERLQKLA-DEKVKIFG  153 (1104)
T ss_dssp             CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHH-TTTCCEEEEESSHHHHHHHHHHHHTTS-CTTSCEEE
T ss_pred             CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHH-hcCCeEEEEechHHHHHHHHHHHHHhh-CCCCeEEE
Confidence            478999999988887 9999999999999998877776655 457899999999999999999999966 56666654

>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=99.23  E-value=1.1e-11  Score=85.76  Aligned_cols=56  Identities=14%  Similarity=0.135  Sum_probs=49.0

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhc--CCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~--~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|+|+++++|||+|||+++.++++..+...  +.++++++|+++|.+|.++++.++.
T Consensus        49 ~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  106 (220)
T 1t6n_A           49 ILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFS  106 (220)
T ss_dssp             HTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHHHT
T ss_pred             hCCCCEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEeCCHHHHHHHHHHHHHHH
Confidence            4688999999999999999999999876542  3489999999999999999998874

>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=99.22  E-value=1.6e-11  Score=102.54  Aligned_cols=72  Identities=25%  Similarity=0.374  Sum_probs=64.5

Q ss_pred             hhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCc
Q psy2029          60 FKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF  132 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~  132 (138)
                      .++++|.++++.+.+ +++++++|||+|||+++.+++++.+. .+.+++|++|+++|++|++++|++.+...|+
T Consensus       184 ~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~-~g~rvlvl~PtraLa~Q~~~~l~~~~~~Vgl  256 (1108)
T 3l9o_A          184 TLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLK-NKQRVIYTSPIKALSNQKYRELLAEFGDVGL  256 (1108)
T ss_dssp             CCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHH-TTCEEEEEESSHHHHHHHHHHHHHHTSSEEE
T ss_pred             CCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHh-cCCeEEEEcCcHHHHHHHHHHHHHHhCCccE
Confidence            478899999988887 99999999999999999999988764 4789999999999999999999999875544

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.21  E-value=1.2e-11  Score=95.51  Aligned_cols=57  Identities=23%  Similarity=0.348  Sum_probs=51.1

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhc----CCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIK----QKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~----~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|+++++|||+|||+++.+++...+.+.    ++++++++|+++|..|..+++.+++.
T Consensus        17 ~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~   77 (555)
T 3tbk_A           17 KKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFE   77 (555)
T ss_dssp             HTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHH
T ss_pred             hCCCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhc
Confidence            4789999999999999999999999877653    67999999999999999999998854

>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=99.21  E-value=3.6e-11  Score=97.32  Aligned_cols=77  Identities=19%  Similarity=0.301  Sum_probs=66.5

Q ss_pred             hhhhhhhHHHhhhhc-------cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCc
Q psy2029          60 FKFYLEGKCLEMIQN-------KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF  132 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~-------~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~  132 (138)
                      .++++|.++++.+.+       .+.++.+|||+|||+++.+++++.+.. +.++++++|+++|+.|.++.+++++.+.|+
T Consensus       368 ~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~-g~qvlvlaPtr~La~Q~~~~l~~~~~~~gi  446 (780)
T 1gm5_A          368 KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA-GFQTAFMVPTSILAIQHYRRTVESFSKFNI  446 (780)
T ss_dssp             CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH-TSCEEEECSCHHHHHHHHHHHHHHHTCSSC
T ss_pred             CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHc-CCeEEEEeCcHHHHHHHHHHHHHHhhhcCc
Confidence            688999999854432       488999999999999999999987764 789999999999999999999999988888


Q ss_pred             eeeec
Q psy2029         133 YLEVL  137 (138)
Q Consensus       133 ~v~~~  137 (138)
                      +|..+
T Consensus       447 ~v~~l  451 (780)
T 1gm5_A          447 HVALL  451 (780)
T ss_dssp             CEEEC
T ss_pred             eEEEE
Confidence            77643

>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=99.21  E-value=2e-11  Score=94.91  Aligned_cols=79  Identities=20%  Similarity=0.321  Sum_probs=68.4

Q ss_pred             hhHHHHHHHHHH-HHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHH
Q psy2029          44 SLVHEKYQSLAK-AAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        44 aL~~q~~~~l~~-~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~  121 (138)
                      .|..+..+.+.+ +++..+.++|.++++.+.+ +++++.+|||+|||+++.++++.    ..++++|++|+++|+.|+++
T Consensus         8 ~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~----~~g~~lvi~P~~aL~~q~~~   83 (523)
T 1oyw_A            8 NLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALL----LNGLTVVVSPLISLMKDQVD   83 (523)
T ss_dssp             SHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHH----SSSEEEEECSCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHH----hCCCEEEECChHHHHHHHHH
Confidence            345667777777 5677889999999988887 99999999999999999999875    36789999999999999999


Q ss_pred             HHHHH
Q psy2029         122 SLAKA  126 (138)
Q Consensus       122 ~~~~~  126 (138)
                      .++++
T Consensus        84 ~l~~~   88 (523)
T 1oyw_A           84 QLQAN   88 (523)
T ss_dssp             HHHHT
T ss_pred             HHHHc
Confidence            99876

>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=99.20  E-value=1.6e-11  Score=94.99  Aligned_cols=57  Identities=18%  Similarity=0.374  Sum_probs=50.8

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhc----CCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIK----QKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~----~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|+++++|||+|||+++.++++..+.+.    ++++++++|+++|..|..+++.+++.
T Consensus        20 ~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~   80 (556)
T 4a2p_A           20 INGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFE   80 (556)
T ss_dssp             HTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHG
T ss_pred             HcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhc
Confidence            4788999999999999999999998877653    67999999999999999999998754

>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=99.19  E-value=2.9e-11  Score=82.99  Aligned_cols=74  Identities=16%  Similarity=0.184  Sum_probs=60.9

Q ss_pred             hhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh-----CCCeEEEEccchhHHHH-HHHHHHHHhhhcCc
Q psy2029          60 FKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI-----KQKSAIFILPYISLVHE-KYQSLAKAAEEFKF  132 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~-----~~~~~~~i~P~~~l~~q-~~~~~~~~~~~~~~  132 (138)
                      .++++|.++++.+.+ +++++.+|||+|||+++.+++++.+..     .+.++++++|+++|+.| ..+.++++... ++
T Consensus        33 ~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~~~~~~~~~~-~~  111 (216)
T 3b6e_A           33 QLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKK-WY  111 (216)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTHHHHHTT-TS
T ss_pred             CchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHHHHHHHHhcc-Cc
Confidence            578999999987777 999999999999999999988876654     25789999999999999 66777777543 34


Q ss_pred             ee
Q psy2029         133 YL  134 (138)
Q Consensus       133 ~v  134 (138)
                      .+
T Consensus       112 ~v  113 (216)
T 3b6e_A          112 RV  113 (216)
T ss_dssp             CE
T ss_pred             eE
Confidence            43

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.19  E-value=2.9e-11  Score=100.29  Aligned_cols=71  Identities=25%  Similarity=0.370  Sum_probs=62.8

Q ss_pred             hhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcC
Q psy2029          60 FKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFK  131 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~  131 (138)
                      .++++|.++++.+.+ +++++++|||+|||+++.++++..+. .+.+++|++|+++|++|++++|++.+...|
T Consensus        86 ~L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~-~g~rvL~l~PtkaLa~Q~~~~l~~~~~~vg  157 (1010)
T 2xgj_A           86 TLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLK-NKQRVIYTSPIKALSNQKYRELLAEFGDVG  157 (1010)
T ss_dssp             CCCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHH-TTCEEEEEESSHHHHHHHHHHHHHHHSCEE
T ss_pred             CCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhc-cCCeEEEECChHHHHHHHHHHHHHHhCCEE
Confidence            378999999988877 99999999999999999988887664 478999999999999999999999876443

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.19  E-value=4.8e-11  Score=91.97  Aligned_cols=70  Identities=16%  Similarity=0.201  Sum_probs=61.5

Q ss_pred             hhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhh
Q psy2029          60 FKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEE  129 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~  129 (138)
                      .++++|.++++.+.+ ++.++++|||+|||+++..++.+.+...+.++++++|+++|+.|.+++|+++...
T Consensus       113 ~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~~~~~~~  183 (510)
T 2oca_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLF  183 (510)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHCSSEEEEEESSHHHHHHHHHHHHHTTSS
T ss_pred             CCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCCCCeEEEEECcHHHHHHHHHHHHHhhcC
Confidence            578899999987776 8999999999999999988888777665669999999999999999999988443

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=99.19  E-value=1.4e-11  Score=93.87  Aligned_cols=56  Identities=16%  Similarity=0.160  Sum_probs=50.5

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +++|+|+++++|||||||++|..+++..+.+.+.++++++|+++|+.|+++.+...
T Consensus         5 l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~~~~~lil~Ptr~La~Q~~~~l~~~   60 (440)
T 1yks_A            5 LKKGMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGL   60 (440)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTTS
T ss_pred             hhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhcCCeEEEEcchHHHHHHHHHHHhcC
Confidence            46899999999999999999999999877777789999999999999999988654

>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=99.17  E-value=1.4e-11  Score=91.31  Aligned_cols=54  Identities=15%  Similarity=0.255  Sum_probs=48.2

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      +++++++|||+|||+++.++++..+..  .+.++++++|+++|.+|.++.+.+++.
T Consensus        45 ~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~  100 (395)
T 3pey_A           45 RNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGK  100 (395)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEECCCHHHHHHHHHHHHHHhc
Confidence            899999999999999999999987654  456999999999999999999988753

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.17  E-value=2.6e-11  Score=91.18  Aligned_cols=55  Identities=31%  Similarity=0.424  Sum_probs=48.5

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|+|+++++|||+|||+++..+++..+ .++.++++++|+++|+.|.++.+.+++
T Consensus        34 ~~~~~~lv~apTGsGKT~~~l~~~~~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~   88 (414)
T 3oiy_A           34 VQGKSFTMVAPTGVGKTTFGMMTALWLA-RKGKKSALVFPTVTLVKQTLERLQKLA   88 (414)
T ss_dssp             TTTCCEECCSCSSSSHHHHHHHHHHHHH-TTTCCEEEEESSHHHHHHHHHHHHHHC
T ss_pred             hcCCCEEEEeCCCCCHHHHHHHHHHHHh-cCCCEEEEEECCHHHHHHHHHHHHHHc
Confidence            5789999999999999998888877644 568899999999999999999998863

>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=99.17  E-value=4e-11  Score=98.81  Aligned_cols=80  Identities=14%  Similarity=0.214  Sum_probs=68.6

Q ss_pred             HhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC----CCeEEEEccchhHHHHHHHHHHHHhhhcCc
Q psy2029          58 EEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK----QKSAIFILPYISLVHEKYQSLAKAAEEFKF  132 (138)
Q Consensus        58 ~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~----~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~  132 (138)
                      ...+.++|.++++.+.+ +++++.+|||+|||+++.+++++.+...    +.++++++|+++|+.|+++++++++...++
T Consensus       246 ~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~  325 (936)
T 4a2w_A          246 TKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGY  325 (936)
T ss_dssp             --CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHHhcccCc
Confidence            44578899999988877 9999999999999999999998877653    678999999999999999999999987777


Q ss_pred             eeeec
Q psy2029         133 YLEVL  137 (138)
Q Consensus       133 ~v~~~  137 (138)
                      ++..+
T Consensus       326 ~v~~~  330 (936)
T 4a2w_A          326 SVQGI  330 (936)
T ss_dssp             CEEEE
T ss_pred             eEEEE
Confidence            76543

>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=99.16  E-value=5.3e-11  Score=88.93  Aligned_cols=57  Identities=16%  Similarity=0.304  Sum_probs=50.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+++++++|||+|||+++.++++..+..  .+.++++++|+++|..|..+.+.+++.
T Consensus        75 ~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~  133 (414)
T 3eiq_A           75 IKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGD  133 (414)
T ss_dssp             HTTCCEEECCCSCSSSHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHGG
T ss_pred             hCCCCEEEECCCCCcccHHHHHHHHHHHhhcCCceeEEEEeChHHHHHHHHHHHHHHhc
Confidence            578899999999999999999999987655  466899999999999999999988754

>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=99.15  E-value=1.3e-10  Score=87.58  Aligned_cols=69  Identities=19%  Similarity=0.275  Sum_probs=61.6

Q ss_pred             hhhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhh
Q psy2029          60 FKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE  128 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~  128 (138)
                      .++++|.++++.+.+.++++.+|||+|||+.+..+++..+...+.++++++|+++|+.|..+++++++.
T Consensus         9 ~l~~~Q~~~i~~~~~~~~ll~~~tG~GKT~~~~~~~~~~~~~~~~~~liv~P~~~L~~q~~~~~~~~~~   77 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESFRRLFN   77 (494)
T ss_dssp             CCCHHHHHHHHHGGGSCEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSSHHHHHHHHHHHHHHBC
T ss_pred             CccHHHHHHHHHHhhCCEEEEcCCCCCHHHHHHHHHHHHHhcCCCeEEEEECCHHHHHHHHHHHHHHhC
Confidence            478899999977666699999999999999999998887766678999999999999999999999964

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A

Probab=99.14  E-value=2.6e-11  Score=92.90  Aligned_cols=54  Identities=19%  Similarity=0.150  Sum_probs=48.8

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK   55 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~   55 (138)
                      .+|+++++++|||||||+++.++++..+.+.+.++++++|+++|+.|+++.+..
T Consensus        19 ~~~~~vlv~a~TGsGKT~~~~l~il~~~~~~~~~~lvl~Ptr~La~Q~~~~l~g   72 (459)
T 2z83_A           19 RKRQMTVLDLHPGSGKTRKILPQIIKDAIQQRLRTAVLAPTRVVAAEMAEALRG   72 (459)
T ss_dssp             STTCEEEECCCTTSCTTTTHHHHHHHHHHHTTCCEEEEECSHHHHHHHHHHTTT
T ss_pred             hcCCcEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEECchHHHHHHHHHHhcC
Confidence            467899999999999999999999988877788999999999999999988753

>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=99.14  E-value=8.1e-11  Score=91.71  Aligned_cols=54  Identities=20%  Similarity=0.240  Sum_probs=48.1

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcC------CeEEEEcchhhhHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQ------KSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~------~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +|+|++++||||+|||++|.++++.++.+..      .++++++|+++|+.|+++++.++
T Consensus       110 ~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lil~Ptr~La~Q~~~~~~~~  169 (563)
T 3i5x_A          110 EDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKI  169 (563)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHHHHHHHHHHHHH
T ss_pred             CCCeEEEECCCCCCccHHHHHHHHHHHHhccccccCCeeEEEEcCcHHHHHHHHHHHHHH
Confidence            5789999999999999999999998876632      48999999999999999998875

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.13  E-value=3.4e-11  Score=95.87  Aligned_cols=57  Identities=25%  Similarity=0.358  Sum_probs=50.5

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcC----CeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQ----KSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~----~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|+++++|||+|||+++.++++.++....    +++++++|+++|..|..+++.+++.
T Consensus        26 l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L~~Q~~~~~~~~~~   86 (696)
T 2ykg_A           26 MKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVFSKYFE   86 (696)
T ss_dssp             HTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             HcCCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHHHHHHHHHHHHHhc
Confidence            57899999999999999999999998776532    7999999999999999999988753

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.13  E-value=4.2e-11  Score=91.06  Aligned_cols=52  Identities=21%  Similarity=0.274  Sum_probs=46.6

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLA   54 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~   54 (138)
                      +|+++++++|||||||++|+.++++.+.+.+.++++++|+++|.+|.++.+.
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~~g~~~lvl~Pt~~La~Q~~~~~~   52 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVKKRLRTVILAPTRVVASEMYEALR   52 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTT
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEECcHHHHHHHHHHHhC
Confidence            5789999999999999999999887777778899999999999999998774

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.12  E-value=9.9e-11  Score=93.79  Aligned_cols=54  Identities=31%  Similarity=0.520  Sum_probs=49.4

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK   55 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~   55 (138)
                      .+++|+++++|||||||+++.+++++.+.+++++++|++|+++|+.|.++++..
T Consensus        44 ~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~il~i~P~r~La~q~~~~~~~   97 (715)
T 2va8_A           44 LEGNRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAIYVTPLRALTNEKYLTFKD   97 (715)
T ss_dssp             TTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCSEEEEECSCHHHHHHHHHHHGG
T ss_pred             cCCCcEEEEcCCCCcHHHHHHHHHHHHHHHCCCeEEEEeCcHHHHHHHHHHHHH
Confidence            578899999999999999999999988776788999999999999999999854

>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=99.12  E-value=5.6e-11  Score=96.40  Aligned_cols=57  Identities=18%  Similarity=0.374  Sum_probs=51.2

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhc----CCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIK----QKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~----~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|+++++|||+|||+++.+++...+.+.    ++++++++|+++|..|..+++.+++.
T Consensus       261 l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~Pt~~L~~Q~~~~~~~~~~  321 (797)
T 4a2q_A          261 INGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFE  321 (797)
T ss_dssp             HTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHG
T ss_pred             HhCCCEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHhcc
Confidence            4789999999999999999999999877663    67999999999999999999999854

>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=99.12  E-value=8e-11  Score=98.43  Aligned_cols=55  Identities=29%  Similarity=0.434  Sum_probs=50.0

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|++++++||||||||++|.++++..+ .++++++|++|+++|++|+++++.+.+
T Consensus       197 ~~g~dvLV~ApTGSGKTlva~l~i~~~l-~~g~rvlvl~PtraLa~Q~~~~l~~~~  251 (1108)
T 3l9o_A          197 DRGESVLVSAHTSAGKTVVAEYAIAQSL-KNKQRVIYTSPIKALSNQKYRELLAEF  251 (1108)
T ss_dssp             TTTCCEEEECCSSSHHHHHHHHHHHHHH-HTTCEEEEEESSHHHHHHHHHHHHHHT
T ss_pred             HcCCCEEEECCCCCChHHHHHHHHHHHH-hcCCeEEEEcCcHHHHHHHHHHHHHHh
Confidence            5789999999999999999999999866 458899999999999999999998864

>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=99.11  E-value=6.1e-11  Score=88.76  Aligned_cols=56  Identities=18%  Similarity=0.307  Sum_probs=49.4

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|+|+++++|||+|||+++.++++..+..  .+.++++++|+++|..|.++++.+++
T Consensus        72 ~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  129 (410)
T 2j0s_A           72 IKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALG  129 (410)
T ss_dssp             HTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHHHHHHHHHHHHHT
T ss_pred             hCCCCEEEECCCCCCchHHHHHHHHHHHhhccCCceEEEEcCcHHHHHHHHHHHHHHh
Confidence            578899999999999999999999986643  46799999999999999999988764

>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=99.11  E-value=6.4e-11  Score=95.02  Aligned_cols=55  Identities=35%  Similarity=0.642  Sum_probs=49.9

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ++|+|+++++|||||||+++.++++..+.+++++++|++|+++|+.|+++++.++
T Consensus        37 ~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~~l~i~P~raLa~q~~~~~~~l   91 (720)
T 2zj8_A           37 LEGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPLKALAEEKFQEFQDW   91 (720)
T ss_dssp             GGTCEEEEECCGGGCHHHHHHHHHHHHHHHHCSEEEEECSSGGGHHHHHHHTGGG
T ss_pred             cCCCcEEEEcCCccHHHHHHHHHHHHHHHhCCCEEEEEcCcHHHHHHHHHHHHHH
Confidence            5688999999999999999999999888767899999999999999999998643

>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=99.11  E-value=5e-11  Score=94.99  Aligned_cols=70  Identities=19%  Similarity=0.191  Sum_probs=62.3

Q ss_pred             hhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC-----CCeEEEEccchhHHHHH-HHHHHHHhhh
Q psy2029          60 FKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK-----QKSAIFILPYISLVHEK-YQSLAKAAEE  129 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~-----~~~~~~i~P~~~l~~q~-~~~~~~~~~~  129 (138)
                      .++++|.++++.+.+ +++++.+|||+|||+++.+++++.+...     +.++++++|+++|+.|+ .+++++++..
T Consensus         7 ~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~   83 (699)
T 4gl2_A            7 QLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKK   83 (699)
T ss_dssp             CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHHTHHHHHTT
T ss_pred             CccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHHHHHHHcCc
Confidence            478899999988887 9999999999999999999998877652     27899999999999999 9999999865

>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=99.10  E-value=1.4e-10  Score=86.48  Aligned_cols=54  Identities=13%  Similarity=0.194  Sum_probs=47.2

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++++++++|||+|||+++.++++..+..  .+.++++++|+++|..|..+.+.++.
T Consensus        64 ~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~  119 (412)
T 3fht_A           64 PQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMG  119 (412)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHT
T ss_pred             CCeEEEECCCCchHHHHHHHHHHHHhhhcCCCCCEEEECCCHHHHHHHHHHHHHHH
Confidence            3899999999999999999999987765  34489999999999999998888763

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*

Probab=99.10  E-value=4.8e-10  Score=90.68  Aligned_cols=92  Identities=13%  Similarity=0.111  Sum_probs=74.7

Q ss_pred             hhhHHHHHHHHHHHHHh----hhhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHH
Q psy2029          43 ISLVHEKYQSLAKAAEE----FKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHE  118 (138)
Q Consensus        43 ~aL~~q~~~~l~~~~~~----~~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q  118 (138)
                      ..+..+.+..+++.+..    .++++|..+++.+.+.+ +..++||+|||+++.+|++..... +..+++++|+++||.|
T Consensus        53 d~~lpeafA~vrea~~R~lg~~p~~VQ~~~i~~ll~G~-Iaem~TGsGKTlaf~LP~l~~~l~-g~~vlVltPTreLA~Q  130 (853)
T 2fsf_A           53 ENLIPEAFAVVREASKRVFGMRHFDVQLLGGMVLNERC-IAEMRTGEGKTLTATLPAYLNALT-GKGVHVVTVNDYLAQR  130 (853)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHSSE-EEECCTTSCHHHHHHHHHHHHHTT-SSCCEEEESSHHHHHH
T ss_pred             hhhhHHHHHHHHHHHHHHcCCCCChHHHhhcccccCCe-eeeecCCchHHHHHHHHHHHHHHc-CCcEEEEcCCHHHHHH
Confidence            33444555555554433    57899999999888744 999999999999999999876554 6789999999999999


Q ss_pred             HHHHHHHHhhhcCceeee
Q psy2029         119 KYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus       119 ~~~~~~~~~~~~~~~v~~  136 (138)
                      .++.+..++..+|++|..
T Consensus       131 ~~e~~~~l~~~lgl~v~~  148 (853)
T 2fsf_A          131 DAENNRPLFEFLGLTVGI  148 (853)
T ss_dssp             HHHHHHHHHHHTTCCEEE
T ss_pred             HHHHHHHHHHhcCCeEEE
Confidence            999999999999988764

>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=99.10  E-value=1.1e-10  Score=86.55  Aligned_cols=55  Identities=15%  Similarity=0.135  Sum_probs=48.3

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ++|+++++++|||+|||+++.++++..+..  .+.++++++|+++|.+|..+++.++
T Consensus        43 ~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L~~q~~~~~~~~   99 (391)
T 1xti_A           43 ILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERF   99 (391)
T ss_dssp             TTTCCEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHHH
T ss_pred             hcCCcEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCCHHHHHHHHHHHHHH
Confidence            578899999999999999999999887654  2458999999999999999888876

>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=99.10  E-value=2.8e-10  Score=88.50  Aligned_cols=52  Identities=25%  Similarity=0.537  Sum_probs=46.2

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|+|+++++|||+|||++|.++++.    .++++++++|+++|.+|+.+.+.+.+
T Consensus        38 l~g~d~lv~apTGsGKTl~~~lp~l~----~~g~~lvi~P~~aL~~q~~~~l~~~g   89 (523)
T 1oyw_A           38 LSGRDCLVVMPTGGGKSLCYQIPALL----LNGLTVVVSPLISLMKDQVDQLQANG   89 (523)
T ss_dssp             HTTCCEEEECSCHHHHHHHHHHHHHH----SSSEEEEECSCHHHHHHHHHHHHHTT
T ss_pred             HcCCCEEEECCCCcHHHHHHHHHHHH----hCCCEEEECChHHHHHHHHHHHHHcC
Confidence            57899999999999999999999874    36789999999999999999987753

>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=99.09  E-value=6.1e-10  Score=87.82  Aligned_cols=52  Identities=27%  Similarity=0.455  Sum_probs=46.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|+|+++.+|||+|||++|.++++.    .++++++++|+++|..|+.+.+...+
T Consensus        57 l~g~d~lv~~pTGsGKTl~~~lpal~----~~g~~lVisP~~~L~~q~~~~l~~~g  108 (591)
T 2v1x_A           57 MAGKEVFLVMPTGGGKSLCYQLPALC----SDGFTLVICPLISLMEDQLMVLKQLG  108 (591)
T ss_dssp             HTTCCEEEECCTTSCTTHHHHHHHHT----SSSEEEEECSCHHHHHHHHHHHHHHT
T ss_pred             HcCCCEEEEECCCChHHHHHHHHHHH----cCCcEEEEeCHHHHHHHHHHHHHhcC
Confidence            57899999999999999999999875    46799999999999999999988763

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.09  E-value=1.1e-10  Score=96.88  Aligned_cols=55  Identities=29%  Similarity=0.434  Sum_probs=49.1

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|+++++++|||+|||++|.+++...+ .++.+++|++|+++|++|+++++.+.+
T Consensus        99 ~~g~~vLV~apTGSGKTlva~lai~~~l-~~g~rvL~l~PtkaLa~Q~~~~l~~~~  153 (1010)
T 2xgj_A           99 DRGESVLVSAHTSAGKTVVAEYAIAQSL-KNKQRVIYTSPIKALSNQKYRELLAEF  153 (1010)
T ss_dssp             HHTCEEEEECCTTSCHHHHHHHHHHHHH-HTTCEEEEEESSHHHHHHHHHHHHHHH
T ss_pred             HcCCCEEEECCCCCChHHHHHHHHHHHh-ccCCeEEEECChHHHHHHHHHHHHHHh
Confidence            4688999999999999999999888765 458899999999999999999998864

>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=99.09  E-value=9.2e-11  Score=89.81  Aligned_cols=53  Identities=11%  Similarity=0.180  Sum_probs=46.6

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhc--CCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~--~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++++++||||||||++|.++++.++...  +.++++++|+++|..|+++.+.++.
T Consensus       132 ~~~l~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~  186 (479)
T 3fmp_B          132 QNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMG  186 (479)
T ss_dssp             CEEEEECCSSSSHHHHHHHHHHTTCCTTSCSCCEEEECSSHHHHHHHHHHHHHHH
T ss_pred             CcEEEEcCCCCchhHHHHHHHHHHHhhcCCCCcEEEEeChHHHHHHHHHHHHHHH
Confidence            8999999999999999999999876542  3389999999999999998888764

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.08  E-value=2.3e-10  Score=89.71  Aligned_cols=55  Identities=20%  Similarity=0.216  Sum_probs=48.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhc------CCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIK------QKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~------~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +|++++++||||+|||++|.++++..+...      +.++++++|+++|+.|+.+++.++.
T Consensus        59 ~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lvl~Ptr~La~Q~~~~~~~~~  119 (579)
T 3sqw_A           59 EDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIH  119 (579)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEcCCCcHHHHHHHHHHHHHHHhccccccCCCeEEEEcchHHHHHHHHHHHHHHH
Confidence            578999999999999999999999887653      2489999999999999999988763

>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=99.08  E-value=1.1e-10  Score=87.00  Aligned_cols=56  Identities=16%  Similarity=0.226  Sum_probs=49.1

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|+++++++|||+|||+++.++++..+..  .+.++++++|+++|..|..+.+.+++
T Consensus        56 ~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~  113 (400)
T 1s2m_A           56 ITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLG  113 (400)
T ss_dssp             HHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHT
T ss_pred             hcCCCEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcCCHHHHHHHHHHHHHHh
Confidence            467899999999999999999999987654  35589999999999999999988764

>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=99.07  E-value=1.5e-10  Score=84.11  Aligned_cols=52  Identities=23%  Similarity=0.293  Sum_probs=46.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|+++++++|||+|||+++..+++.    .+.++++++|+++|.+|.++.+.+++
T Consensus        29 ~~~~~~lv~~~TGsGKT~~~~~~~~~----~~~~~liv~P~~~L~~q~~~~~~~~~   80 (337)
T 2z0m_A           29 LQGKNVVVRAKTGSGKTAAYAIPILE----LGMKSLVVTPTRELTRQVASHIRDIG   80 (337)
T ss_dssp             HTTCCEEEECCTTSSHHHHHHHHHHH----HTCCEEEECSSHHHHHHHHHHHHHHT
T ss_pred             hcCCCEEEEcCCCCcHHHHHHHHHHh----hcCCEEEEeCCHHHHHHHHHHHHHHh
Confidence            46889999999999999999888775    37899999999999999999998864

>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=99.07  E-value=8.4e-11  Score=87.24  Aligned_cols=56  Identities=16%  Similarity=0.227  Sum_probs=49.2

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|+++++++|||+|||+++.++++..+..  .+.++++++|+++|..|..+.+.++.
T Consensus        56 ~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L~~q~~~~~~~~~  113 (394)
T 1fuu_A           56 IEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALA  113 (394)
T ss_dssp             HHTCCEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHT
T ss_pred             hCCCCEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEEcCCHHHHHHHHHHHHHHh
Confidence            467899999999999999999999987654  45699999999999999999988764

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=99.07  E-value=8.6e-11  Score=93.09  Aligned_cols=54  Identities=15%  Similarity=0.186  Sum_probs=49.3

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHH
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLA   54 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~   54 (138)
                      +++|+|++++||||||||+++.++++..+..++.++++++|+++|+.|+++.+.
T Consensus       183 l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~~~~~vLvl~PtreLa~Qi~~~l~  236 (618)
T 2whx_A          183 FRKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALR  236 (618)
T ss_dssp             GSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTT
T ss_pred             HhcCCeEEEEcCCCCCHHHHHHHHHHHHHHhCCCeEEEEcChHHHHHHHHHHhc
Confidence            367899999999999999999999998887777899999999999999998874

>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase, translocation, secretion, protein transport; 2.18A {Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A 3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A

Probab=99.06  E-value=7e-10  Score=89.83  Aligned_cols=78  Identities=15%  Similarity=0.152  Sum_probs=68.0

Q ss_pred             HHHhhhhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceee
Q psy2029          56 AAEEFKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLE  135 (138)
Q Consensus        56 ~~~~~~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~  135 (138)
                      .+. .++++|..+++.+.+.+ +..++||+|||+++.+|++..... +..+++++|+++||.|.++.+..++..+|++|.
T Consensus        80 lG~-~pt~VQ~~~ip~ll~G~-Iaea~TGeGKTlaf~LP~~l~aL~-g~~vlVltptreLA~qd~e~~~~l~~~lgl~v~  156 (844)
T 1tf5_A           80 TGM-FPFKVQLMGGVALHDGN-IAEMKTGEGKTLTSTLPVYLNALT-GKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVG  156 (844)
T ss_dssp             HSC-CCCHHHHHHHHHHHTTS-EEECCTTSCHHHHHHHHHHHHHTT-SSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEE
T ss_pred             cCC-CCcHHHHHhhHHHhCCC-EEEccCCcHHHHHHHHHHHHHHHc-CCCEEEEeCCHHHHHHHHHHHHHHHhhcCCeEE
Confidence            345 68999999999888844 999999999999999999865543 678999999999999999999999999998876


Q ss_pred             e
Q psy2029         136 V  136 (138)
Q Consensus       136 ~  136 (138)
                      .
T Consensus       157 ~  157 (844)
T 1tf5_A          157 L  157 (844)
T ss_dssp             E
T ss_pred             E
Confidence            4

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.06  E-value=3.2e-10  Score=94.01  Aligned_cols=68  Identities=18%  Similarity=0.260  Sum_probs=59.7

Q ss_pred             hhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhh
Q psy2029          60 FKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE  128 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~  128 (138)
                      .+.++|.++++.+.+ +++++.+|||+|||+++.+++...+ ..+.+++|++|+++|+.|+++++++.+.
T Consensus        39 ~l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~-~~g~~vlvl~PtraLa~Q~~~~l~~~~~  107 (997)
T 4a4z_A           39 ELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAH-RNMTKTIYTSPIKALSNQKFRDFKETFD  107 (997)
T ss_dssp             CCCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHH-HTTCEEEEEESCGGGHHHHHHHHHTTC-
T ss_pred             CCCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHH-hcCCeEEEEeCCHHHHHHHHHHHHHHcC
Confidence            368899999988887 9999999999999999988887654 4578999999999999999999999865

>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=99.05  E-value=1.8e-10  Score=82.75  Aligned_cols=55  Identities=22%  Similarity=0.378  Sum_probs=46.8

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++++.++++|||+|||+++..++...+.+.++++++++|+++|.+|..+++.+++
T Consensus       127 ~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~l~~~~  181 (282)
T 1rif_A          127 VNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYR  181 (282)
T ss_dssp             HHSEEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECSSHHHHHHHHHHHHHHT
T ss_pred             hcCCeEEEcCCCCCcHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHHHHHhc
Confidence            3567899999999999999888777655445599999999999999999998874

>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=99.05  E-value=9.3e-11  Score=89.61  Aligned_cols=54  Identities=17%  Similarity=0.230  Sum_probs=47.4

Q ss_pred             CCCccE-EEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHH
Q psy2029           2 VQNKNC-VLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK   55 (138)
Q Consensus         2 ~~~~~~-~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~   55 (138)
                      ++++++ ++++|||||||+++..+++.++..++.++++++|+++|.+|+++.+..
T Consensus        16 l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~lvl~Ptr~La~Q~~~~l~g   70 (451)
T 2jlq_A           16 FRKKRLTIMDLHPGAGKTKRILPSIVREALLRRLRTLILAPTRVVAAEMEEALRG   70 (451)
T ss_dssp             GSTTCEEEECCCTTSSCCTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTT
T ss_pred             HhcCCeEEEECCCCCCHhhHHHHHHHHHHHhcCCcEEEECCCHHHHHHHHHHhcC
Confidence            566666 999999999999999999887777788999999999999999988743

>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=99.04  E-value=2.8e-10  Score=94.80  Aligned_cols=58  Identities=26%  Similarity=0.277  Sum_probs=51.1

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEF   60 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~   60 (138)
                      ++|+|++++||||||||+ +.++++..+..++.++++++|+++|+.|+++.+.+++...
T Consensus        69 l~g~dvlv~apTGSGKTl-~~lp~l~~~~~~~~~~lil~PtreLa~Q~~~~l~~l~~~~  126 (1054)
T 1gku_B           69 LRKESFAATAPTGVGKTS-FGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKA  126 (1054)
T ss_dssp             HTTCCEECCCCBTSCSHH-HHHHHHHHHHTTSCCEEEEESCHHHHHHHHHHHHHHHTTT
T ss_pred             HhCCCEEEEcCCCCCHHH-HHHHHHHHHhhcCCeEEEEeccHHHHHHHHHHHHHHHhhc
Confidence            578999999999999998 7778777777778899999999999999999999886543

>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=99.04  E-value=2.1e-10  Score=78.62  Aligned_cols=56  Identities=21%  Similarity=0.331  Sum_probs=46.0

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh-----cCCeEEEEcchhhhHHH-HHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI-----KQKSAIFILPYISLVHE-KYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-----~~~~~l~v~P~~aL~~q-~~~~l~~~~   57 (138)
                      ++++++++++|||+|||+++..++...+.+     .+.++++++|+++|.+| ..+.+.++.
T Consensus        46 ~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~~~~~~~~  107 (216)
T 3b6e_A           46 LEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFL  107 (216)
T ss_dssp             HTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTHHHHH
T ss_pred             hcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHHHHHHHHh
Confidence            467899999999999999999988876544     25799999999999999 556666653

>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A

Probab=99.03  E-value=1.7e-09  Score=87.93  Aligned_cols=91  Identities=15%  Similarity=0.098  Sum_probs=72.9

Q ss_pred             hhHHHHHHHHHHHHHh----hhhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHH
Q psy2029          44 SLVHEKYQSLAKAAEE----FKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEK  119 (138)
Q Consensus        44 aL~~q~~~~l~~~~~~----~~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~  119 (138)
                      .+..+.+..+++.+..    .++++|..+++.+.+.+ +..++||+|||+++.+|++..... +..+++++|++.|+.|.
T Consensus        91 ~~lpeafA~vrEa~~R~lG~rP~~VQ~~~ip~Ll~G~-Iaem~TGeGKTLa~~LP~~l~aL~-g~~v~VvTpTreLA~Qd  168 (922)
T 1nkt_A           91 DLLPEAFAVAREAAWRVLDQRPFDVQVMGAAALHLGN-VAEMKTGEGKTLTCVLPAYLNALA-GNGVHIVTVNDYLAKRD  168 (922)
T ss_dssp             HHHHHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHTTE-EEECCTTSCHHHHTHHHHHHHHTT-TSCEEEEESSHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHhHhcCC-EEEecCCCccHHHHHHHHHHHHHh-CCCeEEEeCCHHHHHHH
Confidence            3334444444443322    57899999999888744 999999999999999999765554 67899999999999999


Q ss_pred             HHHHHHHhhhcCceeee
Q psy2029         120 YQSLAKAAEEFKFYLEV  136 (138)
Q Consensus       120 ~~~~~~~~~~~~~~v~~  136 (138)
                      ++.+..++..+|++|..
T Consensus       169 ae~m~~l~~~lGLsv~~  185 (922)
T 1nkt_A          169 SEWMGRVHRFLGLQVGV  185 (922)
T ss_dssp             HHHHHHHHHHTTCCEEE
T ss_pred             HHHHHHHHhhcCCeEEE
Confidence            99999999999998864

>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=99.03  E-value=6.4e-10  Score=93.37  Aligned_cols=88  Identities=14%  Similarity=0.181  Sum_probs=68.6

Q ss_pred             HHHHHHHHHHHhhhhhhhhHHHhhhhc-------cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHH
Q psy2029          48 EKYQSLAKAAEEFKFYLEGKCLEMIQN-------KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKY  120 (138)
Q Consensus        48 q~~~~l~~~~~~~~~~~Q~~~~~~~~~-------~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~  120 (138)
                      ...+.+.+.+...++++|.++++.+.+       .+.++++|||+|||.+++++++..+. .+.++++++|+++|++|.+
T Consensus       591 ~~~~~~~~~f~~~~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~-~g~~vlvlvPt~~La~Q~~  669 (1151)
T 2eyq_A          591 EQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD-NHKQVAVLVPTTLLAQQHY  669 (1151)
T ss_dssp             HHHHHHHHTCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT-TTCEEEEECSSHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHH-hCCeEEEEechHHHHHHHH
Confidence            344555443333468999999955432       38899999999999999888877554 4779999999999999999


Q ss_pred             HHHHHHhhhcCceeee
Q psy2029         121 QSLAKAAEEFKFYLEV  136 (138)
Q Consensus       121 ~~~~~~~~~~~~~v~~  136 (138)
                      +.+++++...++++..
T Consensus       670 ~~~~~~~~~~~i~v~~  685 (1151)
T 2eyq_A          670 DNFRDRFANWPVRIEM  685 (1151)
T ss_dssp             HHHHHHSTTTTCCEEE
T ss_pred             HHHHHHhhcCCCeEEE
Confidence            9999998877776654

>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=99.02  E-value=3e-10  Score=83.30  Aligned_cols=55  Identities=20%  Similarity=0.184  Sum_probs=47.7

Q ss_pred             CC-ccEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           3 QN-KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         3 ~~-~~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +| +++++++|||+|||+++..+++..+.. .+.++++++|+++|.+|..+++.++.
T Consensus        42 ~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~   98 (367)
T 1hv8_A           42 NDEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQVADEIESLK   98 (367)
T ss_dssp             HTCSEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCEEEECCCCChHHHHHHHHHHHHhcccCCCcEEEEcCCHHHHHHHHHHHHHHh
Confidence            45 699999999999999999998876554 46699999999999999999988864

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.01  E-value=2.9e-10  Score=87.64  Aligned_cols=54  Identities=22%  Similarity=0.388  Sum_probs=47.7

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +++++++++|||+|||+++..++...+.+.++++++++|+++|.+|.++++.++
T Consensus       127 ~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~~~~  180 (510)
T 2oca_A          127 VNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDY  180 (510)
T ss_dssp             HHSEEEEECCSTTTHHHHHHHHHHHHHHHCSSEEEEEESSHHHHHHHHHHHHHT
T ss_pred             hcCCcEEEeCCCCCHHHHHHHHHHHHHhCCCCeEEEEECcHHHHHHHHHHHHHh
Confidence            457899999999999999988888766555559999999999999999999876

>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=99.00  E-value=1.8e-10  Score=94.99  Aligned_cols=57  Identities=18%  Similarity=0.374  Sum_probs=50.5

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhc----CCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIK----QKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~----~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|+++++|||+|||+++.+++...+...    ++++++++|+++|..|.++++.+++.
T Consensus       261 l~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~  321 (936)
T 4a2w_A          261 INGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFE  321 (936)
T ss_dssp             HTTCCEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHH
T ss_pred             HcCCCEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHHhc
Confidence            5789999999999999999999998866553    67999999999999999999998754

>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=99.00  E-value=2.9e-10  Score=91.01  Aligned_cols=53  Identities=36%  Similarity=0.662  Sum_probs=47.8

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK   55 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~   55 (138)
                      ++|+|+++++|||||||+++.+++++.+. ++++++|++|+++|+.|.+++++.
T Consensus        38 ~~~~~~lv~apTGsGKT~~~~l~il~~~~-~~~~~l~i~P~r~La~q~~~~~~~   90 (702)
T 2p6r_A           38 FSGKNLLLAMPTAAGKTLLAEMAMVREAI-KGGKSLYVVPLRALAGEKYESFKK   90 (702)
T ss_dssp             TTCSCEEEECSSHHHHHHHHHHHHHHHHH-TTCCEEEEESSHHHHHHHHHHHTT
T ss_pred             hCCCcEEEEcCCccHHHHHHHHHHHHHHH-hCCcEEEEeCcHHHHHHHHHHHHH
Confidence            56889999999999999999999998765 478999999999999999999853

>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=98.99  E-value=1.7e-10  Score=91.45  Aligned_cols=66  Identities=12%  Similarity=0.076  Sum_probs=58.1

Q ss_pred             hhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHH
Q psy2029          59 EFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLA  124 (138)
Q Consensus        59 ~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~  124 (138)
                      ....|+|..+++.+.+ +++++.+|||+|||+++.+++++++...+.+++|++|+++|+.|+++.++
T Consensus       170 ~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~~~~~vLvl~PtreLa~Qi~~~l~  236 (618)
T 2whx_A          170 RIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALR  236 (618)
T ss_dssp             CCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTT
T ss_pred             ccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHhCCCeEEEEcChHHHHHHHHHHhc
Confidence            3456777666777777 99999999999999999999999988777899999999999999998886

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=98.99  E-value=5.5e-10  Score=88.50  Aligned_cols=57  Identities=14%  Similarity=0.188  Sum_probs=51.6

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      .+|+++++.||||+|||++++++++.++...+.+++|++|++++..|..+++.....
T Consensus        20 ~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~~~kvli~t~T~~l~~Qi~~el~~l~~   76 (620)
T 4a15_A           20 QKSYGVALESPTGSGKTIMALKSALQYSSERKLKVLYLVRTNSQEEQVIKELRSLSS   76 (620)
T ss_dssp             HHSSEEEEECCTTSCHHHHHHHHHHHHHHHHTCEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             HcCCCEEEECCCCCCHHHHHHHHHHHhhhhcCCeEEEECCCHHHHHHHHHHHHHHhh
Confidence            368899999999999999999999998877788999999999999999999887644

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=98.99  E-value=3e-10  Score=90.71  Aligned_cols=54  Identities=20%  Similarity=0.159  Sum_probs=49.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +|+|+++++|||||||++|.++++..+...+.++++++|+++|+.|+++.+..+
T Consensus       240 ~g~dvlv~apTGSGKTl~~ll~il~~l~~~~~~~lilaPTr~La~Q~~~~l~~~  293 (673)
T 2wv9_A          240 KRQLTVLDLHPGAGKTRRILPQIIKDAIQKRLRTAVLAPTRVVAAEMAEALRGL  293 (673)
T ss_dssp             TTCEEEECCCTTTTTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTTS
T ss_pred             cCCeEEEEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEccHHHHHHHHHHHHhcC
Confidence            789999999999999999999999887777889999999999999999888543

>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=98.98  E-value=9.3e-10  Score=84.01  Aligned_cols=63  Identities=22%  Similarity=0.231  Sum_probs=55.9

Q ss_pred             hhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          60 FKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      .++++|.++++.+.+ .+.++.+|||+|||++++.++.+.    +.++++++|+++|+.|..++|+++
T Consensus        93 ~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~----~~~~Lvl~P~~~L~~Q~~~~~~~~  156 (472)
T 2fwr_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL----STPTLIVVPTLALAEQWKERLGIF  156 (472)
T ss_dssp             CBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH----CSCEEEEESSHHHHHHHHHHGGGG
T ss_pred             CcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc----CCCEEEEECCHHHHHHHHHHHHhC
Confidence            478899999987777 789999999999999998877653    678999999999999999999984

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=98.97  E-value=1.8e-09  Score=85.56  Aligned_cols=75  Identities=13%  Similarity=0.157  Sum_probs=62.3

Q ss_pred             hhhhhhHHH----hhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceee
Q psy2029          61 KFYLEGKCL----EMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLE  135 (138)
Q Consensus        61 ~~~~Q~~~~----~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~  135 (138)
                      +.+.|.+..    +.+.+ +++++.+|||+|||++++++++..+...+.+++|++|+++++.|..+++..+....++++.
T Consensus         4 ~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~~~kvli~t~T~~l~~Qi~~el~~l~~~~~~~~~   83 (620)
T 4a15_A            4 NRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSERKLKVLYLVRTNSQEEQVIKELRSLSSTMKIRAI   83 (620)
T ss_dssp             -CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHHHTCEEEEEESSHHHHHHHHHHHHHHHHHSCCCEE
T ss_pred             CCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhhcCCeEEEECCCHHHHHHHHHHHHHHhhccCeEEE
Confidence            455666665    33445 8999999999999999999999988777889999999999999999999998876666554

>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=98.96  E-value=2.2e-10  Score=87.53  Aligned_cols=63  Identities=17%  Similarity=0.100  Sum_probs=52.7

Q ss_pred             hhhhhhHHHhhhhc-cce-EEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHH
Q psy2029          61 KFYLEGKCLEMIQN-KNC-VLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLA  124 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~-~~~-ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~  124 (138)
                      +.++|. +++.+.+ ++. ++.+|||+|||+++.+++++.+...+.+++|++|+++|+.|+++.+.
T Consensus         5 ~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~lvl~Ptr~La~Q~~~~l~   69 (451)
T 2jlq_A            5 GEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALLRRLRTLILAPTRVVAAEMEEALR   69 (451)
T ss_dssp             CSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTT
T ss_pred             CCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHhcCCcEEEECCCHHHHHHHHHHhc
Confidence            345564 5666665 555 89999999999999999998888778899999999999999999885

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=98.95  E-value=7.6e-10  Score=91.76  Aligned_cols=54  Identities=24%  Similarity=0.364  Sum_probs=48.2

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ++|++++++||||||||+++.+++...+ .++.+++|++|+++|..|+++++.+.
T Consensus        52 l~g~~vlv~apTGsGKTlv~~~~i~~~~-~~g~~vlvl~PtraLa~Q~~~~l~~~  105 (997)
T 4a4z_A           52 EQGDSVFVAAHTSAGKTVVAEYAIAMAH-RNMTKTIYTSPIKALSNQKFRDFKET  105 (997)
T ss_dssp             HTTCEEEEECCTTSCSHHHHHHHHHHHH-HTTCEEEEEESCGGGHHHHHHHHHTT
T ss_pred             HcCCCEEEEECCCCcHHHHHHHHHHHHH-hcCCeEEEEeCCHHHHHHHHHHHHHH
Confidence            5789999999999999999998888754 45889999999999999999999885

>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=98.94  E-value=1.8e-09  Score=81.38  Aligned_cols=55  Identities=24%  Similarity=0.396  Sum_probs=48.9

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +++ ++++.+|||+|||+++..++...+...+.++++++|+++|..|..+++.++.
T Consensus        22 ~~~-~~ll~~~tG~GKT~~~~~~~~~~~~~~~~~~liv~P~~~L~~q~~~~~~~~~   76 (494)
T 1wp9_A           22 KET-NCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESFRRLF   76 (494)
T ss_dssp             GGS-CEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSSHHHHHHHHHHHHHHB
T ss_pred             hhC-CEEEEcCCCCCHHHHHHHHHHHHHhcCCCeEEEEECCHHHHHHHHHHHHHHh
Confidence            455 8999999999999999999888766668899999999999999999998873

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=98.94  E-value=6.4e-10  Score=92.99  Aligned_cols=55  Identities=31%  Similarity=0.424  Sum_probs=48.3

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|+|++++||||||||++++.+++..+ .++.++++++|+++|+.|+++.+.+++
T Consensus        91 l~g~dvlv~ApTGSGKTl~~l~~il~~~-~~~~~~Lil~PtreLa~Q~~~~l~~l~  145 (1104)
T 4ddu_A           91 VQGKSFTMVAPTGVGKTTFGMMTALWLA-RKGKKSALVFPTVTLVKQTLERLQKLA  145 (1104)
T ss_dssp             TTTCCEEECCSTTCCHHHHHHHHHHHHH-TTTCCEEEEESSHHHHHHHHHHHHTTS
T ss_pred             HcCCCEEEEeCCCCcHHHHHHHHHHHHH-hcCCeEEEEechHHHHHHHHHHHHHhh
Confidence            6789999999999999998877777644 568899999999999999999998854

>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=98.94  E-value=3e-10  Score=90.51  Aligned_cols=56  Identities=23%  Similarity=0.346  Sum_probs=49.4

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhc-C----CeEEEEcchhhhHHHH-HHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIK-Q----KSAIFILPYISLVHEK-YQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~-~----~~~l~v~P~~aL~~q~-~~~l~~~~   57 (138)
                      ++|+++++++|||+|||+++.+++...+... .    +++++++|+++|..|. .+++.+++
T Consensus        20 l~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~   81 (699)
T 4gl2_A           20 LEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFL   81 (699)
T ss_dssp             HSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHHTHHHHH
T ss_pred             HhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHHHHHHHc
Confidence            5688999999999999999999998876552 2    7999999999999999 99998875

>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=98.94  E-value=7.2e-10  Score=84.89  Aligned_cols=54  Identities=20%  Similarity=0.215  Sum_probs=48.8

Q ss_pred             hhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHH
Q psy2029          71 MIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLA  124 (138)
Q Consensus        71 ~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~  124 (138)
                      .+.+ +++++.+|||+|||+++.+++++.+...+.+++|++|+++|+.|+++.++
T Consensus        17 ~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~~~~~~lvl~Ptr~La~Q~~~~l~   71 (459)
T 2z83_A           17 MLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQQRLRTAVLAPTRVVAAEMAEALR   71 (459)
T ss_dssp             GGSTTCEEEECCCTTSCTTTTHHHHHHHHHHHTTCCEEEEECSHHHHHHHHHHTT
T ss_pred             HHhcCCcEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEECchHHHHHHHHHHhc
Confidence            3444 88999999999999999999999888778899999999999999999886

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=98.93  E-value=3.4e-10  Score=90.46  Aligned_cols=67  Identities=16%  Similarity=0.090  Sum_probs=55.8

Q ss_pred             hhhhhhh-----HHHhhhh------c-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          60 FKFYLEG-----KCLEMIQ------N-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        60 ~~~~~Q~-----~~~~~~~------~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      .+.++|.     .+++.+.      + +++++.+|||+|||+++++++++.+...+.+++|++|+++|+.|+++.++.+
T Consensus       215 ~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~~~~~~lilaPTr~La~Q~~~~l~~~  293 (673)
T 2wv9_A          215 YVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQKRLRTAVLAPTRVVAAEMAEALRGL  293 (673)
T ss_dssp             EEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTTS
T ss_pred             ccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEccHHHHHHHHHHHHhcC
Confidence            5667788     7775544      5 9999999999999999999999988777889999999999999999988754

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=98.92  E-value=2.4e-09  Score=75.30  Aligned_cols=63  Identities=22%  Similarity=0.235  Sum_probs=53.7

Q ss_pred             hhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          60 FKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      .+.++|.+++..+.+ .+.++++|||+|||.++..++.+    .+.++++++|+++|++|..++++++
T Consensus        93 ~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~----~~~~~liv~P~~~L~~q~~~~~~~~  156 (237)
T 2fz4_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINE----LSTPTLIVVPTLALAEQWKERLGIF  156 (237)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHH----SCSCEEEEESSHHHHHHHHHHHGGG
T ss_pred             CcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHH----cCCCEEEEeCCHHHHHHHHHHHHhC
Confidence            357789999877766 78999999999999999776654    2678999999999999999999883

>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=98.92  E-value=8.9e-10  Score=83.99  Aligned_cols=52  Identities=17%  Similarity=0.153  Sum_probs=48.0

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      +++++.+|||+|||+++++++++.+...+.+++|++|+++|+.|+++.++.+
T Consensus         9 ~~vlv~a~TGSGKT~~~l~~~l~~~~~~~~~~lil~Ptr~La~Q~~~~l~~~   60 (440)
T 1yks_A            9 MTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGL   60 (440)
T ss_dssp             CEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTTS
T ss_pred             CCEEEEcCCCCCHHHHHHHHHHHHHHhcCCeEEEEcchHHHHHHHHHHHhcC
Confidence            8999999999999999999999988877789999999999999999988744

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=98.91  E-value=1.5e-09  Score=82.44  Aligned_cols=50  Identities=22%  Similarity=0.273  Sum_probs=45.7

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLA  124 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~  124 (138)
                      +++++.+|||+|||+++++++++.+...+.+++|++|+++|++|.++.+.
T Consensus         3 ~~~lv~a~TGsGKT~~~l~~~l~~~~~~g~~~lvl~Pt~~La~Q~~~~~~   52 (431)
T 2v6i_A            3 ELTVLDLHPGAGKTRRVLPQLVREAVKKRLRTVILAPTRVVASEMYEALR   52 (431)
T ss_dssp             CEEEEECCTTSCTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTT
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEECcHHHHHHHHHHHhC
Confidence            68899999999999999999997777778899999999999999988775

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=98.88  E-value=8.5e-09  Score=84.02  Aligned_cols=75  Identities=13%  Similarity=0.111  Sum_probs=66.0

Q ss_pred             hhhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          60 FKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      .++++|..+++.+.+.+ +..+.||+|||+++.++++..... +..+++++|++.||.|.++.+..++..+|++|..
T Consensus        79 ~Pt~VQ~~~ip~LlqG~-IaeakTGeGKTLvf~Lp~~L~aL~-G~qv~VvTPTreLA~Qdae~m~~l~~~lGLsv~~  153 (997)
T 2ipc_A           79 RHFDVQLIGGAVLHEGK-IAEMKTGEGKTLVATLAVALNALT-GKGVHVVTVNDYLARRDAEWMGPVYRGLGLSVGV  153 (997)
T ss_dssp             CCCHHHHHHHHHHHTTS-EEECCSTHHHHHHHHHHHHHHHTT-CSCCEEEESSHHHHHHHHHHHHHHHHTTTCCEEE
T ss_pred             CCcHHHHhhcccccCCc-eeeccCCCchHHHHHHHHHHHHHh-CCCEEEEeCCHHHHHHHHHHHHHHHHhcCCeEEE
Confidence            57899999998888744 899999999999999999755554 6689999999999999999999999999998764

>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=98.87  E-value=2.4e-09  Score=86.75  Aligned_cols=53  Identities=21%  Similarity=0.338  Sum_probs=47.7

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      .|+++++|||||||++|.++++..+. .+.++++++|+++|+.|.++++.++..
T Consensus       390 ~~~Ll~a~TGSGKTlvall~il~~l~-~g~qvlvlaPtr~La~Q~~~~l~~~~~  442 (780)
T 1gm5_A          390 MNRLLQGDVGSGKTVVAQLAILDNYE-AGFQTAFMVPTSILAIQHYRRTVESFS  442 (780)
T ss_dssp             CCCEEECCSSSSHHHHHHHHHHHHHH-HTSCEEEECSCHHHHHHHHHHHHHHHT
T ss_pred             CcEEEEcCCCCCHHHHHHHHHHHHHH-cCCeEEEEeCcHHHHHHHHHHHHHHhh
Confidence            48999999999999999999998654 588999999999999999999988753

>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=98.84  E-value=2.6e-08  Score=69.67  Aligned_cols=68  Identities=16%  Similarity=0.099  Sum_probs=57.6

Q ss_pred             hhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCC----CeEEEEccchhHHHHHHHHHHHHhh
Q psy2029          61 KFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQ----KSAIFILPYISLVHEKYQSLAKAAE  128 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~----~~~~~i~P~~~l~~q~~~~~~~~~~  128 (138)
                      .+++|.++++.+.+ +++++.+|||+|||.....++++.....+    .+++++.|+++++.|.++.+.+...
T Consensus        62 ~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~  134 (235)
T 3llm_A           62 VKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERG  134 (235)
T ss_dssp             GGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTT
T ss_pred             hHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhc
Confidence            57889999988887 89999999999999888888887766533    3899999999999999998886643

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=98.83  E-value=4.3e-09  Score=82.26  Aligned_cols=71  Identities=20%  Similarity=0.241  Sum_probs=57.9

Q ss_pred             hhhhhhHHHh----hhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceee
Q psy2029          61 KFYLEGKCLE----MIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLE  135 (138)
Q Consensus        61 ~~~~Q~~~~~----~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~  135 (138)
                      +++.|.+...    .+.+ +++++.+|||+|||++++++++.    .+.+++|++|+++|+.|..+++..+....++++.
T Consensus         4 ~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~----~~~~v~i~~pt~~l~~q~~~~~~~l~~~~~~~~~   79 (551)
T 3crv_A            4 LRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLE----VKPKVLFVVRTHNEFYPIYRDLTKIREKRNITFS   79 (551)
T ss_dssp             CCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHH----HCSEEEEEESSGGGHHHHHHHHTTCCCSSCCCEE
T ss_pred             CCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHh----CCCeEEEEcCCHHHHHHHHHHHHHHhhhcCccEE
Confidence            4677777663    3445 88999999999999999999987    3789999999999999999999888655555543

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=98.79  E-value=5.8e-09  Score=81.51  Aligned_cols=51  Identities=24%  Similarity=0.337  Sum_probs=45.8

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .+|+++++.||||+|||++++++++.    .+.+++|++|+++|.+|..+++...
T Consensus        20 ~~~~~~~~~a~TGtGKT~~~l~p~l~----~~~~v~i~~pt~~l~~q~~~~~~~l   70 (551)
T 3crv_A           20 RNNFLVALNAPTGSGKTLFSLLVSLE----VKPKVLFVVRTHNEFYPIYRDLTKI   70 (551)
T ss_dssp             HTTCEEEEECCTTSSHHHHHHHHHHH----HCSEEEEEESSGGGHHHHHHHHTTC
T ss_pred             HcCCcEEEECCCCccHHHHHHHHHHh----CCCeEEEEcCCHHHHHHHHHHHHHH
Confidence            36889999999999999999999887    4789999999999999998887765

>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=98.78  E-value=6e-09  Score=79.54  Aligned_cols=51  Identities=22%  Similarity=0.340  Sum_probs=45.1

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ++++++++++|||+|||+++..++...    +.++++++|+++|..|..+++.++
T Consensus       106 ~~~~~~ll~~~TGsGKT~~~l~~i~~~----~~~~Lvl~P~~~L~~Q~~~~~~~~  156 (472)
T 2fwr_A          106 LVDKRGCIVLPTGSGKTHVAMAAINEL----STPTLIVVPTLALAEQWKERLGIF  156 (472)
T ss_dssp             TTTTEEEEECCTTSCHHHHHHHHHHHH----CSCEEEEESSHHHHHHHHHHGGGG
T ss_pred             HhcCCEEEEeCCCCCHHHHHHHHHHHc----CCCEEEEECCHHHHHHHHHHHHhC
Confidence            456789999999999999998887753    789999999999999999998885

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=98.77  E-value=6.5e-09  Score=73.09  Aligned_cols=51  Identities=22%  Similarity=0.345  Sum_probs=43.5

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ++++++++++|||+|||.++..++..    .+.++++++|+++|.+|..+++.++
T Consensus       106 ~~~~~~ll~~~tG~GKT~~a~~~~~~----~~~~~liv~P~~~L~~q~~~~~~~~  156 (237)
T 2fz4_A          106 LVDKRGCIVLPTGSGKTHVAMAAINE----LSTPTLIVVPTLALAEQWKERLGIF  156 (237)
T ss_dssp             TTTSEEEEEESSSTTHHHHHHHHHHH----SCSCEEEEESSHHHHHHHHHHHGGG
T ss_pred             HhCCCEEEEeCCCCCHHHHHHHHHHH----cCCCEEEEeCCHHHHHHHHHHHHhC
Confidence            45678999999999999999777664    3688999999999999998887763

>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=98.76  E-value=1.3e-08  Score=71.16  Aligned_cols=55  Identities=16%  Similarity=0.099  Sum_probs=45.3

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcC----CeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQ----KSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~----~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .+|+++++++|||||||..+..+++......+    .+++++.|++++..|..+++...
T Consensus        74 ~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~  132 (235)
T 3llm_A           74 SQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFE  132 (235)
T ss_dssp             HHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHT
T ss_pred             hcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHH
Confidence            35789999999999999888888777665533    38999999999999998887654

>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=98.73  E-value=2.3e-08  Score=84.04  Aligned_cols=50  Identities=16%  Similarity=0.224  Sum_probs=44.9

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ++++++|||+|||+++..+++..+. .+.++++++|+++|++|.++++.+.
T Consensus       626 d~ll~~~TGsGKT~val~aa~~~~~-~g~~vlvlvPt~~La~Q~~~~~~~~  675 (1151)
T 2eyq_A          626 DRLVCGDVGFGKTEVAMRAAFLAVD-NHKQVAVLVPTTLLAQQHYDNFRDR  675 (1151)
T ss_dssp             EEEEECCCCTTTHHHHHHHHHHHHT-TTCEEEEECSSHHHHHHHHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHHH-hCCeEEEEechHHHHHHHHHHHHHH
Confidence            8999999999999999988887544 5789999999999999999998865

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.72  E-value=9.8e-09  Score=80.10  Aligned_cols=51  Identities=22%  Similarity=0.223  Sum_probs=44.5

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .+|+++++.||||+|||++++++++.    .+.+++|++|+++|.+|..+++...
T Consensus        24 ~~~~~~~~~a~TGtGKT~~~l~~~~~----~~~~~~~~~~t~~l~~q~~~~~~~l   74 (540)
T 2vl7_A           24 KHGKTLLLNAKPGLGKTVFVEVLGMQ----LKKKVLIFTRTHSQLDSIYKNAKLL   74 (540)
T ss_dssp             HTTCEEEEECCTTSCHHHHHHHHHHH----HTCEEEEEESCHHHHHHHHHHHGGG
T ss_pred             HcCCCEEEEcCCCCcHHHHHHHHHHh----CCCcEEEEcCCHHHHHHHHHHHHhc
Confidence            36789999999999999999988765    3789999999999999999877663

>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=98.72  E-value=1.3e-08  Score=82.57  Aligned_cols=58  Identities=16%  Similarity=0.153  Sum_probs=48.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF   62 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~   62 (138)
                      ++|+  +..|+||+|||++|.+|++.+.+. +..+++++|++.|+.|..+.+..++...+.
T Consensus        96 l~G~--Iaea~TGeGKTlaf~LP~~l~aL~-g~~vlVltptreLA~qd~e~~~~l~~~lgl  153 (844)
T 1tf5_A           96 HDGN--IAEMKTGEGKTLTSTLPVYLNALT-GKGVHVVTVNEYLASRDAEQMGKIFEFLGL  153 (844)
T ss_dssp             HTTS--EEECCTTSCHHHHHHHHHHHHHTT-SSCEEEEESSHHHHHHHHHHHHHHHHHTTC
T ss_pred             hCCC--EEEccCCcHHHHHHHHHHHHHHHc-CCCEEEEeCCHHHHHHHHHHHHHHHhhcCC
Confidence            4666  999999999999999999855443 778999999999999999999888665443

>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=98.71  E-value=1.1e-08  Score=82.96  Aligned_cols=58  Identities=14%  Similarity=0.058  Sum_probs=48.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF   62 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~   62 (138)
                      ++|+  +..|+||+|||++|.+|++.+.+ .+..+++++|++.|+.|..+.+.+++...+.
T Consensus        87 l~G~--Iaem~TGsGKTlaf~LP~l~~~l-~g~~vlVltPTreLA~Q~~e~~~~l~~~lgl  144 (853)
T 2fsf_A           87 NERC--IAEMRTGEGKTLTATLPAYLNAL-TGKGVHVVTVNDYLAQRDAENNRPLFEFLGL  144 (853)
T ss_dssp             HSSE--EEECCTTSCHHHHHHHHHHHHHT-TSSCCEEEESSHHHHHHHHHHHHHHHHHTTC
T ss_pred             cCCe--eeeecCCchHHHHHHHHHHHHHH-cCCcEEEEcCCHHHHHHHHHHHHHHHHhcCC
Confidence            4565  89999999999999999986554 3678999999999999999999988665443

>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=98.70  E-value=2e-08  Score=80.01  Aligned_cols=51  Identities=16%  Similarity=0.103  Sum_probs=44.0

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .++++++++||||||||.++.+++++    ++.+++++.|+++|..|..+.+.+.
T Consensus       230 ~~~~~vlv~ApTGSGKT~a~~l~ll~----~g~~vLVl~PTReLA~Qia~~l~~~  280 (666)
T 3o8b_A          230 QSFQVAHLHAPTGSGKSTKVPAAYAA----QGYKVLVLNPSVAATLGFGAYMSKA  280 (666)
T ss_dssp             SSCEEEEEECCTTSCTTTHHHHHHHH----TTCCEEEEESCHHHHHHHHHHHHHH
T ss_pred             HcCCeEEEEeCCchhHHHHHHHHHHH----CCCeEEEEcchHHHHHHHHHHHHHH
Confidence            46789999999999999998887665    4679999999999999999877654

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=98.66  E-value=3.3e-08  Score=79.04  Aligned_cols=51  Identities=29%  Similarity=0.288  Sum_probs=40.9

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|++++++||||||||+.++.    .+.. .++.+|+.|+++|+.|+++++.+.+
T Consensus       153 l~rk~vlv~apTGSGKT~~al~----~l~~-~~~gl~l~PtR~LA~Qi~~~l~~~g  203 (677)
T 3rc3_A          153 MQRKIIFHSGPTNSGKTYHAIQ----KYFS-AKSGVYCGPLKLLAHEIFEKSNAAG  203 (677)
T ss_dssp             SCCEEEEEECCTTSSHHHHHHH----HHHH-SSSEEEEESSHHHHHHHHHHHHHTT
T ss_pred             cCCCEEEEEcCCCCCHHHHHHH----HHHh-cCCeEEEeCHHHHHHHHHHHHHhcC
Confidence            5789999999999999994433    3333 3556999999999999999988764

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.65  E-value=5.3e-08  Score=75.99  Aligned_cols=63  Identities=19%  Similarity=0.169  Sum_probs=51.7

Q ss_pred             hhhhhhhHHHh----hhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          60 FKFYLEGKCLE----MIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        60 ~~~~~Q~~~~~----~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      .+++.|.+...    .+.+ +++++.+|||+|||++++++++..    +.+++|++|+++|++|..+++.++
T Consensus         7 ~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~----~~~~~~~~~t~~l~~q~~~~~~~l   74 (540)
T 2vl7_A            7 QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQL----KKKVLIFTRTHSQLDSIYKNAKLL   74 (540)
T ss_dssp             --CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH----TCEEEEEESCHHHHHHHHHHHGGG
T ss_pred             CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC----CCcEEEEcCCHHHHHHHHHHHHhc
Confidence            46778888763    3445 899999999999999999988653    689999999999999999888774

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=98.62  E-value=1.8e-08  Score=79.08  Aligned_cols=68  Identities=16%  Similarity=0.220  Sum_probs=41.9

Q ss_pred             hhhhhhhHHHhhhh-----c-cceEEEeecCCCchHhHHHHHHHHHHh--------CCCeEEEEccchhHHHHHH-HHHH
Q psy2029          60 FKFYLEGKCLEMIQ-----N-KNCVLSIPTSGGKTLVGEILIMKELKI--------KQKSAIFILPYISLVHEKY-QSLA  124 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~-----~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--------~~~~~~~i~P~~~l~~q~~-~~~~  124 (138)
                      .++++|.++++.+.     . +++++++|||+|||++++..+.+.+..        ..++++|++|+++|+.|.. +.|+
T Consensus       178 ~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~~~  257 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKTFT  257 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHHHHTTCCSSCSSSCCCEEEEEC-----------CCT
T ss_pred             CchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHHHHHHHHhcccccccccCCCeEEEEeCCHHHHHHHHHHHHH
Confidence            47789999985442     2 668999999999999985554443332        3479999999999999999 7776


Q ss_pred             HHh
Q psy2029         125 KAA  127 (138)
Q Consensus       125 ~~~  127 (138)
                      .+.
T Consensus       258 ~~~  260 (590)
T 3h1t_A          258 PFG  260 (590)
T ss_dssp             TTC
T ss_pred             hcc
Confidence            553

>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=98.59  E-value=3.9e-08  Score=78.37  Aligned_cols=62  Identities=16%  Similarity=0.103  Sum_probs=50.0

Q ss_pred             hhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHh
Q psy2029          62 FYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA  127 (138)
Q Consensus        62 ~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~  127 (138)
                      ++.|....+.+.+ +++++.+|||+|||..+.+++++    .+.++++++|+++|+.|.++.+.+.+
T Consensus       219 ~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~----~g~~vLVl~PTReLA~Qia~~l~~~~  281 (666)
T 3o8b_A          219 FTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAA----QGYKVLVLNPSVAATLGFGAYMSKAH  281 (666)
T ss_dssp             CCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHH----TTCCEEEEESCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHH----CCCeEEEEcchHHHHHHHHHHHHHHh
Confidence            3445555555656 88999999999999998887765    46699999999999999999887654

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=98.54  E-value=3.4e-08  Score=77.47  Aligned_cols=52  Identities=19%  Similarity=0.282  Sum_probs=31.8

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhh--------cCCeEEEEcchhhhHHHHH-HHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKI--------KQKSAIFILPYISLVHEKY-QSLAKA   56 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~--------~~~~~l~v~P~~aL~~q~~-~~l~~~   56 (138)
                      +++++++|||+|||+++...+...+..        .++++++++|+++|.+|.. +.+..+
T Consensus       199 ~~~ll~~~TGsGKT~~~~~~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~~~~~  259 (590)
T 3h1t_A          199 KRSLITMATGTGKTVVAFQISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKTFTPF  259 (590)
T ss_dssp             SEEEEEECTTSCHHHHHHHHHHHHHHTTCCSSCSSSCCCEEEEEC-----------CCTTT
T ss_pred             CceEEEecCCCChHHHHHHHHHHHHhcccccccccCCCeEEEEeCCHHHHHHHHHHHHHhc
Confidence            578999999999999986655543332        3579999999999999998 666544

>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=98.51  E-value=9.1e-08  Score=77.95  Aligned_cols=57  Identities=12%  Similarity=0.046  Sum_probs=47.6

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFK   61 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~   61 (138)
                      ++|+  +..|+||+|||++|.+|++.+.+. +..+++++|++.|+.|..+.+.+++...+
T Consensus       124 l~G~--Iaem~TGeGKTLa~~LP~~l~aL~-g~~v~VvTpTreLA~Qdae~m~~l~~~lG  180 (922)
T 1nkt_A          124 HLGN--VAEMKTGEGKTLTCVLPAYLNALA-GNGVHIVTVNDYLAKRDSEWMGRVHRFLG  180 (922)
T ss_dssp             HTTE--EEECCTTSCHHHHTHHHHHHHHTT-TSCEEEEESSHHHHHHHHHHHHHHHHHTT
T ss_pred             hcCC--EEEecCCCccHHHHHHHHHHHHHh-CCCeEEEeCCHHHHHHHHHHHHHHHhhcC
Confidence            4565  999999999999999999755553 67899999999999999999988765443

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=98.43  E-value=1.6e-07  Score=76.73  Aligned_cols=59  Identities=15%  Similarity=0.143  Sum_probs=48.9

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhhh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFY   63 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~   63 (138)
                      ++|+  +..|+||+|||++|.+|++.+.+. +..+++++|++.|+.|.++.+.+++...+..
T Consensus        92 lqG~--IaeakTGeGKTLvf~Lp~~L~aL~-G~qv~VvTPTreLA~Qdae~m~~l~~~lGLs  150 (997)
T 2ipc_A           92 HEGK--IAEMKTGEGKTLVATLAVALNALT-GKGVHVVTVNDYLARRDAEWMGPVYRGLGLS  150 (997)
T ss_dssp             HTTS--EEECCSTHHHHHHHHHHHHHHHTT-CSCCEEEESSHHHHHHHHHHHHHHHHTTTCC
T ss_pred             cCCc--eeeccCCCchHHHHHHHHHHHHHh-CCCEEEEeCCHHHHHHHHHHHHHHHHhcCCe
Confidence            4565  899999999999999999755553 6789999999999999999999986654433

>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=98.39  E-value=7.5e-07  Score=68.37  Aligned_cols=69  Identities=19%  Similarity=0.133  Sum_probs=52.9

Q ss_pred             hhhhhhhHHHhhh----hc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHHHHHHHhhhc
Q psy2029          60 FKFYLEGKCLEMI----QN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAEEF  130 (138)
Q Consensus        60 ~~~~~Q~~~~~~~----~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~~~~~~~~~~  130 (138)
                      .+.++|.++++.+    .. .++++..++|.|||+.++..+ ..+..  ...++++|+| .+|+.|..+++++++...
T Consensus        37 ~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i-~~~~~~~~~~~~LIv~P-~~l~~qw~~e~~~~~~~~  112 (500)
T 1z63_A           37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVF-SDAKKENELTPSLVICP-LSVLKNWEEELSKFAPHL  112 (500)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHH-HHHHHTTCCSSEEEEEC-STTHHHHHHHHHHHCTTS
T ss_pred             cchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHH-HHHHhcCCCCCEEEEcc-HHHHHHHHHHHHHHCCCc
Confidence            4678888887433    23 788999999999999985544 44443  2468999999 679999999999997543

>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=98.39  E-value=6.1e-07  Score=74.38  Aligned_cols=66  Identities=14%  Similarity=0.171  Sum_probs=53.1

Q ss_pred             hhhhhhHHHhhhhc---cceEEEeecCCCchHhHHHHHHHHHHhC-CCeEEEEccchhHHHHHHHHHHHHh
Q psy2029          61 KFYLEGKCLEMIQN---KNCVLSIPTSGGKTLVGEILIMKELKIK-QKSAIFILPYISLVHEKYQSLAKAA  127 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~---~~~ii~~ptg~GKt~~~~~~~l~~~~~~-~~~~~~i~P~~~l~~q~~~~~~~~~  127 (138)
                      ++++|.+++..+..   .+++++.+||.|||.++...+.+.+... ..++++|+|+ +|+.|..+++.+++
T Consensus       154 LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g~~~rvLIVvP~-sLl~Qw~~E~~~~f  223 (968)
T 3dmq_A          154 LIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPE-TLQHQWLVEMLRRF  223 (968)
T ss_dssp             CCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTSSCCCEEEECCT-TTHHHHHHHHHHHS
T ss_pred             CcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEeCH-HHHHHHHHHHHHHh
Confidence            68899998854443   5788999999999999977666554442 3589999999 99999999998875

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=98.36  E-value=5.3e-07  Score=72.14  Aligned_cols=48  Identities=29%  Similarity=0.334  Sum_probs=38.6

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHh
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA  127 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~  127 (138)
                      +++++++|||+|||..+    ++.+.. ..+.+|++|+++|+.|+++.+++..
T Consensus       156 k~vlv~apTGSGKT~~a----l~~l~~-~~~gl~l~PtR~LA~Qi~~~l~~~g  203 (677)
T 3rc3_A          156 KIIFHSGPTNSGKTYHA----IQKYFS-AKSGVYCGPLKLLAHEIFEKSNAAG  203 (677)
T ss_dssp             EEEEEECCTTSSHHHHH----HHHHHH-SSSEEEEESSHHHHHHHHHHHHHTT
T ss_pred             CEEEEEcCCCCCHHHHH----HHHHHh-cCCeEEEeCHHHHHHHHHHHHHhcC
Confidence            78899999999999844    334433 3456999999999999999998863

>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=98.35  E-value=1.7e-06  Score=70.28  Aligned_cols=80  Identities=14%  Similarity=0.019  Sum_probs=55.2

Q ss_pred             HHHHHHHHHHHHhhhhhhhhHHHhhhh-c-cceEEEeecCCCchHhHHHHHHHHHHhC--CCeEEEEccchhHHHHHHHH
Q psy2029          47 HEKYQSLAKAAEEFKFYLEGKCLEMIQ-N-KNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQS  122 (138)
Q Consensus        47 ~q~~~~l~~~~~~~~~~~Q~~~~~~~~-~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~--~~~~~~i~P~~~l~~q~~~~  122 (138)
                      ....+.+...+ ..+.+.|.+.++... + .++++.+|||+|||...-..++......  +.+++++.|+++|+.|+++.
T Consensus        81 ~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTtllp~ll~~~~~~~~~g~~ilvl~P~r~La~q~~~~  159 (773)
T 2xau_A           81 PKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPRRVAAMSVAQR  159 (773)
T ss_dssp             HHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHCGGGGTCEEEEEESCHHHHHHHHHH
T ss_pred             HHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHHHHHHHHHHhccccCCCceEEecCchHHHHHHHHHH
Confidence            34445554444 567888888885544 4 6789999999999993222222222122  56799999999999999987


Q ss_pred             HHHHh
Q psy2029         123 LAKAA  127 (138)
Q Consensus       123 ~~~~~  127 (138)
                      +.+..
T Consensus       160 l~~~~  164 (773)
T 2xau_A          160 VAEEM  164 (773)
T ss_dssp             HHHHT
T ss_pred             HHHHh
Confidence            76543

>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=98.35  E-value=5e-07  Score=75.28  Aligned_cols=68  Identities=13%  Similarity=0.031  Sum_probs=53.4

Q ss_pred             hhhhhhhHHHhhhhc---------------cceEEEeecCCCchHhHHHHHHHHHHhC--CCeEEEEccchhHHHHHHHH
Q psy2029          60 FKFYLEGKCLEMIQN---------------KNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQS  122 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~---------------~~~ii~~ptg~GKt~~~~~~~l~~~~~~--~~~~~~i~P~~~l~~q~~~~  122 (138)
                      .+.++|..+++.+.+               ++.++.+|||+|||+++ +++++.+...  ..++++++|+++|+.|..+.
T Consensus       271 ~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~~~~~~rvLvlvpr~eL~~Q~~~~  349 (1038)
T 2w00_A          271 VMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATELDFIDKVFFVVDRKDLDYQTMKE  349 (1038)
T ss_dssp             ECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTTCTTCCEEEEEECGGGCCHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHhcCCCceEEEEeCcHHHHHHHHHH
Confidence            367889888854321               57899999999999998 6666655432  36899999999999999999


Q ss_pred             HHHHhh
Q psy2029         123 LAKAAE  128 (138)
Q Consensus       123 ~~~~~~  128 (138)
                      |.++..
T Consensus       350 f~~f~~  355 (1038)
T 2w00_A          350 YQRFSP  355 (1038)
T ss_dssp             HHTTST
T ss_pred             HHHhcc
Confidence            988754

>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=98.32  E-value=6.2e-07  Score=74.74  Aligned_cols=52  Identities=13%  Similarity=0.104  Sum_probs=41.6

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ++++++++|||||||+++ +++...+..  ...++++++|.++|..|..+++..+
T Consensus       300 ~~~gli~~~TGSGKT~t~-~~l~~ll~~~~~~~rvLvlvpr~eL~~Q~~~~f~~f  353 (1038)
T 2w00_A          300 ESGGYIWHTTGSGKTLTS-FKAARLATELDFIDKVFFVVDRKDLDYQTMKEYQRF  353 (1038)
T ss_dssp             GGSEEEEECTTSSHHHHH-HHHHHHHTTCTTCCEEEEEECGGGCCHHHHHHHHTT
T ss_pred             CCCEEEEecCCCCHHHHH-HHHHHHHHhcCCCceEEEEeCcHHHHHHHHHHHHHh
Confidence            468999999999999998 554554433  2359999999999999998887665

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=98.23  E-value=1.2e-05  Score=64.81  Aligned_cols=74  Identities=16%  Similarity=0.070  Sum_probs=61.0

Q ss_pred             hhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          61 KFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      ++++|...+-.+.+ .-+..+.||+|||+++.+|++-.++. +..+.+++|+..||.+-++.+..++..+|+.|..
T Consensus        76 ~~dvQligg~~L~~-G~iaEM~TGEGKTLva~lp~~lnAL~-G~~vhVvT~ndyLA~rdae~m~~l~~~Lglsvg~  149 (822)
T 3jux_A           76 PFDVQVMGGIALHE-GKVAEMKTGEGKTLAATMPIYLNALI-GKGVHLVTVNDYLARRDALWMGPVYLFLGLRVGV  149 (822)
T ss_dssp             CCHHHHHHHHHHHT-TCEEECCTTSCHHHHTHHHHHHHHTT-SSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEEE
T ss_pred             CcHHHHHHHHHHhC-CChhhccCCCCccHHHHHHHHHHHhc-CCceEEEeccHHHHHhHHHHHHHHHHHhCCEEEE
Confidence            56666655554444 33889999999999999999866665 6778999999999999999999999999998864

>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=98.18  E-value=3.4e-06  Score=68.46  Aligned_cols=53  Identities=17%  Similarity=0.066  Sum_probs=38.7

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhc--CCeEEEEcchhhhHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQSLAK   55 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~--~~~~l~v~P~~aL~~q~~~~l~~   55 (138)
                      +++++++++|||||||......+.......  +.+++++.|+++|..|+.+.+.+
T Consensus       108 ~~~~vii~gpTGSGKTtllp~ll~~~~~~~~~g~~ilvl~P~r~La~q~~~~l~~  162 (773)
T 2xau_A          108 NNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPRRVAAMSVAQRVAE  162 (773)
T ss_dssp             HCSEEEEECCTTSSHHHHHHHHHHHHHCGGGGTCEEEEEESCHHHHHHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHhccccCCCceEEecCchHHHHHHHHHHHHH
Confidence            456899999999999994333333322222  56799999999999998877654

>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=98.12  E-value=4.8e-06  Score=63.87  Aligned_cols=54  Identities=22%  Similarity=0.185  Sum_probs=41.9

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      .+.++++..|||+|||+.+...+...... ..+++++++| .+|..|..+++.++.
T Consensus        55 ~~~~~ilad~~GlGKT~~ai~~i~~~~~~~~~~~~LIv~P-~~l~~qw~~e~~~~~  109 (500)
T 1z63_A           55 LGFGICLADDMGLGKTLQTIAVFSDAKKENELTPSLVICP-LSVLKNWEEELSKFA  109 (500)
T ss_dssp             TTCCEEECCCTTSCHHHHHHHHHHHHHHTTCCSSEEEEEC-STTHHHHHHHHHHHC
T ss_pred             CCCCEEEEeCCCCcHHHHHHHHHHHHHhcCCCCCEEEEcc-HHHHHHHHHHHHHHC
Confidence            46789999999999999986555543222 3468999999 678899999988874

>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=98.03  E-value=9.2e-06  Score=67.39  Aligned_cols=52  Identities=17%  Similarity=0.300  Sum_probs=42.0

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +.+++++.|||+|||+++...+...+.. ..+++++++|+ +|..|..+++.+.
T Consensus       170 ~~~~LLad~tGlGKTi~Ai~~i~~l~~~g~~~rvLIVvP~-sLl~Qw~~E~~~~  222 (968)
T 3dmq_A          170 APRVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPE-TLQHQWLVEMLRR  222 (968)
T ss_dssp             SCEEEECCCTTSCHHHHHHHHHHHHHHTSSCCCEEEECCT-TTHHHHHHHHHHH
T ss_pred             CCCEEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEeCH-HHHHHHHHHHHHH
Confidence            4578999999999999997777664433 23489999999 9999999998664

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=97.91  E-value=2.9e-05  Score=63.19  Aligned_cols=69  Identities=16%  Similarity=0.159  Sum_probs=52.8

Q ss_pred             hhhhhhHHHhhh----hc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHHHHHHHhhhc
Q psy2029          61 KFYLEGKCLEMI----QN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAEEF  130 (138)
Q Consensus        61 ~~~~Q~~~~~~~----~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~~~~~~~~~~  130 (138)
                      +.++|.+++..+    .. .+.++..++|.|||+.++..+...+..  ..+++++|+| .+|+.|..++|.+++...
T Consensus       237 Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P-~sll~qW~~E~~~~~p~~  312 (800)
T 3mwy_W          237 LRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVP-LSTMPAWLDTFEKWAPDL  312 (800)
T ss_dssp             CCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECC-TTTHHHHHHHHHHHSTTC
T ss_pred             cCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEEC-chHHHHHHHHHHHHCCCc
Confidence            567888887422    24 899999999999999986655443322  4578999999 789999999999997543

>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=97.81  E-value=6.4e-05  Score=59.78  Aligned_cols=69  Identities=25%  Similarity=0.266  Sum_probs=52.4

Q ss_pred             hhhhhhhHHHhhh---------hc-cceEEEeecCCCchHhHHHHHHHHHHhC------CCeEEEEccchhHHHHHHHHH
Q psy2029          60 FKFYLEGKCLEMI---------QN-KNCVLSIPTSGGKTLVGEILIMKELKIK------QKSAIFILPYISLVHEKYQSL  123 (138)
Q Consensus        60 ~~~~~Q~~~~~~~---------~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~------~~~~~~i~P~~~l~~q~~~~~  123 (138)
                      .+.++|.+.+..+         .. .++++..++|.|||+.++..+...+...      ..++++|+|. +|+.|..+++
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~~~~~~p~~~~~LiV~P~-sll~qW~~E~  133 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNEV  133 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHHHHhCccccCCCCcEEEEecH-HHHHHHHHHH
Confidence            4678888887433         23 6789999999999999966665544331      2468999996 7999999999


Q ss_pred             HHHhhh
Q psy2029         124 AKAAEE  129 (138)
Q Consensus       124 ~~~~~~  129 (138)
                      .+++..
T Consensus       134 ~~~~~~  139 (644)
T 1z3i_X          134 GKWLGG  139 (644)
T ss_dssp             HHHHGG
T ss_pred             HHHcCC
Confidence            999754

>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=97.58  E-value=0.0001  Score=59.45  Aligned_cols=54  Identities=19%  Similarity=0.110  Sum_probs=45.3

Q ss_pred             EEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhh
Q psy2029           8 VLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKF   62 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~   62 (138)
                      |..+.||+|||+++.+|++-+.+. |..+.+++|+..|+.+-.+.+.+.....+.
T Consensus        92 iaEM~TGEGKTLva~lp~~lnAL~-G~~vhVvT~ndyLA~rdae~m~~l~~~Lgl  145 (822)
T 3jux_A           92 VAEMKTGEGKTLAATMPIYLNALI-GKGVHLVTVNDYLARRDALWMGPVYLFLGL  145 (822)
T ss_dssp             EEECCTTSCHHHHTHHHHHHHHTT-SSCEEEEESSHHHHHHHHHHHHHHHHHTTC
T ss_pred             hhhccCCCCccHHHHHHHHHHHhc-CCceEEEeccHHHHHhHHHHHHHHHHHhCC
Confidence            889999999999999998855554 788999999999999988888887654443

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=97.55  E-value=0.00015  Score=59.08  Aligned_cols=54  Identities=20%  Similarity=0.215  Sum_probs=42.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++.++++..++|.|||+.+...+...+..  ..+++|+++| .+|..|-.+++.++.
T Consensus       254 ~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P-~sll~qW~~E~~~~~  309 (800)
T 3mwy_W          254 KGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVP-LSTMPAWLDTFEKWA  309 (800)
T ss_dssp             TTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECC-TTTHHHHHHHHHHHS
T ss_pred             cCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEEC-chHHHHHHHHHHHHC
Confidence            57899999999999999986665543222  4668899999 677888888888764

>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=97.49  E-value=0.00024  Score=56.18  Aligned_cols=70  Identities=14%  Similarity=0.094  Sum_probs=53.2

Q ss_pred             hhhhhHHHhhhhc-cceEEEeecCCCch--HhHHHHHHHHHHh-CCCeEEEEccchhHHHHHHHHHHHHhhhcC
Q psy2029          62 FYLEGKCLEMIQN-KNCVLSIPTSGGKT--LVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAAEEFK  131 (138)
Q Consensus        62 ~~~Q~~~~~~~~~-~~~ii~~ptg~GKt--~~~~~~~l~~~~~-~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~  131 (138)
                      .++|..+++.... +.+++..|+|+|||  +.+++..+..+.. .+.++++++||...+.+..+.+......++
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~~~~~~vll~APTg~AA~~L~e~~~~~~~~l~  224 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGKALRQLP  224 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHTHHHHHSS
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhhcCCCeEEEEeCChhHHHHHHHHHHHHHhcCC
Confidence            5779988876666 88899999999999  5555555554322 346899999999999998888776655443

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=97.45  E-value=0.0031  Score=43.41  Aligned_cols=39  Identities=21%  Similarity=0.254  Sum_probs=30.9

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      .|.-+++.+++|+|||..+.-.+.+.+.+.+.+++|+.-
T Consensus        29 ~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s~   67 (251)
T 2zts_A           29 EGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTL   67 (251)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEES
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeecc
Confidence            466789999999999999977777666666778888753

>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=97.35  E-value=0.00046  Score=54.88  Aligned_cols=54  Identities=30%  Similarity=0.343  Sum_probs=41.1

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhc------CCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIK------QKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~------~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++.++|+..+||.|||+.+...+...+...      .+++|+++|. +|..|-.+++.++.
T Consensus        78 ~~~g~ILad~mGlGKT~~~i~~i~~l~~~~~~~~p~~~~~LiV~P~-sll~qW~~E~~~~~  137 (644)
T 1z3i_X           78 NSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNEVGKWL  137 (644)
T ss_dssp             TCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHHHHHHH
T ss_pred             CCCCeEeeeCCCchHHHHHHHHHHHHHHhCccccCCCCcEEEEecH-HHHHHHHHHHHHHc
Confidence            456789999999999999876666543321      2468999996 77788888888874

>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=97.23  E-value=0.00049  Score=54.45  Aligned_cols=55  Identities=18%  Similarity=0.114  Sum_probs=39.7

Q ss_pred             CCCccEEEEccCCcchHH--HHHHHHHHHHh-hcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTL--VGEILIMKELK-IKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~--~~~~~~~~~~~-~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +.+..+++++|+|+|||.  .+.+..+..+. ..+.+++++.|+.....+..+.+...
T Consensus       162 l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~~~~~~vll~APTg~AA~~L~e~~~~~  219 (608)
T 1w36_D          162 LTRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGKA  219 (608)
T ss_dssp             HTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHTHH
T ss_pred             hcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhhcCCCeEEEEeCChhHHHHHHHHHHHH
Confidence            356789999999999994  44555554332 23558999999999888777665543

>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=97.19  E-value=0.0059  Score=44.41  Aligned_cols=41  Identities=15%  Similarity=-0.029  Sum_probs=30.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhc-----CCeEEEEcchh
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIK-----QKSAIFILPYI   43 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~-----~~~~l~v~P~~   43 (138)
                      .|+.+++.+|+|+|||..+...+.......     +.+++|+.--.
T Consensus       106 ~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~  151 (324)
T 2z43_A          106 TRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEG  151 (324)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSS
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCC
Confidence            467789999999999999877766533322     56888886443

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=97.18  E-value=0.024  Score=41.02  Aligned_cols=129  Identities=14%  Similarity=0.024  Sum_probs=68.8

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH--h--h-------h--hhhhhH--
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE--E--F-------K--FYLEGK--   67 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~--~--~-------~--~~~Q~~--   67 (138)
                      .|.-+++.+++|+|||..+...+..... .+.+++|+..--. ..+...++.....  .  .       +  -.++..  
T Consensus        67 ~G~l~li~G~pG~GKTtl~l~ia~~~a~-~g~~vl~~slE~s-~~~l~~R~~~~~~~i~~~~l~~~~~~l~~~~~~~l~~  144 (315)
T 3bh0_A           67 RRNFVLIAARPSMGKTAFALKQAKNMSD-NDDVVNLHSLEMG-KKENIKRLIVTAGSINAQKIKAARRDFASEDWGKLSM  144 (315)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHHHT-TTCEEEEEESSSC-HHHHHHHHHHHHTTCCHHHHHSCHHHHCSSCHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHH-cCCeEEEEECCCC-HHHHHHHHHHHHcCCCHHHHhcCCCCCCHHHHHHHHH
Confidence            5677899999999999988776665443 4578888753211 1333344332210  0  0       0  011111  


Q ss_pred             HHhhhhccceEEEeecCCCchHhHHHHHHHHHHh-CCCe--EEEEccchhH------------HHHHHHHHHHHhhhcCc
Q psy2029          68 CLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKS--AIFILPYISL------------VHEKYQSLAKAAEEFKF  132 (138)
Q Consensus        68 ~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~--~~~i~P~~~l------------~~q~~~~~~~~~~~~~~  132 (138)
                      +...+.+.++.+.-+.  +-+...+...++++.. .+.+  .++|.+...+            +.+..+.++.+++.+++
T Consensus       145 a~~~l~~~~i~i~d~~--~~~~~~i~~~i~~l~~~~~~~~~lVVID~l~~l~~~~~~~~r~~~i~~~~~~Lk~lAk~~~i  222 (315)
T 3bh0_A          145 AIGEISNSNINIFDKA--GQSVNYIWSKTRQTKRKNPGKRVIVMIDYLQLLEPAKANDSRTNQISQISRDLKKMARELDV  222 (315)
T ss_dssp             HHHHHHTSCEEEECCS--CCBHHHHHHHHHHHHHTSSSCCEEEEEECGGGSBCSCTTSCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHhCCCEEEECCC--CCCHHHHHHHHHHHHHhcCCCCeEEEEeCchhcCCCCCCCCHHHHHHHHHHHHHHHHHHhCC
Confidence            1112222344433322  2445555555565554 3556  7777665443            23455677788888877


Q ss_pred             eee
Q psy2029         133 YLE  135 (138)
Q Consensus       133 ~v~  135 (138)
                      .|.
T Consensus       223 ~vi  225 (315)
T 3bh0_A          223 VVI  225 (315)
T ss_dssp             EEE
T ss_pred             eEE
Confidence            654

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=97.04  E-value=0.0014  Score=52.11  Aligned_cols=50  Identities=18%  Similarity=0.143  Sum_probs=39.3

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      -.+|.+|.|+|||.+....+. ++..++.++|+++|+..-++++.+.+...
T Consensus       207 ~~lI~GPPGTGKT~ti~~~I~-~l~~~~~~ILv~a~TN~AvD~i~erL~~~  256 (646)
T 4b3f_X          207 LAIIHGPPGTGKTTTVVEIIL-QAVKQGLKVLCCAPSNIAVDNLVERLALC  256 (646)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH-HHHHTTCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             ceEEECCCCCCHHHHHHHHHH-HHHhCCCeEEEEcCchHHHHHHHHHHHhc
Confidence            469999999999987654444 45567889999999988888888777543

>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=96.92  E-value=0.0012  Score=52.25  Aligned_cols=52  Identities=15%  Similarity=0.222  Sum_probs=39.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAK   55 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~   55 (138)
                      .+...+|.+|.|+|||.+....+. ++.. .+.++++++|+..-+++..+.+.+
T Consensus       194 ~~~~~li~GppGTGKT~~~~~~i~-~l~~~~~~~ilv~a~tn~A~~~l~~~l~~  246 (624)
T 2gk6_A          194 QRPLSLIQGPPGTGKTVTSATIVY-HLARQGNGPVLVCAPSNIAVDQLTEKIHQ  246 (624)
T ss_dssp             TCSEEEEECCTTSCHHHHHHHHHH-HHHTSSSCCEEEEESSHHHHHHHHHHHHT
T ss_pred             cCCCeEEECCCCCCHHHHHHHHHH-HHHHcCCCeEEEEeCcHHHHHHHHHHHHh
Confidence            345679999999999987644433 3444 577999999999888888777654

>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=96.92  E-value=0.021  Score=41.93  Aligned_cols=103  Identities=10%  Similarity=-0.029  Sum_probs=55.1

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh-----cCCeEEEEcchhhhHHHHHH-HHHHHHHhhhhhhhhHHHhhhhccc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI-----KQKSAIFILPYISLVHEKYQ-SLAKAAEEFKFYLEGKCLEMIQNKN   76 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-----~~~~~l~v~P~~aL~~q~~~-~l~~~~~~~~~~~Q~~~~~~~~~~~   76 (138)
                      .|+-+++.+|.|+|||..+...+......     .+++++|+..-..+..+... .....    +++.+. +    . .+
T Consensus       121 ~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~~~~~~~----g~~~~~-~----l-~~  190 (343)
T 1v5w_A          121 SMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDIADRF----NVDHDA-V----L-DN  190 (343)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHHHHHHT----TCCHHH-H----H-HT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHHHHHHc----CCCHHH-H----H-hc
Confidence            46778999999999999987776654332     36788888654433222222 22222    222211 1    1 23


Q ss_pred             eEEEeecCCCchHhHHHHHHHHHH-h--CCCeEEEEccchhHH
Q psy2029          77 CVLSIPTSGGKTLVGEILIMKELK-I--KQKSAIFILPYISLV  116 (138)
Q Consensus        77 ~ii~~ptg~GKt~~~~~~~l~~~~-~--~~~~~~~i~P~~~l~  116 (138)
                      +.+.-+. ++......+..+..+. .  .+.+.++|....++.
T Consensus       191 l~~~~~~-~~e~~~~ll~~l~~~i~~~~~~~~lvVIDsl~~l~  232 (343)
T 1v5w_A          191 VLYARAY-TSEHQMELLDYVAAKFHEEAGIFKLLIIDSIMALF  232 (343)
T ss_dssp             EEEEECC-STTHHHHHHHHHHHHHHHSCSSEEEEEEETSGGGH
T ss_pred             eeEeecC-CHHHHHHHHHHHHHHHHhcCCCccEEEEechHHHH
Confidence            4444333 3333333333333333 3  456778887766554

>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=96.86  E-value=0.0027  Score=50.09  Aligned_cols=53  Identities=15%  Similarity=0.040  Sum_probs=40.9

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhc---CCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIK---QKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~---~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +..++|.||.|||||.+...-+...+.+.   ..++++++++.....+..+.+.+.
T Consensus        22 ~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~aa~e~~~rl~~~   77 (647)
T 3lfu_A           22 RSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQL   77 (647)
T ss_dssp             SSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEeccHHHHHHHHHHHHHH
Confidence            45789999999999998766665533332   258999999999888888877664

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=96.85  E-value=0.043  Score=41.59  Aligned_cols=130  Identities=9%  Similarity=-0.033  Sum_probs=68.0

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH--h--h-------hhhhhh--HHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE--E--F-------KFYLEG--KCL   69 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~--~--~-------~~~~Q~--~~~   69 (138)
                      .|.-+++.+|+|+|||..+.-.+.......+.+++|+..--. ..+...++.....  .  .       .-.|+.  .+.
T Consensus       199 ~G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~slE~~-~~~l~~R~~~~~~~i~~~~l~~g~l~~~~~~~~~~a~  277 (444)
T 2q6t_A          199 PGSLNIIAARPAMGKTAFALTIAQNAALKEGVGVGIYSLEMP-AAQLTLRMMCSEARIDMNRVRLGQLTDRDFSRLVDVA  277 (444)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEESSSC-HHHHHHHHHHHHTTCCTTTCCGGGCCHHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEECCCC-HHHHHHHHHHHHcCCCHHHHhCCCCCHHHHHHHHHHH
Confidence            466789999999999999877777655444668888653211 1233333322110  0  0       001111  111


Q ss_pred             hhhhccceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHH---------------HHHHHHHHHHhhhcCce
Q psy2029          70 EMIQNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLV---------------HEKYQSLAKAAEEFKFY  133 (138)
Q Consensus        70 ~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~---------------~q~~~~~~~~~~~~~~~  133 (138)
                      ..+...++.+.-+  .+-+..-+...++++.. .+.+.++|.+...+.               .+..+.++.++..+++.
T Consensus       278 ~~l~~~~l~i~d~--~~~s~~~l~~~~~~l~~~~~~~lIvID~l~~~~~~~~~~~~~~r~~~i~~i~~~Lk~lAke~~v~  355 (444)
T 2q6t_A          278 SRLSEAPIYIDDT--PDLTLMEVRARARRLVSQNQVGLIIIDYLQLMSGPGSGKSGENRQQEIAAISRGLKALARELGIP  355 (444)
T ss_dssp             HHHHTSCEEEECC--TTCBHHHHHHHHHHHHHHSCCCEEEEECGGGCBCC-------CHHHHHHHHHHHHHHHHHHHTSC
T ss_pred             HHHhcCCEEEECC--CCCCHHHHHHHHHHHHHHcCCCEEEEcChhhcCCCcCCCCCCCHHHHHHHHHHHHHHHHHHhCCe
Confidence            1222233333322  33344444455555543 467777776654332               34556677777777766


Q ss_pred             ee
Q psy2029         134 LE  135 (138)
Q Consensus       134 v~  135 (138)
                      |.
T Consensus       356 vi  357 (444)
T 2q6t_A          356 II  357 (444)
T ss_dssp             EE
T ss_pred             EE
Confidence            53

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=96.81  E-value=0.0031  Score=51.47  Aligned_cols=53  Identities=17%  Similarity=0.217  Sum_probs=40.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .+...+|.+|.|+|||.+....+. ++.. .+.++++++|+..-+++..+.+.+.
T Consensus       374 ~~~~~lI~GppGTGKT~~i~~~i~-~l~~~~~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          374 QRPLSLIQGPPGTGKTVTSATIVY-HLSKIHKDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             TCSEEEEECSTTSSHHHHHHHHHH-HHHHHHCCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             cCCCEEEECCCCCCHHHHHHHHHH-HHHhCCCCeEEEEcCcHHHHHHHHHHHHhh
Confidence            345679999999999987644443 3433 5789999999998888888777654

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=96.80  E-value=0.053  Score=39.90  Aligned_cols=129  Identities=13%  Similarity=0.081  Sum_probs=70.1

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH----hh-------hhhhhhHHH--
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE----EF-------KFYLEGKCL--   69 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~----~~-------~~~~Q~~~~--   69 (138)
                      .|.-+++.+++|+|||..+.-.+..... .+.+++|+..--. ..|...++.....    ..       .-.|+....  
T Consensus        45 ~G~LiiIaG~pG~GKTt~al~ia~~~a~-~g~~Vl~fSlEms-~~ql~~Rlls~~~~v~~~~l~~g~Ls~~e~~~l~~a~  122 (338)
T 4a1f_A           45 KGSLVIIGARPSMGKTSLMMNMVLSALN-DDRGVAVFSLEMS-AEQLALRALSDLTSINMHDLESGRLDDDQWENLAKCF  122 (338)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHHH-TTCEEEEEESSSC-HHHHHHHHHHHHHCCCHHHHHHTCCCHHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHH-cCCeEEEEeCCCC-HHHHHHHHHHHhhCCCHHHHhcCCCCHHHHHHHHHHH
Confidence            4667899999999999998766665443 5778888753111 1233333322110    00       112222111  


Q ss_pred             hhhhccceEEEeecCCCchHhHHHHHHHHHHh-C-CCeEEEEccchhH------------HHHHHHHHHHHhhhcCceee
Q psy2029          70 EMIQNKNCVLSIPTSGGKTLVGEILIMKELKI-K-QKSAIFILPYISL------------VHEKYQSLAKAAEEFKFYLE  135 (138)
Q Consensus        70 ~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~-~-~~~~~~i~P~~~l------------~~q~~~~~~~~~~~~~~~v~  135 (138)
                      ..+.+.++.+. .+ .+-+..-+...++++.. + +...++|.+...+            +.+..+.++.+++.+++.|.
T Consensus       123 ~~l~~~~l~I~-d~-~~~si~~i~~~ir~l~~~~gg~~lIVIDyLqlm~~~~~~~~r~~ei~~isr~LK~lAkel~vpVi  200 (338)
T 4a1f_A          123 DHLSQKKLFFY-DK-SYVRIEQIRLQLRKLKSQHKELGIAFIDYLQLMSGSKATKERHEQIAEISRELKTLARELEIPII  200 (338)
T ss_dssp             HHHHHSCEEEE-CC-TTCCHHHHHHHHHHHHHHCTTEEEEEEEEEECCCTHHHHHHCCCCHHHHHHHHHHHHHHHTSCEE
T ss_pred             HHHhcCCeEEe-CC-CCCcHHHHHHHHHHHHHhcCCCCEEEEechHHhcCCCCCCChHHHHHHHHHHHHHHHHHcCCeEE
Confidence            22223344332 22 33355555556666654 3 4566666543322            45667888888888887764

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=96.76  E-value=0.073  Score=40.45  Aligned_cols=38  Identities=11%  Similarity=0.064  Sum_probs=29.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      .|+-+++.+|+|+|||..+...+.......+.+++|+.
T Consensus       202 ~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s  239 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFS  239 (454)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEE
Confidence            56778999999999999987776665444466788875

>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=96.75  E-value=0.03  Score=38.25  Aligned_cols=39  Identities=15%  Similarity=0.026  Sum_probs=28.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhc-----CCeEEEEcc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIK-----QKSAIFILP   41 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~-----~~~~l~v~P   41 (138)
                      .|+-+.+.+|+|+|||..+...+...+...     +.+++|+.-
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~   66 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDT   66 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEES
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEEC
Confidence            467889999999999998876665433322     567788753

>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=96.74  E-value=0.016  Score=41.84  Aligned_cols=42  Identities=14%  Similarity=0.005  Sum_probs=30.0

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh-----------cC----CeEEEEcchhh
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI-----------KQ----KSAIFILPYIS   44 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-----------~~----~~~l~v~P~~a   44 (138)
                      .|+-+++.+|.|+|||..+...+....+.           .+    .+++|+.--..
T Consensus        97 ~g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~  153 (322)
T 2i1q_A           97 SQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGT  153 (322)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCC
Confidence            45678999999999999987776653322           23    68888865433

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=96.73  E-value=0.072  Score=40.54  Aligned_cols=129  Identities=14%  Similarity=0.023  Sum_probs=70.6

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH--H--h---hh------hhhhh--H
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA--E--E---FK------FYLEG--K   67 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~--~--~---~~------~~~Q~--~   67 (138)
                      .|.-+++.|++|+|||..+.-.+.....+ +.+++|+..--. ..|...++....  .  .   .+      ..|+.  .
T Consensus       196 ~G~liiIaG~pG~GKTtlal~ia~~~a~~-g~~vl~fSlEms-~~ql~~R~~~~~~~i~~~~l~~g~~~l~~~~~~~l~~  273 (444)
T 3bgw_A          196 RRNFVLIAARPSMGKTAFALKQAKNMSDN-DDVVNLHSLEMG-KKENIKRLIVTAGSINAQKIKAARRDFASEDWGKLSM  273 (444)
T ss_dssp             SSCEEEEEECSSSSHHHHHHHHHHHHHHT-TCEEEEECSSSC-TTHHHHHHHHHHSCCCHHHHHHTGGGTCCSCHHHHHH
T ss_pred             CCcEEEEEeCCCCChHHHHHHHHHHHHHc-CCEEEEEECCCC-HHHHHHHHHHHHcCCCHHHHhcccCCCCHHHHHHHHH
Confidence            46678999999999999987777765544 778888753211 123333332211  0  0   00      01111  1


Q ss_pred             HHhhhhccceEEEeecCCCchHhHHHHHHHHHHh-CCCe--EEEEccchhH------------HHHHHHHHHHHhhhcCc
Q psy2029          68 CLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKS--AIFILPYISL------------VHEKYQSLAKAAEEFKF  132 (138)
Q Consensus        68 ~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~--~~~i~P~~~l------------~~q~~~~~~~~~~~~~~  132 (138)
                      +...+.+.++.+.-+  .+-+...+...++++.. .+.+  .++|.+...+            +.+..+.++.+++.+++
T Consensus       274 a~~~l~~~~l~i~d~--~~~s~~~i~~~ir~l~~~~~~~~~lIVID~Lq~~~~~~~~~~r~~~i~~i~~~Lk~lAke~~v  351 (444)
T 3bgw_A          274 AIGEISNSNINIFDK--AGQSVNYIWSKTRQTKRKNPGKRVIVMIDYLQLLEPAKANDSRTNQISQISRDLKKMARELDV  351 (444)
T ss_dssp             HHHHHHTSCEEEECC--SSCBHHHHHHHHHHHHHHSCSSCEEEEEECSTTSBCSCSSSCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHhcCCEEEECC--CCCCHHHHHHHHHHHHHHhCCCCeEEEEecHHhccCCCCCCCHHHHHHHHHHHHHHHHHHhCC
Confidence            112222334443322  24555555555666543 4556  7777654322            34556778888888887


Q ss_pred             eee
Q psy2029         133 YLE  135 (138)
Q Consensus       133 ~v~  135 (138)
                      .|.
T Consensus       352 ~vi  354 (444)
T 3bgw_A          352 VVI  354 (444)
T ss_dssp             EEE
T ss_pred             eEE
Confidence            764

>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=96.73  E-value=0.0026  Score=41.99  Aligned_cols=37  Identities=16%  Similarity=0.111  Sum_probs=25.1

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      +|+.+++++|+|+|||..+...+-....+.+.+++++
T Consensus        37 ~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~~   73 (180)
T 3ec2_A           37 EGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFF   73 (180)
T ss_dssp             GCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCEE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEEE
Confidence            4678999999999999887554443222345455553

>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=96.73  E-value=0.023  Score=38.24  Aligned_cols=35  Identities=14%  Similarity=0.102  Sum_probs=27.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      .|+-+++.+|+|+|||..+...+.    ..+.+++|+.-
T Consensus        19 ~G~~~~i~G~~GsGKTtl~~~l~~----~~~~~v~~i~~   53 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLALQTGL----LSGKKVAYVDT   53 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHH----HHCSEEEEEES
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH----HcCCcEEEEEC
Confidence            567789999999999988866655    34778888753

>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=96.62  E-value=0.0086  Score=47.17  Aligned_cols=68  Identities=12%  Similarity=-0.023  Sum_probs=52.7

Q ss_pred             hhhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhC---CCeEEEEccchhHHHHHHHHHHHHhh
Q psy2029          60 FKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIK---QKSAIFILPYISLVHEKYQSLAKAAE  128 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~---~~~~~~i~P~~~l~~q~~~~~~~~~~  128 (138)
                      .+.+-|.+++. ..+..+++.++.|+|||.+....+.+.+...   +.+++++++++..+.+..+.+.+...
T Consensus         9 ~Ln~~Q~~av~-~~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~aa~e~~~rl~~~~~   79 (647)
T 3lfu_A            9 SLNDKQREAVA-APRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLMG   79 (647)
T ss_dssp             TCCHHHHHHHT-CCSSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHHHHHHHHHHHHHHC
T ss_pred             cCCHHHHHHHh-CCCCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEeccHHHHHHHHHHHHHHhc
Confidence            35566777765 1237889999999999999877776655542   35899999999999999999988754

>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=96.62  E-value=0.11  Score=39.88  Aligned_cols=131  Identities=8%  Similarity=-0.067  Sum_probs=69.6

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhh------------hh--hhhhH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEF------------KF--YLEGK   67 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~------------~~--~~Q~~   67 (138)
                      ..|+-+++.+++|+|||..+.-.+.......+.+++|+.---. ..|...++.......            ..  .+.. 
T Consensus       240 ~~G~l~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s~E~s-~~~l~~r~~~~~~~~~~~~~~~~~~g~l~~~~~~~-  317 (503)
T 1q57_A          240 RGGEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAMLEES-VEETAEDLIGLHNRVRLRQSDSLKREIIENGKFDQ-  317 (503)
T ss_dssp             CTTCEEEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEESSSC-HHHHHHHHHHHHTTSCCTTCHHHHHHHHHTSHHHH-
T ss_pred             CCCeEEEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEeccCC-HHHHHHHHHHHHcCCChhhccccccCCCCHHHHHH-
Confidence            3567789999999999999877777644433678888753111 123334332211100            00  0000 


Q ss_pred             HHhhh-hccceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhH------------HHHHHHHHHHHhhhcCce
Q psy2029          68 CLEMI-QNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISL------------VHEKYQSLAKAAEEFKFY  133 (138)
Q Consensus        68 ~~~~~-~~~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l------------~~q~~~~~~~~~~~~~~~  133 (138)
                      ..... .+.++.+.-+ .+.-+...+...++++.. .+.+.++|.+...+            +.+..+.++.+++.+++.
T Consensus       318 ~~~~~~~~~~l~i~~~-~~~~~~~~i~~~i~~~~~~~~~~lvVID~l~~l~~~~~~~~~~~~~~~~~~~Lk~lak~~~i~  396 (503)
T 1q57_A          318 WFDELFGNDTFHLYDS-FAEAETDRLLAKLAYMRSGLGCDVIILDHISIVVSASGESDERKMIDNLMTKLKGFAKSTGVV  396 (503)
T ss_dssp             HHHHHHTTTCEEEECC-C---CHHHHHHHHHHHHHTTCCSEEEEECTTCCCSCCSCCCHHHHHHHHHHHHHHHHHHHTCE
T ss_pred             HHHHHhccCCEEEECC-CCCCCHHHHHHHHHHHHHhcCCCEEEEccchhcCCCCCCCCHHHHHHHHHHHHHHHHHHHCCe
Confidence            11111 1244444322 222444455555555543 46777888776543            235667788888888776


Q ss_pred             ee
Q psy2029         134 LE  135 (138)
Q Consensus       134 v~  135 (138)
                      |.
T Consensus       397 vi  398 (503)
T 1q57_A          397 LV  398 (503)
T ss_dssp             EE
T ss_pred             EE
Confidence            54

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=96.60  E-value=0.0079  Score=47.78  Aligned_cols=65  Identities=14%  Similarity=0.069  Sum_probs=49.8

Q ss_pred             hhhhhhHHHhhhhc--cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          61 KFYLEGKCLEMIQN--KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~--~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      +.+.|.+++.....  .-.++.-|.|+|||....-.+. ++..++.++++++|+..-|++..+.+...
T Consensus       190 LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~~I~-~l~~~~~~ILv~a~TN~AvD~i~erL~~~  256 (646)
T 4b3f_X          190 LDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIIL-QAVKQGLKVLCCAPSNIAVDNLVERLALC  256 (646)
T ss_dssp             CCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHHHHH-HHHHTTCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHHHHH-HHHhCCCeEEEEcCchHHHHHHHHHHHhc
Confidence            45678888755543  3457999999999988755444 45556889999999999999988888654

>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=96.58  E-value=0.044  Score=40.22  Aligned_cols=89  Identities=16%  Similarity=0.170  Sum_probs=53.8

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeec
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPT   83 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~pt   83 (138)
                      -+.+.+|.|+|||..++..+...... .+++++|+..--++....   .++.+               .+ .++++..|+
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~~r---a~~lG---------------vd~d~llv~~~~   91 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITPAY---LRSMG---------------VDPERVIHTPVQ   91 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCHHH---HHHTT---------------CCGGGEEEEECS
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhHHH---HHHhC---------------CCHHHeEEEcCC
Confidence            57899999999999998877765443 278999988755554321   22221               12 456666665


Q ss_pred             CCCchHhHH-HHHHHHH---HhCCCeEEEEccchhHH
Q psy2029          84 SGGKTLVGE-ILIMKEL---KIKQKSAIFILPYISLV  116 (138)
Q Consensus        84 g~GKt~~~~-~~~l~~~---~~~~~~~~~i~P~~~l~  116 (138)
                      .    .--. +.+++.+   .+...+.++|....+|.
T Consensus        92 ~----~E~~~l~i~~~l~~i~~~~~~lvVIDSI~aL~  124 (333)
T 3io5_A           92 S----LEQLRIDMVNQLDAIERGEKVVVFIDSLGNLA  124 (333)
T ss_dssp             B----HHHHHHHHHHHHHTCCTTCCEEEEEECSTTCB
T ss_pred             C----HHHHHHHHHHHHHHhhccCceEEEEecccccc
Confidence            2    2222 3333443   23456777777766663

>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=96.56  E-value=0.0059  Score=48.38  Aligned_cols=65  Identities=11%  Similarity=0.114  Sum_probs=49.1

Q ss_pred             hhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          61 KFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      +.+.|..++..... ...++..|.|+|||....-.+ ..+.. .+.++++++|+..-+.+..+.+.+.
T Consensus       181 ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~~~i-~~l~~~~~~~ilv~a~tn~A~~~l~~~l~~~  247 (624)
T 2gk6_A          181 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIV-YHLARQGNGPVLVCAPSNIAVDQLTEKIHQT  247 (624)
T ss_dssp             CCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHHHHH-HHHHTSSSCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHHHHH-HHHHHcCCCeEEEEeCcHHHHHHHHHHHHhc
Confidence            45667777755555 677899999999998875444 44444 5789999999999998888877654

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=96.56  E-value=0.0067  Score=49.55  Aligned_cols=65  Identities=12%  Similarity=0.147  Sum_probs=49.8

Q ss_pred             hhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          61 KFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      +.+.|..++..... ...++..|.|+|||.+..-.+. .+.. .+.++++++|+..-+.+..+.+.+.
T Consensus       361 Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~~~i~-~l~~~~~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          361 LNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVY-HLSKIHKDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             CCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHHHHH-HHHHHHCCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHH-HHHhCCCCeEEEEcCcHHHHHHHHHHHHhh
Confidence            44667777765555 6678999999999988754443 3433 5789999999999999999888765

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=96.52  E-value=0.0038  Score=45.26  Aligned_cols=36  Identities=22%  Similarity=0.129  Sum_probs=26.6

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHh-hcCCeEEEEc
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELK-IKQKSAIFIL   40 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~-~~~~~~l~v~   40 (138)
                      +.++++++|+|+|||..+...+. .+. ..+.+++++.
T Consensus       152 ~~~lll~G~~GtGKT~La~aia~-~~~~~~g~~v~~~~  188 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLAAMAH-ELSEKKGVSTTLLH  188 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHH-HHHHHSCCCEEEEE
T ss_pred             CceEEEECCCCCCHHHHHHHHHH-HHHHhcCCcEEEEE
Confidence            57899999999999988754444 344 5566777653

>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=96.48  E-value=0.046  Score=41.13  Aligned_cols=39  Identities=13%  Similarity=0.011  Sum_probs=28.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh-----cCCeEEEEcc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI-----KQKSAIFILP   41 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-----~~~~~l~v~P   41 (138)
                      .|+-+.+.+|.|+|||..+...+...+..     .+.+++|+.-
T Consensus       177 ~Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~  220 (400)
T 3lda_A          177 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDT  220 (400)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEES
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeC
Confidence            56788999999999999887555443332     2467888754

>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=96.44  E-value=0.0045  Score=50.55  Aligned_cols=52  Identities=15%  Similarity=0.210  Sum_probs=38.6

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAK   55 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~   55 (138)
                      .+...+|.+|.|+|||.+....+ .++.. .+.++++++|+..-+++..+.+.+
T Consensus       370 ~~~~~lI~GppGTGKT~ti~~~i-~~l~~~~~~~ilv~a~tn~A~~~l~~~l~~  422 (800)
T 2wjy_A          370 QRPLSLIQGPPGTGKTVTSATIV-YHLARQGNGPVLVCAPSNIAVDQLTEKIHQ  422 (800)
T ss_dssp             TSSEEEEECCTTSCHHHHHHHHH-HHHHTTCSSCEEEEESSHHHHHHHHHHHHT
T ss_pred             cCCeEEEEcCCCCCHHHHHHHHH-HHHHHcCCCcEEEEcCcHHHHHHHHHHHHH
Confidence            34567999999999998764333 34444 577999999998887777776654

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=96.31  E-value=0.0063  Score=41.79  Aligned_cols=38  Identities=18%  Similarity=0.277  Sum_probs=29.0

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      .|+.+++.+|+|+|||..+...+.... ..+.+++|+..
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~~~~~~~-~~~~~v~~~~~   59 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQQFLWNGL-KMGEPGIYVAL   59 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHHH-HTTCCEEEEES
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHH-hcCCeEEEEEc
Confidence            567889999999999999866655533 45778888753

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=96.30  E-value=0.0063  Score=40.81  Aligned_cols=34  Identities=24%  Similarity=0.240  Sum_probs=24.3

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      .++++++|+|+|||..+...+ ..+...+.+++++
T Consensus        55 ~~~~l~G~~GtGKT~la~~i~-~~~~~~~~~~~~~   88 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAAIA-NELAKRNVSSLIV   88 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHHHH-HHHHTTTCCEEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHH-HHHHHcCCeEEEE
Confidence            689999999999999875443 3344445666654

>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=96.25  E-value=0.17  Score=38.50  Aligned_cols=36  Identities=17%  Similarity=-0.001  Sum_probs=26.1

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      +..+++.+|+|+|||..+...+.. +..++.+++++.
T Consensus        97 ~~vI~lvG~~GsGKTTt~~kLA~~-l~~~G~kVllv~  132 (433)
T 3kl4_A           97 PFIIMLVGVQGSGKTTTAGKLAYF-YKKRGYKVGLVA  132 (433)
T ss_dssp             SEEEEECCCTTSCHHHHHHHHHHH-HHHTTCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH-HHHcCCeEEEEe
Confidence            456788999999999877554443 445678887764

>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19

Probab=96.17  E-value=0.01  Score=47.26  Aligned_cols=53  Identities=13%  Similarity=0.099  Sum_probs=40.1

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhh---cCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKI---KQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~---~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +.+++|.|+.|||||.+...-+...+.+   ...+++++++++....+..+.+...
T Consensus        15 ~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lTfT~~Aa~em~~Rl~~~   70 (673)
T 1uaa_A           15 TGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQT   70 (673)
T ss_dssp             SSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCChHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHH
Confidence            4588999999999998876655543333   2358999999988888887777654

>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=96.14  E-value=0.086  Score=40.81  Aligned_cols=39  Identities=18%  Similarity=0.158  Sum_probs=28.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcch
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPY   42 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~   42 (138)
                      .|+.+.+.+|.|+|||..+...+-.. ...+.+++|+.+-
T Consensus       280 ~G~i~~i~G~~GsGKSTLl~~l~g~~-~~~G~~vi~~~~e  318 (525)
T 1tf7_A          280 KDSIILATGATGTGKTLLVSRFVENA-CANKERAILFAYE  318 (525)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHHH-HTTTCCEEEEESS
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHH-HhCCCCEEEEEEe
Confidence            57788999999999998876655432 2346677777653

>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=96.11  E-value=0.011  Score=46.40  Aligned_cols=47  Identities=11%  Similarity=-0.032  Sum_probs=34.9

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKY   50 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~   50 (138)
                      .+..+++.+|.|+|||.+... +...+...+.++++++|+........
T Consensus       203 ~~~~~~I~G~pGTGKTt~i~~-l~~~l~~~g~~Vl~~ApT~~Aa~~L~  249 (574)
T 3e1s_A          203 GHRLVVLTGGPGTGKSTTTKA-VADLAESLGLEVGLCAPTGKAARRLG  249 (574)
T ss_dssp             TCSEEEEECCTTSCHHHHHHH-HHHHHHHTTCCEEEEESSHHHHHHHH
T ss_pred             hCCEEEEEcCCCCCHHHHHHH-HHHHHHhcCCeEEEecCcHHHHHHhH
Confidence            456889999999999977533 33445557889999999987665443

>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=96.11  E-value=0.015  Score=47.53  Aligned_cols=65  Identities=11%  Similarity=0.107  Sum_probs=48.4

Q ss_pred             hhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          61 KFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      +.+.|..++..... ...++..|.|+|||....-. +..+.. .+.++++++|+..-+.+..+.+.+.
T Consensus       357 Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti~~~-i~~l~~~~~~~ilv~a~tn~A~~~l~~~l~~~  423 (800)
T 2wjy_A          357 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATI-VYHLARQGNGPVLVCAPSNIAVDQLTEKIHQT  423 (800)
T ss_dssp             CCHHHHHHHHHHHTSSEEEEECCTTSCHHHHHHHH-HHHHHTTCSSCEEEEESSHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHhccCCeEEEEcCCCCCHHHHHHHH-HHHHHHcCCCcEEEEcCcHHHHHHHHHHHHHh
Confidence            35567777755545 66789999999999876443 444544 5789999999998888888777654

>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A*

Probab=96.08  E-value=0.01  Score=50.51  Aligned_cols=54  Identities=13%  Similarity=0.163  Sum_probs=41.6

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhc-----CCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIK-----QKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~-----~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .+.+++|.|..|||||.+..-=+...+.+.     ..+++++++|++...+..+.+...
T Consensus        22 ~~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~Tft~~aa~e~~~ri~~~   80 (1232)
T 3u4q_A           22 TGQDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAEA   80 (1232)
T ss_dssp             CSSCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEECSSHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEEeccHHHHHHHHHHHHHH
Confidence            367999999999999998766555544441     248999999999888887777664

>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=96.08  E-value=0.11  Score=35.10  Aligned_cols=39  Identities=18%  Similarity=0.030  Sum_probs=26.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh-----cCCeEEEEcc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI-----KQKSAIFILP   41 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-----~~~~~l~v~P   41 (138)
                      .|+-+.+.+|+|||||..+...+-.....     .+++++++..
T Consensus        24 ~G~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~   67 (231)
T 4a74_A           24 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDT   67 (231)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEES
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEEC
Confidence            46778999999999998875554432221     1446777654

>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B*

Probab=96.01  E-value=0.017  Score=46.49  Aligned_cols=53  Identities=15%  Similarity=-0.006  Sum_probs=39.9

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhc---CCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIK---QKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~---~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +.+++|.|+.|||||.+...-+...+.+.   ..++++++.++....+..+++...
T Consensus        24 ~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~vTFTnkAA~Em~~Rl~~~   79 (724)
T 1pjr_A           24 EGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSL   79 (724)
T ss_dssp             SSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHH
Confidence            45889999999999998766555534332   248999999998887777776654

>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=95.98  E-value=0.038  Score=41.41  Aligned_cols=70  Identities=19%  Similarity=0.144  Sum_probs=55.8

Q ss_pred             hhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHHHHHHHHHHHHhhhc
Q psy2029          61 KFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAAEEF  130 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~~q~~~~~~~~~~~~  130 (138)
                      +.++|...+..+.. +..++..|-+.|||.+....++..+.. .+.++++++|+...+.+.++.++.++...
T Consensus       164 L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~~~g~~v~~vA~t~~qA~~vf~~i~~mi~~~  235 (385)
T 2o0j_A          164 LRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNKDKAVGILAHKGSMSAEVLDRTKQAIELL  235 (385)
T ss_dssp             CCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHSSSSCEEEEEESSHHHHHHHHHHHHHHHHHS
T ss_pred             CCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHhCCCCeEEEEeCCHHHHHHHHHHHHHHHHhC
Confidence            47788888765444 668899999999999887777765554 45689999999999999998888877654

>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=95.98  E-value=0.02  Score=43.55  Aligned_cols=44  Identities=16%  Similarity=0.195  Sum_probs=31.9

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCC-eEEEEcchhhhHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQK-SAIFILPYISLVHEKY   50 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~-~~l~v~P~~aL~~q~~   50 (138)
                      ++++.+|.|+|||.+... +...+...+. +++.++|+.....+..
T Consensus        47 ~~li~G~aGTGKT~ll~~-~~~~l~~~~~~~il~~a~T~~Aa~~l~   91 (459)
T 3upu_A           47 HVTINGPAGTGATTLTKF-IIEALISTGETGIILAAPTHAAKKILS   91 (459)
T ss_dssp             EEEEECCTTSCHHHHHHH-HHHHHHHTTCCCEEEEESSHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHH-HHHHHHhcCCceEEEecCcHHHHHHHH
Confidence            899999999999987643 3334555554 7888999876554443

>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=95.98  E-value=0.096  Score=36.94  Aligned_cols=24  Identities=21%  Similarity=0.266  Sum_probs=20.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .|+-+++.+|.|+|||..+...+.
T Consensus        29 ~G~i~~i~G~~GsGKTtl~~~l~~   52 (279)
T 1nlf_A           29 AGTVGALVSPGGAGKSMLALQLAA   52 (279)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHH
Confidence            577889999999999988866655

>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=95.93  E-value=0.012  Score=44.32  Aligned_cols=42  Identities=10%  Similarity=0.132  Sum_probs=29.6

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLV   46 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~   46 (138)
                      ..++++.+|||||||... -.++..++..+.+++++-|.-++.
T Consensus        53 ~~h~~i~G~tGsGKs~~~-~~li~~~~~~g~~viv~Dpkge~~   94 (437)
T 1e9r_A           53 PRHLLVNGATGTGKSVLL-RELAYTGLLRGDRMVIVDPNGDML   94 (437)
T ss_dssp             GGCEEEEECTTSSHHHHH-HHHHHHHHHTTCEEEEEEETTHHH
T ss_pred             cceEEEECCCCCCHHHHH-HHHHHHHHHCCCcEEEEeCCCchh
Confidence            458999999999999875 334444555677777777765543

>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=95.93  E-value=0.013  Score=39.91  Aligned_cols=37  Identities=14%  Similarity=0.133  Sum_probs=25.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      .+.++++++|+|+|||..+...+.. +...+.++.++.
T Consensus        51 ~~~~~ll~G~~G~GKT~la~~l~~~-~~~~~~~~~~~~   87 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLIHAACAR-ANELERRSFYIP   87 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHHHHHHHH-HHHTTCCEEEEE
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHH-HHHcCCeEEEEE
Confidence            3578999999999999988554443 333355555543

>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=95.93  E-value=0.036  Score=43.65  Aligned_cols=70  Identities=17%  Similarity=0.133  Sum_probs=56.1

Q ss_pred             hhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhC-CCeEEEEccchhHHHHHHHHHHHHhhhc
Q psy2029          61 KFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIK-QKSAIFILPYISLVHEKYQSLAKAAEEF  130 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~-~~~~~~i~P~~~l~~q~~~~~~~~~~~~  130 (138)
                      +.++|...+..+.. +..++..|-+.|||......++..+... +.+++++.|+...+.+.++.++.++...
T Consensus       164 l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~~~~~i~~va~t~~qA~~~~~~i~~~i~~~  235 (592)
T 3cpe_A          164 LRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNKDKAVGILAHKGSMSAEVLDRTKQAIELL  235 (592)
T ss_dssp             CCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTSSSCEEEEEESSHHHHHHHHHHHHHHHTTS
T ss_pred             CCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhCCCCeEEEEECCHHHHHHHHHHHHHHHHhC
Confidence            46788888765555 7788999999999998876666666543 4589999999999999998888887655

>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=95.91  E-value=0.026  Score=49.54  Aligned_cols=93  Identities=20%  Similarity=0.170  Sum_probs=61.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhhhhHHHhhhhccceEEEee
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIQNKNCVLSIP   82 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~ii~~p   82 (138)
                      .|+.+.+.+|.|||||..++..+.+... ++++++|+.+-.+|....   ++..+.+.              .+++++-|
T Consensus      1430 rg~~iei~g~~~sGkttl~~~~~a~~~~-~g~~~~~i~~e~~~~~~~---~~~~Gv~~--------------~~l~~~~p 1491 (1706)
T 3cmw_A         1430 MGRIVEIYGPESSGKTTLTLQVIAAAQR-EGKTCAFIDAEHALDPIY---ARKLGVDI--------------DNLLCSQP 1491 (1706)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHH-TTCCEEEECTTSCCCHHH---HHHTTCCG--------------GGCEEECC
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHh-cCCeEEEEecCCCCCHHH---HHHcCCCH--------------HHeEEeCC
Confidence            4678999999999999999888877544 589999998877765433   22222211              44566666


Q ss_pred             cCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHHH
Q psy2029          83 TSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVH  117 (138)
Q Consensus        83 tg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~~  117 (138)
                      +.+    --.+.++.++.. .....++|.|.-||+.
T Consensus      1492 ~~~----e~~l~~~~~~~~s~~~~~vvvDsv~al~~ 1523 (1706)
T 3cmw_A         1492 DTG----EQALEICDALARSGAVDVIVVDSVAALTP 1523 (1706)
T ss_dssp             SSH----HHHHHHHHHHHHHTCCSEEEESCSTTCCC
T ss_pred             CcH----HHHHHHHHHHHHcCCCCEEEEccHHhCCc
Confidence            543    222455555554 5567888777766653

>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=95.85  E-value=0.41  Score=36.47  Aligned_cols=39  Identities=10%  Similarity=-0.009  Sum_probs=27.8

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc--chhh
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL--PYIS   44 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~--P~~a   44 (138)
                      .-+++++|+|+|||..+.-.+.. +..++.+++++.  |+++
T Consensus       101 ~vIlivG~~G~GKTTt~~kLA~~-l~~~G~kVllv~~D~~R~  141 (443)
T 3dm5_A          101 TILLMVGIQGSGKTTTVAKLARY-FQKRGYKVGVVCSDTWRP  141 (443)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH-HHTTTCCEEEEECCCSST
T ss_pred             eEEEEECcCCCCHHHHHHHHHHH-HHHCCCeEEEEeCCCcch
Confidence            45789999999999887555443 455677887764  4554

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=95.83  E-value=0.0069  Score=38.70  Aligned_cols=23  Identities=13%  Similarity=0.011  Sum_probs=19.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      .+.++++++|+|+|||.++-...
T Consensus        23 ~~~~vll~G~~GtGKt~lA~~i~   45 (145)
T 3n70_A           23 TDIAVWLYGAPGTGRMTGARYLH   45 (145)
T ss_dssp             CCSCEEEESSTTSSHHHHHHHHH
T ss_pred             CCCCEEEECCCCCCHHHHHHHHH
Confidence            45789999999999999986543

>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=95.83  E-value=0.025  Score=45.03  Aligned_cols=74  Identities=11%  Similarity=0.055  Sum_probs=54.1

Q ss_pred             hhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHh---CCCeEEEEccchhHHHHHHHHHHHHhhhc---Cceee
Q psy2029          62 FYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKI---KQKSAIFILPYISLVHEKYQSLAKAAEEF---KFYLE  135 (138)
Q Consensus        62 ~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~---~~~~~~~i~P~~~l~~q~~~~~~~~~~~~---~~~v~  135 (138)
                      .+-|.+++.. .+.++++.++.|+|||.+....+.+.+..   ...++++++.++..+.+..+.+.+.....   ++.|.
T Consensus         4 ~~~Q~~av~~-~~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lTfT~~Aa~em~~Rl~~~l~~~~~~~~~v~   82 (673)
T 1uaa_A            4 NPGQQQAVEF-VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLGRKEARGLMIS   82 (673)
T ss_dssp             CHHHHHHHHC-CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSCTTTTTTSEEE
T ss_pred             CHHHHHHHhC-CCCCEEEEeCCCCChHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHcCcccccCCEEE
Confidence            3456666532 13788899999999999887777665554   24689999999999999999998875432   34454


Q ss_pred             e
Q psy2029         136 V  136 (138)
Q Consensus       136 ~  136 (138)
                      .
T Consensus        83 T   83 (673)
T 1uaa_A           83 T   83 (673)
T ss_dssp             E
T ss_pred             e
Confidence            4

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=95.80  E-value=0.028  Score=40.53  Aligned_cols=36  Identities=14%  Similarity=0.004  Sum_probs=25.6

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      +.++++++|+|+|||..+-..+.. +...+.+++++.
T Consensus        37 ~~~lll~G~~GtGKT~la~~i~~~-~~~~~~~~~~i~   72 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLLQAAGNE-AKKRGYRVIYSS   72 (324)
T ss_dssp             CSSEEEECSSSSSHHHHHHHHHHH-HHHTTCCEEEEE
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHH-HHHCCCEEEEEE
Confidence            468999999999999887554433 333456677754

>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=95.80  E-value=0.03  Score=44.01  Aligned_cols=59  Identities=10%  Similarity=-0.022  Sum_probs=44.6

Q ss_pred             hhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHH
Q psy2029          62 FYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        62 ~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~  121 (138)
                      .+.|..++..... ..+++..|.|+|||... ..++..+...+.++++++|+...+.+..+
T Consensus       191 ~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i-~~l~~~l~~~g~~Vl~~ApT~~Aa~~L~e  250 (574)
T 3e1s_A          191 SEEQASVLDQLAGHRLVVLTGGPGTGKSTTT-KAVADLAESLGLEVGLCAPTGKAARRLGE  250 (574)
T ss_dssp             CHHHHHHHHHHTTCSEEEEECCTTSCHHHHH-HHHHHHHHHTTCCEEEEESSHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhCCEEEEEcCCCCCHHHHH-HHHHHHHHhcCCeEEEecCcHHHHHHhHh
Confidence            4567777766655 88899999999999776 33445555567899999999988766544

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=95.77  E-value=0.017  Score=39.14  Aligned_cols=37  Identities=22%  Similarity=0.193  Sum_probs=27.0

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      .|+.+.+.+|+|+|||..+...+... ...+++++|+.
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~l~~~~-~~~~~~v~~~~   58 (235)
T 2w0m_A           22 QGFFIALTGEPGTGKTIFSLHFIAKG-LRDGDPCIYVT   58 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHHHH-HHHTCCEEEEE
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHH-HHCCCeEEEEE
Confidence            46788999999999998876555433 33467777764

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=95.74  E-value=0.014  Score=37.74  Aligned_cols=37  Identities=14%  Similarity=0.060  Sum_probs=25.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      .|+.+.+.+|+|+|||..+-..+-. +...+.+++|+.
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~~i~~~-~~~~g~~~~~~~   71 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQAWVAQ-ALEAGKNAAYID   71 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHHHHHHH-HHTTTCCEEEEE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHH-HHhcCCcEEEEc
Confidence            4678999999999999877554433 223455566653

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=95.70  E-value=0.0056  Score=39.11  Aligned_cols=20  Identities=10%  Similarity=0.022  Sum_probs=17.2

Q ss_pred             CCccEEEEccCCcchHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGE   22 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~   22 (138)
                      .+.++++++|+|+|||.++-
T Consensus        26 ~~~~vll~G~~GtGKt~lA~   45 (143)
T 3co5_A           26 RTSPVFLTGEAGSPFETVAR   45 (143)
T ss_dssp             CSSCEEEEEETTCCHHHHHG
T ss_pred             CCCcEEEECCCCccHHHHHH
Confidence            35689999999999998874

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=95.64  E-value=0.1  Score=46.61  Aligned_cols=92  Identities=21%  Similarity=0.159  Sum_probs=54.8

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhhhhHHHhhhhccceEEEee
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCLEMIQNKNCVLSIP   82 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~~~~ii~~p   82 (138)
                      .|+++++++|+|+|||..+...+.... .++.++.|+..--++....   .+.+    +.+.          .++.+..|
T Consensus      1426 ~g~~vll~GppGtGKT~LA~ala~ea~-~~G~~v~Fi~~e~~~~~l~---a~~~----G~dl----------~~l~v~~~ 1487 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQVIAAAQ-REGKTCAFIDAEHALDPIY---ARKL----GVDI----------DNLLCSQP 1487 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHH-TTTCCEEEECTTSCCCHHH---HHHT----TCCT----------TTCEEECC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH-HcCCcEEEEEcccccCHHH---HHHc----CCCc----------hhceeecC
Confidence            478999999999999999977777654 3588999987654433222   2222    2111          22344444


Q ss_pred             cCCCchHhHHHHHHHHHH-hCCCeEEEEccchhHH
Q psy2029          83 TSGGKTLVGEILIMKELK-IKQKSAIFILPYISLV  116 (138)
Q Consensus        83 tg~GKt~~~~~~~l~~~~-~~~~~~~~i~P~~~l~  116 (138)
                      .. +.   -.+..++++. +...+.|+|.+..+++
T Consensus      1488 ~~-~E---~~l~~~~~lvr~~~~~lVVIDsi~al~ 1518 (2050)
T 3cmu_A         1488 DT-GE---QALEICDALARSGAVDVIVVDSVAALT 1518 (2050)
T ss_dssp             SS-HH---HHHHHHHHHHHHTCCSEEEESCGGGCC
T ss_pred             Ch-HH---HHHHHHHHHHhcCCCCEEEEcChhHhc
Confidence            32 22   2233344333 3567888888875444

>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=95.60  E-value=0.017  Score=39.98  Aligned_cols=40  Identities=18%  Similarity=0.069  Sum_probs=30.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchh
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYI   43 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~   43 (138)
                      .|.-.++.+|.|+|||..+.-.+.+ +..++.+++++.|..
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~~r-~~~~g~kVli~~~~~   50 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRLHR-LEYADVKYLVFKPKI   50 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHHHH-HHHTTCCEEEEEECC
T ss_pred             CcEEEEEECCCCCcHHHHHHHHHHH-HHhcCCEEEEEEecc
Confidence            3556688999999999888666554 445688999887754

>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=95.59  E-value=0.087  Score=42.43  Aligned_cols=76  Identities=9%  Similarity=-0.035  Sum_probs=56.2

Q ss_pred             hhhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHh---CCCeEEEEccchhHHHHHHHHHHHHhhhc--Ccee
Q psy2029          60 FKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKI---KQKSAIFILPYISLVHEKYQSLAKAAEEF--KFYL  134 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~---~~~~~~~i~P~~~l~~q~~~~~~~~~~~~--~~~v  134 (138)
                      .+.+-|.+++.. .+.++++.++.|+|||.+....+.+.+..   ...++++++.|+..+.+..+.+.+.....  ++.|
T Consensus        11 ~Ln~~Q~~av~~-~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~vTFTnkAA~Em~~Rl~~~l~~~~~~~~v   89 (724)
T 1pjr_A           11 HLNKEQQEAVRT-TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLGGAAEDVWI   89 (724)
T ss_dssp             TSCHHHHHHHHC-CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHHGGGGTTSEE
T ss_pred             hCCHHHHHHHhC-CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHhcccccCcEE
Confidence            355667777643 23788999999999999987777766654   23589999999999999999998875432  4444


Q ss_pred             ee
Q psy2029         135 EV  136 (138)
Q Consensus       135 ~~  136 (138)
                      ..
T Consensus        90 ~T   91 (724)
T 1pjr_A           90 ST   91 (724)
T ss_dssp             EE
T ss_pred             ee
Confidence            43

>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=95.54  E-value=0.022  Score=40.60  Aligned_cols=39  Identities=8%  Similarity=-0.053  Sum_probs=27.4

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      -.|+-+++.+|+|+|||..+...+.....+.+.+++|+.
T Consensus        33 ~~G~~~~i~G~~G~GKTTl~~~ia~~~~~~~G~~v~~~~   71 (296)
T 1cr0_A           33 RGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAM   71 (296)
T ss_dssp             CTTCEEEEEESTTSSHHHHHHHHHHHHHHTSCCCEEEEE
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHHcCCeEEEEe
Confidence            357788999999999998876655543333354777764

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=95.45  E-value=0.028  Score=37.51  Aligned_cols=40  Identities=25%  Similarity=0.232  Sum_probs=29.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchh
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYI   43 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~   43 (138)
                      .|.-.++++|.|+|||..+.-.+.+ ....+.+++++.|..
T Consensus         2 ~g~i~vi~G~~gsGKTT~ll~~~~~-~~~~g~~v~~~~~~~   41 (184)
T 2orw_A            2 SGKLTVITGPMYSGKTTELLSFVEI-YKLGKKKVAVFKPKI   41 (184)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHH-HHHTTCEEEEEEEC-
T ss_pred             ccEEEEEECCCCCCHHHHHHHHHHH-HHHCCCeEEEEeecc
Confidence            4666789999999999987555554 334577888887763

>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=95.35  E-value=0.024  Score=42.07  Aligned_cols=39  Identities=23%  Similarity=0.439  Sum_probs=27.1

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcch
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPY   42 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~   42 (138)
                      .+.++++.+|||+|||...-..+... ...+.+++++-|.
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~~~~~~-~~~~~~~~~~D~~   72 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKMLLLRE-YMQGSRVIIIDPE   72 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHH-HTTTCCEEEEESS
T ss_pred             ccCceEEEcCCCCCHHHHHHHHHHHH-HHCCCEEEEEeCC
Confidence            45689999999999998775555443 3345666665553

>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=95.27  E-value=0.045  Score=46.66  Aligned_cols=65  Identities=11%  Similarity=0.073  Sum_probs=50.6

Q ss_pred             hhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhC-----CCeEEEEccchhHHHHHHHHHHHHh
Q psy2029          62 FYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIK-----QKSAIFILPYISLVHEKYQSLAKAA  127 (138)
Q Consensus        62 ~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~-----~~~~~~i~P~~~l~~q~~~~~~~~~  127 (138)
                      .+-|..++... +.++++.++.|||||.+-.-.+++.+...     ..+++++++|++.+.+..+.+.+..
T Consensus        12 t~eQ~~~i~~~-~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~Tft~~aa~e~~~ri~~~l   81 (1232)
T 3u4q_A           12 TDDQWNAIVST-GQDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAEAL   81 (1232)
T ss_dssp             CHHHHHHHHCC-SSCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEECSSHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHhCC-CCCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEEeccHHHHHHHHHHHHHHH
Confidence            44566665322 48999999999999999877777766552     2489999999999999999888754

>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=95.22  E-value=0.032  Score=40.18  Aligned_cols=38  Identities=32%  Similarity=0.226  Sum_probs=25.8

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      .++.+.+.+|+|+|||..+...+.....+.|.+++++.
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~  141 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFIT  141 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEe
Confidence            35678899999999998775544432223466777763

>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=95.22  E-value=0.044  Score=43.77  Aligned_cols=48  Identities=19%  Similarity=0.122  Sum_probs=38.4

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ...+.+.||||||++..-.+..    .++.+++++|...+..|.++++..++
T Consensus        30 ~~~l~g~tgs~kt~~~a~~~~~----~~~~~lvv~~~~~~A~ql~~el~~~~   77 (664)
T 1c4o_A           30 FVTLLGATGTGKTVTMAKVIEA----LGRPALVLAPNKILAAQLAAEFRELF   77 (664)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHH----HTCCEEEEESSHHHHHHHHHHHHHHC
T ss_pred             cEEEEcCCCcHHHHHHHHHHHH----hCCCEEEEecCHHHHHHHHHHHHHHC
Confidence            4578899999999886433322    25678999999999999999999884

>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=95.21  E-value=0.08  Score=42.29  Aligned_cols=50  Identities=22%  Similarity=0.203  Sum_probs=40.0

Q ss_pred             ceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhh
Q psy2029          76 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEE  129 (138)
Q Consensus        76 ~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~  129 (138)
                      ...+...||+|||+...-.+ +..   ++++++|+|...++.|.+++|+.++.+
T Consensus        30 ~~~l~g~tgs~kt~~~a~~~-~~~---~~~~lvv~~~~~~A~ql~~el~~~~~~   79 (664)
T 1c4o_A           30 FVTLLGATGTGKTVTMAKVI-EAL---GRPALVLAPNKILAAQLAAEFRELFPE   79 (664)
T ss_dssp             EEEEEECTTSCHHHHHHHHH-HHH---TCCEEEEESSHHHHHHHHHHHHHHCTT
T ss_pred             cEEEEcCCCcHHHHHHHHHH-HHh---CCCEEEEecCHHHHHHHHHHHHHHCCC
Confidence            45678899999998875333 322   557999999999999999999999754

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=95.12  E-value=0.039  Score=38.99  Aligned_cols=21  Identities=19%  Similarity=0.150  Sum_probs=17.4

Q ss_pred             CCccEEEEccCCcchHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      .|+.+.+++|||||||...-.
T Consensus        24 ~g~~v~i~Gp~GsGKSTll~~   44 (261)
T 2eyu_A           24 KMGLILVTGPTGSGKSTTIAS   44 (261)
T ss_dssp             SSEEEEEECSTTCSHHHHHHH
T ss_pred             CCCEEEEECCCCccHHHHHHH
Confidence            577889999999999977533

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=95.12  E-value=0.02  Score=37.26  Aligned_cols=23  Identities=35%  Similarity=0.180  Sum_probs=18.5

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ..++++++|.|+|||..+...+.
T Consensus        43 ~~~~ll~G~~G~GKT~l~~~~~~   65 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAIVEGLAQ   65 (195)
T ss_dssp             SCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCceEEECCCCCCHHHHHHHHHH
Confidence            36799999999999988755443

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=95.02  E-value=0.017  Score=37.59  Aligned_cols=24  Identities=33%  Similarity=0.254  Sum_probs=19.1

Q ss_pred             CccEEEEccCCcchHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      ..++++++|+|+|||..+...+..
T Consensus        43 ~~~vll~G~~G~GKT~la~~~~~~   66 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIVEGLAIK   66 (187)
T ss_dssp             SCEEEEESCGGGCHHHHHHHHHHH
T ss_pred             CCceEEECCCCCCHHHHHHHHHHH
Confidence            457899999999999887555443

>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=95.01  E-value=0.038  Score=40.95  Aligned_cols=42  Identities=21%  Similarity=0.098  Sum_probs=31.0

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhh
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISL   45 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL   45 (138)
                      .|+-+++.+|.|+|||..+...+.. +...+++++|+..-.++
T Consensus        60 ~G~i~~I~GppGsGKSTLal~la~~-~~~~gg~VlyId~E~s~  101 (356)
T 3hr8_A           60 RGRIVEIFGQESSGKTTLALHAIAE-AQKMGGVAAFIDAEHAL  101 (356)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHH-HHHTTCCEEEEESSCCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH-HHhcCCeEEEEeccccc
Confidence            4667899999999999988666554 33457889998654443

>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=95.00  E-value=0.037  Score=40.78  Aligned_cols=38  Identities=24%  Similarity=0.177  Sum_probs=29.7

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      .|+-+++.+|.|+|||..+...+.... ..+.+++|+..
T Consensus        60 ~G~iv~I~G~pGsGKTtLal~la~~~~-~~g~~vlyi~~   97 (349)
T 2zr9_A           60 RGRVIEIYGPESSGKTTVALHAVANAQ-AAGGIAAFIDA   97 (349)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHH-HTTCCEEEEES
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH-hCCCeEEEEEC
Confidence            467789999999999999877766543 35778888764

>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=94.99  E-value=0.036  Score=37.38  Aligned_cols=40  Identities=23%  Similarity=0.110  Sum_probs=29.8

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchh
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYI   43 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~   43 (138)
                      +|.=.++++|.|+|||..++-.+.+ ...++.+++++.|.+
T Consensus         7 ~g~i~v~~G~mgsGKTT~ll~~a~r-~~~~g~kV~v~k~~~   46 (191)
T 1xx6_A            7 HGWVEVIVGPMYSGKSEELIRRIRR-AKIAKQKIQVFKPEI   46 (191)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHH-HHHTTCCEEEEEEC-
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHH-HHHCCCEEEEEEecc
Confidence            3455688999999999887666555 445688999988864

>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=94.90  E-value=0.031  Score=42.30  Aligned_cols=36  Identities=17%  Similarity=0.227  Sum_probs=23.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      .|+.+++.+|||||||..... ++..+....+++++.
T Consensus       166 ~ggii~I~GpnGSGKTTlL~a-llg~l~~~~g~I~~~  201 (418)
T 1p9r_A          166 PHGIILVTGPTGSGKSTTLYA-GLQELNSSERNILTV  201 (418)
T ss_dssp             SSEEEEEECSTTSCHHHHHHH-HHHHHCCTTSCEEEE
T ss_pred             cCCeEEEECCCCCCHHHHHHH-HHhhcCCCCCEEEEe
Confidence            456789999999999977533 333333334555554

>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=94.88  E-value=0.042  Score=40.66  Aligned_cols=39  Identities=23%  Similarity=0.180  Sum_probs=30.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcch
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPY   42 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~   42 (138)
                      .|..+++.+|.|+|||..+...+.... ..+.+++|+..-
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~~~-~~g~~vlyid~E  100 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAAAQ-REGKTCAFIDAE  100 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHH-HTTCCEEEEESS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH-HCCCeEEEEeCC
Confidence            466789999999999999977766543 357788887653

>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=94.86  E-value=0.053  Score=40.27  Aligned_cols=36  Identities=19%  Similarity=0.142  Sum_probs=23.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhc-CCeEEEE
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIK-QKSAIFI   39 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~-~~~~l~v   39 (138)
                      .|+.+++++|||||||...-..+- .+... .++++.+
T Consensus       135 ~g~~i~ivG~~GsGKTTll~~l~~-~~~~~~~g~I~~~  171 (372)
T 2ewv_A          135 KMGLILVTGPTGSGKSTTIASMID-YINQTKSYHIITI  171 (372)
T ss_dssp             SSEEEEEECSSSSSHHHHHHHHHH-HHHHHSCCEEEEE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHh-hcCcCCCcEEEEe
Confidence            567889999999999977533322 22223 4666544

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=94.85  E-value=0.023  Score=37.57  Aligned_cols=23  Identities=22%  Similarity=0.160  Sum_probs=18.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      ..|+-+.+++|+|||||...-..
T Consensus         3 ~~g~~i~i~GpsGsGKSTL~~~L   25 (180)
T 1kgd_A            3 HMRKTLVLLGAHGVGRRHIKNTL   25 (180)
T ss_dssp             CCCCEEEEECCTTSSHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHH
Confidence            35778899999999999887543

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=94.82  E-value=0.019  Score=42.35  Aligned_cols=23  Identities=30%  Similarity=0.154  Sum_probs=18.0

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +..+++++|||+|||.++...+.
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA~   62 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLAA   62 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHT
T ss_pred             CceEEEECCCCCCHHHHHHHHHH
Confidence            34689999999999998855443

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=94.77  E-value=0.023  Score=44.11  Aligned_cols=19  Identities=21%  Similarity=0.170  Sum_probs=16.8

Q ss_pred             CCccEEEEccCCcchHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVG   21 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~   21 (138)
                      .|.++++++|||||||...
T Consensus       259 ~g~~i~I~GptGSGKTTlL  277 (511)
T 2oap_1          259 HKFSAIVVGETASGKTTTL  277 (511)
T ss_dssp             TTCCEEEEESTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5778999999999999775

>3bs4_A Uncharacterized protein PH0321; structural genomics, unknown function, PSI-2, protein struct initiative; 1.60A {Pyrococcus horikoshii}

Probab=94.77  E-value=0.044  Score=38.85  Aligned_cols=53  Identities=6%  Similarity=-0.080  Sum_probs=34.3

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ..|..+++.+.+|+|||..+...+...+ .++.+++|+.-.-. ..+..+++..+
T Consensus        19 ~~gs~~li~g~p~~~~~~l~~qfl~~g~-~~Ge~~~~~~~~e~-~~~l~~~~~~~   71 (260)
T 3bs4_A           19 KHSLILIHEEDASSRGKDILFYILSRKL-KSDNLVGMFSISYP-LQLIIRILSRF   71 (260)
T ss_dssp             TTCEEEEEECSGGGCHHHHHHHHHHHHH-HTTCEEEEEECSSC-HHHHHHHHHHT
T ss_pred             CCCcEEEEEeCCCccHHHHHHHHHHHHH-HCCCcEEEEEEeCC-HHHHHHHHHHc
Confidence            4677889987888888866666666544 45889999764222 23445555444

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=94.72  E-value=0.024  Score=40.35  Aligned_cols=22  Identities=18%  Similarity=0.051  Sum_probs=18.1

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .++++++|+|+|||.++-..+.
T Consensus        68 ~~vll~G~~GtGKT~la~~la~   89 (309)
T 3syl_A           68 LHMSFTGNPGTGKTTVALKMAG   89 (309)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999998855444

>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=94.67  E-value=0.058  Score=39.91  Aligned_cols=36  Identities=17%  Similarity=0.187  Sum_probs=22.8

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhc-CCeEEEE
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIK-QKSAIFI   39 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~-~~~~l~v   39 (138)
                      .+..+++++|||||||...-. +...+... +++++.+
T Consensus       122 ~~g~i~I~GptGSGKTTlL~~-l~g~~~~~~~~~i~t~  158 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTTLAA-MLDYLNNTKYHHILTI  158 (356)
T ss_dssp             SSEEEEEECSTTSCHHHHHHH-HHHHHHHHCCCEEEEE
T ss_pred             CCCEEEEECCCCCCHHHHHHH-HHhcccCCCCcEEEEc
Confidence            456889999999999977533 22223233 4555544

>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=94.65  E-value=0.055  Score=41.12  Aligned_cols=61  Identities=13%  Similarity=0.159  Sum_probs=40.7

Q ss_pred             hhhhhhHHHhh----hhc--cceEEEeecCCCchHhHHHHHHHHHHhCCC-eEEEEccchhHHHHHHHH
Q psy2029          61 KFYLEGKCLEM----IQN--KNCVLSIPTSGGKTLVGEILIMKELKIKQK-SAIFILPYISLVHEKYQS  122 (138)
Q Consensus        61 ~~~~Q~~~~~~----~~~--~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~-~~~~i~P~~~l~~q~~~~  122 (138)
                      +.+-|..++..    +.+  ..+++..|.|+|||.+.. .++..+...+. +++.++|+...+.+..+.
T Consensus        26 Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll~-~~~~~l~~~~~~~il~~a~T~~Aa~~l~~~   93 (459)
T 3upu_A           26 LTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLTK-FIIEALISTGETGIILAAPTHAAKKILSKL   93 (459)
T ss_dssp             CCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHHH-HHHHHHHHTTCCCEEEEESSHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHHH-HHHHHHHhcCCceEEEecCcHHHHHHHHhh
Confidence            34455555532    222  488999999999998774 44455555444 789999998777655543

>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=94.64  E-value=0.052  Score=40.34  Aligned_cols=39  Identities=21%  Similarity=0.242  Sum_probs=29.8

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcch
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPY   42 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~   42 (138)
                      .|.-+++.+|.|+|||..+...+.... ..+.+++|+..-
T Consensus        73 ~G~li~I~G~pGsGKTtlal~la~~~~-~~g~~vlyi~~E  111 (366)
T 1xp8_A           73 RGRITEIYGPESGGKTTLALAIVAQAQ-KAGGTCAFIDAE  111 (366)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHH-HTTCCEEEEESS
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHHH-HCCCeEEEEECC
Confidence            466789999999999999877666543 357788888643

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=94.51  E-value=0.025  Score=41.31  Aligned_cols=25  Identities=16%  Similarity=0.054  Sum_probs=20.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      .+.++++++|+|+|||.++-..+..
T Consensus        44 ~~~~lli~GpPGTGKT~~v~~v~~~   68 (318)
T 3te6_A           44 QNKLFYITNADDSTKFQLVNDVMDE   68 (318)
T ss_dssp             CCCEEEEECCCSHHHHHHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHH
Confidence            4568999999999999988665543

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=94.49  E-value=0.029  Score=37.56  Aligned_cols=24  Identities=21%  Similarity=0.178  Sum_probs=19.7

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .++.+++.+|.|||||.++-..+-
T Consensus        24 ~~~~i~l~G~~GsGKsTl~~~La~   47 (199)
T 3vaa_A           24 AMVRIFLTGYMGAGKTTLGKAFAR   47 (199)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHH
Confidence            467889999999999999855543

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=94.43  E-value=0.03  Score=40.84  Aligned_cols=24  Identities=13%  Similarity=0.169  Sum_probs=19.6

Q ss_pred             CccEEEEccCCcchHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      ++++++++|+|+|||.++...+..
T Consensus        70 ~~~vLl~GppGtGKT~la~~la~~   93 (368)
T 3uk6_A           70 GRAVLIAGQPGTGKTAIAMGMAQA   93 (368)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999998655443

>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=94.42  E-value=0.028  Score=39.44  Aligned_cols=23  Identities=22%  Similarity=0.307  Sum_probs=18.7

Q ss_pred             ccEEEEccCCcchHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      .++++++|+|+|||.++-..+..
T Consensus        65 ~~vLl~G~~GtGKT~la~~ia~~   87 (272)
T 1d2n_A           65 VSVLLEGPPHSGKTALAAKIAEE   87 (272)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHHHH
Confidence            57899999999999988655443

>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=94.42  E-value=0.092  Score=39.81  Aligned_cols=37  Identities=11%  Similarity=-0.015  Sum_probs=25.6

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhc--CCeEEEEcc
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILP   41 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~--~~~~l~v~P   41 (138)
                      ..++++++|+|+|||..+-..+-. +...  +.+++++..
T Consensus       130 ~~~lll~Gp~G~GKTtLa~aia~~-l~~~~~~~~v~~v~~  168 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSIGNY-VVQNEPDLRVMYITS  168 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHHHHH-HHHHCCSSCEEEEEH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH-HHHhCCCCeEEEeeH
Confidence            457999999999999887544433 3332  567777543

>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=94.41  E-value=0.032  Score=39.96  Aligned_cols=24  Identities=25%  Similarity=0.371  Sum_probs=19.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .++.+++++|+|+|||..+-..+-
T Consensus        48 ~~~~vLL~Gp~GtGKT~la~ala~   71 (301)
T 3cf0_A           48 PSKGVLFYGPPGCGKTLLAKAIAN   71 (301)
T ss_dssp             CCSEEEEECSSSSSHHHHHHHHHH
T ss_pred             CCceEEEECCCCcCHHHHHHHHHH
Confidence            356799999999999999855443

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=94.37  E-value=0.037  Score=37.22  Aligned_cols=24  Identities=17%  Similarity=0.157  Sum_probs=19.5

Q ss_pred             CCCccEEEEccCCcchHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      ..|..+++++|+|||||.++...+
T Consensus        10 ~~~~~i~l~G~sGsGKsTl~~~L~   33 (204)
T 2qor_A           10 ARIPPLVVCGPSGVGKGTLIKKVL   33 (204)
T ss_dssp             CCCCCEEEECCTTSCHHHHHHHHH
T ss_pred             ccCCEEEEECCCCCCHHHHHHHHH
Confidence            457788999999999998875543

>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=94.31  E-value=0.033  Score=37.65  Aligned_cols=22  Identities=36%  Similarity=0.326  Sum_probs=17.9

Q ss_pred             CCccEEEEccCCcchHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      .|.-+++++|+|+|||.++-..
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~~L   28 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVREAV   28 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHHHHH
Confidence            4667899999999999887544

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=94.30  E-value=0.042  Score=38.67  Aligned_cols=24  Identities=29%  Similarity=0.379  Sum_probs=19.1

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ...++++++|+|+|||.++-..+.
T Consensus        50 ~~~~~ll~G~~GtGKT~la~~la~   73 (285)
T 3h4m_A           50 PPKGILLYGPPGTGKTLLAKAVAT   73 (285)
T ss_dssp             CCSEEEEESSSSSSHHHHHHHHHH
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHH
Confidence            346799999999999998855443

>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=94.30  E-value=0.028  Score=38.47  Aligned_cols=24  Identities=13%  Similarity=0.087  Sum_probs=18.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .|.-+++.+|||+|||..+.-.+.
T Consensus        33 ~g~~ilI~GpsGsGKStLA~~La~   56 (205)
T 2qmh_A           33 YGLGVLITGDSGVGKSETALELVQ   56 (205)
T ss_dssp             TTEEEEEECCCTTTTHHHHHHHHT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            456689999999999977755443

>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=94.28  E-value=0.035  Score=40.78  Aligned_cols=24  Identities=42%  Similarity=0.502  Sum_probs=19.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .+.++++.+|+|+|||.++-..+.
T Consensus        50 ~~~~vll~GppGtGKT~la~~ia~   73 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLAETLAR   73 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHH
Confidence            346899999999999999855543

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=94.27  E-value=0.031  Score=39.64  Aligned_cols=23  Identities=30%  Similarity=0.398  Sum_probs=18.9

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ++++++.+|+|+|||.++-..+-
T Consensus        54 ~~~vll~Gp~GtGKT~la~~la~   76 (297)
T 3b9p_A           54 AKGLLLFGPPGNGKTLLARAVAT   76 (297)
T ss_dssp             CSEEEEESSSSSCHHHHHHHHHH
T ss_pred             CCeEEEECcCCCCHHHHHHHHHH
Confidence            46899999999999998865443

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=94.26  E-value=0.034  Score=38.83  Aligned_cols=23  Identities=22%  Similarity=0.244  Sum_probs=18.8

Q ss_pred             CCccEEEEccCCcchHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      .+.++++++|+|+|||.++-...
T Consensus        28 ~~~~vll~G~~GtGKt~la~~i~   50 (265)
T 2bjv_A           28 LDKPVLIIGERGTGKELIASRLH   50 (265)
T ss_dssp             SCSCEEEECCTTSCHHHHHHHHH
T ss_pred             CCCCEEEECCCCCcHHHHHHHHH
Confidence            35689999999999999885543

>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=94.24  E-value=0.037  Score=36.49  Aligned_cols=23  Identities=26%  Similarity=0.312  Sum_probs=18.8

Q ss_pred             CCCccEEEEccCCcchHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      -+|+.+.+.+|.|||||.++-..
T Consensus         7 ~~g~~i~l~G~~GsGKSTl~~~L   29 (191)
T 1zp6_A            7 LGGNILLLSGHPGSGKSTIAEAL   29 (191)
T ss_dssp             CTTEEEEEEECTTSCHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHH
Confidence            35778899999999999887443

>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=94.19  E-value=0.04  Score=39.00  Aligned_cols=23  Identities=35%  Similarity=0.341  Sum_probs=19.0

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ..++++++|+|+|||.++-..+.
T Consensus        50 ~~~vll~G~~GtGKT~la~~la~   72 (310)
T 1ofh_A           50 PKNILMIGPTGVGKTEIARRLAK   72 (310)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999998865544

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=94.17  E-value=0.039  Score=36.74  Aligned_cols=22  Identities=27%  Similarity=0.422  Sum_probs=18.2

Q ss_pred             CCccEEEEccCCcchHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      .|+-+.+.+|+|||||.++-..
T Consensus         6 ~g~ii~l~Gp~GsGKSTl~~~L   27 (205)
T 3tr0_A            6 KANLFIISAPSGAGKTSLVRAL   27 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHHHHH
Confidence            5777899999999999887543

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=94.17  E-value=0.036  Score=36.38  Aligned_cols=23  Identities=35%  Similarity=0.215  Sum_probs=19.0

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +.++++++|+|||||.++...+-
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~   27 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAK   27 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            56789999999999999865543

>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=94.15  E-value=0.04  Score=38.11  Aligned_cols=23  Identities=30%  Similarity=0.406  Sum_probs=18.5

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ..++++++|+|+|||.++...+.
T Consensus        39 ~~~vll~G~~GtGKT~la~~la~   61 (262)
T 2qz4_A           39 PKGALLLGPPGCGKTLLAKAVAT   61 (262)
T ss_dssp             CCEEEEESCTTSSHHHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHH
Confidence            35789999999999998865544

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=94.14  E-value=0.04  Score=35.71  Aligned_cols=22  Identities=32%  Similarity=0.555  Sum_probs=18.3

Q ss_pred             CCccEEEEccCCcchHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      .+..+.+.+|.|||||.++-..
T Consensus         3 ~~~~i~l~G~~GsGKSTl~~~L   24 (173)
T 1kag_A            3 EKRNIFLVGPMGAGKSTIGRQL   24 (173)
T ss_dssp             CCCCEEEECCTTSCHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHHHH
Confidence            4678899999999999987544

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=94.11  E-value=0.035  Score=37.29  Aligned_cols=23  Identities=30%  Similarity=0.372  Sum_probs=16.9

Q ss_pred             CCCccEEEEccCCcchHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      -.|+-+.+++|+|+|||...-..
T Consensus         2 ~~g~~i~lvGpsGaGKSTLl~~L   24 (198)
T 1lvg_A            2 AGPRPVVLSGPSGAGKSTLLKKL   24 (198)
T ss_dssp             ---CCEEEECCTTSSHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHH
Confidence            35778899999999999876443

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=94.06  E-value=0.036  Score=40.95  Aligned_cols=20  Identities=25%  Similarity=0.232  Sum_probs=17.4

Q ss_pred             CCccEEEEccCCcchHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGE   22 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~   22 (138)
                      .|+.+.+++|||||||...-
T Consensus       174 ~G~~i~ivG~sGsGKSTll~  193 (361)
T 2gza_A          174 LERVIVVAGETGSGKTTLMK  193 (361)
T ss_dssp             TTCCEEEEESSSSCHHHHHH
T ss_pred             cCCEEEEECCCCCCHHHHHH
Confidence            57899999999999997753

>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=94.04  E-value=0.036  Score=40.53  Aligned_cols=22  Identities=32%  Similarity=0.317  Sum_probs=17.2

Q ss_pred             CccEEEEccCCcchHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      ..-+++++|||+|||.++...+
T Consensus         3 ~~~i~i~GptgsGKt~la~~La   24 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVMLA   24 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHH
T ss_pred             CcEEEEECCCcCCHHHHHHHHH
Confidence            3456889999999998875443

>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=94.03  E-value=0.024  Score=37.99  Aligned_cols=45  Identities=18%  Similarity=0.135  Sum_probs=27.3

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ++|.+++|||||..++-.+.    . +.+++|+..-.....+..+++...
T Consensus         2 ilV~Gg~~SGKS~~A~~la~----~-~~~~~yiaT~~~~d~e~~~rI~~h   46 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIG----D-APQVLYIATSQILDDEMAARIQHH   46 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHC----S-CSSEEEEECCCC------CHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHh----c-CCCeEEEecCCCCCHHHHHHHHHH
Confidence            58999999999999875432    2 567888876554444444444433

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=94.03  E-value=1.3  Score=33.54  Aligned_cols=43  Identities=19%  Similarity=0.108  Sum_probs=28.8

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhc-CCeEEEEc--chhhhHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIK-QKSAIFIL--PYISLVHE   48 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~-~~~~l~v~--P~~aL~~q   48 (138)
                      ..++++++.|+|||..+.-.+.. +..+ +.+++++.  |.+.-..+
T Consensus       101 ~vI~ivG~~GvGKTT~a~~LA~~-l~~~~G~kVllvd~D~~r~~a~~  146 (433)
T 2xxa_A          101 AVVLMAGLQGAGKTTSVGKLGKF-LREKHKKKVLVVSADVYRPAAIK  146 (433)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH-HHHTSCCCEEEEECCCSSTTHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH-HHHhcCCeEEEEecCCCCccHHH
Confidence            35678899999999887555543 4455 77888764  44443333

>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=93.99  E-value=0.049  Score=35.65  Aligned_cols=23  Identities=30%  Similarity=0.273  Sum_probs=19.1

Q ss_pred             CCccEEEEccCCcchHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      ++.++++++|.|||||.++...+
T Consensus        10 ~~~~i~i~G~~GsGKst~~~~l~   32 (180)
T 3iij_A           10 LLPNILLTGTPGVGKTTLGKELA   32 (180)
T ss_dssp             CCCCEEEECSTTSSHHHHHHHHH
T ss_pred             cCCeEEEEeCCCCCHHHHHHHHH
Confidence            45689999999999999886544

>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=93.98  E-value=0.035  Score=40.47  Aligned_cols=20  Identities=35%  Similarity=0.283  Sum_probs=16.1

Q ss_pred             EEEEccCCcchHHHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +++++|||+|||.++...+-
T Consensus        13 i~i~GptgsGKt~la~~La~   32 (316)
T 3foz_A           13 IFLMGPTASGKTALAIELRK   32 (316)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCccCHHHHHHHHHH
Confidence            58899999999988755443

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=93.87  E-value=0.037  Score=36.34  Aligned_cols=25  Identities=20%  Similarity=0.215  Sum_probs=19.4

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHH
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      |..|..+++.+|.|||||.++-..+
T Consensus         1 m~~g~~I~l~G~~GsGKST~~~~La   25 (186)
T 3cm0_A            1 MDVGQAVIFLGPPGAGKGTQASRLA   25 (186)
T ss_dssp             --CEEEEEEECCTTSCHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHH
Confidence            3467788999999999999885544

>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=93.81  E-value=0.19  Score=36.58  Aligned_cols=23  Identities=22%  Similarity=0.198  Sum_probs=18.4

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ..++++++|.|+|||..+...+.
T Consensus        45 ~~~vll~G~~G~GKT~la~~l~~   67 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFVSKYIFN   67 (384)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCcEEEECCCCCCHHHHHHHHHH
Confidence            35799999999999988755443

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=93.79  E-value=0.052  Score=36.16  Aligned_cols=23  Identities=30%  Similarity=0.241  Sum_probs=18.8

Q ss_pred             CCCccEEEEccCCcchHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      -.|..+.+.+|.|||||..+-..
T Consensus         4 ~~g~~i~l~G~~GsGKSTl~~~L   26 (207)
T 2j41_A            4 EKGLLIVLSGPSGVGKGTVRKRI   26 (207)
T ss_dssp             CCCCEEEEECSTTSCHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHH
Confidence            35778899999999999887543

>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=93.77  E-value=0.15  Score=43.33  Aligned_cols=53  Identities=13%  Similarity=0.075  Sum_probs=37.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcC-----------CeEEEEcchhhhHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQ-----------KSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~-----------~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +| +.+|.|..|||||.+-..-++..+...+           .++|.++-|++=..+..+++.+.
T Consensus        16 ~g-~~lV~AsAGSGKT~~L~~r~lrLll~~g~~~~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~~   79 (1180)
T 1w36_B           16 QG-ERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSN   79 (1180)
T ss_dssp             SS-CEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHH
T ss_pred             CC-CEEEEECCCCCHHHHHHHHHHHHHhcCCcccccCCCCCHHHEEEEeccHHHHHHHHHHHHHH
Confidence            45 4599999999999886665666555322           37899998887666666555543

>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=93.71  E-value=0.052  Score=39.19  Aligned_cols=22  Identities=18%  Similarity=0.308  Sum_probs=18.3

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +++++++|+|+|||.++-..+.
T Consensus        52 ~~vLl~GppGtGKT~la~aia~   73 (322)
T 3eie_A           52 SGILLYGPPGTGKSYLAKAVAT   73 (322)
T ss_dssp             CEEEEECSSSSCHHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHH
Confidence            5799999999999999855544

>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=93.71  E-value=0.061  Score=35.71  Aligned_cols=22  Identities=27%  Similarity=0.262  Sum_probs=17.7

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .++++++|+|+|||..+...+.
T Consensus        39 ~~~ll~G~~G~GKT~l~~~l~~   60 (226)
T 2chg_A           39 PHLLFSGPPGTGKTATAIALAR   60 (226)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            3599999999999988755443

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=93.69  E-value=0.043  Score=38.41  Aligned_cols=21  Identities=24%  Similarity=0.181  Sum_probs=16.8

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .+++++|+|||||.++...+-
T Consensus         3 li~I~G~~GSGKSTla~~La~   23 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAIQIAQ   23 (253)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            468999999999998855443

>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=93.69  E-value=0.045  Score=40.32  Aligned_cols=23  Identities=39%  Similarity=0.512  Sum_probs=18.8

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ..++++++|+|+|||.++-..+.
T Consensus        72 ~~~ill~Gp~GtGKT~la~~la~   94 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMAQTLAK   94 (376)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCEEEECCCCCCHHHHHHHHHH
Confidence            45799999999999999865543

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=93.66  E-value=0.054  Score=39.28  Aligned_cols=22  Identities=18%  Similarity=0.333  Sum_probs=18.5

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +.+++++|.|+|||..+-..+.
T Consensus        46 ~~iLL~GppGtGKT~la~ala~   67 (322)
T 1xwi_A           46 RGILLFGPPGTGKSYLAKAVAT   67 (322)
T ss_dssp             SEEEEESSSSSCHHHHHHHHHH
T ss_pred             ceEEEECCCCccHHHHHHHHHH
Confidence            6799999999999999865544

>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=93.64  E-value=0.056  Score=35.71  Aligned_cols=24  Identities=21%  Similarity=0.325  Sum_probs=19.6

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ++.+++++++.|||||.++-..+-
T Consensus         9 ~~~~I~l~G~~GsGKSTv~~~La~   32 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMAEMIAA   32 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            467899999999999999855443

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=93.59  E-value=0.054  Score=38.70  Aligned_cols=23  Identities=17%  Similarity=0.056  Sum_probs=18.3

Q ss_pred             ccEEEEccCCcchHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      ..+++++|+|+|||..+-..+..
T Consensus        37 ~~lLl~GppGtGKT~la~aiA~~   59 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQCELVFRK   59 (293)
T ss_dssp             SEEEEEECTTSCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            46789999999999998655443

>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=93.55  E-value=0.055  Score=41.13  Aligned_cols=24  Identities=21%  Similarity=0.338  Sum_probs=19.5

Q ss_pred             CccEEEEccCCcchHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      ++++++.+|+|+|||..+-..+..
T Consensus        63 ~~~iLl~GppGtGKT~la~ala~~   86 (456)
T 2c9o_A           63 GRAVLLAGPPGTGKTALALAIAQE   86 (456)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEECCCcCCHHHHHHHHHHH
Confidence            468999999999999998655443

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=93.47  E-value=0.052  Score=37.70  Aligned_cols=22  Identities=27%  Similarity=0.413  Sum_probs=17.9

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .++++.+|+|+|||..+-..+.
T Consensus        46 ~~vll~G~~GtGKT~la~~la~   67 (257)
T 1lv7_A           46 KGVLMVGPPGTGKTLLAKAIAG   67 (257)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEECcCCCCHHHHHHHHHH
Confidence            4689999999999988855443

>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=93.47  E-value=0.064  Score=36.39  Aligned_cols=23  Identities=22%  Similarity=0.219  Sum_probs=18.4

Q ss_pred             CCCccEEEEccCCcchHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      ..|+-+++++|+|+|||.+.-..
T Consensus        17 ~~g~~ivl~GPSGaGKsTL~~~L   39 (197)
T 3ney_A           17 QGRKTLVLIGASGVGRSHIKNAL   39 (197)
T ss_dssp             CSCCEEEEECCTTSSHHHHHHHH
T ss_pred             CCCCEEEEECcCCCCHHHHHHHH
Confidence            35677899999999999876443

>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=93.43  E-value=0.066  Score=34.81  Aligned_cols=22  Identities=23%  Similarity=0.215  Sum_probs=18.0

Q ss_pred             CccEEEEccCCcchHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      +..+++++|.|||||.++-..+
T Consensus         3 ~~~i~l~G~~GsGKST~a~~La   24 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIVRCLQ   24 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHH
Confidence            5678999999999999985543

>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=93.35  E-value=0.065  Score=39.39  Aligned_cols=22  Identities=18%  Similarity=0.308  Sum_probs=18.3

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +++++++|+|+|||.++-..+.
T Consensus        85 ~~iLL~GppGtGKT~la~ala~  106 (355)
T 2qp9_X           85 SGILLYGPPGTGKSYLAKAVAT  106 (355)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHH
T ss_pred             ceEEEECCCCCcHHHHHHHHHH
Confidence            5799999999999999865544

>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=93.35  E-value=0.12  Score=37.32  Aligned_cols=36  Identities=17%  Similarity=-0.005  Sum_probs=24.3

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      ++-+.+.+|+|+|||..+...+.. +...+++++++.
T Consensus       104 ~~vi~ivG~~GsGKTTl~~~LA~~-l~~~g~kV~lv~  139 (306)
T 1vma_A          104 PFVIMVVGVNGTGKTTSCGKLAKM-FVDEGKSVVLAA  139 (306)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH-HHHTTCCEEEEE
T ss_pred             CeEEEEEcCCCChHHHHHHHHHHH-HHhcCCEEEEEc
Confidence            445789999999999776444432 334567777653

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=93.34  E-value=0.046  Score=35.82  Aligned_cols=21  Identities=19%  Similarity=0.150  Sum_probs=17.8

Q ss_pred             CCccEEEEccCCcchHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      +|+-+.+.+|.|||||..+-.
T Consensus         8 ~gei~~l~G~nGsGKSTl~~~   28 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFAKK   28 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHH
Confidence            577789999999999988753

>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=93.34  E-value=1.5  Score=31.24  Aligned_cols=36  Identities=19%  Similarity=0.168  Sum_probs=24.5

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      ++.+.+.+|.|+|||..+...+.. +...+++++++-
T Consensus        98 ~~~i~i~g~~G~GKTT~~~~la~~-~~~~~~~v~l~~  133 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTAAKLALY-YKGKGRRPLLVA  133 (295)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHH-HHHTTCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH-HHHcCCeEEEec
Confidence            456678899999999776444433 334577777763

>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=93.34  E-value=0.12  Score=40.10  Aligned_cols=38  Identities=16%  Similarity=0.267  Sum_probs=27.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      .|+.+.+.+|.|||||..+...++..+...+...+++.
T Consensus        38 ~Ge~~~l~G~nGsGKSTL~~~~ll~Gl~~~~~g~i~v~   75 (525)
T 1tf7_A           38 IGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVT   75 (525)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEE
Confidence            57888999999999999887655555555344455553

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=93.31  E-value=0.1  Score=46.62  Aligned_cols=46  Identities=22%  Similarity=0.233  Sum_probs=34.8

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKY   50 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~   50 (138)
                      .|+++++++|+|+|||..+...+.+.+. ++.+++|+.- -.+.++.+
T Consensus      1080 ~g~~vll~G~~GtGKT~la~~~~~ea~k-~Ge~~~Fit~-ee~~~~L~ 1125 (2050)
T 3cmu_A         1080 MGRIVEIYGPESSGKTTLTLQVIAAAQR-EGKTCAFIDA-EHALDPIY 1125 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHT-TTCCEEEECT-TSCCCHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHH-cCCeEEEEEc-cccHHHHH
Confidence            5789999999999999999888877654 4889999753 33333444

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=93.30  E-value=0.06  Score=39.19  Aligned_cols=23  Identities=30%  Similarity=0.342  Sum_probs=18.7

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +.++++++|+|+|||..+...+.
T Consensus        44 ~~~vll~G~~G~GKT~l~~~~~~   66 (387)
T 2v1u_A           44 PSNALLYGLTGTGKTAVARLVLR   66 (387)
T ss_dssp             CCCEEECBCTTSSHHHHHHHHHH
T ss_pred             CCcEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999988755443

>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=93.26  E-value=0.14  Score=36.94  Aligned_cols=36  Identities=17%  Similarity=0.038  Sum_probs=24.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      .|+.+.+.+|+|+|||...-..+.. +...++++.+.
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagl-l~~~~g~V~l~  136 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRY-YQNLGKKVMFC  136 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHH-HHTTTCCEEEE
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH-HHhcCCEEEEE
Confidence            3567889999999999765443332 23356777665

>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=93.26  E-value=0.028  Score=41.21  Aligned_cols=34  Identities=12%  Similarity=0.008  Sum_probs=24.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      .|..+++.+|.|+|||..+...+..    .+.+++|+.
T Consensus       122 ~gsviLI~GpPGsGKTtLAlqlA~~----~G~~VlyIs  155 (331)
T 2vhj_A          122 ASGMVIVTGKGNSGKTPLVHALGEA----LGGKDKYAT  155 (331)
T ss_dssp             ESEEEEEECSCSSSHHHHHHHHHHH----HHTTSCCEE
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHh----CCCCEEEEE
Confidence            3556799999999999998776654    344555543

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=93.22  E-value=0.067  Score=38.58  Aligned_cols=22  Identities=27%  Similarity=0.385  Sum_probs=18.2

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .++++.+|+|+|||.++-..+.
T Consensus        56 ~~vll~G~~GtGKT~la~~ia~   77 (338)
T 3pfi_A           56 DHILFSGPAGLGKTTLANIISY   77 (338)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHH
T ss_pred             CeEEEECcCCCCHHHHHHHHHH
Confidence            4799999999999998865533

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=93.21  E-value=0.065  Score=38.55  Aligned_cols=23  Identities=22%  Similarity=0.313  Sum_probs=18.7

Q ss_pred             CCccEEEEccCCcchHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      .+.++++.+|+|+|||.++-...
T Consensus        24 ~~~~vLi~Ge~GtGKt~lAr~i~   46 (304)
T 1ojl_A           24 SDATVLIHGDSGTGKELVARALH   46 (304)
T ss_dssp             TTSCEEEESCTTSCHHHHHHHHH
T ss_pred             CCCcEEEECCCCchHHHHHHHHH
Confidence            35689999999999999885443

>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=93.17  E-value=0.071  Score=39.15  Aligned_cols=23  Identities=35%  Similarity=0.491  Sum_probs=18.8

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .+++++++|+|+|||.++-..+.
T Consensus       117 ~~~vLl~GppGtGKT~la~aia~  139 (357)
T 3d8b_A          117 PKGILLFGPPGTGKTLIGKCIAS  139 (357)
T ss_dssp             CSEEEEESSTTSSHHHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHH
Confidence            45799999999999998865543

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=93.10  E-value=0.052  Score=39.14  Aligned_cols=23  Identities=22%  Similarity=0.069  Sum_probs=19.1

Q ss_pred             CCccEEEEccCCcchHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      .++++++.+|+|+|||..+-..+
T Consensus        45 ~~~~vll~G~pGtGKT~la~~la   67 (331)
T 2r44_A           45 TGGHILLEGVPGLAKTLSVNTLA   67 (331)
T ss_dssp             HTCCEEEESCCCHHHHHHHHHHH
T ss_pred             cCCeEEEECCCCCcHHHHHHHHH
Confidence            46789999999999998875543

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=93.07  E-value=0.075  Score=39.42  Aligned_cols=23  Identities=22%  Similarity=0.384  Sum_probs=18.9

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ..++++++|+|+|||.++-..+.
T Consensus       148 ~~~vLL~GppGtGKT~la~aia~  170 (389)
T 3vfd_A          148 ARGLLLFGPPGNGKTMLAKAVAA  170 (389)
T ss_dssp             CSEEEEESSTTSCHHHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999998865533

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=93.07  E-value=0.071  Score=39.00  Aligned_cols=21  Identities=33%  Similarity=0.264  Sum_probs=17.2

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .+++++|||||||.++...+.
T Consensus         7 ~i~i~GptGsGKTtla~~La~   27 (323)
T 3crm_A            7 AIFLMGPTAAGKTDLAMALAD   27 (323)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            578999999999998855443

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=93.07  E-value=0.17  Score=33.28  Aligned_cols=36  Identities=17%  Similarity=0.062  Sum_probs=24.9

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      .|..+++.++.|||||.++-..+-. +...+.++.++
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~L~~~-l~~~~~~~~~~   47 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATRLADL-LQKEGYRVEVL   47 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHH-HHHTTCCEEEE
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHH-HHhcCCeEEEe
Confidence            4567899999999999988554432 33345666554

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=93.04  E-value=0.05  Score=39.75  Aligned_cols=19  Identities=32%  Similarity=0.232  Sum_probs=16.7

Q ss_pred             CCccEEEEccCCcchHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVG   21 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~   21 (138)
                      .|+++.+.+|||||||...
T Consensus       170 ~g~~v~i~G~~GsGKTTll  188 (330)
T 2pt7_A          170 IGKNVIVCGGTGSGKTTYI  188 (330)
T ss_dssp             HTCCEEEEESTTSCHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4788999999999999864

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=93.03  E-value=0.087  Score=34.98  Aligned_cols=25  Identities=20%  Similarity=0.109  Sum_probs=20.4

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHH
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      |..|..+++.+|.|||||.++...+
T Consensus         1 m~~~~~I~l~G~~GsGKsT~~~~L~   25 (204)
T 2v54_A            1 MSRGALIVFEGLDKSGKTTQCMNIM   25 (204)
T ss_dssp             CCCCCEEEEECCTTSSHHHHHHHHH
T ss_pred             CCCCcEEEEEcCCCCCHHHHHHHHH
Confidence            4567788999999999999985543

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=93.02  E-value=0.077  Score=36.20  Aligned_cols=22  Identities=23%  Similarity=0.141  Sum_probs=18.0

Q ss_pred             CCccEEEEccCCcchHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      .|+-+.+.+|+|||||...-..
T Consensus        22 ~G~~~~lvGpsGsGKSTLl~~L   43 (218)
T 1z6g_A           22 NIYPLVICGPSGVGKGTLIKKL   43 (218)
T ss_dssp             CCCCEEEECSTTSSHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHH
Confidence            5778899999999999876443

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=93.01  E-value=0.15  Score=37.13  Aligned_cols=35  Identities=11%  Similarity=-0.108  Sum_probs=24.5

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      ++-+.+.+|.|+|||..+...+.. +...+++++++
T Consensus       105 ~~vI~ivG~~G~GKTT~~~~LA~~-l~~~g~kVlli  139 (320)
T 1zu4_A          105 LNIFMLVGVNGTGKTTSLAKMANY-YAELGYKVLIA  139 (320)
T ss_dssp             CEEEEEESSTTSSHHHHHHHHHHH-HHHTTCCEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH-HHHCCCeEEEE
Confidence            445788999999999776444332 33457788776

>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=93.01  E-value=0.05  Score=34.90  Aligned_cols=19  Identities=16%  Similarity=0.246  Sum_probs=16.0

Q ss_pred             cEEEEccCCcchHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~   24 (138)
                      .+++++|.|||||.++...
T Consensus         3 ~I~l~G~~GsGKsT~a~~L   21 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKLL   21 (179)
T ss_dssp             EEEEECCTTSCHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            4689999999999988554

>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=92.99  E-value=0.062  Score=38.41  Aligned_cols=22  Identities=23%  Similarity=0.313  Sum_probs=18.3

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .++++++|+|+|||.++...+.
T Consensus        39 ~~vll~G~~GtGKT~la~~i~~   60 (324)
T 1hqc_A           39 EHLLLFGPPGLGKTTLAHVIAH   60 (324)
T ss_dssp             CCCEEECCTTCCCHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999998855543

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=92.99  E-value=0.061  Score=38.21  Aligned_cols=22  Identities=27%  Similarity=0.279  Sum_probs=18.1

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .++++.+|+|+|||.++-..+.
T Consensus        48 ~~~ll~G~~GtGKt~la~~la~   69 (311)
T 4fcw_A           48 GSFLFLGPTGVGKTELAKTLAA   69 (311)
T ss_dssp             EEEEEESCSSSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHH
Confidence            4789999999999998855444

>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=92.95  E-value=0.12  Score=37.50  Aligned_cols=33  Identities=18%  Similarity=0.215  Sum_probs=23.2

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEE
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIF   38 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~   38 (138)
                      -.|+.+.+.+|+|||||....+.+-  +.  .++++.
T Consensus       124 ~~Ge~vaIvGpsGsGKSTLl~lL~g--l~--~G~I~~  156 (305)
T 2v9p_A          124 PKKNCLAFIGPPNTGKSMLCNSLIH--FL--GGSVLS  156 (305)
T ss_dssp             TTCSEEEEECSSSSSHHHHHHHHHH--HH--TCEEEC
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhh--hc--CceEEE
Confidence            3678889999999999987654433  22  455544

>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=92.93  E-value=0.078  Score=34.45  Aligned_cols=22  Identities=23%  Similarity=0.225  Sum_probs=18.2

Q ss_pred             CCccEEEEccCCcchHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      .|..+.+.+|.|||||.++-..
T Consensus         7 ~g~~i~l~G~~GsGKSTl~~~l   28 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAVASEV   28 (175)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHH
Confidence            4677899999999999887554

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=92.90  E-value=0.081  Score=36.32  Aligned_cols=22  Identities=23%  Similarity=0.357  Sum_probs=17.8

Q ss_pred             CCCccEEEEccCCcchHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      -.|+-+.+++|.|||||...-.
T Consensus        14 ~~G~ii~l~GpsGsGKSTLlk~   35 (219)
T 1s96_A           14 AQGTLYIVSAPSGAGKSSLIQA   35 (219)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHH
Confidence            3577889999999999987644

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=92.90  E-value=0.16  Score=35.25  Aligned_cols=33  Identities=12%  Similarity=-0.090  Sum_probs=24.5

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      ++++.++.|.|||..+.-.+.. +..+|.+++++
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~-l~~~G~~V~v~   40 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHA-QLRQGVRVMAG   40 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHH-HHHTTCCEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHH-HHHCCCCEEEE
Confidence            6899999999999997555554 44567677554

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=92.90  E-value=0.16  Score=36.62  Aligned_cols=37  Identities=19%  Similarity=0.147  Sum_probs=24.6

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      .|+-+.+.+|+|+|||...-..+-. +...++++.+..
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag~-l~~~~g~V~l~g  135 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAHR-LKNEGTKVLMAA  135 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHHH-HHHTTCCEEEEC
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHH-HHHcCCeEEEEe
Confidence            4567789999999999765443322 233567777653

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=92.88  E-value=0.077  Score=39.07  Aligned_cols=21  Identities=29%  Similarity=0.226  Sum_probs=16.7

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      -++|++|||||||.++...+.
T Consensus         9 lI~I~GptgSGKTtla~~La~   29 (340)
T 3d3q_A            9 LIVIVGPTASGKTELSIEVAK   29 (340)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEECCCcCcHHHHHHHHHH
Confidence            468999999999998854433

>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=92.86  E-value=0.47  Score=37.86  Aligned_cols=50  Identities=26%  Similarity=0.244  Sum_probs=39.5

Q ss_pred             ceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhh
Q psy2029          76 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEE  129 (138)
Q Consensus        76 ~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~  129 (138)
                      ...+..-||+|||+...-.+ +.   .++++++|+|...++.|.+++|+.++.+
T Consensus        34 ~~~l~g~~gs~k~~~~a~~~-~~---~~~~~lvv~~~~~~A~~l~~el~~~~~~   83 (661)
T 2d7d_A           34 HQTLLGATGTGKTFTVSNLI-KE---VNKPTLVIAHNKTLAGQLYSEFKEFFPN   83 (661)
T ss_dssp             EEEEEECTTSCHHHHHHHHH-HH---HCCCEEEECSSHHHHHHHHHHHHHHCTT
T ss_pred             cEEEECcCCcHHHHHHHHHH-HH---hCCCEEEEECCHHHHHHHHHHHHHHcCC
Confidence            45677889999998774333 22   2557999999999999999999999754

>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=92.85  E-value=0.15  Score=44.91  Aligned_cols=40  Identities=23%  Similarity=0.199  Sum_probs=32.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchh
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYI   43 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~   43 (138)
                      .|+++++++|+|+|||..+...+...+. .+.+++|+.-..
T Consensus        33 ~G~i~lI~G~pGsGKT~LAlqla~~~~~-~G~~vlYI~te~   72 (1706)
T 3cmw_A           33 MGRIVEIYGPESSGKTTLTLQVIAAAQR-EGKTCAFIDAEH   72 (1706)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHH-TTCCEEEECTTS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhh-CCCceEEEEecC
Confidence            4788999999999999999887776554 477899986543

>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=92.80  E-value=0.21  Score=36.23  Aligned_cols=36  Identities=28%  Similarity=0.287  Sum_probs=24.5

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhc---CCeEEEEc
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIK---QKSAIFIL   40 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~---~~~~l~v~   40 (138)
                      +..+++++|.|+|||..+...+-. +...   +...+++.
T Consensus        45 ~~~vli~G~~G~GKTtl~~~l~~~-~~~~~~~~~~~~~i~   83 (386)
T 2qby_A           45 PNNIFIYGLTGTGKTAVVKFVLSK-LHKKFLGKFKHVYIN   83 (386)
T ss_dssp             CCCEEEEECTTSSHHHHHHHHHHH-HHHHTCSSCEEEEEE
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH-HHHHhcCCceEEEEE
Confidence            568999999999999887554433 3332   44566654

>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=92.77  E-value=0.19  Score=37.65  Aligned_cols=42  Identities=10%  Similarity=0.138  Sum_probs=33.2

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVH  117 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~  117 (138)
                      .++++..|||+|||... ..++..+...+..++++.|-.++..
T Consensus        54 ~h~~i~G~tGsGKs~~~-~~li~~~~~~g~~viv~Dpkge~~~   95 (437)
T 1e9r_A           54 RHLLVNGATGTGKSVLL-RELAYTGLLRGDRMVIVDPNGDMLS   95 (437)
T ss_dssp             GCEEEEECTTSSHHHHH-HHHHHHHHHTTCEEEEEEETTHHHH
T ss_pred             ceEEEECCCCCCHHHHH-HHHHHHHHHCCCcEEEEeCCCchhH
Confidence            89999999999999874 4455555656788999999877753

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=92.74  E-value=0.083  Score=40.19  Aligned_cols=23  Identities=26%  Similarity=0.378  Sum_probs=19.0

Q ss_pred             ccEEEEccCCcchHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      +.+++.+|.|+|||+.+-..+-.
T Consensus       216 rGvLLyGPPGTGKTllAkAiA~e  238 (434)
T 4b4t_M          216 KGALMYGPPGTGKTLLARACAAQ  238 (434)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHH
T ss_pred             CeeEEECcCCCCHHHHHHHHHHH
Confidence            57899999999999998655543

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=92.70  E-value=0.092  Score=35.10  Aligned_cols=23  Identities=17%  Similarity=0.226  Sum_probs=18.6

Q ss_pred             CCccEEEEccCCcchHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      .|..+.+.+|.|||||.++-..+
T Consensus        28 ~g~~i~l~G~~GsGKSTl~~~L~   50 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIAHGVA   50 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHH
Confidence            35678999999999998875543

>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=92.61  E-value=0.038  Score=38.55  Aligned_cols=22  Identities=32%  Similarity=0.416  Sum_probs=18.1

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +++++.+|+|+|||.++...+.
T Consensus        45 ~~vll~G~~GtGKT~la~~la~   66 (268)
T 2r62_A           45 KGVLLVGPPGTGKTLLAKAVAG   66 (268)
T ss_dssp             SCCCCBCSSCSSHHHHHHHHHH
T ss_pred             ceEEEECCCCCcHHHHHHHHHH
Confidence            4689999999999999865544

>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=92.60  E-value=0.089  Score=35.17  Aligned_cols=24  Identities=13%  Similarity=0.012  Sum_probs=18.9

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .|..+.+.+|.|||||.++-..+-
T Consensus        24 ~g~~i~l~G~sGsGKSTl~~~La~   47 (200)
T 3uie_A           24 KGCVIWVTGLSGSGKSTLACALNQ   47 (200)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            466788999999999988755443

>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=92.56  E-value=0.051  Score=39.22  Aligned_cols=23  Identities=13%  Similarity=0.004  Sum_probs=18.6

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ..++++.+|+|+|||.++-..+.
T Consensus        45 ~~~vLl~G~~GtGKT~la~~la~   67 (350)
T 1g8p_A           45 IGGVLVFGDRGTGKSTAVRALAA   67 (350)
T ss_dssp             GCCEEEECCGGGCTTHHHHHHHH
T ss_pred             CceEEEECCCCccHHHHHHHHHH
Confidence            45799999999999998865443

>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=92.54  E-value=0.089  Score=39.72  Aligned_cols=21  Identities=24%  Similarity=0.140  Sum_probs=16.6

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      -++|++|||+|||.++...+.
T Consensus         4 ~i~i~GptgsGKttla~~La~   24 (409)
T 3eph_A            4 VIVIAGTTGVGKSQLSIQLAQ   24 (409)
T ss_dssp             EEEEEECSSSSHHHHHHHHHH
T ss_pred             EEEEECcchhhHHHHHHHHHH
Confidence            468899999999988755443

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=92.51  E-value=0.08  Score=35.90  Aligned_cols=22  Identities=23%  Similarity=0.366  Sum_probs=17.4

Q ss_pred             cEEEEccCCcchHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      -.+++++.|||||..+...+..
T Consensus         7 i~l~tG~pGsGKT~~a~~~~~~   28 (199)
T 2r2a_A            7 ICLITGTPGSGKTLKMVSMMAN   28 (199)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHH
Confidence            4589999999999988555444

>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=92.49  E-value=0.1  Score=35.13  Aligned_cols=22  Identities=32%  Similarity=0.318  Sum_probs=17.6

Q ss_pred             CCCccEEEEccCCcchHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      -.|+-+.+.+|+|||||...-.
T Consensus        18 ~~Gei~~l~GpnGsGKSTLl~~   39 (207)
T 1znw_A           18 AVGRVVVLSGPSAVGKSTVVRC   39 (207)
T ss_dssp             -CCCEEEEECSTTSSHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHH
Confidence            3577889999999999987644

>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=92.46  E-value=0.099  Score=34.19  Aligned_cols=24  Identities=21%  Similarity=0.196  Sum_probs=18.7

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ++..+++.+|.|||||.++-..+-
T Consensus         2 ~~~~I~i~G~~GsGKsT~~~~L~~   25 (192)
T 1kht_A            2 KNKVVVVTGVPGVGSTTSSQLAMD   25 (192)
T ss_dssp             -CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            456789999999999998855443

>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=92.39  E-value=0.11  Score=34.88  Aligned_cols=18  Identities=28%  Similarity=0.313  Sum_probs=14.8

Q ss_pred             cEEEEccCCcchHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~   23 (138)
                      =+++++|+|+|||.+.-.
T Consensus         3 pIVi~GPSG~GK~Tl~~~   20 (186)
T 1ex7_A            3 PIVISGPSGTGKSTLLKK   20 (186)
T ss_dssp             CEEEECCTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            368999999999987643

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=92.36  E-value=0.086  Score=40.15  Aligned_cols=22  Identities=27%  Similarity=0.413  Sum_probs=18.2

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .++++++|+|+|||.++-..+.
T Consensus        51 ~~vLL~GppGtGKTtlAr~ia~   72 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLAEVIAR   72 (447)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHH
Confidence            4789999999999999865544

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=92.34  E-value=0.1  Score=39.34  Aligned_cols=23  Identities=30%  Similarity=0.433  Sum_probs=19.1

Q ss_pred             ccEEEEccCCcchHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      +.+++.+|.|+|||+.+-..+-+
T Consensus       183 rGvLL~GPPGTGKTllAkAiA~e  205 (405)
T 4b4t_J          183 KGVILYGPPGTGKTLLARAVAHH  205 (405)
T ss_dssp             CCEEEESCSSSSHHHHHHHHHHH
T ss_pred             CceEEeCCCCCCHHHHHHHHHHh
Confidence            57899999999999998665554

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=92.26  E-value=0.22  Score=33.72  Aligned_cols=38  Identities=18%  Similarity=0.037  Sum_probs=28.8

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcch
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPY   42 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~   42 (138)
                      |+=.++.+|.|+|||...+-.+.+. ...+.+++++.|.
T Consensus        20 g~l~fiyG~MgsGKTt~Ll~~i~n~-~~~~~kvl~~kp~   57 (195)
T 1w4r_A           20 GQIQVILGPMFSGKSTELMRRVRRF-QIAQYKCLVIKYA   57 (195)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHH-HHTTCCEEEEEET
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHH-HHcCCeEEEEccc
Confidence            3445889999999997766666654 3457899999886

>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=92.24  E-value=0.098  Score=36.19  Aligned_cols=20  Identities=25%  Similarity=0.315  Sum_probs=16.4

Q ss_pred             cEEEEccCCcchHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~   25 (138)
                      .+++.+|+|+|||..+-..+
T Consensus        51 g~ll~G~~G~GKTtl~~~i~   70 (254)
T 1ixz_A           51 GVLLVGPPGVGKTHLARAVA   70 (254)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHH
Confidence            48999999999998875443

>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=92.19  E-value=0.23  Score=36.13  Aligned_cols=34  Identities=24%  Similarity=0.110  Sum_probs=23.4

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhc-CCeEEEEc
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIK-QKSAIFIL   40 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~-~~~~l~v~   40 (138)
                      ++++++|+|+|||..+...+- .+... +...+++.
T Consensus        46 ~~li~G~~G~GKTtl~~~l~~-~~~~~~~~~~~~i~   80 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTLRKLWE-LYKDKTTARFVYIN   80 (389)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH-HHTTSCCCEEEEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHH-HHhhhcCeeEEEEe
Confidence            799999999999988754433 33333 34566654

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=92.18  E-value=0.13  Score=34.47  Aligned_cols=21  Identities=24%  Similarity=0.264  Sum_probs=17.1

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .+++.+|.|+|||..+...+.
T Consensus        47 ~~ll~G~~G~GKT~l~~~~~~   67 (250)
T 1njg_A           47 AYLFSGTRGVGKTSIARLLAK   67 (250)
T ss_dssp             EEEEECSTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            689999999999988755443

>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=92.14  E-value=0.11  Score=33.36  Aligned_cols=20  Identities=25%  Similarity=0.112  Sum_probs=16.5

Q ss_pred             cEEEEccCCcchHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~   25 (138)
                      .+++.+|.|||||.++-..+
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~   22 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLS   22 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            57899999999999885543

>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=92.14  E-value=0.11  Score=39.41  Aligned_cols=22  Identities=18%  Similarity=0.333  Sum_probs=18.4

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +++++++|+|+|||.++-..+.
T Consensus       168 ~~vLL~GppGtGKT~lA~aia~  189 (444)
T 2zan_A          168 RGILLFGPPGTGKSYLAKAVAT  189 (444)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHH
Confidence            6789999999999999865544

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=92.13  E-value=0.092  Score=36.08  Aligned_cols=19  Identities=26%  Similarity=0.364  Sum_probs=16.1

Q ss_pred             ccEEEEccCCcchHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~   23 (138)
                      +++++.+|.|+|||..+..
T Consensus        59 n~ili~GPPGtGKTt~a~a   77 (212)
T 1tue_A           59 NCLVFCGPANTGKSYFGMS   77 (212)
T ss_dssp             SEEEEESCGGGCHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHH
Confidence            4689999999999988843

>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=92.12  E-value=0.4  Score=38.26  Aligned_cols=48  Identities=23%  Similarity=0.203  Sum_probs=37.9

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ...+.+-||||||++..-.+.+    .++.+++++|...+..|.++++..+.
T Consensus        34 ~~~l~g~~gs~k~~~~a~~~~~----~~~~~lvv~~~~~~A~~l~~el~~~~   81 (661)
T 2d7d_A           34 HQTLLGATGTGKTFTVSNLIKE----VNKPTLVIAHNKTLAGQLYSEFKEFF   81 (661)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHH----HCCCEEEECSSHHHHHHHHHHHHHHC
T ss_pred             cEEEECcCCcHHHHHHHHHHHH----hCCCEEEEECCHHHHHHHHHHHHHHc
Confidence            4578899999999876433322    25678999999999999999999884

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=92.12  E-value=0.12  Score=34.47  Aligned_cols=25  Identities=12%  Similarity=0.005  Sum_probs=20.0

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .++..+++.+|.|||||.++...+-
T Consensus         2 m~~~~I~i~G~~GsGKsT~~~~L~~   26 (213)
T 2plr_A            2 KKGVLIAFEGIDGSGKSSQATLLKD   26 (213)
T ss_dssp             CCCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCeEEEEEcCCCCCHHHHHHHHHH
Confidence            3567789999999999998865543

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=92.12  E-value=0.094  Score=40.04  Aligned_cols=42  Identities=10%  Similarity=-0.074  Sum_probs=31.4

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLA   54 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~   54 (138)
                      .++.++.|+|||....-.     .+ ..+.++++|++++.++..+.+.
T Consensus       164 ~~I~G~aGsGKTt~I~~~-----~~-~~~~lVlTpT~~aa~~l~~kl~  205 (446)
T 3vkw_A          164 VLVDGVPGCGKTKEILSR-----VN-FEEDLILVPGRQAAEMIRRRAN  205 (446)
T ss_dssp             EEEEECTTSCHHHHHHHH-----CC-TTTCEEEESCHHHHHHHHHHHT
T ss_pred             EEEEcCCCCCHHHHHHHH-----hc-cCCeEEEeCCHHHHHHHHHHhh
Confidence            479999999999865221     12 2566999999999987777764

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=92.09  E-value=0.11  Score=39.51  Aligned_cols=23  Identities=30%  Similarity=0.427  Sum_probs=19.1

Q ss_pred             ccEEEEccCCcchHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      +.+++.+|.|+|||+.+-..+-.
T Consensus       216 rGvLL~GPPGtGKTllAkAiA~e  238 (437)
T 4b4t_L          216 KGVLLYGPPGTGKTLLAKAVAAT  238 (437)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHHH
Confidence            57899999999999998665544

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=92.00  E-value=0.078  Score=41.03  Aligned_cols=22  Identities=23%  Similarity=0.283  Sum_probs=18.7

Q ss_pred             CCccEEEEccCCcchHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      .|.++++.+|+|+|||..+-..
T Consensus        40 ~~~~VLL~GpPGtGKT~LAraL   61 (500)
T 3nbx_X           40 SGESVFLLGPPGIAKSLIARRL   61 (500)
T ss_dssp             HTCEEEEECCSSSSHHHHHHHG
T ss_pred             cCCeeEeecCchHHHHHHHHHH
Confidence            4679999999999999988544

>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=91.99  E-value=0.13  Score=33.69  Aligned_cols=23  Identities=17%  Similarity=0.187  Sum_probs=18.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      .+..++++++.|||||.++-..+
T Consensus         4 ~~~~I~l~G~~GsGKST~~~~L~   26 (193)
T 2rhm_A            4 TPALIIVTGHPATGKTTLSQALA   26 (193)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHH
Confidence            45678999999999999885543

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=91.90  E-value=0.11  Score=34.28  Aligned_cols=24  Identities=13%  Similarity=0.070  Sum_probs=19.1

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ++..+++.+|.|||||.++-..+-
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~La~   31 (196)
T 2c95_A            8 KTNIIFVVGGPGSGKGTQCEKIVQ   31 (196)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            456789999999999998855443

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=91.90  E-value=0.25  Score=36.60  Aligned_cols=37  Identities=19%  Similarity=0.147  Sum_probs=24.7

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      .|+-+.+.+|+|+|||...-..+-. +...++++++..
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag~-l~~~~G~V~l~g  192 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAHR-LKNEGTKVLMAA  192 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHH-HHHTTCCEEEEC
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHhh-ccccCCEEEEec
Confidence            4667789999999999765443322 233567777653

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=91.89  E-value=0.12  Score=34.84  Aligned_cols=21  Identities=19%  Similarity=0.181  Sum_probs=16.9

Q ss_pred             CCccEEEEccCCcchHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      .|.-+.+.+|+|||||..+-.
T Consensus        21 ~g~~v~I~G~sGsGKSTl~~~   41 (208)
T 3c8u_A           21 GRQLVALSGAPGSGKSTLSNP   41 (208)
T ss_dssp             SCEEEEEECCTTSCTHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHH
Confidence            466778999999999977633

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=91.87  E-value=0.12  Score=39.19  Aligned_cols=23  Identities=22%  Similarity=0.326  Sum_probs=18.8

Q ss_pred             ccEEEEccCCcchHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      +.+++.+|.|+|||+.+-..+-.
T Consensus       207 rGiLL~GPPGtGKT~lakAiA~~  229 (428)
T 4b4t_K          207 RGVLLYGPPGTGKTMLVKAVANS  229 (428)
T ss_dssp             CEEEEESCTTTTHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH
Confidence            56899999999999998665543

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=91.77  E-value=0.11  Score=36.38  Aligned_cols=24  Identities=29%  Similarity=0.355  Sum_probs=20.1

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .|+.+.+.+|.|||||.++-..+-
T Consensus        47 ~g~~i~l~G~~GsGKSTl~~~La~   70 (250)
T 3nwj_A           47 NGRSMYLVGMMGSGKTTVGKIMAR   70 (250)
T ss_dssp             TTCCEEEECSTTSCHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            488999999999999999855543

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=91.76  E-value=0.13  Score=34.51  Aligned_cols=22  Identities=23%  Similarity=0.164  Sum_probs=17.3

Q ss_pred             CCccEEEEccCCcchHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      +|.-+.+.+|+|||||.++-..
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l   26 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQAL   26 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHHHH
Confidence            3556789999999999887443

>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=91.76  E-value=0.12  Score=37.63  Aligned_cols=22  Identities=27%  Similarity=0.397  Sum_probs=18.0

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +++++++|.|+|||..+-+.+-
T Consensus        52 ~~~ll~Gp~G~GKTTLa~~ia~   73 (334)
T 1in4_A           52 DHVLLAGPPGLGKTTLAHIIAS   73 (334)
T ss_dssp             CCEEEESSTTSSHHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHH
Confidence            5789999999999988755443

>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=91.73  E-value=0.15  Score=34.49  Aligned_cols=22  Identities=14%  Similarity=0.217  Sum_probs=17.7

Q ss_pred             CccEEEEccCCcchHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      +..+.+.+|+|||||.++-..+
T Consensus         5 ~~~i~i~G~~GsGKSTl~~~L~   26 (227)
T 1cke_A            5 APVITIDGPSGAGKGTLCKAMA   26 (227)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHH
Confidence            3567899999999998886544

>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=91.68  E-value=0.11  Score=34.26  Aligned_cols=22  Identities=23%  Similarity=0.285  Sum_probs=17.4

Q ss_pred             CccEEEEccCCcchHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      |..+.+.+|.|||||..+-..+
T Consensus         2 g~ii~l~G~~GaGKSTl~~~L~   23 (189)
T 2bdt_A            2 KKLYIITGPAGVGKSTTCKRLA   23 (189)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHh
Confidence            4567899999999998875543

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=91.67  E-value=0.084  Score=36.09  Aligned_cols=23  Identities=39%  Similarity=0.417  Sum_probs=14.0

Q ss_pred             CCccEEEEccCCcchHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      .|+-+.+.+|+|||||.+.-..+
T Consensus        26 ~G~ii~l~Gp~GsGKSTl~~~L~   48 (231)
T 3lnc_A           26 VGVILVLSSPSGCGKTTVANKLL   48 (231)
T ss_dssp             CCCEEEEECSCC----CHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHH
Confidence            46677899999999997764443

>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=91.60  E-value=0.15  Score=36.73  Aligned_cols=22  Identities=23%  Similarity=0.126  Sum_probs=17.8

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .++++.+|.|+|||..+...+.
T Consensus        59 ~~~ll~G~~G~GKT~la~~la~   80 (353)
T 1sxj_D           59 PHMLFYGPPGTGKTSTILALTK   80 (353)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            4699999999999988755444

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=91.59  E-value=0.14  Score=39.03  Aligned_cols=24  Identities=33%  Similarity=0.246  Sum_probs=19.8

Q ss_pred             CccEEEEccCCcchHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      ..|+++.+|+|+|||.++...+..
T Consensus       201 ~~~~LL~G~pG~GKT~la~~la~~  224 (468)
T 3pxg_A          201 KNNPVLIGEPGVGKTAIAEGLAQQ  224 (468)
T ss_dssp             SCEEEEESCTTTTTHHHHHHHHHH
T ss_pred             CCCeEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999998665544

>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=91.56  E-value=0.24  Score=36.39  Aligned_cols=39  Identities=18%  Similarity=0.058  Sum_probs=27.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh--c---CCeEEEEcc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI--K---QKSAIFILP   41 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~---~~~~l~v~P   41 (138)
                      .|+-+.+.+|.|+|||..+...+......  .   +++++|+.-
T Consensus       130 ~G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~  173 (349)
T 1pzn_A          130 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDT  173 (349)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEES
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeC
Confidence            46778999999999998886665542211  2   368788753

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=91.42  E-value=0.098  Score=37.35  Aligned_cols=21  Identities=19%  Similarity=0.219  Sum_probs=17.0

Q ss_pred             CccEEEEccCCcchHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      +.-+++++|.|||||.++-..
T Consensus        33 ~~livl~G~sGsGKSTla~~L   53 (287)
T 1gvn_B           33 PTAFLLGGQPGSGKTSLRSAI   53 (287)
T ss_dssp             CEEEEEECCTTSCTHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHH
Confidence            456799999999999887544

>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=91.40  E-value=0.34  Score=31.98  Aligned_cols=33  Identities=12%  Similarity=-0.105  Sum_probs=21.1

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      -+.+.++.|||||......+ ..+..++.++-.+
T Consensus         6 ~i~i~G~sGsGKTTl~~~L~-~~l~~~g~~v~~i   38 (169)
T 1xjc_A            6 VWQVVGYKHSGKTTLMEKWV-AAAVREGWRVGTV   38 (169)
T ss_dssp             EEEEECCTTSSHHHHHHHHH-HHHHHTTCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHH-HhhHhcCCeeeEE
Confidence            35789999999998764433 3344455555443

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=91.34  E-value=0.16  Score=33.91  Aligned_cols=21  Identities=29%  Similarity=0.132  Sum_probs=17.0

Q ss_pred             CccEEEEccCCcchHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      +..+.+.+|+|||||.++...
T Consensus        21 ~~~i~i~G~~GsGKSTl~~~L   41 (207)
T 2qt1_A           21 TFIIGISGVTNSGKTTLAKNL   41 (207)
T ss_dssp             CEEEEEEESTTSSHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHH
Confidence            456789999999999887543

>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=91.29  E-value=0.37  Score=33.12  Aligned_cols=40  Identities=18%  Similarity=0.095  Sum_probs=28.8

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhh
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYIS   44 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~a   44 (138)
                      |.=.++++|-|+|||..++-.+.+. ..++.+++++.|.+.
T Consensus        28 G~l~vitG~MgsGKTT~lL~~a~r~-~~~g~kVli~k~~~d   67 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELIRRVRRT-QFAKQHAIVFKPCID   67 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHH-HHTTCCEEEEECC--
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHH-HHCCCEEEEEEeccC
Confidence            3334688999999998886666654 456889999988764

>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=91.28  E-value=0.41  Score=32.41  Aligned_cols=38  Identities=11%  Similarity=-0.090  Sum_probs=30.5

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchh
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYI   43 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~   43 (138)
                      .++++..+.|.|||.+|.-.+++.+ ..|.+++++.-.+
T Consensus        29 g~i~v~tG~GkGKTTaA~GlalRA~-g~G~rV~~vQF~K   66 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAARAV-GHGKNVGVVQFIK   66 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHH-HTTCCEEEEESSC
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHH-HCCCeEEEEEeeC
Confidence            4889999999999999977777644 5688999985443

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=91.27  E-value=0.25  Score=33.66  Aligned_cols=52  Identities=17%  Similarity=0.199  Sum_probs=33.9

Q ss_pred             hhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHH
Q psy2029          72 IQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLA  124 (138)
Q Consensus        72 ~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~  124 (138)
                      +.. .-+++..++|+|||..+.-.+...+...+.+++|+.-. .-.++..+.+.
T Consensus        27 l~~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s~E-~~~~~~~~~~~   79 (251)
T 2zts_A           27 FPEGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTLE-ERARDLRREMA   79 (251)
T ss_dssp             EETTCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEESS-SCHHHHHHHHH
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeeccc-CCHHHHHHHHH
Confidence            444 56679999999999999766665555556677777543 23344444443

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=91.23  E-value=0.15  Score=32.96  Aligned_cols=19  Identities=11%  Similarity=-0.073  Sum_probs=15.7

Q ss_pred             cEEEEccCCcchHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~   24 (138)
                      .+++++|.|||||.++-..
T Consensus         4 ~I~i~G~~GsGKST~a~~L   22 (181)
T 1ly1_A            4 IILTIGCPGSGKSTWAREF   22 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHH
T ss_pred             EEEEecCCCCCHHHHHHHH
Confidence            4789999999999987443

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=91.23  E-value=0.37  Score=32.18  Aligned_cols=35  Identities=17%  Similarity=0.074  Sum_probs=22.7

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      +.-+.+.+|.|||||.++....- .+...+..+.+.
T Consensus        22 ~~~i~i~G~~GsGKstl~~~l~~-~~~~~~~~v~~~   56 (201)
T 1rz3_A           22 RLVLGIDGLSRSGKTTLANQLSQ-TLREQGISVCVF   56 (201)
T ss_dssp             SEEEEEEECTTSSHHHHHHHHHH-HHHHTTCCEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH-HHhhcCCeEEEe
Confidence            45678999999999988754332 222345555553

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=91.19  E-value=0.16  Score=38.73  Aligned_cols=23  Identities=35%  Similarity=0.341  Sum_probs=18.7

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .+++++.+|+|+|||.++-..+-
T Consensus        50 ~~~iLl~GppGtGKT~lar~lA~   72 (444)
T 1g41_A           50 PKNILMIGPTGVGKTEIARRLAK   72 (444)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHH
T ss_pred             CceEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999998855443

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=91.12  E-value=0.19  Score=33.44  Aligned_cols=24  Identities=21%  Similarity=0.250  Sum_probs=19.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .+..+++.++.|||||.++-..+-
T Consensus         9 ~~~~I~l~G~~GsGKST~~~~L~~   32 (212)
T 2wwf_A            9 KGKFIVFEGLDRSGKSTQSKLLVE   32 (212)
T ss_dssp             CSCEEEEEESTTSSHHHHHHHHHH
T ss_pred             cCCEEEEEcCCCCCHHHHHHHHHH
Confidence            466789999999999998865543

>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=91.11  E-value=0.17  Score=38.99  Aligned_cols=21  Identities=29%  Similarity=0.460  Sum_probs=17.7

Q ss_pred             ccEEEEccCCcchHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      .++++.+|+|+|||.++-..+
T Consensus       239 ~~vLL~GppGtGKT~lAraia  259 (489)
T 3hu3_A          239 RGILLYGPPGTGKTLIARAVA  259 (489)
T ss_dssp             CEEEEECSTTSSHHHHHHHHH
T ss_pred             CcEEEECcCCCCHHHHHHHHH
Confidence            579999999999999885543

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=91.10  E-value=0.14  Score=39.33  Aligned_cols=23  Identities=30%  Similarity=0.390  Sum_probs=19.0

Q ss_pred             ccEEEEccCCcchHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      +.+++.+|.|+|||+.+-..+-+
T Consensus       244 rGILLyGPPGTGKTlLAkAiA~e  266 (467)
T 4b4t_H          244 KGILLYGPPGTGKTLCARAVANR  266 (467)
T ss_dssp             SEEEECSCTTSSHHHHHHHHHHH
T ss_pred             CceEeeCCCCCcHHHHHHHHHhc
Confidence            57899999999999998655543

>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=91.08  E-value=0.18  Score=32.35  Aligned_cols=18  Identities=11%  Similarity=0.064  Sum_probs=14.7

Q ss_pred             cEEEEccCCcchHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~   23 (138)
                      -.++.+|+|+|||.+...
T Consensus        25 ~~~I~G~NGsGKStil~A   42 (149)
T 1f2t_A           25 INLIIGQNGSGKSSLLDA   42 (149)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            458899999999988544

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=91.08  E-value=0.15  Score=35.81  Aligned_cols=20  Identities=25%  Similarity=0.315  Sum_probs=16.3

Q ss_pred             cEEEEccCCcchHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~   25 (138)
                      .+++.+|+|+|||..+-..+
T Consensus        75 gvll~Gp~GtGKTtl~~~i~   94 (278)
T 1iy2_A           75 GVLLVGPPGVGKTHLARAVA   94 (278)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             eEEEECCCcChHHHHHHHHH
Confidence            48999999999998875443

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=91.01  E-value=0.26  Score=39.78  Aligned_cols=22  Identities=27%  Similarity=0.282  Sum_probs=18.1

Q ss_pred             cEEEEccCCcchHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      ++++++|+|+|||.++-..+..
T Consensus       523 ~~Ll~Gp~GtGKT~lA~ala~~  544 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELARALAES  544 (758)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6999999999999998655443

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=90.96  E-value=0.18  Score=35.87  Aligned_cols=21  Identities=29%  Similarity=0.295  Sum_probs=17.8

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .+++.+|.|+|||+.+...+.
T Consensus       106 ~~~l~GppgtGKt~~a~ala~  126 (267)
T 1u0j_A          106 TIWLFGPATTGKTNIAEAIAH  126 (267)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            589999999999999975544

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=90.91  E-value=0.16  Score=39.51  Aligned_cols=24  Identities=21%  Similarity=0.209  Sum_probs=19.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .|..+++.+|+|+|||..+-..+.
T Consensus       107 ~g~~vll~Gp~GtGKTtlar~ia~  130 (543)
T 3m6a_A          107 KGPILCLAGPPGVGKTSLAKSIAK  130 (543)
T ss_dssp             CSCEEEEESSSSSSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            467899999999999998854433

>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=90.90  E-value=3.5  Score=29.95  Aligned_cols=36  Identities=19%  Similarity=-0.007  Sum_probs=24.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      .|.-+.+.+|+|+|||...-..+.. +...++++++.
T Consensus       128 ~g~vi~lvG~nGaGKTTll~~Lag~-l~~~~g~V~l~  163 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTTIAKLANW-LKNHGFSVVIA  163 (328)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHH-HHHTTCCEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH-HHhcCCEEEEE
Confidence            3567789999999999765443332 33456777665

>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=90.81  E-value=4.2  Score=30.73  Aligned_cols=36  Identities=19%  Similarity=0.168  Sum_probs=24.9

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      +..+.+.+|.|+|||..+...+.. +...+++++++-
T Consensus        98 ~~vi~i~G~~GsGKTT~~~~LA~~-l~~~g~~Vllvd  133 (425)
T 2ffh_A           98 RNLWFLVGLQGSGKTTTAAKLALY-YKGKGRRPLLVA  133 (425)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHH-HHTTTCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH-HHHcCCeEEEee
Confidence            445678899999999877554443 344577777763

>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=90.79  E-value=0.22  Score=37.81  Aligned_cols=35  Identities=17%  Similarity=0.107  Sum_probs=25.4

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      ..+++++|+|+|||..+.-.+.. +...+.+++++.
T Consensus       100 ~vI~ivG~~GvGKTTla~~La~~-l~~~G~kVllv~  134 (432)
T 2v3c_C          100 NVILLVGIQGSGKTTTAAKLARY-IQKRGLKPALIA  134 (432)
T ss_dssp             CCEEEECCSSSSTTHHHHHHHHH-HHHHHCCEEEEC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH-HHHcCCeEEEEe
Confidence            47889999999999877554443 334577887764

>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=90.79  E-value=0.18  Score=38.92  Aligned_cols=32  Identities=19%  Similarity=0.172  Sum_probs=22.9

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      +.+++++|+|+|||.++...+.. +   +...+.+-
T Consensus        78 ~~lLL~GppGtGKTtla~~la~~-l---~~~~i~in  109 (516)
T 1sxj_A           78 RAAMLYGPPGIGKTTAAHLVAQE-L---GYDILEQN  109 (516)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHH-T---TCEEEEEC
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH-c---CCCEEEEe
Confidence            57899999999999988655443 2   44555553

>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=90.74  E-value=0.31  Score=35.03  Aligned_cols=36  Identities=19%  Similarity=-0.034  Sum_probs=24.9

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      +..+.+++|.|+|||..+...+.. +...+++++++-
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~-~~~~g~~v~l~~  133 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYF-YKKKGFKVGLVG  133 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHH-HHHTTCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH-HHHCCCeEEEEe
Confidence            456778899999999776554443 334577887763

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=90.71  E-value=0.18  Score=40.66  Aligned_cols=24  Identities=33%  Similarity=0.225  Sum_probs=19.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ...|+++.+|+|+|||.++...+.
T Consensus       200 ~~~~vLL~G~pGtGKT~la~~la~  223 (758)
T 3pxi_A          200 TKNNPVLIGEPGVGKTAIAEGLAQ  223 (758)
T ss_dssp             SSCEEEEESCTTTTTHHHHHHHHH
T ss_pred             CCCCeEEECCCCCCHHHHHHHHHH
Confidence            346899999999999999865544

>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=90.71  E-value=0.19  Score=32.74  Aligned_cols=24  Identities=25%  Similarity=0.133  Sum_probs=18.9

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .|..+.+.++.|||||.++-..+-
T Consensus         4 ~g~~i~l~G~~GsGKST~~~~L~~   27 (179)
T 2pez_A            4 RGCTVWLTGLSGAGKTTVSMALEE   27 (179)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            467789999999999988755433

>3of5_A Dethiobiotin synthetase; structural genomics, center for structural genomics of infec diseases, csgid, ligase; 1.52A {Francisella tularensis subsp}

Probab=90.71  E-value=0.41  Score=32.96  Aligned_cols=34  Identities=21%  Similarity=0.218  Sum_probs=22.6

Q ss_pred             EEEEcc-CCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           7 CVLSIP-TSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         7 ~~~~~p-tg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      ++|.+. ||+|||.++...+. .+.+++.++.+.=|
T Consensus         7 i~Itgt~t~vGKT~vt~~L~~-~l~~~G~~V~~~KP   41 (228)
T 3of5_A            7 FFIIGTDTEVGKTYISTKLIE-VCEHQNIKSLCLKP   41 (228)
T ss_dssp             EEEEESSSSSCHHHHHHHHHH-HHHHTTCCEEEECS
T ss_pred             EEEEeCCCCCCHHHHHHHHHH-HHHHCCCeeEEecc
Confidence            444444 89999999854443 46667777777544

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=90.71  E-value=0.19  Score=38.24  Aligned_cols=23  Identities=26%  Similarity=0.339  Sum_probs=19.1

Q ss_pred             ccEEEEccCCcchHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      +.+++.+|.|+|||+.+-..+-+
T Consensus       217 rGvLLyGPPGTGKTlLAkAiA~e  239 (437)
T 4b4t_I          217 KGVILYGAPGTGKTLLAKAVANQ  239 (437)
T ss_dssp             SEEEEESSTTTTHHHHHHHHHHH
T ss_pred             CCCceECCCCchHHHHHHHHHHH
Confidence            57899999999999998665554

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=90.68  E-value=0.18  Score=32.94  Aligned_cols=23  Identities=9%  Similarity=-0.021  Sum_probs=17.8

Q ss_pred             CCccEEEEccCCcchHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      .+..+++.++.|||||.++...+
T Consensus         2 ~~~~I~l~G~~GsGKsT~a~~L~   24 (196)
T 1tev_A            2 KPLVVFVLGGPGAGKGTQCARIV   24 (196)
T ss_dssp             -CEEEEEECCTTSSHHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHH
Confidence            35568999999999999885543

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=90.66  E-value=0.18  Score=33.56  Aligned_cols=21  Identities=29%  Similarity=0.359  Sum_probs=17.1

Q ss_pred             ccEEEEccCCcchHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      ..+++++|.|||||.++-..+
T Consensus        19 ~~I~l~G~~GsGKSTla~~L~   39 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVGEAIA   39 (202)
T ss_dssp             SCEEEECSTTSCHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            357999999999999885543

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=90.61  E-value=0.23  Score=33.32  Aligned_cols=21  Identities=33%  Similarity=0.253  Sum_probs=17.0

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .+++.+|.|||||.++-..+-
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIE   22 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            578999999999998865443

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=90.57  E-value=0.22  Score=33.20  Aligned_cols=24  Identities=21%  Similarity=0.159  Sum_probs=19.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ++..+++.++.|||||.++...+-
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~L~~   31 (215)
T 1nn5_A            8 RGALIVLEGVDRAGKSTQSRKLVE   31 (215)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            466789999999999999865543

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=90.56  E-value=0.21  Score=34.81  Aligned_cols=23  Identities=17%  Similarity=0.183  Sum_probs=18.6

Q ss_pred             CCccEEEEccCCcchHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      .|..+.+.+|.|||||.++-..+
T Consensus        26 ~g~~I~I~G~~GsGKSTl~k~La   48 (252)
T 4e22_A           26 IAPVITVDGPSGAGKGTLCKALA   48 (252)
T ss_dssp             TSCEEEEECCTTSSHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHH
Confidence            35678899999999998885554

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=90.54  E-value=0.2  Score=34.08  Aligned_cols=22  Identities=18%  Similarity=0.129  Sum_probs=17.7

Q ss_pred             CccEEEEccCCcchHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      +..+++.+|.|||||.++-..+
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La   28 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRIT   28 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHH
Confidence            4568999999999999885443

>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=90.52  E-value=0.25  Score=32.14  Aligned_cols=19  Identities=16%  Similarity=0.319  Sum_probs=15.5

Q ss_pred             cEEEEccCCcchHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~   24 (138)
                      -.++.+|+|||||.+....
T Consensus        28 ~~~i~G~NGsGKStll~ai   46 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGDAI   46 (182)
T ss_dssp             EEEEEECTTSSHHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHHH
Confidence            5689999999999886543

>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga maritima} PDB: 3qg5_A 3tho_A*

Probab=90.50  E-value=0.18  Score=37.19  Aligned_cols=18  Identities=28%  Similarity=0.283  Sum_probs=14.8

Q ss_pred             cEEEEccCCcchHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~   23 (138)
                      -.++++|+|||||.+...
T Consensus        25 ~~~i~G~NGaGKTTll~a   42 (365)
T 3qf7_A           25 ITVVEGPNGAGKSSLFEA   42 (365)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            457899999999987644

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=90.44  E-value=0.21  Score=32.43  Aligned_cols=21  Identities=24%  Similarity=0.191  Sum_probs=17.3

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ++++.+|.|||||.++-..+-
T Consensus         6 ~i~i~G~~GsGKsTla~~La~   26 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAK   26 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHH
Confidence            688999999999998855543

>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=90.35  E-value=0.2  Score=33.71  Aligned_cols=20  Identities=35%  Similarity=0.370  Sum_probs=16.6

Q ss_pred             cEEEEccCCcchHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~   25 (138)
                      ++++.+|.|||||.++...+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~   21 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIV   21 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            57899999999999885543

>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=90.20  E-value=0.2  Score=36.96  Aligned_cols=19  Identities=16%  Similarity=0.113  Sum_probs=15.4

Q ss_pred             cEEEEccCCcchHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~   24 (138)
                      -.++++|||+|||.+....
T Consensus        27 l~vi~G~NGaGKT~ileAI   45 (371)
T 3auy_A           27 IVAIIGENGSGKSSIFEAV   45 (371)
T ss_dssp             EEEEEECTTSSHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHH
Confidence            4588999999999886543

>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=90.18  E-value=0.24  Score=32.37  Aligned_cols=22  Identities=27%  Similarity=0.315  Sum_probs=17.6

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ..++++++.|||||.++-..+-
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~   24 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAK   24 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999855443

>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=90.15  E-value=0.42  Score=37.01  Aligned_cols=36  Identities=17%  Similarity=0.047  Sum_probs=24.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      .|.-+.+.+|+|+|||...-..+.. +...++++++.
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAgl-l~~~~G~V~l~  327 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLARQ-FEQQGKSVMLA  327 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHHH-HHHTTCCEEEE
T ss_pred             CCeEEEEECCCcccHHHHHHHHHHH-hhhcCCeEEEe
Confidence            4567789999999999765443322 33356777775

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=90.14  E-value=0.21  Score=35.34  Aligned_cols=20  Identities=30%  Similarity=0.483  Sum_probs=16.5

Q ss_pred             cEEEEccCCcchHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~   25 (138)
                      .+++.+|.|+|||..+-..+
T Consensus        46 GvlL~Gp~GtGKTtLakala   65 (274)
T 2x8a_A           46 GVLLAGPPGCGKTLLAKAVA   65 (274)
T ss_dssp             EEEEESSTTSCHHHHHHHHH
T ss_pred             eEEEECCCCCcHHHHHHHHH
Confidence            48999999999998875443

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=90.08  E-value=0.24  Score=32.60  Aligned_cols=23  Identities=22%  Similarity=0.059  Sum_probs=18.0

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +..+++++|.|||||.++-..+-
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~   34 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVE   34 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            34678999999999998855443

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=89.84  E-value=0.27  Score=32.65  Aligned_cols=23  Identities=22%  Similarity=0.169  Sum_probs=18.2

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +..+++++|.|||||.++-..+-
T Consensus        20 ~~~I~l~G~~GsGKST~a~~La~   42 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQAVKLAE   42 (201)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            34678999999999998855443

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=89.74  E-value=0.2  Score=34.72  Aligned_cols=19  Identities=16%  Similarity=0.233  Sum_probs=16.5

Q ss_pred             CCccEEEEccCCcchHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVG   21 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~   21 (138)
                      .|+-+.+.+|.|||||...
T Consensus        30 ~Ge~~~iiG~nGsGKSTLl   48 (235)
T 3tif_A           30 EGEFVSIMGPSGSGKSTML   48 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHH
Confidence            5778899999999999765

>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=89.72  E-value=0.59  Score=31.39  Aligned_cols=33  Identities=24%  Similarity=0.140  Sum_probs=23.1

Q ss_pred             EEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           8 VLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      +...-+|.|||.++.-.+.. +..++.|++++=|
T Consensus         6 v~s~kgGvGKTt~a~nLa~~-la~~G~rVll~dp   38 (224)
T 1byi_A            6 VTGTDTEVGKTVASCALLQA-AKAAGYRTAGYKP   38 (224)
T ss_dssp             EEESSTTSCHHHHHHHHHHH-HHHTTCCEEEECS
T ss_pred             EEECCCCCCHHHHHHHHHHH-HHHCCCCEEEEcc
Confidence            44556899999888555443 5556889988755

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=89.71  E-value=0.27  Score=33.16  Aligned_cols=24  Identities=25%  Similarity=0.180  Sum_probs=19.0

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .+..+++.+|.|||||.++-..+-
T Consensus         3 ~~~~I~l~G~~GsGKsT~a~~La~   26 (220)
T 1aky_A            3 ESIRMVLIGPPGAGKGTQAPNLQE   26 (220)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            356789999999999998855443

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=89.70  E-value=0.47  Score=31.39  Aligned_cols=42  Identities=26%  Similarity=0.218  Sum_probs=26.8

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHE  118 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q  118 (138)
                      .++++.-|+|+|||..+.. +...+...+.+++++ ....+..+
T Consensus        55 ~~~~l~G~~GtGKT~la~~-i~~~~~~~~~~~~~~-~~~~~~~~   96 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAA-IANELAKRNVSSLIV-YVPELFRE   96 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHH-HHHHHHTTTCCEEEE-EHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHH-HHHHHHHcCCeEEEE-EhHHHHHH
Confidence            5788999999999998844 444454445555554 33344433

>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=89.68  E-value=0.26  Score=31.66  Aligned_cols=22  Identities=23%  Similarity=0.164  Sum_probs=17.5

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ..+++.++.|||||.++-..+-
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~   24 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELAR   24 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999998855443

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=89.62  E-value=0.28  Score=33.14  Aligned_cols=23  Identities=17%  Similarity=0.179  Sum_probs=18.4

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +..+++.+|.|||||.++-..+-
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~   27 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKT   27 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45789999999999998865443

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=89.59  E-value=0.24  Score=38.99  Aligned_cols=24  Identities=21%  Similarity=0.407  Sum_probs=19.7

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .|+++++.+|+|+|||..+-..+-
T Consensus        59 ~g~~vll~Gp~GtGKTtlar~ia~   82 (604)
T 3k1j_A           59 QKRHVLLIGEPGTGKSMLGQAMAE   82 (604)
T ss_dssp             TTCCEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHhc
Confidence            578999999999999998855433

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=89.43  E-value=0.27  Score=31.63  Aligned_cols=22  Identities=23%  Similarity=0.176  Sum_probs=18.1

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .++.+.++.|||||.++-..+-
T Consensus         8 ~~i~l~G~~GsGKSTva~~La~   29 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELGL   29 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHH
Confidence            4789999999999999865543

>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=89.43  E-value=0.71  Score=30.91  Aligned_cols=36  Identities=17%  Similarity=0.091  Sum_probs=23.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHh-hcCCeEEEE
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELK-IKQKSAIFI   39 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~-~~~~~~l~v   39 (138)
                      .|..+++.++.|||||..+-...-. +. +.+...+++
T Consensus        24 ~~~~i~~~G~~GsGKsT~~~~l~~~-l~~~~g~~~~~~   60 (211)
T 1m7g_A           24 RGLTIWLTGLSASGKSTLAVELEHQ-LVRDRRVHAYRL   60 (211)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHH-HHHHHCCCEEEE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHH-hccccCCcEEEE
Confidence            4667889999999999887554332 22 234344554

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=89.37  E-value=1.3  Score=31.91  Aligned_cols=83  Identities=11%  Similarity=-0.054  Sum_probs=47.6

Q ss_pred             cchhhhHHHHHHHHHHH-H----HhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccch
Q psy2029          40 LPYISLVHEKYQSLAKA-A----EEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYI  113 (138)
Q Consensus        40 ~P~~aL~~q~~~~l~~~-~----~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~  113 (138)
                      .+...+..+.++++++. +    ...+++-=......+.. .-+++..++|.|||..+.-.+...+. ++.+++|+.-- 
T Consensus        28 ~~~~~~~~~~~~~~~~~~~~~~~i~TG~~~LD~~lgGl~~G~l~li~G~pG~GKTtl~l~ia~~~a~-~g~~vl~~slE-  105 (315)
T 3bh0_A           28 GSIDEALVTVYEEIESADGNITGVPSGFTELDRMTYGYKRRNFVLIAARPSMGKTAFALKQAKNMSD-NDDVVNLHSLE-  105 (315)
T ss_dssp             CCCHHHHHHHHHHHHTCSSSCCSBCCSCHHHHHHHSSBCTTCEEEEECCTTSSHHHHHHHHHHHHHT-TTCEEEEEESS-
T ss_pred             ccHHHHHHHHHHHHHhccCCCCCccCChHHHHhhcCCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHH-cCCeEEEEECC-
Confidence            46666666777766653 1    11222222222233444 56679999999999988766655443 35678887643 


Q ss_pred             hHHHHHHHHHH
Q psy2029         114 SLVHEKYQSLA  124 (138)
Q Consensus       114 ~l~~q~~~~~~  124 (138)
                      .-..|....+.
T Consensus       106 ~s~~~l~~R~~  116 (315)
T 3bh0_A          106 MGKKENIKRLI  116 (315)
T ss_dssp             SCHHHHHHHHH
T ss_pred             CCHHHHHHHHH
Confidence            33344444443

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=89.30  E-value=0.25  Score=38.01  Aligned_cols=22  Identities=32%  Similarity=0.388  Sum_probs=17.9

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +.+++.+|+|+|||..+-..+-
T Consensus        50 ~gvLL~GppGtGKT~Laraia~   71 (476)
T 2ce7_A           50 KGILLVGPPGTGKTLLARAVAG   71 (476)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            4689999999999998855443

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=89.28  E-value=0.34  Score=34.22  Aligned_cols=21  Identities=29%  Similarity=0.284  Sum_probs=17.4

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (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            589999999999988855544

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=89.24  E-value=0.34  Score=34.35  Aligned_cols=21  Identities=24%  Similarity=0.230  Sum_probs=17.5

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ++++++|.|+|||..+...+.
T Consensus        48 ~~ll~G~~G~GKT~la~~l~~   68 (327)
T 1iqp_A           48 HLLFAGPPGVGKTTAALALAR   68 (327)
T ss_dssp             EEEEESCTTSSHHHHHHHHHH
T ss_pred             eEEEECcCCCCHHHHHHHHHH
Confidence            689999999999988865544

>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=89.20  E-value=0.56  Score=36.44  Aligned_cols=25  Identities=12%  Similarity=0.198  Sum_probs=19.8

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      ++.++++.++||||||...-..+..
T Consensus       166 ~~pHlLIaG~TGSGKSt~L~~li~s  190 (512)
T 2ius_A          166 KMPHLLVAGTTGSGASVGVNAMILS  190 (512)
T ss_dssp             GSCSEEEECCTTSSHHHHHHHHHHH
T ss_pred             cCceEEEECCCCCCHHHHHHHHHHH
Confidence            4578999999999999887555544

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=89.20  E-value=0.31  Score=39.30  Aligned_cols=24  Identities=29%  Similarity=0.254  Sum_probs=19.7

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .+.++++++|+|+|||.++...+.
T Consensus       206 ~~~~vlL~G~~GtGKT~la~~la~  229 (758)
T 1r6b_X          206 RKNNPLLVGESGVGKTAIAEGLAW  229 (758)
T ss_dssp             SSCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCCeEEEcCCCCCHHHHHHHHHH
Confidence            356899999999999998865544

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=89.20  E-value=0.28  Score=32.82  Aligned_cols=24  Identities=17%  Similarity=0.153  Sum_probs=19.7

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .|.-+++.+|.|+|||..+...+.
T Consensus        15 ~G~gvli~G~SGaGKStlal~L~~   38 (181)
T 3tqf_A           15 DKMGVLITGEANIGKSELSLALID   38 (181)
T ss_dssp             TTEEEEEEESSSSSHHHHHHHHHH
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHH
Confidence            577889999999999988765554

>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=89.17  E-value=0.41  Score=31.13  Aligned_cols=44  Identities=18%  Similarity=0.132  Sum_probs=27.3

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHH-hCCCeEEEEccchhHHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELK-IKQKSAIFILPYISLVHEKY  120 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~-~~~~~~~~i~P~~~l~~q~~  120 (138)
                      +.+.+.-|+|+|||..+...+ ..+. ..+.+++| .+...+..+..
T Consensus        39 ~~~~l~G~~G~GKTtL~~~i~-~~~~~~~g~~~~~-~~~~~~~~~~~   83 (180)
T 3ec2_A           39 KGLTFVGSPGVGKTHLAVATL-KAIYEKKGIRGYF-FDTKDLIFRLK   83 (180)
T ss_dssp             CEEEECCSSSSSHHHHHHHHH-HHHHHHSCCCCCE-EEHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHH-HHHHHHcCCeEEE-EEHHHHHHHHH
Confidence            677899999999998885443 3443 33444444 34455554433

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=89.12  E-value=0.29  Score=32.49  Aligned_cols=19  Identities=21%  Similarity=0.246  Sum_probs=15.9

Q ss_pred             cEEEEccCCcchHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~   24 (138)
                      .+.+.+|.|||||.++-..
T Consensus         3 ~i~i~G~~GsGKSTl~~~L   21 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMF   21 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHH
Confidence            5789999999999987554

>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=89.12  E-value=0.29  Score=34.20  Aligned_cols=36  Identities=17%  Similarity=0.086  Sum_probs=23.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      .+..++++++.|||||..+-..+-. +.+.+...+++
T Consensus         3 ~~~lIvl~G~pGSGKSTla~~La~~-L~~~g~~~i~~   38 (260)
T 3a4m_A            3 DIMLIILTGLPGVGKSTFSKNLAKI-LSKNNIDVIVL   38 (260)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHH-HHHTTCCEEEE
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHH-HHhCCCEEEEE
Confidence            4457899999999999988554332 33334444433

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=89.05  E-value=0.29  Score=31.90  Aligned_cols=36  Identities=17%  Similarity=0.004  Sum_probs=23.1

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchh
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYI   43 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~   43 (138)
                      .+++.+|.|||||.++...+-. +.+.+..+.++ |.-
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~-l~~~g~~~~~~-~~~   38 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEI-LDNQGINNKII-NYG   38 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHH-HHTTTCCEEEE-EHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH-HHhcCceEEEE-ECC
Confidence            4789999999999988554432 33334444444 543

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=89.04  E-value=0.32  Score=33.21  Aligned_cols=23  Identities=26%  Similarity=0.212  Sum_probs=18.6

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +.++++.++.|||||..+...+-
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La~   38 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLAK   38 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45789999999999998855543

>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=89.01  E-value=0.29  Score=31.88  Aligned_cols=20  Identities=10%  Similarity=-0.007  Sum_probs=16.6

Q ss_pred             cEEEEccCCcchHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~   25 (138)
                      .+++.++.|||||.++-..+
T Consensus         8 ~I~l~G~~GsGKsT~~~~L~   27 (194)
T 1qf9_A            8 VVFVLGGPGSGKGTQCANIV   27 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            57899999999999885543

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=88.95  E-value=0.31  Score=32.12  Aligned_cols=19  Identities=21%  Similarity=0.223  Sum_probs=16.0

Q ss_pred             cEEEEccCCcchHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~   24 (138)
                      .+.+.++.|||||.++-..
T Consensus        10 ~I~i~G~~GsGKST~~~~L   28 (203)
T 1uf9_A           10 IIGITGNIGSGKSTVAALL   28 (203)
T ss_dssp             EEEEEECTTSCHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            5789999999999988554

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=88.94  E-value=0.38  Score=31.19  Aligned_cols=21  Identities=19%  Similarity=0.045  Sum_probs=17.0

Q ss_pred             CCccEEEEccCCcchHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      .|+-+.+.+|.|+|||...-.
T Consensus        32 ~Ge~v~L~G~nGaGKTTLlr~   52 (158)
T 1htw_A           32 KAIMVYLNGDLGAGKTTLTRG   52 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            566778999999999977643

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=88.88  E-value=0.28  Score=35.52  Aligned_cols=20  Identities=25%  Similarity=0.125  Sum_probs=16.9

Q ss_pred             EEEEccCCcchHHHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +++++|.|+|||..+...+.
T Consensus        49 ~ll~Gp~G~GKTtla~~la~   68 (340)
T 1sxj_C           49 LLFYGPPGTGKTSTIVALAR   68 (340)
T ss_dssp             EEEECSSSSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            89999999999988865544

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=88.82  E-value=0.22  Score=34.47  Aligned_cols=20  Identities=10%  Similarity=0.004  Sum_probs=17.0

Q ss_pred             CCccEEEEccCCcchHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGE   22 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~   22 (138)
                      .|+-+.+.+|.|||||...-
T Consensus        30 ~Ge~~~i~G~nGsGKSTLl~   49 (237)
T 2cbz_A           30 EGALVAVVGQVGCGKSSLLS   49 (237)
T ss_dssp             TTCEEEEECSTTSSHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            57788999999999997753

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=88.81  E-value=0.34  Score=32.59  Aligned_cols=21  Identities=19%  Similarity=0.178  Sum_probs=17.2

Q ss_pred             CccEEEEccCCcchHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      +..+.+.++.|||||.++-..
T Consensus         4 ~~~I~i~G~~GSGKST~~~~L   24 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTVANAF   24 (218)
T ss_dssp             CEEEEEECCTTSCHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHH
Confidence            456789999999999987554

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=88.74  E-value=0.34  Score=31.01  Aligned_cols=21  Identities=29%  Similarity=0.246  Sum_probs=16.9

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .+++.++.|||||.++-..+-
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSR   22 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            578999999999998855433

>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=88.68  E-value=0.35  Score=33.28  Aligned_cols=22  Identities=23%  Similarity=0.212  Sum_probs=17.6

Q ss_pred             CccEEEEccCCcchHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      +..+.+.+|.|||||..+-..+
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La   48 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIA   48 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHH
Confidence            4578999999999998875443

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=88.62  E-value=0.33  Score=33.56  Aligned_cols=22  Identities=14%  Similarity=0.051  Sum_probs=18.0

Q ss_pred             CccEEEEccCCcchHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      +..+++.+|.|||||.++...+
T Consensus        29 ~~~I~l~G~~GsGKsT~a~~L~   50 (243)
T 3tlx_A           29 DGRYIFLGAPGSGKGTQSLNLK   50 (243)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHH
Confidence            4568999999999999885554

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=88.62  E-value=0.32  Score=35.26  Aligned_cols=21  Identities=24%  Similarity=0.264  Sum_probs=17.1

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .+++++|.|+|||..+...+.
T Consensus        40 ~~ll~G~~G~GKT~la~~la~   60 (373)
T 1jr3_A           40 AYLFSGTRGVGKTSIARLLAK   60 (373)
T ss_dssp             EEEEESCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            479999999999988855543

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=88.61  E-value=0.27  Score=39.63  Aligned_cols=21  Identities=33%  Similarity=0.264  Sum_probs=17.7

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ++++++|+|+|||.++-..+.
T Consensus       490 ~~ll~G~~GtGKT~la~~la~  510 (758)
T 1r6b_X          490 SFLFAGPTGVGKTEVTVQLSK  510 (758)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHH
Confidence            689999999999999865444

>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=88.53  E-value=0.6  Score=39.57  Aligned_cols=36  Identities=31%  Similarity=0.264  Sum_probs=27.0

Q ss_pred             EEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchh
Q psy2029           8 VLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYI   43 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~   43 (138)
                      +|.|..|||||.+...-+...+.+  .+.++++++|..
T Consensus         5 lV~agAGSGKT~~l~~ri~~ll~~~~~~~~il~lVP~q   42 (1166)
T 3u4q_B            5 FLVGRSGSGKTKLIINSIQDELRRAPFGKPIIFLVPDQ   42 (1166)
T ss_dssp             EEEECTTSSHHHHHHHHHHHHHHHCTTSSCEEEECCGG
T ss_pred             EEEeCCCCChHHHHHHHHHHHHHhCCCCCcEEEEecCc
Confidence            789999999999987766554433  246899998854

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=88.44  E-value=0.81  Score=34.74  Aligned_cols=41  Identities=10%  Similarity=-0.112  Sum_probs=29.9

Q ss_pred             hhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccc
Q psy2029          71 MIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPY  112 (138)
Q Consensus        71 ~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~  112 (138)
                      .+.. .-+++..++|.|||..++-.+...+.. +.+++|+.--
T Consensus       193 Gl~~G~liiIaG~pG~GKTtlal~ia~~~a~~-g~~vl~fSlE  234 (444)
T 3bgw_A          193 GYKRRNFVLIAARPSMGKTAFALKQAKNMSDN-DDVVNLHSLE  234 (444)
T ss_dssp             SBCSSCEEEEEECSSSSHHHHHHHHHHHHHHT-TCEEEEECSS
T ss_pred             CCCCCcEEEEEeCCCCChHHHHHHHHHHHHHc-CCEEEEEECC
Confidence            3444 556799999999999997766665544 6788887653

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=88.43  E-value=0.37  Score=33.23  Aligned_cols=22  Identities=27%  Similarity=0.116  Sum_probs=17.3

Q ss_pred             CCccEEEEccCCcchHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      .|.-+-+.+|.|||||.++-..
T Consensus        24 ~g~iigI~G~~GsGKSTl~k~L   45 (245)
T 2jeo_A           24 RPFLIGVSGGTASGKSTVCEKI   45 (245)
T ss_dssp             CSEEEEEECSTTSSHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHH
Confidence            3556779999999999887543

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=88.40  E-value=0.27  Score=38.81  Aligned_cols=19  Identities=5%  Similarity=0.062  Sum_probs=16.6

Q ss_pred             cEEEEccCCcchHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~   24 (138)
                      ++++.+|+|+|||..+-..
T Consensus       329 ~vLL~GppGtGKT~LAr~l  347 (595)
T 3f9v_A          329 HILIIGDPGTAKSQMLQFI  347 (595)
T ss_dssp             CEEEEESSCCTHHHHHHSS
T ss_pred             ceEEECCCchHHHHHHHHH
Confidence            8999999999999987443

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=88.39  E-value=0.29  Score=35.37  Aligned_cols=21  Identities=24%  Similarity=0.210  Sum_probs=17.1

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ++++++|.|+|||..+...+-
T Consensus        38 ~~ll~Gp~G~GKTtl~~~la~   58 (354)
T 1sxj_E           38 HLLLYGPNGTGKKTRCMALLE   58 (354)
T ss_dssp             CEEEECSTTSSHHHHHHTHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            489999999999988755443

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=88.35  E-value=0.36  Score=31.84  Aligned_cols=18  Identities=17%  Similarity=0.148  Sum_probs=14.7

Q ss_pred             cEEEEccCCcchHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~   23 (138)
                      .+.+.+|.|+|||...-.
T Consensus         2 ~i~l~G~nGsGKTTLl~~   19 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKK   19 (178)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            568899999999977633

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=88.33  E-value=0.62  Score=33.47  Aligned_cols=34  Identities=24%  Similarity=0.168  Sum_probs=24.6

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHH-hCCCeEEEE
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELK-IKQKSAIFI  109 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~-~~~~~~~~i  109 (138)
                      .++++.-|+|+|||..+... ...+. ..+.+++|+
T Consensus       153 ~~lll~G~~GtGKT~La~ai-a~~~~~~~g~~v~~~  187 (308)
T 2qgz_A          153 KGLYLYGDMGIGKSYLLAAM-AHELSEKKGVSTTLL  187 (308)
T ss_dssp             CEEEEECSTTSSHHHHHHHH-HHHHHHHSCCCEEEE
T ss_pred             ceEEEECCCCCCHHHHHHHH-HHHHHHhcCCcEEEE
Confidence            67889999999999988544 44555 555666554

>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=88.22  E-value=1.9  Score=33.81  Aligned_cols=53  Identities=21%  Similarity=0.150  Sum_probs=38.3

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +.+++..|-++|||.+....++..+.. .+.+++++.|+.....+.++.+....
T Consensus       179 r~~~i~~~Rq~GKS~~~a~~~l~~~~~~~~~~i~~va~t~~qA~~~~~~i~~~i  232 (592)
T 3cpe_A          179 RMTVCNLSRQLGKTTVVAIFLAHFVCFNKDKAVGILAHKGSMSAEVLDRTKQAI  232 (592)
T ss_dssp             SEEEEEECSSSCHHHHHHHHHHHHHHTSSSCEEEEEESSHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEcCccChHHHHHHHHHHHHHhCCCCeEEEEECCHHHHHHHHHHHHHHH
Confidence            457899999999997765544443443 45589999999987777776665553

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=88.18  E-value=0.27  Score=34.16  Aligned_cols=22  Identities=23%  Similarity=0.193  Sum_probs=17.6

Q ss_pred             CccEEEEccCCcchHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      +..+++++|.|||||.++-..+
T Consensus        32 ~~~i~l~G~~GsGKSTla~~L~   53 (253)
T 2p5t_B           32 PIAILLGGQSGAGKTTIHRIKQ   53 (253)
T ss_dssp             CEEEEEESCGGGTTHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHH
Confidence            4567999999999999875443

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=88.16  E-value=0.38  Score=32.46  Aligned_cols=23  Identities=22%  Similarity=0.198  Sum_probs=18.4

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +..+++.+|.|||||..+-..+-
T Consensus         5 ~~~I~l~G~~GsGKsT~a~~La~   27 (217)
T 3be4_A            5 KHNLILIGAPGSGKGTQCEFIKK   27 (217)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            45789999999999998855543

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=88.15  E-value=0.38  Score=31.87  Aligned_cols=20  Identities=20%  Similarity=0.018  Sum_probs=16.2

Q ss_pred             ccEEEEccCCcchHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~   24 (138)
                      ..+++.+|.|||||.++-..
T Consensus        16 ~~I~l~G~~GsGKsT~~~~L   35 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQCEKL   35 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHH
Confidence            35789999999999987444

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=88.13  E-value=0.29  Score=34.80  Aligned_cols=20  Identities=10%  Similarity=0.019  Sum_probs=17.0

Q ss_pred             CCccEEEEccCCcchHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGE   22 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~   22 (138)
                      .|+-+.+.+|.|||||...-
T Consensus        33 ~Ge~~~iiGpnGsGKSTLl~   52 (275)
T 3gfo_A           33 RGEVTAILGGNGVGKSTLFQ   52 (275)
T ss_dssp             TTSEEEEECCTTSSHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            57778999999999998753

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=88.12  E-value=0.28  Score=33.36  Aligned_cols=22  Identities=23%  Similarity=0.137  Sum_probs=17.6

Q ss_pred             CCccEEEEccCCcchHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      .|+.+.+.+|.|||||...-+.
T Consensus        21 ~Ge~~~liG~nGsGKSTLl~~l   42 (208)
T 3b85_A           21 TNTIVFGLGPAGSGKTYLAMAK   42 (208)
T ss_dssp             HCSEEEEECCTTSSTTHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHH
Confidence            4677889999999999776443

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=88.11  E-value=0.41  Score=31.97  Aligned_cols=20  Identities=25%  Similarity=0.270  Sum_probs=16.1

Q ss_pred             CccEEEEccCCcchHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~   23 (138)
                      |+.+.+.+|.|+|||...-.
T Consensus         1 G~~i~i~G~nG~GKTTll~~   20 (189)
T 2i3b_A            1 ARHVFLTGPPGVGKTTLIHK   20 (189)
T ss_dssp             CCCEEEESCCSSCHHHHHHH
T ss_pred             CCEEEEECCCCChHHHHHHH
Confidence            46688999999999976544

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=88.09  E-value=0.35  Score=32.47  Aligned_cols=21  Identities=14%  Similarity=0.192  Sum_probs=17.0

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ++++.+|.|||||.++-..+-
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIME   22 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            578999999999998855443

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=88.08  E-value=0.82  Score=30.25  Aligned_cols=36  Identities=25%  Similarity=0.260  Sum_probs=25.1

Q ss_pred             eEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccch
Q psy2029          77 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYI  113 (138)
Q Consensus        77 ~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~  113 (138)
                      .+++.|.|+|||..++-. +.++...+.+++++.|..
T Consensus         6 ~vi~G~~gsGKTT~ll~~-~~~~~~~g~~v~~~~~~~   41 (184)
T 2orw_A            6 TVITGPMYSGKTTELLSF-VEIYKLGKKKVAVFKPKI   41 (184)
T ss_dssp             EEEEESTTSSHHHHHHHH-HHHHHHTTCEEEEEEEC-
T ss_pred             EEEECCCCCCHHHHHHHH-HHHHHHCCCeEEEEeecc
Confidence            457888999999887443 444444567888887763

>3qks_A DNA double-strand break repair RAD50 ATPase; RECA-like fold, coiled-coils, ATPase, exonuclease, endonucle binding, DNA binding; HET: DNA; 2.10A {Pyrococcus furiosus} PDB: 3qkr_A*

Probab=88.00  E-value=0.4  Score=32.27  Aligned_cols=18  Identities=11%  Similarity=0.064  Sum_probs=14.7

Q ss_pred             cEEEEccCCcchHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~   23 (138)
                      -.++.+|+|+|||.+...
T Consensus        25 ~~~I~G~NgsGKStil~a   42 (203)
T 3qks_A           25 INLIIGQNGSGKSSLLDA   42 (203)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             eEEEEcCCCCCHHHHHHH
Confidence            458899999999987644

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=87.93  E-value=0.31  Score=33.42  Aligned_cols=20  Identities=10%  Similarity=0.049  Sum_probs=16.7

Q ss_pred             CCccEEEEccCCcchHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGE   22 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~   22 (138)
                      .|+-+.+.+|.|||||...-
T Consensus        29 ~Ge~~~iiG~nGsGKSTLl~   48 (224)
T 2pcj_A           29 KGEFVSIIGASGSGKSTLLY   48 (224)
T ss_dssp             TTCEEEEEECTTSCHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            57778899999999997753

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=87.92  E-value=0.24  Score=45.49  Aligned_cols=19  Identities=26%  Similarity=0.508  Sum_probs=17.2

Q ss_pred             CCccEEEEccCCcchHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVG   21 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~   21 (138)
                      .++++++++|+|+|||..+
T Consensus      1266 ~~~~vLL~GPpGtGKT~la 1284 (2695)
T 4akg_A         1266 SKRGIILCGPPGSGKTMIM 1284 (2695)
T ss_dssp             HTCEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4689999999999999887

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=87.91  E-value=0.4  Score=31.55  Aligned_cols=21  Identities=10%  Similarity=0.109  Sum_probs=16.7

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .+++.++.|||||..+-..+-
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~   22 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISK   22 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHH
Confidence            468999999999998755433

>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=87.85  E-value=1.4  Score=33.86  Aligned_cols=49  Identities=8%  Similarity=0.042  Sum_probs=38.1

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      |....+.+-|||||+++..-.+.    ..++.+++++|......+.++++..+
T Consensus        14 ~~~~~l~g~~gs~ka~~~a~l~~----~~~~p~lvv~~~~~~A~~l~~~l~~~   62 (483)
T 3hjh_A           14 GEQRLLGELTGAACATLVAEIAE----RHAGPVVLIAPDMQNALRLHDEISQF   62 (483)
T ss_dssp             TCEEEEECCCTTHHHHHHHHHHH----HSSSCEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCeEEEeCCCchHHHHHHHHHHH----HhCCCEEEEeCCHHHHHHHHHHHHhh
Confidence            45678899999999987533222    24667899999999999999998876

>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=87.81  E-value=0.39  Score=31.95  Aligned_cols=19  Identities=21%  Similarity=0.244  Sum_probs=15.7

Q ss_pred             cEEEEccCCcchHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~   24 (138)
                      .+.+.+|.|||||.++-..
T Consensus         4 ~i~l~G~~GsGKST~~~~L   22 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLF   22 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            4678999999999987554

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=87.81  E-value=0.38  Score=33.94  Aligned_cols=22  Identities=14%  Similarity=0.205  Sum_probs=17.9

Q ss_pred             CCCccEEEEccCCcchHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      -.|+-+.+.+|.|||||...-+
T Consensus        44 ~~Ge~~~l~G~NGsGKSTLlk~   65 (267)
T 2zu0_C           44 HPGEVHAIMGPNGSGKSTLSAT   65 (267)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHHHH
Confidence            3577889999999999987643

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=87.79  E-value=0.29  Score=31.74  Aligned_cols=22  Identities=23%  Similarity=0.179  Sum_probs=13.5

Q ss_pred             CCccEEEEccCCcchHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      ++..+++.++.|||||.++-..
T Consensus         4 ~~~~I~l~G~~GsGKST~a~~L   25 (183)
T 2vli_A            4 RSPIIWINGPFGVGKTHTAHTL   25 (183)
T ss_dssp             -CCEEEEECCC----CHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHH
Confidence            3556889999999999988554

>3zq6_A Putative arsenical pump-driving ATPase; tail-anchored, membrane protein; HET: ADP; 2.11A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=87.69  E-value=0.8  Score=33.06  Aligned_cols=34  Identities=15%  Similarity=0.098  Sum_probs=25.1

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      -+++++..|.|||.++...+.. +.+.+.|++++-
T Consensus        16 i~v~sgKGGvGKTTvA~~LA~~-lA~~G~rVLlvD   49 (324)
T 3zq6_A           16 FVFIGGKGGVGKTTISAATALW-MARSGKKTLVIS   49 (324)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH-HHHTTCCEEEEE
T ss_pred             EEEEeCCCCchHHHHHHHHHHH-HHHCCCcEEEEe
Confidence            4578899999999888665554 445677887764

>3qkt_A DNA double-strand break repair RAD50 ATPase; RECA-like fold, coiled-coils, ATP binding, DNA bindi MRE11, replication; HET: DNA ANP; 1.90A {Pyrococcus furiosus} PDB: 3qku_A* 1ii8_A 3qks_B* 3qkr_B* 1ii8_B

Probab=87.68  E-value=0.39  Score=34.91  Aligned_cols=18  Identities=11%  Similarity=0.064  Sum_probs=14.9

Q ss_pred             cEEEEccCCcchHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~   23 (138)
                      -.++++|+|+|||.+...
T Consensus        25 ~~~i~G~NGsGKS~lleA   42 (339)
T 3qkt_A           25 INLIIGQNGSGKSSLLDA   42 (339)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            347899999999988764

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=87.66  E-value=0.5  Score=33.38  Aligned_cols=22  Identities=23%  Similarity=0.102  Sum_probs=17.8

Q ss_pred             cEEEEccCCcchHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      ++++++|.|+|||..+...+..
T Consensus        44 ~~ll~G~~G~GKt~la~~l~~~   65 (323)
T 1sxj_B           44 HMIISGMPGIGKTTSVHCLAHE   65 (323)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEECcCCCCHHHHHHHHHHH
Confidence            4899999999999888655443

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=87.63  E-value=1.4  Score=33.40  Aligned_cols=40  Identities=13%  Similarity=0.055  Sum_probs=29.1

Q ss_pred             hhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEcc
Q psy2029          72 IQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP  111 (138)
Q Consensus        72 ~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P  111 (138)
                      +.. .-+++..++|.|||..+.-.+.......+.+++|+..
T Consensus       200 l~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s~  240 (454)
T 2r6a_A          200 FQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSL  240 (454)
T ss_dssp             BCTTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEES
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEEC
Confidence            444 5567999999999999977666554444667888764

>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=87.62  E-value=0.74  Score=31.69  Aligned_cols=37  Identities=19%  Similarity=0.116  Sum_probs=26.2

Q ss_pred             ceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccch
Q psy2029          76 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYI  113 (138)
Q Consensus        76 ~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~  113 (138)
                      -.+++-|.|+|||..++ ..+.++...+.+++++-|..
T Consensus        14 i~litG~mGsGKTT~ll-~~~~r~~~~g~kVli~~~~~   50 (223)
T 2b8t_A           14 IEFITGPMFAGKTAELI-RRLHRLEYADVKYLVFKPKI   50 (223)
T ss_dssp             EEEEECSTTSCHHHHHH-HHHHHHHHTTCCEEEEEECC
T ss_pred             EEEEECCCCCcHHHHHH-HHHHHHHhcCCEEEEEEecc
Confidence            34577888999998874 44455555677888886654

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=87.61  E-value=0.3  Score=33.85  Aligned_cols=21  Identities=24%  Similarity=0.406  Sum_probs=17.4

Q ss_pred             CCccEEEEccCCcchHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      .|+.+.+.+|.|||||...-+
T Consensus        27 ~Ge~~~i~G~nGsGKSTLl~~   47 (243)
T 1mv5_A           27 PNSIIAFAGPSGGGKSTIFSL   47 (243)
T ss_dssp             TTEEEEEECCTTSSHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            577789999999999987643

>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=87.60  E-value=0.98  Score=29.74  Aligned_cols=30  Identities=20%  Similarity=0.079  Sum_probs=18.9

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeE
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSA   36 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~   36 (138)
                      -+.+++|.|+|||......+- .+...+.++
T Consensus         8 ~i~i~G~sGsGKTTl~~~l~~-~l~~~g~~v   37 (174)
T 1np6_A            8 LLAFAAWSGTGKTTLLKKLIP-ALCARGIRP   37 (174)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH-HHHHTTCCE
T ss_pred             EEEEEeCCCCCHHHHHHHHHH-hccccCCce
Confidence            368899999999977544332 233344433

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=87.55  E-value=0.33  Score=34.09  Aligned_cols=21  Identities=24%  Similarity=0.495  Sum_probs=17.5

Q ss_pred             CCccEEEEccCCcchHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      .|+.+.+.+|.|||||...-+
T Consensus        45 ~Ge~~~i~G~nGsGKSTLl~~   65 (260)
T 2ghi_A           45 SGTTCALVGHTGSGKSTIAKL   65 (260)
T ss_dssp             TTCEEEEECSTTSSHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            577889999999999987633

>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=87.53  E-value=1.9  Score=32.90  Aligned_cols=55  Identities=11%  Similarity=0.089  Sum_probs=34.4

Q ss_pred             ceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEc--cchhHHHHHHHHHHHHhhhcCcee
Q psy2029          76 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL--PYISLVHEKYQSLAKAAEEFKFYL  134 (138)
Q Consensus        76 ~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~--P~~~l~~q~~~~~~~~~~~~~~~v  134 (138)
                      -++++.|+|+|||..+.-.+. .+...+.+++++.  |.++-+   +++++.+....|+.+
T Consensus       102 vIlivG~~G~GKTTt~~kLA~-~l~~~G~kVllv~~D~~R~aa---~eqL~~~~~~~gvpv  158 (443)
T 3dm5_A          102 ILLMVGIQGSGKTTTVAKLAR-YFQKRGYKVGVVCSDTWRPGA---YHQLRQLLDRYHIEV  158 (443)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH-HHHTTTCCEEEEECCCSSTHH---HHHHHHHHGGGTCEE
T ss_pred             EEEEECcCCCCHHHHHHHHHH-HHHHCCCeEEEEeCCCcchhH---HHHHHHHHHhcCCcE
Confidence            446888999999998865553 3445566766665  555544   344555555555543

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=87.50  E-value=0.55  Score=35.83  Aligned_cols=45  Identities=11%  Similarity=-0.006  Sum_probs=32.6

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAK  125 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~  125 (138)
                      +-.++..+.|+|||....    +.+ . ..+.++++|+++++++..+.+.+
T Consensus       162 ~v~~I~G~aGsGKTt~I~----~~~-~-~~~~lVlTpT~~aa~~l~~kl~~  206 (446)
T 3vkw_A          162 KVVLVDGVPGCGKTKEIL----SRV-N-FEEDLILVPGRQAAEMIRRRANA  206 (446)
T ss_dssp             EEEEEEECTTSCHHHHHH----HHC-C-TTTCEEEESCHHHHHHHHHHHTT
T ss_pred             cEEEEEcCCCCCHHHHHH----HHh-c-cCCeEEEeCCHHHHHHHHHHhhh
Confidence            344689999999996552    211 1 25679999999999888777753

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=87.42  E-value=0.37  Score=33.57  Aligned_cols=21  Identities=14%  Similarity=0.178  Sum_probs=17.4

Q ss_pred             CCccEEEEccCCcchHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      .|+-+.+.+|.|||||...-+
T Consensus        34 ~Ge~~~i~G~nGsGKSTLl~~   54 (247)
T 2ff7_A           34 QGEVIGIVGRSGSGKSTLTKL   54 (247)
T ss_dssp             TTCEEEEECSTTSSHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            577889999999999987633

>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=87.42  E-value=0.87  Score=35.61  Aligned_cols=35  Identities=14%  Similarity=0.138  Sum_probs=26.1

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      +-+++++..|.|||.++...+.. +.+.|.|++++-
T Consensus         9 ~i~~~sgkGGvGKTT~a~~lA~~-lA~~G~rVLlvd   43 (589)
T 1ihu_A            9 PYLFFTGKGGVGKTSISCATAIR-LAEQGKRVLLVS   43 (589)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHH-HHHTTCCEEEEE
T ss_pred             EEEEEeCCCcCHHHHHHHHHHHH-HHHCCCcEEEEE
Confidence            45688999999999888665554 445678888853

>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=87.36  E-value=2.3  Score=31.71  Aligned_cols=52  Identities=21%  Similarity=0.158  Sum_probs=37.8

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +.+++..|-+.|||.+....++..+.. .+.+++++.|+..-..+.++.+..+
T Consensus       179 R~~vi~~sRq~GKT~l~a~~~l~~a~~~~g~~v~~vA~t~~qA~~vf~~i~~m  231 (385)
T 2o0j_A          179 RMTVCNLSRQLGKTTVVAIFLAHFVCFNKDKAVGILAHKGSMSAEVLDRTKQA  231 (385)
T ss_dssp             SEEEEEECSSSCHHHHHHHHHHHHHHSSSSCEEEEEESSHHHHHHHHHHHHHH
T ss_pred             cEEEEEEcCcCChhHHHHHHHHHHHHhCCCCeEEEEeCCHHHHHHHHHHHHHH
Confidence            347899999999998776655543333 4568999999988776666665554

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=87.35  E-value=0.25  Score=35.69  Aligned_cols=20  Identities=20%  Similarity=0.308  Sum_probs=17.2

Q ss_pred             CCccEEEEccCCcchHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGE   22 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~   22 (138)
                      .|+.+.+.+|+|||||...-
T Consensus        79 ~Ge~vaivG~sGsGKSTLl~   98 (306)
T 3nh6_A           79 PGQTLALVGPSGAGKSTILR   98 (306)
T ss_dssp             TTCEEEEESSSCHHHHHHHH
T ss_pred             CCCEEEEECCCCchHHHHHH
Confidence            57788999999999998753

>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=87.34  E-value=0.78  Score=31.01  Aligned_cols=32  Identities=22%  Similarity=0.183  Sum_probs=22.9

Q ss_pred             EEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           8 VLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      +.+...|.|||.++...+.. +..++.+++++-
T Consensus         7 v~s~kgGvGKTt~a~~LA~~-la~~g~~VlliD   38 (237)
T 1g3q_A            7 IVSGKGGTGKTTVTANLSVA-LGDRGRKVLAVD   38 (237)
T ss_dssp             EECSSTTSSHHHHHHHHHHH-HHHTTCCEEEEE
T ss_pred             EecCCCCCCHHHHHHHHHHH-HHhcCCeEEEEe
Confidence            45667899999888665553 445678888874

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=87.32  E-value=0.27  Score=32.36  Aligned_cols=20  Identities=15%  Similarity=0.096  Sum_probs=15.5

Q ss_pred             cEEEEccCCcchHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~   25 (138)
                      .+.+.+|+|||||......+
T Consensus         4 ~v~IvG~SGsGKSTL~~~L~   23 (171)
T 2f1r_A            4 ILSIVGTSDSGKTTLITRMM   23 (171)
T ss_dssp             EEEEEESCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            46789999999998765443

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=87.27  E-value=0.44  Score=31.05  Aligned_cols=21  Identities=19%  Similarity=0.039  Sum_probs=16.7

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .+.+.++.|||||.++...+-
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~   22 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYE   22 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            367899999999998855543

>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=87.25  E-value=0.88  Score=37.32  Aligned_cols=24  Identities=33%  Similarity=0.210  Sum_probs=19.7

Q ss_pred             CccEEEEccCCcchHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      ..++++++|.|+|||.++...+..
T Consensus       191 ~~~vlL~G~pG~GKT~la~~la~~  214 (854)
T 1qvr_A          191 KNNPVLIGEPGVGKTAIVEGLAQR  214 (854)
T ss_dssp             CCCCEEEECTTSCHHHHHHHHHHH
T ss_pred             CCceEEEcCCCCCHHHHHHHHHHH
Confidence            357999999999999988666554

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=87.20  E-value=0.36  Score=33.81  Aligned_cols=20  Identities=15%  Similarity=0.253  Sum_probs=17.0

Q ss_pred             CCccEEEEccCCcchHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGE   22 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~   22 (138)
                      .|+.+.+.+|.|||||...-
T Consensus        32 ~Ge~~~liG~nGsGKSTLlk   51 (257)
T 1g6h_A           32 KGDVTLIIGPNGSGKSTLIN   51 (257)
T ss_dssp             TTCEEEEECSTTSSHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            57778899999999998753

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=87.18  E-value=0.49  Score=32.96  Aligned_cols=21  Identities=29%  Similarity=0.484  Sum_probs=17.6

Q ss_pred             CCccEEEEccCCcchHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      .|+-+.+.+|.|||||...-+
T Consensus        28 ~Ge~~~l~G~nGsGKSTLlk~   48 (250)
T 2d2e_A           28 KGEVHALMGPNGAGKSTLGKI   48 (250)
T ss_dssp             TTCEEEEECSTTSSHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            577788999999999987644

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=87.18  E-value=0.39  Score=32.99  Aligned_cols=20  Identities=20%  Similarity=0.116  Sum_probs=16.9

Q ss_pred             CCccEEEEccCCcchHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGE   22 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~   22 (138)
                      .|+-+.+.+|.|||||...-
T Consensus        33 ~Ge~~~i~G~nGsGKSTLl~   52 (229)
T 2pze_A           33 RGQLLAVAGSTGAGKTSLLM   52 (229)
T ss_dssp             TTCEEEEECCTTSSHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            57778899999999997753

>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=87.17  E-value=0.31  Score=39.98  Aligned_cols=22  Identities=27%  Similarity=0.279  Sum_probs=18.1

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .++++.+|+|+|||.++-..+.
T Consensus       589 ~~vLl~Gp~GtGKT~lA~~la~  610 (854)
T 1qvr_A          589 GSFLFLGPTGVGKTELAKTLAA  610 (854)
T ss_dssp             EEEEEBSCSSSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4789999999999998855444

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=87.16  E-value=0.41  Score=37.03  Aligned_cols=21  Identities=29%  Similarity=0.351  Sum_probs=17.2

Q ss_pred             ccEEEEccCCcchHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      +.+++.+|+|+|||..+-..+
T Consensus        65 ~GvLL~GppGtGKTtLaraIa   85 (499)
T 2dhr_A           65 KGVLLVGPPGVGKTHLARAVA   85 (499)
T ss_dssp             SEEEEECSSSSSHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHH
Confidence            358999999999999885543

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=87.03  E-value=0.45  Score=34.38  Aligned_cols=21  Identities=10%  Similarity=-0.034  Sum_probs=16.7

Q ss_pred             CCccEEEEccCCcchHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      .|.-+-+.+|+|||||..+-.
T Consensus        89 ~g~ivgI~G~sGsGKSTL~~~  109 (312)
T 3aez_A           89 VPFIIGVAGSVAVGKSTTARV  109 (312)
T ss_dssp             CCEEEEEECCTTSCHHHHHHH
T ss_pred             CCEEEEEECCCCchHHHHHHH
Confidence            355678999999999987744

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=87.01  E-value=0.94  Score=30.64  Aligned_cols=47  Identities=17%  Similarity=0.164  Sum_probs=30.6

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSL  123 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~  123 (138)
                      ..+++..|+|+|||..+.-.+...+ ..+.+++|+.... ...+..+.+
T Consensus        24 ~~~~i~G~~GsGKTtl~~~~~~~~~-~~~~~v~~~~~e~-~~~~~~~~~   70 (247)
T 2dr3_A           24 NVVLLSGGPGTGKTIFSQQFLWNGL-KMGEPGIYVALEE-HPVQVRQNM   70 (247)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHH-HTTCCEEEEESSS-CHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHH-hcCCeEEEEEccC-CHHHHHHHH
Confidence            5667999999999999865554433 3467788876543 233443333

>2woo_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; 3.01A {Schizosaccharomyces pombe}

Probab=86.98  E-value=0.93  Score=32.85  Aligned_cols=33  Identities=18%  Similarity=0.145  Sum_probs=24.5

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      -+++++..|.|||.++...+.. +.+.|.|++++
T Consensus        21 i~v~sgkGGvGKTTva~~LA~~-lA~~G~rVllv   53 (329)
T 2woo_A           21 WIFVGGKGGVGKTTTSCSLAIQ-MSKVRSSVLLI   53 (329)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHH-HHTSSSCEEEE
T ss_pred             EEEEeCCCCCcHHHHHHHHHHH-HHHCCCeEEEE
Confidence            3577899999999888655554 44567788875

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=86.98  E-value=0.53  Score=35.03  Aligned_cols=23  Identities=22%  Similarity=0.424  Sum_probs=18.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      .|+.+.+.+|.|+|||..+-..+
T Consensus       168 ~~~~i~l~G~~GsGKSTl~~~l~  190 (377)
T 1svm_A          168 KKRYWLFKGPIDSGKTTLAAALL  190 (377)
T ss_dssp             TCCEEEEECSTTSSHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHH
Confidence            46788999999999998775444

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=86.97  E-value=0.42  Score=32.64  Aligned_cols=21  Identities=19%  Similarity=0.139  Sum_probs=17.4

Q ss_pred             CCccEEEEccCCcchHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      .|+-+.+.+|.|||||...-+
T Consensus        34 ~Ge~~~iiG~NGsGKSTLlk~   54 (214)
T 1sgw_A           34 KGNVVNFHGPNGIGKTTLLKT   54 (214)
T ss_dssp             TTCCEEEECCTTSSHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            577888999999999987643

>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=86.97  E-value=0.88  Score=30.47  Aligned_cols=25  Identities=16%  Similarity=0.101  Sum_probs=19.2

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELK  100 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~  100 (138)
                      .++++.-|+|+|||..+...+ +.+.
T Consensus        53 ~~~ll~G~~G~GKT~la~~l~-~~~~   77 (242)
T 3bos_A           53 QAIYLWGPVKSGRTHLIHAAC-ARAN   77 (242)
T ss_dssp             SEEEEECSTTSSHHHHHHHHH-HHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHH-HHHH
Confidence            788999999999999885443 3443

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=86.97  E-value=0.38  Score=33.32  Aligned_cols=21  Identities=19%  Similarity=0.098  Sum_probs=17.3

Q ss_pred             CCccEEEEccCCcchHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      .|+-+.+.+|.|||||...-+
T Consensus        31 ~Ge~~~l~G~nGsGKSTLl~~   51 (240)
T 1ji0_A           31 RGQIVTLIGANGAGKTTTLSA   51 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            577788999999999987533

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=86.92  E-value=0.41  Score=33.79  Aligned_cols=20  Identities=15%  Similarity=0.219  Sum_probs=17.0

Q ss_pred             CCccEEEEccCCcchHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGE   22 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~   22 (138)
                      .|+-+.+.+|.|||||...-
T Consensus        36 ~Ge~~~liG~nGsGKSTLl~   55 (266)
T 4g1u_C           36 SGEMVAIIGPNGAGKSTLLR   55 (266)
T ss_dssp             TTCEEEEECCTTSCHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHH
Confidence            57788999999999998753

>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=86.88  E-value=1  Score=31.06  Aligned_cols=32  Identities=22%  Similarity=0.082  Sum_probs=23.2

Q ss_pred             EEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           8 VLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      +.+...|.|||.++...+.. +..++.+++++-
T Consensus         7 v~s~kgGvGKTt~a~~LA~~-la~~g~~VlliD   38 (263)
T 1hyq_A            7 VASGKGGTGKTTITANLGVA-LAQLGHDVTIVD   38 (263)
T ss_dssp             EEESSSCSCHHHHHHHHHHH-HHHTTCCEEEEE
T ss_pred             EECCCCCCCHHHHHHHHHHH-HHhCCCcEEEEE
Confidence            55778899999888665543 445677888874

>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=86.77  E-value=0.49  Score=33.85  Aligned_cols=19  Identities=21%  Similarity=0.195  Sum_probs=15.2

Q ss_pred             ccEEEEccCCcchHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~   23 (138)
                      .-+.+.+|+|||||.++-.
T Consensus        32 ~ii~I~G~sGsGKSTla~~   50 (290)
T 1odf_A           32 LFIFFSGPQGSGKSFTSIQ   50 (290)
T ss_dssp             EEEEEECCTTSSHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            3467899999999988743

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=86.73  E-value=0.88  Score=35.24  Aligned_cols=36  Identities=17%  Similarity=0.042  Sum_probs=25.6

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      ..+.+++++|+|||..+.-.+.. +..++.+++++..
T Consensus       102 ~vI~ivG~~GvGKTTl~~kLA~~-l~~~G~kVllVd~  137 (504)
T 2j37_W          102 NVIMFVGLQGSGKTTTCSKLAYY-YQRKGWKTCLICA  137 (504)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH-HHHTTCCEEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH-HHhCCCeEEEEec
Confidence            36788999999999887555543 4445777777653

>3nwn_A Kinesin-like protein KIF9; motor domain, ADP, structural genomics, structural consortium, SGC, contractIle protein; HET: ADP; 2.00A {Homo sapiens}

Probab=86.71  E-value=0.28  Score=36.34  Aligned_cols=19  Identities=26%  Similarity=0.212  Sum_probs=14.9

Q ss_pred             CCCccE--EEEccCCcchHHH
Q psy2029           2 VQNKNC--VLSIPTSGGKTLV   20 (138)
Q Consensus         2 ~~~~~~--~~~~ptg~GKt~~   20 (138)
                      ++|.|+  +..++||||||..
T Consensus       101 l~G~N~tifAYGQTGSGKTyT  121 (359)
T 3nwn_A          101 LDGYNGTIMCYGQTGAGKTYT  121 (359)
T ss_dssp             HTTCCEEEEEEESTTSSHHHH
T ss_pred             hCCCCEEEEEeCCCCCCccEE
Confidence            456655  7789999999975

>3t0q_A AGR253WP; kinesin, alpha and beta proteins, P-loop containing nucleosi triphosphate hydrolases, microtubule motor protein; HET: ADP; 2.35A {Ashbya gossypii}

Probab=86.64  E-value=0.33  Score=35.80  Aligned_cols=20  Identities=25%  Similarity=0.155  Sum_probs=15.7

Q ss_pred             CCCccE--EEEccCCcchHHHH
Q psy2029           2 VQNKNC--VLSIPTSGGKTLVG   21 (138)
Q Consensus         2 ~~~~~~--~~~~ptg~GKt~~~   21 (138)
                      ++|.|+  +..++||||||..-
T Consensus        82 l~G~n~tifAYGqTGSGKTyTm  103 (349)
T 3t0q_A           82 LDGYNVCIFAYGQTGSGKTYTM  103 (349)
T ss_dssp             GTTCEEEEEEECSTTSSHHHHH
T ss_pred             HCCcceeEEEeCCCCCCCceEe
Confidence            567665  66899999999764

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=86.60  E-value=0.4  Score=33.70  Aligned_cols=20  Identities=10%  Similarity=0.031  Sum_probs=16.8

Q ss_pred             CCccEEEEccCCcchHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGE   22 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~   22 (138)
                      .|+-+.+.+|.|||||...-
T Consensus        31 ~Ge~~~liG~nGsGKSTLlk   50 (262)
T 1b0u_A           31 AGDVISIIGSSGSGKSTFLR   50 (262)
T ss_dssp             TTCEEEEECCTTSSHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            57778899999999997753

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=86.53  E-value=0.41  Score=33.72  Aligned_cols=21  Identities=19%  Similarity=0.251  Sum_probs=17.3

Q ss_pred             CCccEEEEccCCcchHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      .|+-+.+.+|.|||||...-+
T Consensus        32 ~Ge~~~liG~nGsGKSTLl~~   52 (266)
T 2yz2_A           32 EGECLLVAGNTGSGKSTLLQI   52 (266)
T ss_dssp             TTCEEEEECSTTSSHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHH
Confidence            577788999999999987533

>1f9v_A Kinesin-like protein KAR3; kinesin-related protein, motor protein, microtubinding proteinbule, contractIle protein; HET: ADP; 1.30A {Saccharomyces cerevisiae} SCOP: c.37.1.9 PDB: 1f9t_A* 1f9w_A* 1f9u_A* 3kar_A*

Probab=86.36  E-value=0.34  Score=35.75  Aligned_cols=20  Identities=25%  Similarity=0.189  Sum_probs=15.4

Q ss_pred             CCCccE--EEEccCCcchHHHH
Q psy2029           2 VQNKNC--VLSIPTSGGKTLVG   21 (138)
Q Consensus         2 ~~~~~~--~~~~ptg~GKt~~~   21 (138)
                      ++|.|+  +..++||||||..-
T Consensus        81 l~G~n~tifAYGqTGSGKTyTM  102 (347)
T 1f9v_A           81 LDGYNVCIFAYGQTGSGKTFTM  102 (347)
T ss_dssp             GGTCCEEEEEECCTTSSHHHHH
T ss_pred             cCCceeEEEEECCCCCCCcEec
Confidence            466665  67899999999753

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=86.30  E-value=0.43  Score=33.51  Aligned_cols=21  Identities=29%  Similarity=0.226  Sum_probs=17.4

Q ss_pred             CCccEEEEccCCcchHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      .|+-+.+.+|.|||||...-+
T Consensus        40 ~Gei~~l~G~NGsGKSTLlk~   60 (256)
T 1vpl_A           40 EGEIFGLIGPNGAGKTTTLRI   60 (256)
T ss_dssp             TTCEEEEECCTTSSHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHH
Confidence            577889999999999987533

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=86.26  E-value=3.8  Score=29.95  Aligned_cols=40  Identities=13%  Similarity=0.146  Sum_probs=29.0

Q ss_pred             hhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEcc
Q psy2029          71 MIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP  111 (138)
Q Consensus        71 ~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P  111 (138)
                      .+.. .-+++..++|.|||..+.-.+...+. .+.+++|+..
T Consensus        42 Gl~~G~LiiIaG~pG~GKTt~al~ia~~~a~-~g~~Vl~fSl   82 (338)
T 4a1f_A           42 GFNKGSLVIIGARPSMGKTSLMMNMVLSALN-DDRGVAVFSL   82 (338)
T ss_dssp             SBCTTCEEEEEECTTSCHHHHHHHHHHHHHH-TTCEEEEEES
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHH-cCCeEEEEeC
Confidence            3444 55679999999999998766655444 5677888765

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=86.15  E-value=0.53  Score=33.76  Aligned_cols=21  Identities=14%  Similarity=0.124  Sum_probs=16.6

Q ss_pred             CccEEEEccCCcchHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      |.-+-+.+|.|||||.++-..
T Consensus        80 g~iigI~G~~GsGKSTl~~~L  100 (308)
T 1sq5_A           80 PYIISIAGSVAVGKSTTARVL  100 (308)
T ss_dssp             CEEEEEEECTTSSHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHH
Confidence            456788999999999887443

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=86.14  E-value=0.47  Score=33.53  Aligned_cols=21  Identities=29%  Similarity=0.397  Sum_probs=17.3

Q ss_pred             CCccEEEEccCCcchHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      .|+.+.+.+|.|||||...-+
T Consensus        44 ~Ge~~~i~G~nGsGKSTLlk~   64 (271)
T 2ixe_A           44 PGKVTALVGPNGSGKSTVAAL   64 (271)
T ss_dssp             TTCEEEEECSTTSSHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            577789999999999977533

>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=85.98  E-value=1.1  Score=32.76  Aligned_cols=33  Identities=15%  Similarity=0.063  Sum_probs=24.2

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      +++++.-|.|||.++...+.. +.+.+.|++++-
T Consensus        29 ~v~sgKGGvGKTTvA~~LA~~-lA~~G~rVLlvD   61 (349)
T 3ug7_A           29 IMFGGKGGVGKTTMSAATGVY-LAEKGLKVVIVS   61 (349)
T ss_dssp             EEEECSSSTTHHHHHHHHHHH-HHHSSCCEEEEE
T ss_pred             EEEeCCCCccHHHHHHHHHHH-HHHCCCeEEEEe
Confidence            577889999999888555554 445677887764

>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=85.96  E-value=1.2  Score=31.00  Aligned_cols=40  Identities=18%  Similarity=0.022  Sum_probs=30.0

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhh
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYIS   44 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~a   44 (138)
                      |.=.++++|-|+|||..++-.+.+. ...+.+++++-|.+.
T Consensus        19 g~l~v~~G~MgsGKTT~lL~~~~r~-~~~g~kvli~kp~~D   58 (234)
T 2orv_A           19 GQIQVILGPMFSGKSTELMRRVRRF-QIAQYKCLVIKYAKD   58 (234)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHH-HTTTCCEEEEEETTC
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHH-HHCCCeEEEEeecCC
Confidence            3444778888999998876666654 446889999888764

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=85.92  E-value=0.46  Score=33.51  Aligned_cols=21  Identities=19%  Similarity=0.238  Sum_probs=17.4

Q ss_pred             CCccEEEEccCCcchHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      .|+-+.+.+|.|||||...-+
T Consensus        49 ~Gei~~liG~NGsGKSTLlk~   69 (263)
T 2olj_A           49 EGEVVVVIGPSGSGKSTFLRC   69 (263)
T ss_dssp             TTCEEEEECCTTSSHHHHHHH
T ss_pred             CCCEEEEEcCCCCcHHHHHHH
Confidence            577788999999999987643

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=85.91  E-value=0.63  Score=31.79  Aligned_cols=23  Identities=26%  Similarity=0.440  Sum_probs=18.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      .+..+.+.+|.|||||.++-..+
T Consensus        15 ~~~~i~i~G~~gsGKst~~~~l~   37 (236)
T 1q3t_A           15 KTIQIAIDGPASSGKSTVAKIIA   37 (236)
T ss_dssp             CCCEEEEECSSCSSHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHH
Confidence            35678899999999999885544

---

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	9e-05
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	2e-04
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	0.001

>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 = 38.4 bits (88), Expect = 9e-05
 Identities = 8/63 (12%), Positives = 25/63 (39%), Gaps = 1/63 (1%)

Query: 70  EMI-QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE 128
           ++  + +  ++ +    GKT      I++E   +    + + P   +  E  ++L     
Sbjct: 4   DIFRKKRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAPTRVVAAEMEEALRGLPI 63

Query: 129 EFK 131
            ++
Sbjct: 64  RYQ 66

>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 = 8/59 (13%), Positives = 23/59 (38%)

Query: 3  QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFK 61
          + +  ++ +    GKT      I++E   +    + + P   +  E  ++L      ++
Sbjct: 8  KKRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAPTRVVAAEMEEALRGLPIRYQ 66

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 34.8 bits (78), Expect = 0.001
 Identities = 13/67 (19%), Positives = 25/67 (37%)

Query: 67  KCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA 126
                 +  NC++ +PT  GKTL+  ++    L       + + P   LV +  +S  + 
Sbjct: 16  VIYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESFRRL 75

Query: 127 AEEFKFY 133
                  
Sbjct: 76  FNLPPEK 82

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	138
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.66
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.63
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.63
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.6
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.56
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.56
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.55
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.54
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.54
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.53
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.49
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.44
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.43
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.4
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.39
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.39
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.37
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.37
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.34
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.33
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.33
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.3
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.25
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.25
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.17
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.17
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.15
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.08
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.04
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.02
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	98.98
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	98.98
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	98.95
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	98.95
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	98.94
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	98.88
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	98.88
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.83
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	98.83
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	98.73
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	97.85
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	97.56
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.52
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	97.47
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	97.43
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.42
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	97.32
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	97.24
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.08
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	97.07
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	96.76
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	96.72
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	96.72
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	96.59
d1okkd2	207	GTPase domain of the signal recognition particle r	96.58
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	96.53
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	96.38
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	96.36
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	96.32
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	96.29
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	96.17
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	96.1
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	96.05
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	96.0
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	95.99
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	95.91
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	95.91
d1vmaa2	213	GTPase domain of the signal recognition particle r	95.9
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	95.81
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	95.81
d1j8yf2	211	GTPase domain of the signal sequence recognition p	95.78
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	95.74
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	95.73
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	95.72
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	95.58
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	95.53
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	95.52
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	95.44
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	95.42
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	95.38
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	95.29
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	95.27
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	95.18
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	95.18
d2qy9a2	211	GTPase domain of the signal recognition particle r	95.17
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	95.14
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	95.08
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	95.02
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	94.92
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	94.88
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	94.74
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	94.73
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	94.7
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	94.69
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	94.67
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	94.62
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	94.62
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	94.58
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	94.57
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	94.5
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	94.49
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	94.39
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	94.3
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	94.28
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	94.24
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	94.23
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	94.08
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	93.82
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	93.78
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	93.74
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	93.62
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	93.54
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	93.47
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	93.42
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	93.3
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	93.28
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	93.24
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	93.08
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	93.0
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	92.98
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	92.96
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	92.89
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	92.84
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	92.74
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	92.66
d1ls1a2	207	GTPase domain of the signal sequence recognition p	92.58
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	92.54
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	92.5
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	92.37
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	92.3
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	92.18
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	92.05
d1vmaa2	213	GTPase domain of the signal recognition particle r	91.89
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	91.84
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	91.81
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	91.74
d2qy9a2	211	GTPase domain of the signal recognition particle r	91.66
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	91.65
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	91.65
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	91.55
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	91.53
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	91.5
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	91.48
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	91.42
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	91.32
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	91.27
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	91.26
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	91.26
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	91.1
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	91.05
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	90.94
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	90.88
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	90.86
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	90.57
d1j8yf2	211	GTPase domain of the signal sequence recognition p	90.53
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	90.5
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	90.44
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	90.42
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	90.39
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	90.26
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	90.1
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	90.09
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	90.08
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	90.07
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	90.07
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	90.02
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	89.99
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	89.88
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	89.57
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	89.56
d1c9ka_	180	Adenosylcobinamide kinase/adenosylcobinamide phosp	89.14
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	89.09
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	88.97
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	88.97
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	88.95
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	88.91
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	88.89
d1g2912	240	Maltose transport protein MalK, N-terminal domain	88.73
d2awna2	232	Maltose transport protein MalK, N-terminal domain	88.6
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	88.53
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	88.45
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	88.09
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	87.89
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	87.56
d1okkd2	207	GTPase domain of the signal recognition particle r	87.46
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	87.0
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	86.96
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	86.9
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	86.89
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	86.77
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	86.73
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	86.61
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	86.52
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	86.51
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	86.37
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	86.34
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	86.28
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	86.25
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	85.78
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	85.67
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	85.44
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	85.19
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	85.14
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	85.06
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	84.81
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	84.75
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	84.7
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	84.51
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	84.5
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	84.43
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	84.31
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	84.15
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	83.99
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	83.96
d2ncda_	368	Kinesin motor Ncd (non-claret disjunctional) {Frui	83.78
d1tuea_	205	Replication protein E1 helicase domain {Human papi	83.68
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	83.56
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	83.37
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	83.23
d2zfia1	349	Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090	83.12
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	83.0
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	83.0
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	82.97
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	82.62
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	82.36
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	82.22
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	82.08
d1xpua3	289	Transcription termination factor Rho, ATPase domai	82.06
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	81.72
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	81.55
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	81.51
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	81.5
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	81.48
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	81.42
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	81.27
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	81.12
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	80.92
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	80.88
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	80.47
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	80.24
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	80.15
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	80.12

>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=99.66  E-value=7.3e-17  Score=111.45  Aligned_cols=92  Identities=14%  Similarity=0.194  Sum_probs=83.4

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~  121 (138)
                      |.....+.+.+.++..+.++|..++|.+.+ +|+++.+|||+|||+++.+++++.+..  .+.++++++|+++|+.|.++
T Consensus        24 L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~~~~~~lil~PtreLa~Qi~~  103 (222)
T d2j0sa1          24 LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQK  103 (222)
T ss_dssp             CCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHHHHHHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhcccccccccccccCceeEEecchHHHHHHHHH
Confidence            667888999999999999999999998888 999999999999999999999998865  35689999999999999999


Q ss_pred             HHHHHhhhcCceeee
Q psy2029         122 SLAKAAEEFKFYLEV  136 (138)
Q Consensus       122 ~~~~~~~~~~~~v~~  136 (138)
                      .++++....++++..
T Consensus       104 ~~~~l~~~~~i~~~~  118 (222)
T d2j0sa1         104 GLLALGDYMNVQCHA  118 (222)
T ss_dssp             HHHHHTTTTTCCEEE
T ss_pred             HHHHHhCccceeEEE
Confidence            999999888877654

>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=99.63  E-value=3.8e-16  Score=107.52  Aligned_cols=91  Identities=12%  Similarity=0.127  Sum_probs=81.5

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~  121 (138)
                      |.....+.+.+.++..+.++|..++|.+.. +|+++.+|||+|||+++++++++.+..  .+.++++++|+++|+.|.++
T Consensus        19 L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~~~~~~alil~Pt~eL~~Q~~~   98 (218)
T d2g9na1          19 LSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQK   98 (218)
T ss_dssp             CCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheecccccCccEEEEcccchhhhhHHH
Confidence            556788888888999999999999988887 999999999999999999999998864  45789999999999999999


Q ss_pred             HHHHHhhhcCceee
Q psy2029         122 SLAKAAEEFKFYLE  135 (138)
Q Consensus       122 ~~~~~~~~~~~~v~  135 (138)
                      .+.++....+..+.
T Consensus        99 ~~~~~~~~~~~~~~  112 (218)
T d2g9na1          99 VVMALGDYMGASCH  112 (218)
T ss_dssp             HHHHHHTTTTCCEE
T ss_pred             HHhhhccccceeEE
Confidence            99999988876654

>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=99.63  E-value=3.7e-16  Score=108.42  Aligned_cols=83  Identities=20%  Similarity=0.137  Sum_probs=70.0

Q ss_pred             HHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhc
Q psy2029          52 SLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEF  130 (138)
Q Consensus        52 ~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~  130 (138)
                      ++.+.+...++++|..+++.+.+ +++++.+|||+|||.++.++++.... ++++++|++|+++|++|+++++++++...
T Consensus        35 ~~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~-~~~rvliv~Pt~~La~Q~~~~l~~~~~~~  113 (237)
T d1gkub1          35 EFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLAL-KGKRCYVIFPTSLLVIQAAETIRKYAEKA  113 (237)
T ss_dssp             HHHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHT-TSCCEEEEESCHHHHHHHHHHHHHHHTTT
T ss_pred             HHHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHH-hcCeEEEEeccHHHHHHHHHHHHHHHHHc
Confidence            33333445789999999988888 99999999999999999888886554 47899999999999999999999999888


Q ss_pred             Cceee
Q psy2029         131 KFYLE  135 (138)
Q Consensus       131 ~~~v~  135 (138)
                      ++.+.
T Consensus       114 ~~~~~  118 (237)
T d1gkub1         114 GVGTE  118 (237)
T ss_dssp             CCSGG
T ss_pred             CCceE
Confidence            76643

>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=99.60  E-value=8e-16  Score=105.07  Aligned_cols=87  Identities=14%  Similarity=0.133  Sum_probs=78.5

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~  121 (138)
                      |..+..+.+.+.++..+.++|..++|.+.+ +|+++.+|||+|||+++.+++++++..  .+.++++++|+++|+.|..+
T Consensus         8 L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~lil~PtreL~~qi~~   87 (207)
T d1t6na_           8 LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISK   87 (207)
T ss_dssp             CCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHH
T ss_pred             cCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeecccCCCceEEEEeccchhhHHHHH
Confidence            557788899999999999999999998888 999999999999999999999998765  34689999999999999999


Q ss_pred             HHHHHhhhcC
Q psy2029         122 SLAKAAEEFK  131 (138)
Q Consensus       122 ~~~~~~~~~~  131 (138)
                      .++.+....+
T Consensus        88 ~~~~~~~~~~   97 (207)
T d1t6na_          88 EYERFSKYMP   97 (207)
T ss_dssp             HHHHHTTTST
T ss_pred             HHHHHHhhCC
Confidence            9999987663

>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=99.56  E-value=6e-15  Score=99.41  Aligned_cols=78  Identities=18%  Similarity=0.208  Sum_probs=67.8

Q ss_pred             hhhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeeec
Q psy2029          60 FKFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEVL  137 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~~  137 (138)
                      .+.++|.+++....++|.++++|||+|||+++.+++...+...+.+++|++|+++|++|.++++++++...+.++..+
T Consensus         9 ~pr~~Q~~~~~~~~~~n~lv~~pTGsGKT~i~~~~~~~~~~~~~~~il~i~P~~~L~~q~~~~~~~~~~~~~~~v~~~   86 (200)
T d1wp9a1           9 QPRIYQEVIYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVAL   86 (200)
T ss_dssp             CCCHHHHHHHHHGGGSCEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEE
T ss_pred             CCCHHHHHHHHHHhcCCeEEEeCCCCcHHHHHHHHHHHHHHhcCCcEEEEcCchHHHHHHHHHHHHhhcccccceeee
Confidence            467889999887777899999999999999999888877777778999999999999999999999987776666543

>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=99.56  E-value=1e-15  Score=103.83  Aligned_cols=85  Identities=26%  Similarity=0.373  Sum_probs=69.6

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSL  123 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~  123 (138)
                      +.+...+.+.+.+++.++|+|.++++.+.+ +++++++|||+|||.++.++++..+.. +++++|++|+++|++|..+.+
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~-~~~vl~l~P~~~L~~q~~~~~   88 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK-GGKSLYVVPLRALAGEKYESF   88 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT-TCCEEEEESSHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhc-cCcceeecccHHHHHHHHHHH
Confidence            445555666666777899999999988877 999999999999999999988887664 678999999999999999999


Q ss_pred             HHHhhhc
Q psy2029         124 AKAAEEF  130 (138)
Q Consensus       124 ~~~~~~~  130 (138)
                      ++++...
T Consensus        89 ~~~~~~~   95 (202)
T d2p6ra3          89 KKWEKIG   95 (202)
T ss_dssp             TTTTTTT
T ss_pred             HHHhhcc
Confidence            8876543

>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=99.55  E-value=3.4e-15  Score=101.83  Aligned_cols=86  Identities=14%  Similarity=0.159  Sum_probs=77.2

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~  121 (138)
                      |..+..+.+.+.++..+.++|..++|.+.+ +|+++.+|||+|||+++.+++++++..  .+.++++++|+++|+.|.++
T Consensus        10 L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~~~~~~~lil~pt~el~~q~~~   89 (206)
T d1veca_          10 LKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQ   89 (206)
T ss_dssp             CCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHHHHHHHHH
T ss_pred             cCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhcccccccCcceEEEeecchhhHHHHH
Confidence            557888999999999999999999998888 999999999999999999999998765  35689999999999999999


Q ss_pred             HHHHHhhhc
Q psy2029         122 SLAKAAEEF  130 (138)
Q Consensus       122 ~~~~~~~~~  130 (138)
                      .+..+....
T Consensus        90 ~~~~~~~~~   98 (206)
T d1veca_          90 ICIQVSKHM   98 (206)
T ss_dssp             HHHHHTTTS
T ss_pred             HHHHHhhcc
Confidence            999886554

>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=99.54  E-value=6.3e-15  Score=100.53  Aligned_cols=92  Identities=16%  Similarity=0.133  Sum_probs=79.8

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc--cceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN--KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~--~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~~q~~~  121 (138)
                      |..++.+.+.+.++..+.++|.+++|.+.+  .|+++.+|||+|||+++.+++++.... .+.++++++|+++|+.|..+
T Consensus        11 l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~~~~~~~lil~pt~~l~~q~~~   90 (208)
T d1hv8a1          11 LSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQVAD   90 (208)
T ss_dssp             CCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHHHHHHHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeecccccccccccCcceEEEeeccccchhhhh
Confidence            556788888888888999999999987654  589999999999999999999886654 45789999999999999999


Q ss_pred             HHHHHhhhcCceeee
Q psy2029         122 SLAKAAEEFKFYLEV  136 (138)
Q Consensus       122 ~~~~~~~~~~~~v~~  136 (138)
                      .++++....+.++..
T Consensus        91 ~~~~~~~~~~~~v~~  105 (208)
T d1hv8a1          91 EIESLKGNKNLKIAK  105 (208)
T ss_dssp             HHHHHHCSSCCCEEE
T ss_pred             hhhhhcccCCeEEEE
Confidence            999999888777654

>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=99.54  E-value=1.7e-15  Score=105.47  Aligned_cols=91  Identities=14%  Similarity=0.071  Sum_probs=79.1

Q ss_pred             HHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh-----------CCCeEEEEccch
Q psy2029          46 VHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI-----------KQKSAIFILPYI  113 (138)
Q Consensus        46 ~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~-----------~~~~~~~i~P~~  113 (138)
                      .++..+.+.+.++..+.++|..++|.+.+ +|+++.+|||+|||+++++++++++..           .+.++++++|++
T Consensus        29 ~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~~~~~~~alil~pt~  108 (238)
T d1wrba1          29 DPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTR  108 (238)
T ss_dssp             CCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSH
T ss_pred             CHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccccccccCCCCceEEEeccch
Confidence            34555667777888999999999998888 999999999999999999999999854           245799999999


Q ss_pred             hHHHHHHHHHHHHhhhcCceeee
Q psy2029         114 SLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus       114 ~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      +|+.|..+.+.......++++..
T Consensus       109 el~~q~~~~~~~~~~~~~~~~~~  131 (238)
T d1wrba1         109 ELAIQILSESQKFSLNTPLRSCV  131 (238)
T ss_dssp             HHHHHHHHHHHHHHTTSSCCEEE
T ss_pred             hhhcchheeeeecccCCCcEEEE
Confidence            99999999999999888877654

>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=99.53  E-value=1.2e-14  Score=99.47  Aligned_cols=92  Identities=13%  Similarity=0.110  Sum_probs=81.4

Q ss_pred             hhHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHH
Q psy2029          44 SLVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKY  120 (138)
Q Consensus        44 aL~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~  120 (138)
                      .|..+..+.+.+.++..+.++|..++|.+.+ +|+++.+|||+|||+++.+++++.+..  .+.++++++|+++++.|..
T Consensus        16 ~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~lil~pt~el~~q~~   95 (212)
T d1qdea_          16 ELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQ   95 (212)
T ss_dssp             TCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhccCCCcceEEEcccHHHhhhhh
Confidence            4667888999999999999999999998887 999999999999999999999998865  4568999999999999999


Q ss_pred             HHHHHHhhhcCceee
Q psy2029         121 QSLAKAAEEFKFYLE  135 (138)
Q Consensus       121 ~~~~~~~~~~~~~v~  135 (138)
                      +.+..........+.
T Consensus        96 ~~~~~~~~~~~~~~~  110 (212)
T d1qdea_          96 KVVMALAFHMDIKVH  110 (212)
T ss_dssp             HHHHHHTTTSCCCEE
T ss_pred             hhhccccccccccee
Confidence            999988776655543

>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=99.49  E-value=1.5e-14  Score=100.14  Aligned_cols=59  Identities=25%  Similarity=0.296  Sum_probs=51.5

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhhh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFK   61 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~   61 (138)
                      ++|+|++++||||+|||+++.++++... .+++++++++|+++|++|.+++++++....+
T Consensus        56 l~g~~~~i~apTGsGKT~~~~~~~~~~~-~~~~rvliv~Pt~~La~Q~~~~l~~~~~~~~  114 (237)
T d1gkub1          56 LRKESFAATAPTGVGKTSFGLAMSLFLA-LKGKRCYVIFPTSLLVIQAAETIRKYAEKAG  114 (237)
T ss_dssp             HTTCCEECCCCBTSCSHHHHHHHHHHHH-TTSCCEEEEESCHHHHHHHHHHHHHHHTTTC
T ss_pred             HCCCCEEEEecCCChHHHHHHHHHHHHH-HhcCeEEEEeccHHHHHHHHHHHHHHHHHcC
Confidence            6899999999999999999988887654 4578999999999999999999998865443

>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=99.44  E-value=4.5e-14  Score=95.71  Aligned_cols=70  Identities=19%  Similarity=0.326  Sum_probs=62.4

Q ss_pred             HHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhc
Q psy2029          57 AEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEF  130 (138)
Q Consensus        57 ~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~  130 (138)
                      +++.+.++|.++++.+.+ +|+++++|||+|||+++.+++++    ...++++++|+++|++|+.+.++.++...
T Consensus        22 g~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~----~~~~~~~v~P~~~L~~q~~~~l~~~~~~~   92 (206)
T d1oywa2          22 GYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALL----LNGLTVVVSPLISLMKDQVDQLQANGVAA   92 (206)
T ss_dssp             CCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHH----SSSEEEEECSCHHHHHHHHHHHHHTTCCE
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhh----ccCceEEeccchhhhhhHHHHHHhhcccc
Confidence            566778999999988877 99999999999999999988875    47899999999999999999999886554

>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=99.43  E-value=3e-14  Score=98.13  Aligned_cols=58  Identities=17%  Similarity=0.296  Sum_probs=51.6

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      ++|+|+++.||||||||++|.+|+++++..  ++.++++++|+++|+.|.++.+..++..
T Consensus        52 l~g~dvi~~a~TGSGKTlayllPil~~l~~~~~~~~~lil~PtreLa~Qi~~~~~~l~~~  111 (222)
T d2j0sa1          52 IKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDY  111 (222)
T ss_dssp             HTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTT
T ss_pred             HCCCCeEEEcCcchhhhhhhcccccccccccccCceeEEecchHHHHHHHHHHHHHHhCc
Confidence            689999999999999999999999988755  3558999999999999999999888643

>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=99.40  E-value=3.3e-13  Score=90.67  Aligned_cols=55  Identities=24%  Similarity=0.408  Sum_probs=49.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      .++|+++++|||+|||+++..++...+.+.++++++++|+++|++|..+++.+++
T Consensus        22 ~~~n~lv~~pTGsGKT~i~~~~~~~~~~~~~~~il~i~P~~~L~~q~~~~~~~~~   76 (200)
T d1wp9a1          22 KETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESFRRLF   76 (200)
T ss_dssp             GGSCEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSSHHHHHHHHHHHHHHB
T ss_pred             hcCCeEEEeCCCCcHHHHHHHHHHHHHHhcCCcEEEEcCchHHHHHHHHHHHHhh
Confidence            4678999999999999999988887777778899999999999999999998874

>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=99.39  E-value=7.5e-14  Score=95.84  Aligned_cols=59  Identities=15%  Similarity=0.287  Sum_probs=52.2

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHHHhh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAEEF   60 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~~~~   60 (138)
                      ++|+|++++||||||||++|.+++++++..  ++.++++++|+++|+.|.++.+..+....
T Consensus        47 l~g~dvl~~a~TGsGKTlayllp~l~~i~~~~~~~~alil~Pt~eL~~Q~~~~~~~~~~~~  107 (218)
T d2g9na1          47 IKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYM  107 (218)
T ss_dssp             HHTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHHTTT
T ss_pred             HcCCCEEEEcccchhhhhhhhhhhhheecccccCccEEEEcccchhhhhHHHHHhhhcccc
Confidence            679999999999999999999999998754  45689999999999999999998875543

>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=99.39  E-value=3.1e-13  Score=91.99  Aligned_cols=59  Identities=14%  Similarity=0.120  Sum_probs=51.3

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      +++|+|+++.||||||||++|.+|+++.+..  .+.++++++|+++|+.|.++.++.....
T Consensus        35 il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~lil~PtreL~~qi~~~~~~~~~~   95 (207)
T d1t6na_          35 AILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKY   95 (207)
T ss_dssp             HHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHHHTTT
T ss_pred             HHcCCCeEEEeccccccccccccceeeeecccCCCceEEEEeccchhhHHHHHHHHHHHhh
Confidence            3689999999999999999999999987654  3458999999999999999999887543

>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=99.37  E-value=1.7e-13  Score=95.18  Aligned_cols=82  Identities=15%  Similarity=0.112  Sum_probs=62.1

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhh-----------cCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhhhhHHH
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKI-----------KQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEGKCL   69 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-----------~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q~~~~   69 (138)
                      +++|+|++++||||||||++|.+++++++..           .+.++++++|+++|+.|.++.+...+...+........
T Consensus        55 il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~~~~~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g  134 (238)
T d1wrba1          55 ILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYG  134 (238)
T ss_dssp             HHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECS
T ss_pred             hhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccccccccCCCCceEEEeccchhhhcchheeeeecccCCCcEEEEEec
Confidence            3689999999999999999999999998754           23479999999999999999988876654433222111


Q ss_pred             --------hhhhc-cceEEEee
Q psy2029          70 --------EMIQN-KNCVLSIP   82 (138)
Q Consensus        70 --------~~~~~-~~~ii~~p   82 (138)
                              ..... .++++++|
T Consensus       135 ~~~~~~~~~~~~~~~~ivV~TP  156 (238)
T d1wrba1         135 GADTHSQIREVQMGCHLLVATP  156 (238)
T ss_dssp             SSCSHHHHHHHSSCCSEEEECH
T ss_pred             cchhhHHHhhcccCCceeecCH
Confidence                    11223 67788888

>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=99.37  E-value=6.5e-13  Score=90.16  Aligned_cols=92  Identities=15%  Similarity=0.141  Sum_probs=82.1

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~  121 (138)
                      |.....+.+.+.++..+.++|..++|.+.+ +|+++.+|||+|||+++.+++++.+..  .+.+++++.|+.+++.|...
T Consensus         8 L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (206)
T d1s2ma1           8 LKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQ   87 (206)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccccccccceeeccchhhhhhhhh
Confidence            557788889889999999999999998887 999999999999999999999988765  35688999999999999999


Q ss_pred             HHHHHhhhcCceeee
Q psy2029         122 SLAKAAEEFKFYLEV  136 (138)
Q Consensus       122 ~~~~~~~~~~~~v~~  136 (138)
                      .+..+....++++..
T Consensus        88 ~~~~~~~~~~~~~~~  102 (206)
T d1s2ma1          88 VVRTLGKHCGISCMV  102 (206)
T ss_dssp             HHHHHTTTTTCCEEE
T ss_pred             hhhhcccccCeeEEe
Confidence            999999888887654

>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=99.34  E-value=8.2e-13  Score=89.76  Aligned_cols=56  Identities=16%  Similarity=0.220  Sum_probs=49.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|+|++++||||||||++|.+|+++++..  ++.++++++|+++|+.|.++.+....
T Consensus        38 l~g~dvl~~a~TGsGKTlayllP~l~~~~~~~~~~~~lil~pt~el~~q~~~~~~~~~   95 (206)
T d1veca_          38 LSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVS   95 (206)
T ss_dssp             HTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHHHHHHHHHHHHHHT
T ss_pred             HcCCCEEeeccCccccccccccchhhcccccccCcceEEEeecchhhHHHHHHHHHHh
Confidence            689999999999999999999999987654  35589999999999999999887764

>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=99.33  E-value=3.5e-13  Score=91.08  Aligned_cols=55  Identities=35%  Similarity=0.617  Sum_probs=48.5

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|+|+++++|||+|||.++.+++...+. +++++++++|+++|.+|.++.+.++.
T Consensus        38 ~~~~~~il~apTGsGKT~~a~l~i~~~~~-~~~~vl~l~P~~~L~~q~~~~~~~~~   92 (202)
T d2p6ra3          38 FSGKNLLLAMPTAAGKTLLAEMAMVREAI-KGGKSLYVVPLRALAGEKYESFKKWE   92 (202)
T ss_dssp             TTCSCEEEECSSHHHHHHHHHHHHHHHHH-TTCCEEEEESSHHHHHHHHHHHTTTT
T ss_pred             HcCCCEEEEcCCCCchhHHHHHHHHHHhh-ccCcceeecccHHHHHHHHHHHHHHh
Confidence            57899999999999999999888887654 47799999999999999999987753

>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=99.33  E-value=5.2e-13  Score=90.34  Aligned_cols=53  Identities=25%  Similarity=0.515  Sum_probs=47.8

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|+++++|||||||++|.++++.    +.+++++++|+++|.+|..+++++.+.
T Consensus        38 l~g~~vlv~apTGsGKT~~~~~~~~~----~~~~~~~v~P~~~L~~q~~~~l~~~~~   90 (206)
T d1oywa2          38 LSGRDCLVVMPTGGGKSLCYQIPALL----LNGLTVVVSPLISLMKDQVDQLQANGV   90 (206)
T ss_dssp             HTTCCEEEECSCHHHHHHHHHHHHHH----SSSEEEEECSCHHHHHHHHHHHHHTTC
T ss_pred             HcCCCEEEEcCCCCCCcchhhhhhhh----ccCceEEeccchhhhhhHHHHHHhhcc
Confidence            57899999999999999999888765    578999999999999999999988754

>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=99.30  E-value=5.6e-13  Score=94.53  Aligned_cols=57  Identities=14%  Similarity=0.159  Sum_probs=50.0

Q ss_pred             CCCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           1 MVQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         1 ~~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +.+|+++++.||||||||++++.+++....+++.++++++|+++|++|.++++.+.+
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~~~~~lvi~Ptr~La~q~~~~l~~~~   62 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAPTRVVAAEMEEALRGLP   62 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHTTTSC
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHhcCCEEEEEccHHHHHHHHHHHHhcCC
Confidence            367899999999999999988778887777788999999999999999998886653

>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=99.25  E-value=3.8e-12  Score=86.18  Aligned_cols=86  Identities=15%  Similarity=0.075  Sum_probs=74.5

Q ss_pred             hHHHHHHHHHHHHHhhhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHH
Q psy2029          45 LVHEKYQSLAKAAEEFKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        45 L~~q~~~~l~~~~~~~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~  121 (138)
                      |.+.+.+.+.+.++..+.++|.+++|.+.+ +|+++.+|||+|||+++.+++++.+..  .....+++.|...++.+.++
T Consensus         8 L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (209)
T d1q0ua_           8 FQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQIYH   87 (209)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHH
T ss_pred             cCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeeccccccccccccccccccccchhHHHHH
Confidence            456777888888899999999999988877 999999999999999999999988765  24578999999999999999


Q ss_pred             HHHHHhhhc
Q psy2029         122 SLAKAAEEF  130 (138)
Q Consensus       122 ~~~~~~~~~  130 (138)
                      .+.......
T Consensus        88 ~~~~~~~~~   96 (209)
T d1q0ua_          88 ETLKITKFC   96 (209)
T ss_dssp             HHHHHHTTS
T ss_pred             HHHhhhccc
Confidence            888776554

>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=99.25  E-value=1.6e-12  Score=88.36  Aligned_cols=58  Identities=19%  Similarity=0.186  Sum_probs=49.8

Q ss_pred             CCC-ccEEEEccCCcchHHHHHHHHHHHHhh-cCCeEEEEcchhhhHHHHHHHHHHHHHh
Q psy2029           2 VQN-KNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLVHEKYQSLAKAAEE   59 (138)
Q Consensus         2 ~~~-~~~~~~~ptg~GKt~~~~~~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l~~~~~~   59 (138)
                      ++| .|+++++|||+|||+++.+++.++... ++.++++++|+++|+.|.++.+..++..
T Consensus        39 l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~~~~~~~lil~pt~~l~~q~~~~~~~~~~~   98 (208)
T d1hv8a1          39 LNDEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQVADEIESLKGN   98 (208)
T ss_dssp             HHTCSEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHHHHHHHHHHHHHHHCS
T ss_pred             HcCCCCeeeechhcccccceeecccccccccccCcceEEEeeccccchhhhhhhhhhccc
Confidence            456 499999999999999999999886655 4569999999999999999999887643

>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=99.17  E-value=1.6e-11  Score=83.68  Aligned_cols=57  Identities=16%  Similarity=0.201  Sum_probs=50.2

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      ++|+|+++++|||||||++|.++++.++..  ++.++++++|+++++.|.+..+.....
T Consensus        45 l~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~lil~pt~el~~q~~~~~~~~~~  103 (212)
T d1qdea_          45 IEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAF  103 (212)
T ss_dssp             HTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTT
T ss_pred             HcCCCEEeecccccchhhhhHhhhHhhhhccCCCcceEEEcccHHHhhhhhhhhccccc
Confidence            689999999999999999999999988754  456899999999999999998877643

>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=99.17  E-value=3.6e-11  Score=85.14  Aligned_cols=70  Identities=16%  Similarity=0.201  Sum_probs=57.7

Q ss_pred             hhhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhh
Q psy2029          60 FKFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEE  129 (138)
Q Consensus        60 ~~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~  129 (138)
                      .+.+.|.+++..+.+ ++.++.+|||+|||+++...+.......+.++++++|+++|++|.+++|.+++..
T Consensus       113 ~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i~~~~~~~~~~k~Liivp~~~Lv~Q~~~~f~~~~~~  183 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLF  183 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECSSHHHHHHHHHHHHHHTSC
T ss_pred             ccchHHHHHHHHHHhcCCceeEEEcccCccHHHHHHHHHhhhcccceEEEEEcCchhHHHHHHHHHHhhcc
Confidence            367889999866655 8899999999999999876554444445679999999999999999999998643

>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=99.15  E-value=1.9e-11  Score=76.86  Aligned_cols=55  Identities=16%  Similarity=0.146  Sum_probs=46.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .+|++++++||||+|||..+...++....+.+.+++++.|++++.+|.++.+...
T Consensus         5 ~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~~~~vli~~p~~~l~~q~~~~~~~~   59 (140)
T d1yksa1           5 KKGMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGL   59 (140)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTTS
T ss_pred             HcCCcEEEEcCCCCChhHHHHHHHHHHhhhcCceeeeeecchhHHHHHHHHhhhh
Confidence            5789999999999999998877777777777889999999999998888766443

>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=99.08  E-value=2.4e-11  Score=85.88  Aligned_cols=53  Identities=15%  Similarity=0.159  Sum_probs=47.2

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHh
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA  127 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~  127 (138)
                      ++.++.+|||+|||++++.++++.....+.+++|++|+++|++|.++.+++..
T Consensus        10 ~~~lv~~~TGsGKT~~~l~~~~~~~~~~~~~~lvi~Ptr~La~q~~~~l~~~~   62 (305)
T d2bmfa2          10 RLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAPTRVVAAEMEEALRGLP   62 (305)
T ss_dssp             CEEEECCCTTSSTTTTHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHTTTSC
T ss_pred             CcEEEEECCCCCHHHHHHHHHHHHHHhcCCEEEEEccHHHHHHHHHHHHhcCC
Confidence            88899999999999988888888777778899999999999999999887654

>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=99.04  E-value=6.6e-11  Score=80.03  Aligned_cols=81  Identities=12%  Similarity=0.163  Sum_probs=59.3

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHHHhhhhhhhh--------HHHhh
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEG--------KCLEM   71 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~~~~~~~~Q~--------~~~~~   71 (138)
                      ++|+|+++.||||+|||++|.+++.+++..  .+.+++++.|+.++..+....+...+...+.....        .....
T Consensus        36 l~g~dvi~~a~tGsGKTlay~lp~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~  115 (206)
T d1s2ma1          36 ITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILR  115 (206)
T ss_dssp             HHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHH
T ss_pred             HcCCCEEEecCCcchhhhhhccccccccccccccccceeeccchhhhhhhhhhhhhcccccCeeEEeecCccchhhHHHH
Confidence            679999999999999999999999987655  35588999999999988888877765443322211        11122


Q ss_pred             hhc-cceEEEee
Q psy2029          72 IQN-KNCVLSIP   82 (138)
Q Consensus        72 ~~~-~~~ii~~p   82 (138)
                      +.. .++++++|
T Consensus       116 l~~~~~Ili~TP  127 (206)
T d1s2ma1         116 LNETVHILVGTP  127 (206)
T ss_dssp             TTSCCSEEEECH
T ss_pred             hcccceEEEECC
Confidence            333 67777877

>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=99.02  E-value=2.8e-10  Score=76.86  Aligned_cols=65  Identities=26%  Similarity=0.309  Sum_probs=53.9

Q ss_pred             hhhhhhHHHhhhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhh
Q psy2029          61 KFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEE  129 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~  129 (138)
                      +.++|.+++..+.+ .+.++.+|||+|||+++...+ .+   .+.++++++|+++|++|..++++++...
T Consensus        71 Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~~-~~---~~~~~Liv~p~~~L~~q~~~~~~~~~~~  136 (206)
T d2fz4a1          71 LRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAI-NE---LSTPTLIVVPTLALAEQWKERLGIFGEE  136 (206)
T ss_dssp             CCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHH-HH---SCSCEEEEESSHHHHHHHHHHHGGGCGG
T ss_pred             cCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhHH-HH---hcCceeEEEcccchHHHHHHHHHhhccc
Confidence            67899999977766 788999999999999885443 32   4678999999999999999999887644

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=98.98  E-value=1.2e-09  Score=75.10  Aligned_cols=88  Identities=13%  Similarity=0.158  Sum_probs=66.2

Q ss_pred             HHHHHHHHHHhhhhhhhhHHHhhh----hc---cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHH
Q psy2029          49 KYQSLAKAAEEFKFYLEGKCLEMI----QN---KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        49 ~~~~l~~~~~~~~~~~Q~~~~~~~----~~---~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~  121 (138)
                      ..+.+.+.....+.+-|..+...+    ..   .+.++...||+|||.+++.++...+ ..+.++++++|+..|+.|.++
T Consensus        44 ~~~~~~~~lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~-~~g~qv~~l~Pt~~La~Q~~~  122 (233)
T d2eyqa3          44 QYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAV-DNHKQVAVLVPTTLLAQQHYD  122 (233)
T ss_dssp             HHHHHHHTCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHH-TTTCEEEEECSSHHHHHHHHH
T ss_pred             HHHhhhhccccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHH-HcCCceEEEccHHHhHHHHHH
Confidence            334444333334555676666322    22   4668999999999999988777655 458999999999999999999


Q ss_pred             HHHHHhhhcCceeeec
Q psy2029         122 SLAKAAEEFKFYLEVL  137 (138)
Q Consensus       122 ~~~~~~~~~~~~v~~~  137 (138)
                      .|++++.++++.|..+
T Consensus       123 ~~~~~~~~~~~~v~~l  138 (233)
T d2eyqa3         123 NFRDRFANWPVRIEMI  138 (233)
T ss_dssp             HHHHHSTTTTCCEEEE
T ss_pred             HHHHHHhhCCCEEEec
Confidence            9999999998887654

>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=98.98  E-value=2.3e-10  Score=80.92  Aligned_cols=55  Identities=22%  Similarity=0.378  Sum_probs=45.6

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +.++.++.+|||+|||+++...+.....+.+.++++++|+++|++|..+++.+++
T Consensus       127 ~~~~~il~~pTGsGKT~i~~~i~~~~~~~~~~k~Liivp~~~Lv~Q~~~~f~~~~  181 (282)
T d1rifa_         127 VNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYR  181 (282)
T ss_dssp             HHSEEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECSSHHHHHHHHHHHHHHT
T ss_pred             hcCCceeEEEcccCccHHHHHHHHHhhhcccceEEEEEcCchhHHHHHHHHHHhh
Confidence            4567899999999999998665554444456799999999999999999998875

>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=98.95  E-value=3.4e-10  Score=76.30  Aligned_cols=56  Identities=23%  Similarity=0.269  Sum_probs=46.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhc--CCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIK--QKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~--~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++|+|++++||||||||++|.++++..+...  +...+.+.|...+..+....+....
T Consensus        36 l~G~dvii~a~TGSGKTlayllp~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (209)
T d1q0ua_          36 LRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQIYHETLKIT   93 (209)
T ss_dssp             HHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHH
T ss_pred             HCCCCeEeecccccccceeeeeeeccccccccccccccccccccchhHHHHHHHHhhh
Confidence            6899999999999999999999999876552  4477888999988888887776653

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=98.95  E-value=2.2e-09  Score=75.05  Aligned_cols=88  Identities=17%  Similarity=0.245  Sum_probs=68.3

Q ss_pred             HHHHHHHHHHhhhhhhhhHHHhhhh-----c--cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHH
Q psy2029          49 KYQSLAKAAEEFKFYLEGKCLEMIQ-----N--KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQ  121 (138)
Q Consensus        49 ~~~~l~~~~~~~~~~~Q~~~~~~~~-----~--~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~  121 (138)
                      ..+.+.+.....+++-|..++..+.     +  .+.++...+|+|||.+++..++..+. .+.++++++|+..|+.|.++
T Consensus        72 l~~~f~~~LPFeLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~-~g~q~~~m~Pt~~La~Qh~~  150 (264)
T d1gm5a3          72 LAEEFIKSLPFKLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYE-AGFQTAFMVPTSILAIQHYR  150 (264)
T ss_dssp             HHHHHHHHSSSCCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHH-HTSCEEEECSCHHHHHHHHH
T ss_pred             HHHHHHhhccccCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHh-cccceeEEeehHhhhHHHHH
Confidence            3344444333346777888873332     2  56799999999999999888876655 48899999999999999999


Q ss_pred             HHHHHhhhcCceeeec
Q psy2029         122 SLAKAAEEFKFYLEVL  137 (138)
Q Consensus       122 ~~~~~~~~~~~~v~~~  137 (138)
                      .|++++.++|+.+..+
T Consensus       151 ~~~~~f~~~~~~v~~l  166 (264)
T d1gm5a3         151 RTVESFSKFNIHVALL  166 (264)
T ss_dssp             HHHHHHTCSSCCEEEC
T ss_pred             HHHHhhhhccccceee
Confidence            9999999988887654

>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=98.94  E-value=5.7e-10  Score=70.32  Aligned_cols=49  Identities=16%  Similarity=0.135  Sum_probs=40.4

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ...++.+|||||||.++...    +.+.+.++++++|+++|.+|..+.+.+..
T Consensus         9 ~~~ll~apTGsGKT~~~~~~----~~~~~~~vli~~P~~~l~~q~~~~~~~~~   57 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAA----YAAQGYKVLVLNPSVAATLGFGAYMSKAH   57 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHH----HHTTTCCEEEEESCHHHHHHHHHHHHHHH
T ss_pred             CEEEEEeCCCCCHHHHHHHH----HHHcCCcEEEEcChHHHHHHHHHHHHHHh
Confidence            46799999999999876433    23468899999999999999999888763

>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=98.88  E-value=9.4e-10  Score=74.22  Aligned_cols=52  Identities=21%  Similarity=0.341  Sum_probs=42.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +++++.++.+|||+|||+++...+..    .+.++++++|.++|.+|..+++..++
T Consensus        83 ~~~~~~ll~~~tG~GKT~~a~~~~~~----~~~~~Liv~p~~~L~~q~~~~~~~~~  134 (206)
T d2fz4a1          83 LVDKRGCIVLPTGSGKTHVAMAAINE----LSTPTLIVVPTLALAEQWKERLGIFG  134 (206)
T ss_dssp             TTTSEEEEEESSSTTHHHHHHHHHHH----SCSCEEEEESSHHHHHHHHHHHGGGC
T ss_pred             HhCCCcEEEeCCCCCceehHHhHHHH----hcCceeEEEcccchHHHHHHHHHhhc
Confidence            45678899999999999987655432    46789999999999999998887764

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=98.88  E-value=1.4e-09  Score=74.77  Aligned_cols=53  Identities=15%  Similarity=0.162  Sum_probs=47.0

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      .+.++++.||||||.+|..++...+ +.+.++++++|+..|..|.++++.+.+.
T Consensus        77 ~~~LL~GdvGsGKT~V~~~a~~~~~-~~g~qv~~l~Pt~~La~Q~~~~~~~~~~  129 (233)
T d2eyqa3          77 MDRLVCGDVGFGKTEVAMRAAFLAV-DNHKQVAVLVPTTLLAQQHYDNFRDRFA  129 (233)
T ss_dssp             CEEEEECCCCTTTHHHHHHHHHHHH-TTTCEEEEECSSHHHHHHHHHHHHHHST
T ss_pred             cCeEEEcCCCCCcHHHHHHHHHHHH-HcCCceEEEccHHHhHHHHHHHHHHHHh
Confidence            3679999999999999999988755 5699999999999999999999998744

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=98.83  E-value=1.9e-09  Score=67.31  Aligned_cols=52  Identities=17%  Similarity=0.153  Sum_probs=45.5

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      ++.++.+|||+|||..+...++......+.++++++|++++++|..+.+...
T Consensus         8 ~~~il~~~tGsGKT~~~~~~~~~~~~~~~~~vli~~p~~~l~~q~~~~~~~~   59 (140)
T d1yksa1           8 MTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGL   59 (140)
T ss_dssp             CEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTTS
T ss_pred             CcEEEEcCCCCChhHHHHHHHHHHhhhcCceeeeeecchhHHHHHHHHhhhh
Confidence            8889999999999999987778877777889999999999999988776543

>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=98.83  E-value=3.5e-09  Score=66.59  Aligned_cols=52  Identities=15%  Similarity=0.077  Sum_probs=42.9

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhc
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEF  130 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~  130 (138)
                      +..++.+|||+|||.++...+    ...+.++++++|+++|++|..+.+.+++...
T Consensus         9 ~~~ll~apTGsGKT~~~~~~~----~~~~~~vli~~P~~~l~~q~~~~~~~~~~~~   60 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAAY----AAQGYKVLVLNPSVAATLGFGAYMSKAHGVD   60 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHHH----HTTTCCEEEEESCHHHHHHHHHHHHHHHSCC
T ss_pred             CEEEEEeCCCCCHHHHHHHHH----HHcCCcEEEEcChHHHHHHHHHHHHHHhhcc
Confidence            667899999999998764333    3457899999999999999999999886543

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=98.73  E-value=8.8e-09  Score=71.96  Aligned_cols=53  Identities=21%  Similarity=0.313  Sum_probs=46.9

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      .+.++++.||||||.+|..++...+ +.+.++++++|+..|..|.++.+.+++.
T Consensus       105 m~rLL~GdvGSGKT~Va~~a~~~~~-~~g~q~~~m~Pt~~La~Qh~~~~~~~f~  157 (264)
T d1gm5a3         105 MNRLLQGDVGSGKTVVAQLAILDNY-EAGFQTAFMVPTSILAIQHYRRTVESFS  157 (264)
T ss_dssp             CCCEEECCSSSSHHHHHHHHHHHHH-HHTSCEEEECSCHHHHHHHHHHHHHHHT
T ss_pred             ceeeeeccccccccHHHHHHHHHHH-hcccceeEEeehHhhhHHHHHHHHHhhh
Confidence            3669999999999999999988755 4589999999999999999999988854

>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=97.85  E-value=0.00038  Score=47.52  Aligned_cols=133  Identities=10%  Similarity=-0.025  Sum_probs=69.1

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHHhh----hhhhh---------hHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEF----KFYLE---------GKC   68 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~~~----~~~~Q---------~~~   68 (138)
                      ..|+-+++.|++|+|||..+...+.......+.+++|+..--. ..+....+.......    .....         .++
T Consensus        33 ~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s~E~~-~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  111 (277)
T d1cr2a_          33 RGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEES-VEETAEDLIGLHNRVRLRQSDSLKREIIENGKFDQW  111 (277)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEESSSC-HHHHHHHHHHHHTTCCGGGCHHHHHHHHHTSHHHHH
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEeeeccc-hhhHHhHHHHHhhcCCchhhcccccchhhhHHHHHH
Confidence            3567789999999999988877766544556778888764221 122222222211100    00000         111


Q ss_pred             HhhhhccceEEEeecCCCchHhHHHHHHHHHHh-CCCeEEEEccchhHH------------HHHHHHHHHHhhhcCceee
Q psy2029          69 LEMIQNKNCVLSIPTSGGKTLVGEILIMKELKI-KQKSAIFILPYISLV------------HEKYQSLAKAAEEFKFYLE  135 (138)
Q Consensus        69 ~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~-~~~~~~~i~P~~~l~------------~q~~~~~~~~~~~~~~~v~  135 (138)
                      .........+...+....-+.--....++.... .+.+.++|.|...+.            .+....+++++..+++.|.
T Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vvID~l~~l~~~~~~~~~~~~~~~~~~~l~~lA~~~~i~vi  191 (277)
T d1cr2a_         112 FDELFGNDTFHLYDSFAEAETDRLLAKLAYMRSGLGCDVIILDHISIVVSASGESDERKMIDNLMTKLKGFAKSTGVVLV  191 (277)
T ss_dssp             HHHHHSSSCEEEECCC-CCCHHHHHHHHHHHHHTTCCSEEEEEEEEC----------CHHHHHHHHHHHHHHHHHCCEEE
T ss_pred             HHHhhccceeeeeccccchhHHHHHHHhhhhhhccCcceEEEcccccccccccccchhHHHHHHHHHHHHHhhhccccce
Confidence            122223233334444444444444444444433 467888888864442            3345667777777776653

>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=97.56  E-value=7.4e-05  Score=51.61  Aligned_cols=52  Identities=13%  Similarity=0.098  Sum_probs=38.9

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhh---cCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKI---KQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~---~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      .+++|.||.|||||.+...-+.+.+.+   +..+++++++++++++++.+.+.+.
T Consensus        15 ~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn~a~~~i~~~~~~~   69 (306)
T d1uaaa1          15 GPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQT   69 (306)
T ss_dssp             SEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcHHHHHHHHHHHHHh
Confidence            478999999999998875544443322   2358999999999998877776554

>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=97.52  E-value=0.00013  Score=50.83  Aligned_cols=53  Identities=15%  Similarity=-0.006  Sum_probs=41.1

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhc---CCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIK---QKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~---~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      +..++|.||.|||||.+...-+.+.+.+.   ..+++++++++..++++...+.+.
T Consensus        24 ~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~aa~~~~~~~~~~   79 (318)
T d1pjra1          24 EGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSL   79 (318)
T ss_dssp             SSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHHHHHHHHHHHHhh
Confidence            34789999999999998876665544332   248999999999998888877665

>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=97.47  E-value=0.00093  Score=44.45  Aligned_cols=38  Identities=18%  Similarity=0.185  Sum_probs=30.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      .|.-+++.+|+|+|||..+.-.+.+. ..++.+++|+..
T Consensus        25 ~gsl~li~G~pGsGKT~l~~qia~~~-~~~~~~~~~is~   62 (242)
T d1tf7a2          25 KDSIILATGATGTGKTLLVSRFVENA-CANKERAILFAY   62 (242)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHHH-HTTTCCEEEEES
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHH-HHhccccceeec
Confidence            46778999999999999997777764 445778888753

>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=97.43  E-value=0.00087  Score=46.07  Aligned_cols=74  Identities=14%  Similarity=0.106  Sum_probs=58.0

Q ss_pred             hhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhcCceeee
Q psy2029          61 KFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEFKFYLEV  136 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~~~~v~~  136 (138)
                      .+++|....-.+. ..-+..+.||.|||+++.+++.-.... ++.+=+|...--|+.--++.+..+++.+|++|..
T Consensus        81 hyDVQLiGgi~L~-~G~iaem~TGEGKTL~a~l~a~l~al~-g~~vhvvTvNdyLA~RDae~m~~iy~~lGlsvg~  154 (273)
T d1tf5a3          81 PFKVQLMGGVALH-DGNIAEMKTGEGKTLTSTLPVYLNALT-GKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGL  154 (273)
T ss_dssp             CCHHHHHHHHHHH-TTSEEECCTTSCHHHHHHHHHHHHHTT-SSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEEE
T ss_pred             EehhHHHHHHHHH-hhhheeecCCCcchhHHHHHHHHHHhc-CCCceEEecCccccchhhhHHhHHHHHcCCCccc
Confidence            4445544433222 445789999999999999999877665 6667788888889999999999999999999874

>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=97.42  E-value=0.006  Score=40.20  Aligned_cols=53  Identities=19%  Similarity=0.238  Sum_probs=31.5

Q ss_pred             CCCccE-EEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc--hhhhHHHHHHHHHH
Q psy2029           2 VQNKNC-VLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP--YISLVHEKYQSLAK   55 (138)
Q Consensus         2 ~~~~~~-~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P--~~aL~~q~~~~l~~   55 (138)
                      ++..++ ++++|||+|||....-.+.. +..++.++.++..  ++.=..++.+.+.+
T Consensus         7 ~~~~~vi~lvGp~GvGKTTTiaKLA~~-~~~~g~kV~lit~Dt~R~gA~eQL~~~a~   62 (207)
T d1ls1a2           7 LKDRNLWFLVGLQGSGKTTTAAKLALY-YKGKGRRPLLVAADTQRPAAREQLRLLGE   62 (207)
T ss_dssp             CCSSEEEEEECCTTTTHHHHHHHHHHH-HHHTTCCEEEEECCSSCHHHHHHHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHH-HHHCCCcEEEEecccccchHHHHHHHHHH
Confidence            345565 56999999999665443433 4456777766543  45444444444444

>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=97.32  E-value=0.00024  Score=48.94  Aligned_cols=66  Identities=12%  Similarity=0.058  Sum_probs=48.2

Q ss_pred             hhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHh---CCCeEEEEccchhHHHHHHHHHHHHhh
Q psy2029          62 FYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKI---KQKSAIFILPYISLVHEKYQSLAKAAE  128 (138)
Q Consensus        62 ~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~---~~~~~~~i~P~~~l~~q~~~~~~~~~~  128 (138)
                      .+-|.+++.. ...+++|.+|.|+|||.+....+.+.+..   ...++++++++++++++..+.+.+...
T Consensus         3 ~~eQ~~av~~-~~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn~a~~~i~~~~~~~~~   71 (306)
T d1uaaa1           3 NPGQQQAVEF-VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLG   71 (306)
T ss_dssp             CHHHHHHHHC-CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CHHHHHHHhC-CCCCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcHHHHHHHHHHHHHhcC
Confidence            3456666632 23678899999999999876555444333   335899999999999998888877654

>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=97.08  E-value=0.0018  Score=44.71  Aligned_cols=69  Identities=12%  Similarity=-0.058  Sum_probs=51.4

Q ss_pred             hhhhhhHHHhhhhccceEEEeecCCCchHhHHHHHHHHHHhC---CCeEEEEccchhHHHHHHHHHHHHhhhc
Q psy2029          61 KFYLEGKCLEMIQNKNCVLSIPTSGGKTLVGEILIMKELKIK---QKSAIFILPYISLVHEKYQSLAKAAEEF  130 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~~~~ii~~ptg~GKt~~~~~~~l~~~~~~---~~~~~~i~P~~~l~~q~~~~~~~~~~~~  130 (138)
                      +.+-|.+++.. ....++|..|.|+|||.+....+.+.+...   ..+++++++++..+.+....+.+.....
T Consensus        12 L~~eQ~~~v~~-~~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~aa~~~~~~~~~~~~~~   83 (318)
T d1pjra1          12 LNKEQQEAVRT-TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLGGA   83 (318)
T ss_dssp             SCHHHHHHHHC-CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHHGGG
T ss_pred             CCHHHHHHHhC-CCCCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHHHHHHHHHHHHhhcccc
Confidence            34457666642 236788999999999999877666555432   2589999999999999999988765543

>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=97.07  E-value=0.0011  Score=44.19  Aligned_cols=68  Identities=19%  Similarity=0.159  Sum_probs=48.5

Q ss_pred             hhhhhhHHHhhh----hc-cceEEEeecCCCchHhHHHHHHHHHHh--CCCeEEEEccchhHHHHHHHHHHHHhhhc
Q psy2029          61 KFYLEGKCLEMI----QN-KNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAAEEF  130 (138)
Q Consensus        61 ~~~~Q~~~~~~~----~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~--~~~~~~~i~P~~~l~~q~~~~~~~~~~~~  130 (138)
                      +.++|.+++...    .. ..+++.-+.|.|||..++. ++..+..  ...++++|+| ..+..|..+++.++....
T Consensus        13 L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~-~~~~~~~~~~~~~~LIv~p-~~l~~~W~~e~~~~~~~~   87 (230)
T d1z63a1          13 LRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIA-VFSDAKKENELTPSLVICP-LSVLKNWEEELSKFAPHL   87 (230)
T ss_dssp             CCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHH-HHHHHHHTTCCSSEEEEEC-STTHHHHHHHHHHHCTTS
T ss_pred             hhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHH-hhhhhhhcccccccceecc-hhhhhHHHHHHHhhcccc
Confidence            567788777432    22 5578899999999999854 4444443  2367888888 567788889998886543

>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=96.76  E-value=0.00042  Score=51.09  Aligned_cols=23  Identities=35%  Similarity=0.361  Sum_probs=19.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      .-+|+++.+|||+|||+.+--.+
T Consensus        48 ~ksNILliGPTGvGKTlLAr~LA   70 (443)
T d1g41a_          48 TPKNILMIGPTGVGKTEIARRLA   70 (443)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHH
T ss_pred             ccccEEEECCCCCCHHHHHHHHH
Confidence            34799999999999999986544

>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=96.72  E-value=0.0011  Score=43.52  Aligned_cols=39  Identities=15%  Similarity=0.227  Sum_probs=30.7

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      .|+-+++.+|+|+|||..+.-.+...+.+.+.+++|+..
T Consensus        25 ~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s~   63 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTF   63 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEES
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCcccccc
Confidence            467889999999999999876666556666678888754

>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=96.58  E-value=0.004  Score=41.12  Aligned_cols=52  Identities=13%  Similarity=0.024  Sum_probs=32.2

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc--chhhhHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL--PYISLVHEKYQSLAKA   56 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~--P~~aL~~q~~~~l~~~   56 (138)
                      ++-+++++|||+|||....=.+.. +..++.++.++.  .+|.=..++++.+.+.
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA~~-~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~   59 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLGRY-YQNLGKKVMFCAGDTFRAAGGTQLSEWGKR   59 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHH-HHTTTCCEEEECCCCSSTTHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH-HHHCCCcEEEEEeccccccchhhHhhcccc
Confidence            455678999999999665433433 445577777665  3555445555555443

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=96.53  E-value=0.0073  Score=41.58  Aligned_cols=69  Identities=19%  Similarity=0.199  Sum_probs=47.7

Q ss_pred             hhhhhhhHHHhhh---------hc-cceEEEeecCCCchHhHHHHHHHHHHhC-------CCeEEEEccchhHHHHHHHH
Q psy2029          60 FKFYLEGKCLEMI---------QN-KNCVLSIPTSGGKTLVGEILIMKELKIK-------QKSAIFILPYISLVHEKYQS  122 (138)
Q Consensus        60 ~~~~~Q~~~~~~~---------~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~-------~~~~~~i~P~~~l~~q~~~~  122 (138)
                      .+.++|.+.+..+         .. ..+++.-..|.|||+.++- ++..+...       ..++++|+|.. |+.|..++
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qaia-~l~~l~~~~~~~~~~~~~~LIV~P~s-l~~qW~~E  132 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCIT-LIWTLLKQSPDCKPEIDKVIVVSPSS-LVRNWYNE  132 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHH-HHHHHHHCCTTSSCSCSCEEEEECHH-HHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHHH-HHHHHHHhcccccCCCCcEEEEccch-hhHHHHHH
Confidence            3567777776422         12 4578888899999997743 33333321       23689999975 88899999


Q ss_pred             HHHHhhhc
Q psy2029         123 LAKAAEEF  130 (138)
Q Consensus       123 ~~~~~~~~  130 (138)
                      +.+++...
T Consensus       133 i~k~~~~~  140 (298)
T d1z3ix2         133 VGKWLGGR  140 (298)
T ss_dssp             HHHHHGGG
T ss_pred             HHhhcCCc
Confidence            99987653

>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=96.38  E-value=0.00095  Score=47.14  Aligned_cols=41  Identities=27%  Similarity=0.199  Sum_probs=28.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhh
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISL   45 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL   45 (138)
                      .+.|++|++|||||||.... +++. .++...+++.+-...+|
T Consensus       165 ~~~nili~G~tgSGKTT~l~-al~~-~i~~~~rivtiEd~~El  205 (323)
T d1g6oa_         165 IGKNVIVCGGTGSGKTTYIK-SIME-FIPKEERIISIEDTEEI  205 (323)
T ss_dssp             HTCCEEEEESTTSSHHHHHH-HHGG-GSCTTCCEEEEESSCCC
T ss_pred             hCCCEEEEeeccccchHHHH-HHhh-hcccccceeeccchhhh
Confidence            36789999999999998742 3332 34456677777555554

>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=96.36  E-value=0.001  Score=46.49  Aligned_cols=23  Identities=35%  Similarity=0.341  Sum_probs=19.1

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ..++++++|||+|||..|-..+-
T Consensus        49 ~~~iLl~GPpG~GKT~lAkalA~   71 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIARRLAK   71 (309)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHhh
Confidence            46899999999999999965443

>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=96.32  E-value=0.0052  Score=40.68  Aligned_cols=52  Identities=23%  Similarity=0.226  Sum_probs=36.0

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhh--cCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKI--KQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~--~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +..+++.-+.|.|||..+...+. ++..  ...++++++| .++..+-.+++.++.
T Consensus        31 ~~g~iLaDe~GlGKT~~~i~~~~-~~~~~~~~~~~LIv~p-~~l~~~W~~e~~~~~   84 (230)
T d1z63a1          31 GFGICLADDMGLGKTLQTIAVFS-DAKKENELTPSLVICP-LSVLKNWEEELSKFA   84 (230)
T ss_dssp             TCCEEECCCTTSCHHHHHHHHHH-HHHHTTCCSSEEEEEC-STTHHHHHHHHHHHC
T ss_pred             CCCEEEEeCCCCChHHHHHHhhh-hhhhcccccccceecc-hhhhhHHHHHHHhhc
Confidence            34578888999999999855444 3433  3458888888 455566677776653

>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=96.29  E-value=0.0058  Score=40.32  Aligned_cols=43  Identities=14%  Similarity=0.010  Sum_probs=28.3

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKY   50 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~   50 (138)
                      .+++++|+|+|||..+..... .+.+++.+++|+ +...+.++..
T Consensus        38 ~l~l~G~~G~GKTHLl~A~~~-~~~~~~~~~~~~-~~~~~~~~~~   80 (213)
T d1l8qa2          38 PIFIYGSVGTGKTHLLQAAGN-EAKKRGYRVIYS-SADDFAQAMV   80 (213)
T ss_dssp             SEEEECSSSSSHHHHHHHHHH-HHHHTTCCEEEE-EHHHHHHHHH
T ss_pred             cEEEECCCCCcHHHHHHHHHH-HhccCccceEEe-chHHHHHHHH
Confidence            379999999999988744443 455566777775 4444444333

>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=96.17  E-value=0.035  Score=37.11  Aligned_cols=37  Identities=16%  Similarity=0.243  Sum_probs=26.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh----------cCCeEEEEc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI----------KQKSAIFIL   40 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~----------~~~~~l~v~   40 (138)
                      .|+-.++.+++|+|||.++...+.. +..          .+.+++|+.
T Consensus        28 pg~~~~i~G~~G~GKS~l~l~la~~-ia~g~~~~~~~~~~~~~vl~~~   74 (274)
T d1nlfa_          28 AGTVGALVSPGGAGKSMLALQLAAQ-IAGGPDLLEVGELPTGPVIYLP   74 (274)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHH-HHTCCCTTCCCCCCCCCEEEEE
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHH-HHcCCCcccccccCCCceEEEe
Confidence            4667799999999999888666553 322          244788865

>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=96.10  E-value=0.0049  Score=44.35  Aligned_cols=41  Identities=10%  Similarity=0.143  Sum_probs=28.1

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhh
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISL   45 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL   45 (138)
                      .++++|.++||+|||.... .++..++..+..++++-|.-++
T Consensus        50 ~~H~~I~G~tGsGKT~~l~-~li~~~~~~g~~~iiiD~kge~   90 (433)
T d1e9ra_          50 PRHLLVNGATGTGKSVLLR-ELAYTGLLRGDRMVIVDPNGDM   90 (433)
T ss_dssp             GGCEEEEECTTSSHHHHHH-HHHHHHHHTTCEEEEEEETTHH
T ss_pred             cceEEEEeCCCCcHHHHHH-HHHHHHHhCCCCEEEEeCChhH
Confidence            3579999999999997653 3444455556677766665443

>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=96.05  E-value=0.0056  Score=38.20  Aligned_cols=29  Identities=24%  Similarity=0.180  Sum_probs=21.0

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCC
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQK   34 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~   34 (138)
                      +++++.+|.|+|||..+...+ ..+.+++.
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~-~~l~~~~~   30 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKAS-EVLKSSGV   30 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHH-HHHHHTTC
T ss_pred             cEEEEECCCCCcHHHHHHHHH-HHHHHCCC
Confidence            579999999999998765444 44544444

>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=96.00  E-value=0.0048  Score=40.84  Aligned_cols=39  Identities=18%  Similarity=0.030  Sum_probs=28.9

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh-----cCCeEEEEcc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI-----KQKSAIFILP   41 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-----~~~~~l~v~P   41 (138)
                      .|+-+++.+|+|+|||..++..+.+.+..     .+.+++|+.-
T Consensus        35 ~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~   78 (254)
T d1pzna2          35 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDT   78 (254)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEES
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEec
Confidence            46678999999999999998777764432     2457777643

>d1tf5a3 c.37.1.19 (A:1-226,A:349-395) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=95.99  E-value=0.0092  Score=40.85  Aligned_cols=51  Identities=18%  Similarity=0.167  Sum_probs=36.6

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAE   58 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~~   58 (138)
                      -+..+.||-|||+++.+++.-+.+. |+.+-+++..--|...=.+.+.+...
T Consensus        96 ~iaem~TGEGKTL~a~l~a~l~al~-g~~vhvvTvNdyLA~RDae~m~~iy~  146 (273)
T d1tf5a3          96 NIAEMKTGEGKTLTSTLPVYLNALT-GKGVHVVTVNEYLASRDAEQMGKIFE  146 (273)
T ss_dssp             SEEECCTTSCHHHHHHHHHHHHHTT-SSCEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             hheeecCCCcchhHHHHHHHHHHhc-CCCceEEecCccccchhhhHHhHHHH
Confidence            4789999999999999988776664 77777777665565544455555433

>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=95.91  E-value=0.0016  Score=46.63  Aligned_cols=21  Identities=43%  Similarity=0.571  Sum_probs=17.6

Q ss_pred             ccEEEEccCCcchHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      .|+++.+|||+|||..+-..+
T Consensus        69 ~niLfiGPTGvGKTElAk~LA   89 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMAQTLA   89 (364)
T ss_dssp             CCEEEECCTTSSHHHHHHHHH
T ss_pred             cceeeeCCCCccHHHHHHHHH
Confidence            579999999999999985443

>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=95.90  E-value=0.11  Score=34.00  Aligned_cols=48  Identities=15%  Similarity=0.086  Sum_probs=28.4

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc--chhhhHHHHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL--PYISLVHEKYQSLAK   55 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~--P~~aL~~q~~~~l~~   55 (138)
                      +++++|||+|||....=.+.. +..++.++.++.  .+|.=..++.+.+.+
T Consensus        14 i~lvGptGvGKTTTiAKLAa~-~~~~~~kV~lit~Dt~R~gA~eQL~~~a~   63 (213)
T d1vmaa2          14 IMVVGVNGTGKTTSCGKLAKM-FVDEGKSVVLAAADTFRAAAIEQLKIWGE   63 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH-HHHTTCCEEEEEECTTCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH-HHHCCCceEEEeecccccchhHHHHHHhh
Confidence            578999999999655333332 445566766653  345434444444433

>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=95.81  E-value=0.0071  Score=39.90  Aligned_cols=51  Identities=14%  Similarity=-0.004  Sum_probs=33.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHHHHhh-----cCCeEEEEcchhhhHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMKELKI-----KQKSAIFILPYISLVHEKYQS   52 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-----~~~~~l~v~P~~aL~~q~~~~   52 (138)
                      -.|+-+++.+|+|+|||..+...+.+....     ....++++.....+..+....
T Consensus        35 p~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   90 (258)
T d1v5wa_          35 ESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRD   90 (258)
T ss_dssp             CSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHH
T ss_pred             cCCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHHHHHH
Confidence            357788999999999999998877765433     123566665544444333333

>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=95.81  E-value=0.0033  Score=39.25  Aligned_cols=24  Identities=21%  Similarity=0.325  Sum_probs=19.9

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ++.++++.+|.|||||.++-..+-
T Consensus         4 k~~~I~i~G~~GsGKTT~~~~La~   27 (174)
T d1y63a_           4 KGINILITGTPGTGKTSMAEMIAA   27 (174)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHH
Confidence            467899999999999999866544

>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=95.78  E-value=0.0051  Score=40.70  Aligned_cols=33  Identities=18%  Similarity=-0.011  Sum_probs=17.8

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      +++++|||+|||....=.+. ++..++.++.++.
T Consensus        15 i~lvGptGvGKTTTiAKLA~-~~~~~g~kV~lit   47 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLAY-FYKKKGFKVGLVG   47 (211)
T ss_dssp             EEEECSCCC----HHHHHHH-HHHHTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHH-HHHHCCCceEEEE
Confidence            46689999999965433333 2445566766554

>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=95.74  E-value=0.0022  Score=42.18  Aligned_cols=38  Identities=13%  Similarity=0.010  Sum_probs=28.1

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh-----cCCeEEEEc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI-----KQKSAIFIL   40 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~-----~~~~~l~v~   40 (138)
                      .|+-+++.+|+|+|||..+...+.+.+..     .+.+++|+.
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~   75 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYID   75 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEE
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEe
Confidence            57788999999999999987766543321     355777764

>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=95.73  E-value=0.0038  Score=38.25  Aligned_cols=23  Identities=30%  Similarity=0.481  Sum_probs=18.6

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      -+++++.+|.|+|||.++-..+-
T Consensus         2 ~k~I~l~G~~GsGKSTvak~La~   24 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGRQLAQ   24 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH
Confidence            36889999999999998855443

>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=95.72  E-value=0.0038  Score=41.34  Aligned_cols=23  Identities=26%  Similarity=0.397  Sum_probs=18.8

Q ss_pred             ccEEEEccCCcchHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      .++++++|.|+|||.++-+.+-.
T Consensus        36 ~~~L~~GPpGtGKT~lA~~la~~   58 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLAHIIASE   58 (238)
T ss_dssp             CCEEEESSTTSSHHHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHhc
Confidence            47999999999999998665443

>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=95.58  E-value=0.0043  Score=38.70  Aligned_cols=23  Identities=26%  Similarity=0.312  Sum_probs=18.5

Q ss_pred             CCCccEEEEccCCcchHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      +.|+-+++.+|.|||||.++-..
T Consensus         2 ~~g~iI~l~G~~GsGKSTia~~L   24 (176)
T d1zp6a1           2 LGGNILLLSGHPGSGKSTIAEAL   24 (176)
T ss_dssp             CTTEEEEEEECTTSCHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHH
Confidence            35677889999999999987433

>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=95.53  E-value=0.0048  Score=40.92  Aligned_cols=23  Identities=22%  Similarity=0.317  Sum_probs=19.0

Q ss_pred             ccEEEEccCCcchHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      .++++++|+|+|||..+-..+..
T Consensus        36 ~~~Ll~GPpG~GKTtla~~la~~   58 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLAHVIAHE   58 (239)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            47999999999999998665543

>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=95.52  E-value=0.0067  Score=43.82  Aligned_cols=32  Identities=19%  Similarity=0.252  Sum_probs=21.2

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEE
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAI   37 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l   37 (138)
                      .-+++++|||||||... .+++..+.....+++
T Consensus       159 GliLvtGpTGSGKSTTl-~~~l~~~~~~~~~i~  190 (401)
T d1p9ra_         159 GIILVTGPTGSGKSTTL-YAGLQELNSSERNIL  190 (401)
T ss_dssp             EEEEEECSTTSCHHHHH-HHHHHHHCCTTSCEE
T ss_pred             ceEEEEcCCCCCccHHH-HHHhhhhcCCCceEE
Confidence            35799999999999875 445554433334433

>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=95.44  E-value=0.023  Score=40.77  Aligned_cols=48  Identities=13%  Similarity=0.083  Sum_probs=32.4

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhc-------C----CeEEEEcchhhhHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIK-------Q----KSAIFILPYISLVHEKYQSL   53 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~-------~----~~~l~v~P~~aL~~q~~~~l   53 (138)
                      +++|+|..|||||.+...=+++.+...       +    .+++.++-|+.=..+..+++
T Consensus        18 ~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI   76 (485)
T d1w36b1          18 ERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRI   76 (485)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHH
T ss_pred             CeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHH
Confidence            789999999999988766666544431       1    25788877765444444443

>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=95.42  E-value=0.0049  Score=39.39  Aligned_cols=27  Identities=15%  Similarity=-0.013  Sum_probs=22.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKEL   29 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~   29 (138)
                      .|+-+++.+|+|+|||.+++..+.+.+
T Consensus        22 ~G~v~~i~G~~GsGKT~l~l~la~~~~   48 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKTQICHTLAVTCQ   48 (242)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            467889999999999999877776543

>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=95.38  E-value=0.011  Score=39.19  Aligned_cols=34  Identities=24%  Similarity=0.173  Sum_probs=22.4

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhc-CCeEEEE
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIK-QKSAIFI   39 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~-~~~~l~v   39 (138)
                      .++++.+|+|+|||.++-.. .+.+.+. ..+.+++
T Consensus        44 ~~lll~GppGtGKT~l~~~l-~~~l~~~~~~~~~~~   78 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTLRKL-WELYKDKTTARFVYI   78 (276)
T ss_dssp             CEEEEECCTTSSHHHHHHHH-HHHHTTSCCCEEEEE
T ss_pred             CceEEECCCCCCHHHHHHHH-HHHHhcccCCcEEEe
Confidence            57899999999999887543 3334332 2344443

>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=95.29  E-value=0.012  Score=37.98  Aligned_cols=35  Identities=20%  Similarity=0.068  Sum_probs=25.7

Q ss_pred             ccEEEEcc-CCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           5 KNCVLSIP-TSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         5 ~~~~~~~p-tg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      ++..|++- ||.|||.++.-.+.. +.++|.|++++=
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~a-La~~G~rVl~id   37 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQA-AKAAGYRTAGYK   37 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHH-HHHTTCCEEEEC
T ss_pred             ceEEEEECCCCccHHHHHHHHHHH-HHHCCCeEEEEC
Confidence            45667777 799999988555543 566788998874

>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=95.27  E-value=0.006  Score=41.14  Aligned_cols=22  Identities=23%  Similarity=0.303  Sum_probs=18.1

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +++++.+|+|+|||.++-..+-
T Consensus        41 ~~vLL~GppGtGKT~la~alA~   62 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALAAKIAE   62 (246)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHhh
Confidence            4689999999999999865544

>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=95.18  E-value=0.0075  Score=37.36  Aligned_cols=22  Identities=32%  Similarity=0.333  Sum_probs=18.0

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      -++++++|.|||||.++-..+-
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~   26 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELAS   26 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            4788999999999998865544

>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=95.18  E-value=0.026  Score=40.91  Aligned_cols=49  Identities=22%  Similarity=0.196  Sum_probs=38.9

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ++..+.+-||||||++..- +..   +.++.+++++|...++.+.++++..+.
T Consensus        32 ~~q~l~GltGS~ka~~iA~-l~~---~~~rp~LVVt~n~~~A~qL~~dL~~~l   80 (413)
T d1t5la1          32 KHQTLLGATGTGKTFTISN-VIA---QVNKPTLVIAHNKTLAGQLYSELKEFF   80 (413)
T ss_dssp             SEEEEEECTTSCHHHHHHH-HHH---HHTCCEEEECSSHHHHHHHHHHHHHHC
T ss_pred             CcEEEeCCCCcHHHHHHHH-HHH---HhCCCEEEEeCCHHHHHHHHHHHHHHc
Confidence            4578899999999977532 222   236789999999999999999998874

>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=95.17  E-value=0.22  Score=32.52  Aligned_cols=46  Identities=17%  Similarity=0.114  Sum_probs=27.1

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc--hhhhHHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP--YISLVHEKYQSL   53 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P--~~aL~~q~~~~l   53 (138)
                      +++++|||+|||....=.+.. +..++.++.++.-  ++.=..++.+.+
T Consensus        12 i~lvGptGvGKTTTiAKLA~~-~~~~g~kV~lit~Dt~R~gA~eQL~~~   59 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLARQ-FEQQGKSVMLAAGDTFRAAAVEQLQVW   59 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH-HHTTTCCEEEECCCTTCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH-HHHCCCcEEEEecccccccchhhhhhh
Confidence            467999999999665443433 4455667766653  343333444443

>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=95.14  E-value=0.0058  Score=38.15  Aligned_cols=22  Identities=23%  Similarity=0.211  Sum_probs=17.9

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +++++.+|+|+|||..+-..+-
T Consensus         8 K~I~i~G~~GsGKTTla~~La~   29 (192)
T d1lw7a2           8 KTVAILGGESSGKSVLVNKLAA   29 (192)
T ss_dssp             EEEEEECCTTSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5789999999999988855433

>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=95.08  E-value=0.006  Score=40.81  Aligned_cols=20  Identities=20%  Similarity=0.245  Sum_probs=16.6

Q ss_pred             ccEEEEccCCcchHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~   24 (138)
                      +.+++.+|+|+|||..+-..
T Consensus        33 ~~ilL~GpPGtGKT~la~~l   52 (273)
T d1gvnb_          33 TAFLLGGQPGSGKTSLRSAI   52 (273)
T ss_dssp             EEEEEECCTTSCTHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHH
Confidence            45899999999999987443

>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=95.02  E-value=0.0055  Score=37.44  Aligned_cols=16  Identities=13%  Similarity=-0.014  Sum_probs=14.0

Q ss_pred             EEEEccCCcchHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGE   22 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~   22 (138)
                      +++++|+|||||..+-
T Consensus         5 Iii~G~pGsGKTTla~   20 (152)
T d1ly1a_           5 ILTIGCPGSGKSTWAR   20 (152)
T ss_dssp             EEEECCTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6789999999998764

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=94.92  E-value=0.047  Score=39.47  Aligned_cols=52  Identities=23%  Similarity=0.188  Sum_probs=41.1

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhc
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEF  130 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~  130 (138)
                      ++..+..-||+||+++..-.+ +.   .++++++|+|...+|.|.+++++.++.+.
T Consensus        32 ~~q~l~GltGS~ka~~iA~l~-~~---~~rp~LVVt~n~~~A~qL~~dL~~~l~~~   83 (413)
T d1t5la1          32 KHQTLLGATGTGKTFTISNVI-AQ---VNKPTLVIAHNKTLAGQLYSELKEFFPHN   83 (413)
T ss_dssp             SEEEEEECTTSCHHHHHHHHH-HH---HTCCEEEECSSHHHHHHHHHHHHHHCTTS
T ss_pred             CcEEEeCCCCcHHHHHHHHHH-HH---hCCCEEEEeCCHHHHHHHHHHHHHHcCCC
Confidence            567788889999997663222 22   36789999999999999999999997553

>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=94.88  E-value=0.021  Score=35.17  Aligned_cols=33  Identities=21%  Similarity=0.096  Sum_probs=23.8

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      +.++++.|||||..+...+. ++.+++.++.++.
T Consensus         5 i~itG~~GSGKTTL~~~L~~-~l~~~g~~v~v~~   37 (170)
T d1np6a_           5 LAFAAWSGTGKTTLLKKLIP-ALCARGIRPGLIK   37 (170)
T ss_dssp             EEEECCTTSCHHHHHHHHHH-HHHHTTCCEEEEE
T ss_pred             EEEEcCCCCCHHHHHHHHHH-HHHHCCCeEEEec
Confidence            57899999999988755544 3555677776654

>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=94.74  E-value=0.012  Score=36.31  Aligned_cols=20  Identities=20%  Similarity=0.247  Sum_probs=16.3

Q ss_pred             cEEEEccCCcchHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~   25 (138)
                      -+++.+|.|||||.++-..+
T Consensus         4 lI~i~G~~GsGKTTva~~L~   23 (176)
T d2bdta1           4 LYIITGPAGVGKSTTCKRLA   23 (176)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            46899999999999985443

>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=94.73  E-value=0.016  Score=37.72  Aligned_cols=27  Identities=11%  Similarity=-0.054  Sum_probs=22.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKEL   29 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~   29 (138)
                      .|+-+++.+|+|+|||.++...+...+
T Consensus        33 ~G~l~~i~G~~G~GKT~~~l~~a~~~~   59 (258)
T d2i1qa2          33 SQSVTEFAGVFGSGKTQIMHQSCVNLQ   59 (258)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            466789999999999999988777644

>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=94.70  E-value=0.0095  Score=39.16  Aligned_cols=22  Identities=23%  Similarity=0.211  Sum_probs=18.1

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (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            4689999999999988865544

>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=94.69  E-value=0.074  Score=37.61  Aligned_cols=66  Identities=15%  Similarity=0.052  Sum_probs=44.9

Q ss_pred             hhhhhhHHHhhhhc-cceEEEeecCCCchHhHHH--HHHHHHH-hCCCeEEEEccchhHHHHHHHHHHHH
Q psy2029          61 KFYLEGKCLEMIQN-KNCVLSIPTSGGKTLVGEI--LIMKELK-IKQKSAIFILPYISLVHEKYQSLAKA  126 (138)
Q Consensus        61 ~~~~Q~~~~~~~~~-~~~ii~~ptg~GKt~~~~~--~~l~~~~-~~~~~~~~i~P~~~l~~q~~~~~~~~  126 (138)
                      ..++|..++..... +-.+++-|.|+|||.....  ..+.... ..+.+++..+||-.-+....+.....
T Consensus       149 ~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~~~~  218 (359)
T d1w36d1         149 EINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGKA  218 (359)
T ss_dssp             SCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHTHH
T ss_pred             cccHHHHHHHHHHcCCeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHHHHHHHHHHHHHH
Confidence            45678888865555 7778999999999977532  2222222 24568999999987776666655543

>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=94.67  E-value=0.051  Score=37.10  Aligned_cols=52  Identities=27%  Similarity=0.318  Sum_probs=35.6

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhc-------CCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIK-------QKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~-------~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      +..+++.=..|.|||+.+...+.. +...       ..++|+++|.. |..|=.+++.++.
T Consensus        79 ~~g~iLaDemGlGKT~qaia~l~~-l~~~~~~~~~~~~~~LIV~P~s-l~~qW~~Ei~k~~  137 (298)
T d1z3ix2          79 SYGCIMADEMGLGKTLQCITLIWT-LLKQSPDCKPEIDKVIVVSPSS-LVRNWYNEVGKWL  137 (298)
T ss_dssp             CCEEEECCCTTSCHHHHHHHHHHH-HHHCCTTSSCSCSCEEEEECHH-HHHHHHHHHHHHH
T ss_pred             CCceEEEeCCCCCHHHHHHHHHHH-HHHhcccccCCCCcEEEEccch-hhHHHHHHHHhhc
Confidence            456788888999999876443333 3321       23689999975 6677778887764

>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=94.62  E-value=0.012  Score=38.55  Aligned_cols=23  Identities=22%  Similarity=0.138  Sum_probs=18.3

Q ss_pred             ccEEEEccCCcchHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      .++++++|+|+|||..+-..+.+
T Consensus        34 ~~lll~Gp~G~GKTtl~~~i~~~   56 (237)
T d1sxjd2          34 PHMLFYGPPGTGKTSTILALTKE   56 (237)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEEEECCCCCChHHHHHHHHHH
Confidence            35899999999999887665543

>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=94.62  E-value=0.014  Score=36.20  Aligned_cols=24  Identities=21%  Similarity=0.188  Sum_probs=19.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +|..++++++.|||||.++-..+.
T Consensus         5 ~g~~I~l~G~~GsGKTTia~~La~   28 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIARALQV   28 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            566788999999999999855543

>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=94.58  E-value=0.013  Score=38.86  Aligned_cols=22  Identities=23%  Similarity=0.312  Sum_probs=18.0

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .++++++|.|+|||..+-..+.
T Consensus        53 ~~lll~GPpG~GKTt~a~~la~   74 (253)
T d1sxja2          53 RAAMLYGPPGIGKTTAAHLVAQ   74 (253)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHH
Confidence            4689999999999988865544

>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=94.57  E-value=0.045  Score=38.79  Aligned_cols=51  Identities=16%  Similarity=0.047  Sum_probs=33.0

Q ss_pred             CCccEEEEccCCcchHHHHHH--HHHHHHhh-cCCeEEEEcchhhhHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEI--LIMKELKI-KQKSAIFILPYISLVHEKYQSL   53 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~--~~~~~~~~-~~~~~l~v~P~~aL~~q~~~~l   53 (138)
                      .++-+++++|.|+|||.....  ..+....+ ++.+++...|+-.-.....+.+
T Consensus       162 ~~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~  215 (359)
T d1w36d1         162 TRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESL  215 (359)
T ss_dssp             TBSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHH
T ss_pred             cCCeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHHHHHHHHHHH
Confidence            456779999999999976422  22322222 4568999999876554444433

>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=94.50  E-value=0.013  Score=36.57  Aligned_cols=23  Identities=26%  Similarity=0.228  Sum_probs=18.6

Q ss_pred             ccEEEEccCCcchHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      +|+++.+|.|||||.++-..+-.
T Consensus         1 k~I~liG~~GsGKsTi~k~La~~   23 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTLARALAKD   23 (161)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHHH
Confidence            57899999999999998655443

>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=94.49  E-value=0.031  Score=37.99  Aligned_cols=44  Identities=23%  Similarity=0.190  Sum_probs=32.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVH   47 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~   47 (138)
                      .|.-+.+.+|.|+|||..++..+..... ++.+++|+----++..
T Consensus        53 ~g~itei~G~~gsGKTtl~l~~~~~~q~-~g~~~vyidtE~~~~~   96 (263)
T d1u94a1          53 MGRIVEIYGPESSGKTTLTLQVIAAAQR-EGKTCAFIDAEHALDP   96 (263)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHH-TTCCEEEEESSCCCCH
T ss_pred             CceEEEEecCCCcHHHHHHHHHHHHHHc-CCCEEEEEccccccCH
Confidence            3566789999999999999887776544 5788888764434433

>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=94.39  E-value=0.045  Score=37.31  Aligned_cols=46  Identities=22%  Similarity=0.130  Sum_probs=34.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEK   49 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~   49 (138)
                      .|+-..+.+|.|+|||..++..+.... ..+++++|+-.-.++..+.
T Consensus        59 ~g~i~e~~G~~~~GKT~l~l~~~~~~q-~~g~~~vyIDtE~~~~~e~  104 (269)
T d1mo6a1          59 RGRVIEIYGPESSGKTTVALHAVANAQ-AAGGVAAFIDAEHALDPDY  104 (269)
T ss_dssp             SSSEEEEECSSSSSHHHHHHHHHHHHH-HTTCEEEEEESSCCCCHHH
T ss_pred             cceeEEEecCCCcHHHHHHHHHHHHHh-cCCCEEEEEECCccCCHHH
Confidence            456678999999999999977766544 4588999987655555443

>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=94.30  E-value=0.3  Score=30.05  Aligned_cols=22  Identities=23%  Similarity=0.164  Sum_probs=18.1

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +.+++.+|.|||||.++-..+-
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~   24 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELAR   24 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHH
Confidence            4678899999999999866654

>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=94.28  E-value=0.016  Score=37.85  Aligned_cols=22  Identities=23%  Similarity=0.150  Sum_probs=18.0

Q ss_pred             cEEEEccCCcchHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~   27 (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            5899999999999887665543

>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=94.24  E-value=0.017  Score=37.81  Aligned_cols=22  Identities=23%  Similarity=0.102  Sum_probs=18.2

Q ss_pred             cEEEEccCCcchHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      ++++++|.|+|||.++...+.+
T Consensus        38 ~~ll~Gp~G~GKTt~a~~la~~   59 (224)
T d1sxjb2          38 HMIISGMPGIGKTTSVHCLAHE   59 (224)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCchhhHHHHHHH
Confidence            6899999999999988665543

>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=94.23  E-value=0.017  Score=36.73  Aligned_cols=24  Identities=25%  Similarity=0.224  Sum_probs=19.7

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +|..+++.+|.|||||..+...+-
T Consensus         2 ~~~riil~G~pGSGKsT~a~~La~   25 (190)
T d1ak2a1           2 KGVRAVLLGPPGAGKGTQAPKLAK   25 (190)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CccEEEEECCCCCCHHHHHHHHHH
Confidence            467889999999999999865543

>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=94.08  E-value=0.042  Score=37.42  Aligned_cols=45  Identities=20%  Similarity=0.188  Sum_probs=33.2

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHE   48 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q   48 (138)
                      .|+-+.+.+|.|+|||..++..+.... ..+++++|+-.-.++..+
T Consensus        56 ~g~itei~G~~~sGKT~l~l~~~~~aq-k~g~~v~yiDtE~~~~~~  100 (268)
T d1xp8a1          56 RGRITEIYGPESGGKTTLALAIVAQAQ-KAGGTCAFIDAEHALDPV  100 (268)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHH-HTTCCEEEEESSCCCCHH
T ss_pred             CceEEEEecCCccchHHHHHHHHHHHH-hCCCEEEEEECCccCCHH
Confidence            355678999999999999977776644 457889998654455444

>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=93.82  E-value=0.023  Score=38.45  Aligned_cols=23  Identities=26%  Similarity=0.413  Sum_probs=18.9

Q ss_pred             ccEEEEccCCcchHHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      +.+++.+|.|+|||.++-..+..
T Consensus        46 ~~iLL~GppGtGKT~la~~iA~~   68 (256)
T d1lv7a_          46 KGVLMVGPPGTGKTLLAKAIAGE   68 (256)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CeEEeeCCCCCCccHHHHHHHHH
Confidence            56899999999999998666543

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=93.78  E-value=0.058  Score=38.45  Aligned_cols=41  Identities=10%  Similarity=0.143  Sum_probs=32.2

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLV  116 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~  116 (138)
                      +++++..+||+|||... ..++.++...+..++++.|--++.
T Consensus        51 ~H~~I~G~tGsGKT~~l-~~li~~~~~~g~~~iiiD~kge~~   91 (433)
T d1e9ra_          51 RHLLVNGATGTGKSVLL-RELAYTGLLRGDRMVIVDPNGDML   91 (433)
T ss_dssp             GCEEEEECTTSSHHHHH-HHHHHHHHHTTCEEEEEEETTHHH
T ss_pred             ceEEEEeCCCCcHHHHH-HHHHHHHHhCCCCEEEEeCChhHH
Confidence            89999999999999764 445555666678899999987654

>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=93.74  E-value=0.03  Score=34.44  Aligned_cols=23  Identities=22%  Similarity=0.206  Sum_probs=17.8

Q ss_pred             CCccEEEEccCCcchHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      ..+=+++++|.|||||.++-..+
T Consensus         2 ~~kiI~l~G~~GsGKsTva~~L~   24 (178)
T d1qhxa_           2 TTRMIILNGGSSAGKSGIVRCLQ   24 (178)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHH
Confidence            34557889999999999885543

>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=93.62  E-value=0.02  Score=37.80  Aligned_cols=22  Identities=23%  Similarity=0.191  Sum_probs=17.8

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .++++++|.|+|||.++-..+.
T Consensus        34 ~~lll~Gp~G~GKTt~~~~la~   55 (252)
T d1sxje2          34 PHLLLYGPNGTGKKTRCMALLE   55 (252)
T ss_dssp             CCEEEECSTTSSHHHHHHTHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            3689999999999998855544

>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=93.54  E-value=0.026  Score=34.79  Aligned_cols=22  Identities=23%  Similarity=0.199  Sum_probs=17.3

Q ss_pred             CccEEEEccCCcchHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~   25 (138)
                      ++-+++++|.|||||.++-..+
T Consensus         6 ~~iivl~G~~GsGKsT~a~~La   27 (171)
T d1knqa_           6 HHIYVLMGVSGSGKSAVASEVA   27 (171)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHH
Confidence            3456889999999999985543

>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=93.47  E-value=0.054  Score=36.36  Aligned_cols=33  Identities=21%  Similarity=0.243  Sum_probs=23.0

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      +.+++.+|.|+|||..+...+..    .+...+++.+
T Consensus        39 ~giLL~GppGtGKT~l~~ala~~----~~~~~~~i~~   71 (258)
T d1e32a2          39 RGILLYGPPGTGKTLIARAVANE----TGAFFFLING   71 (258)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH----TTCEEEEECH
T ss_pred             ceeEEecCCCCCchHHHHHHHHH----hCCeEEEEEc
Confidence            56899999999999987544443    3445555544

>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=93.42  E-value=0.025  Score=37.97  Aligned_cols=33  Identities=21%  Similarity=0.148  Sum_probs=23.5

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcc
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP   41 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P   41 (138)
                      +.+++.+|.|+|||.++-..+-.    -+...+++-+
T Consensus        43 ~giLl~GppGtGKT~la~aia~~----~~~~~~~i~~   75 (247)
T d1ixza_          43 KGVLLVGPPGVGKTHLARAVAGE----ARVPFITASG   75 (247)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHH----TTCCEEEEEH
T ss_pred             ceEEEecCCCCChhHHHHHHHHH----cCCCEEEEEh
Confidence            46899999999999998665543    2445555543

>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=93.30  E-value=0.036  Score=36.07  Aligned_cols=21  Identities=24%  Similarity=0.373  Sum_probs=17.7

Q ss_pred             CCccEEEEccCCcchHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      +|.-+++++|+|+|||.+.-.
T Consensus         1 ~G~livi~GPSG~GK~tl~~~   21 (205)
T d1s96a_           1 QGTLYIVSAPSGAGKSSLIQA   21 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHH
Confidence            477789999999999988743

>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=93.28  E-value=0.021  Score=36.05  Aligned_cols=23  Identities=26%  Similarity=0.117  Sum_probs=18.0

Q ss_pred             CccEEEEccCCcchHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      |..++++++.|||||.++-..+.
T Consensus        19 g~vI~L~G~pGSGKTTiAk~La~   41 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSMALEE   41 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            44567899999999999865544

>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=93.24  E-value=0.031  Score=35.27  Aligned_cols=21  Identities=38%  Similarity=0.419  Sum_probs=17.3

Q ss_pred             CccEEEEccCCcchHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      |+=+++++|.|+|||.++...
T Consensus         2 G~iivl~GpsG~GK~tl~~~L   22 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTVVRCL   22 (182)
T ss_dssp             CCEEEEECSTTSSHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHH
Confidence            566899999999999886443

>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=93.08  E-value=0.028  Score=39.05  Aligned_cols=21  Identities=33%  Similarity=0.264  Sum_probs=17.4

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ++++++|||+|||..+-..+.
T Consensus        54 ~~lf~Gp~GvGKT~lak~la~   74 (315)
T d1r6bx3          54 SFLFAGPTGVGKTEVTVQLSK   74 (315)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCcchhHHHHHHHHh
Confidence            689999999999998865443

>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=93.00  E-value=0.037  Score=35.03  Aligned_cols=21  Identities=19%  Similarity=0.243  Sum_probs=17.2

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .+++.+|.|||||..+...+-
T Consensus         5 ~I~i~GppGsGKsT~a~~La~   25 (189)
T d1zaka1           5 KVMISGAPASGKGTQCELIKT   25 (189)
T ss_dssp             CEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            578999999999999865443

>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=92.98  E-value=0.038  Score=35.12  Aligned_cols=19  Identities=32%  Similarity=0.366  Sum_probs=15.8

Q ss_pred             cEEEEccCCcchHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~   24 (138)
                      -+++++|+|+|||.+.-..
T Consensus         3 pIvl~GpsG~GK~tl~~~L   21 (186)
T d1gkya_           3 PIVISGPSGTGKSTLLKKL   21 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHH
Confidence            4789999999999877544

>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=92.96  E-value=0.065  Score=33.09  Aligned_cols=34  Identities=15%  Similarity=0.139  Sum_probs=22.2

Q ss_pred             ccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      +-+++.+|.|||||..+...+- ++..++.++..+
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~-~l~~~~~~~~~~   35 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMD-NLRKEGVNYKMV   35 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH-HHHTTTCCCEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHH-HHHHcCCCeEEE
Confidence            4578899999999988754433 344444444443

>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=92.89  E-value=0.042  Score=37.15  Aligned_cols=33  Identities=27%  Similarity=0.296  Sum_probs=23.1

Q ss_pred             CccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      .+.+++++|.|+|||..+...+..    -+...+++.
T Consensus        41 ~~giLL~Gp~GtGKT~l~~ala~~----~~~~~~~~~   73 (265)
T d1r7ra3          41 SKGVLFYGPPGCGKTLLAKAIANE----CQANFISIK   73 (265)
T ss_dssp             CCEEEEBCCTTSSHHHHHHHHHHH----TTCEEEEEC
T ss_pred             CCeEEEECCCCCcchhHHHHHHHH----hCCcEEEEE
Confidence            357899999999999998655443    244445544

>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=92.84  E-value=0.026  Score=35.69  Aligned_cols=15  Identities=20%  Similarity=-0.009  Sum_probs=13.4

Q ss_pred             EEEEccCCcchHHHH
Q psy2029           7 CVLSIPTSGGKTLVG   21 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~   21 (138)
                      ++++++.|||||..+
T Consensus        17 iil~G~pGsGKST~a   31 (172)
T d1yj5a2          17 VVAVGFPGAGKSTFI   31 (172)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            589999999999876

>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=92.74  E-value=0.038  Score=39.24  Aligned_cols=24  Identities=21%  Similarity=0.379  Sum_probs=19.5

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +.+++++.+|.|+|||..+...+-
T Consensus       153 ~~~~~~~~g~~~~gk~~~~~~~~~  176 (362)
T d1svma_         153 KKRYWLFKGPIDSGKTTLAAALLE  176 (362)
T ss_dssp             TCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CcCeEEEECCCCCCHHHHHHHHHH
Confidence            456889999999999999865544

>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=92.66  E-value=0.039  Score=34.24  Aligned_cols=18  Identities=17%  Similarity=0.148  Sum_probs=15.0

Q ss_pred             cEEEEccCCcchHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~   23 (138)
                      .+++.+|.|+|||...-.
T Consensus         2 ki~I~G~~G~GKSTLl~~   19 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLVKK   19 (178)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             EEEEECCCCcHHHHHHHH
Confidence            578999999999987533

>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=92.58  E-value=0.16  Score=32.98  Aligned_cols=59  Identities=17%  Similarity=0.205  Sum_probs=36.0

Q ss_pred             hhccce-EEEeecCCCchHhHHHHHHHHHHhCCCeEEEEcc--chhHHHHHHHHHHHHhhhcCcee
Q psy2029          72 IQNKNC-VLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP--YISLVHEKYQSLAKAAEEFKFYL  134 (138)
Q Consensus        72 ~~~~~~-ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P--~~~l~~q~~~~~~~~~~~~~~~v  134 (138)
                      ..++++ ++.-|+|.|||....-.+.+ +..++.++.++..  +|.-+.++.+.+.+.   +|+.+
T Consensus         7 ~~~~~vi~lvGp~GvGKTTTiaKLA~~-~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~---l~v~~   68 (207)
T d1ls1a2           7 LKDRNLWFLVGLQGSGKTTTAAKLALY-YKGKGRRPLLVAADTQRPAAREQLRLLGEK---VGVPV   68 (207)
T ss_dssp             CCSSEEEEEECCTTTTHHHHHHHHHHH-HHHTTCCEEEEECCSSCHHHHHHHHHHHHH---HTCCE
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHH-HHHCCCcEEEEecccccchHHHHHHHHHHh---cCCcc
Confidence            344555 56899999998877665544 3444566655544  666665555555444   55544

>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=92.54  E-value=0.19  Score=33.39  Aligned_cols=42  Identities=7%  Similarity=-0.087  Sum_probs=31.2

Q ss_pred             hhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccc
Q psy2029          71 MIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPY  112 (138)
Q Consensus        71 ~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~  112 (138)
                      .+.. .-+++..++|.|||..+.-.+.+.+...+.+++|+..-
T Consensus        31 G~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s~E   73 (277)
T d1cr2a_          31 GARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLE   73 (277)
T ss_dssp             SBCTTCEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEESS
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEeeec
Confidence            3444 56679999999999888776666555567888888754

>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=92.50  E-value=0.026  Score=37.51  Aligned_cols=20  Identities=15%  Similarity=-0.019  Sum_probs=15.6

Q ss_pred             EEEEccCCcchHHHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +++++|+|+|||.++-..+-
T Consensus        49 l~l~GppGtGKT~l~~~l~~   68 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLAKFTVK   68 (287)
T ss_dssp             EECTTCCSSSHHHHHHHHHH
T ss_pred             EEeECCCCCCHHHHHHHHHH
Confidence            45679999999998855544

>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=92.37  E-value=0.044  Score=34.18  Aligned_cols=21  Identities=29%  Similarity=0.249  Sum_probs=17.2

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ++++.+|.|||||..+...+-
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~   22 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAEKIVA   22 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            578999999999999865443

>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=92.30  E-value=0.045  Score=34.37  Aligned_cols=18  Identities=22%  Similarity=0.176  Sum_probs=14.8

Q ss_pred             EEEccCCcchHHHHHHHH
Q psy2029           8 VLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~~~   25 (138)
                      -|++|+|||||.++-...
T Consensus        26 gI~G~~GSGKSTla~~L~   43 (198)
T d1rz3a_          26 GIDGLSRSGKTTLANQLS   43 (198)
T ss_dssp             EEEECTTSSHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHH
Confidence            389999999999885543

>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=92.18  E-value=0.048  Score=34.15  Aligned_cols=20  Identities=15%  Similarity=0.235  Sum_probs=16.8

Q ss_pred             cEEEEccCCcchHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILI   25 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~   25 (138)
                      ++++.+|.|||||..+...+
T Consensus         2 ~I~i~G~pGSGKsT~~~~La   21 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIM   21 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            57889999999999985554

>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=92.05  E-value=0.064  Score=34.19  Aligned_cols=18  Identities=39%  Similarity=0.475  Sum_probs=15.1

Q ss_pred             EEEEccCCcchHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~   24 (138)
                      +++++|+|+|||.++-..
T Consensus         3 Ivl~GPsGsGK~tl~~~L   20 (190)
T d1lvga_           3 VVLSGPSGAGKSTLLKKL   20 (190)
T ss_dssp             EEEECCTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            689999999999987443

>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=91.89  E-value=0.35  Score=31.50  Aligned_cols=54  Identities=15%  Similarity=0.019  Sum_probs=32.4

Q ss_pred             eEEEeecCCCchHhHHHHHHHHHHhCCCeEEEE--ccchhHHHHHHHHHHHHhhhcCcee
Q psy2029          77 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI--LPYISLVHEKYQSLAKAAEEFKFYL  134 (138)
Q Consensus        77 ~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i--~P~~~l~~q~~~~~~~~~~~~~~~v  134 (138)
                      ++++-|||.|||....=.+.+. ..++.++.++  ..+|.=+.++.+.+.   +.+|+.+
T Consensus        14 i~lvGptGvGKTTTiAKLAa~~-~~~~~kV~lit~Dt~R~gA~eQL~~~a---~~l~i~~   69 (213)
T d1vmaa2          14 IMVVGVNGTGKTTSCGKLAKMF-VDEGKSVVLAAADTFRAAAIEQLKIWG---ERVGATV   69 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH-HHTTCCEEEEEECTTCHHHHHHHHHHH---HHHTCEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHH-HHCCCceEEEeecccccchhHHHHHHh---hhcCccc
Confidence            4578999999998876555443 4445554333  336666655555544   4455554

>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=91.84  E-value=0.056  Score=33.95  Aligned_cols=22  Identities=27%  Similarity=0.255  Sum_probs=17.7

Q ss_pred             cEEEEccCCcchHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      ++++.+|.|||||..+...+-.
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~   23 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEK   23 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999998655543

>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=91.81  E-value=0.068  Score=33.04  Aligned_cols=22  Identities=27%  Similarity=0.318  Sum_probs=17.7

Q ss_pred             cEEEEccCCcchHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      ++++.++.|+|||.++-..+-.
T Consensus         3 ~IvliG~~G~GKSTig~~La~~   24 (165)
T d2iyva1           3 KAVLVGLPGSGKSTIGRRLAKA   24 (165)
T ss_dssp             SEEEECSTTSSHHHHHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHHHHHH
Confidence            5778899999999998666543

>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=91.74  E-value=0.058  Score=33.79  Aligned_cols=21  Identities=24%  Similarity=0.188  Sum_probs=17.6

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ++++.+|.|||||..+...+-
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~   22 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAE   22 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            678999999999999866543

>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=91.66  E-value=0.31  Score=31.74  Aligned_cols=55  Identities=13%  Similarity=0.045  Sum_probs=33.4

Q ss_pred             eEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEcc--chhHHHHHHHHHHHHhhhcCceee
Q psy2029          77 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP--YISLVHEKYQSLAKAAEEFKFYLE  135 (138)
Q Consensus        77 ~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P--~~~l~~q~~~~~~~~~~~~~~~v~  135 (138)
                      +.+.-|||.|||....=.+.+ +...+.++.++.-  +|.=+.   ++++.|++..|+.+.
T Consensus        12 i~lvGptGvGKTTTiAKLA~~-~~~~g~kV~lit~Dt~R~gA~---eQL~~~a~~l~v~~~   68 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLARQ-FEQQGKSVMLAAGDTFRAAAV---EQLQVWGQRNNIPVI   68 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH-HHTTTCCEEEECCCTTCHHHH---HHHHHHHHHTTCCEE
T ss_pred             EEEECCCCCCHHHHHHHHHHH-HHHCCCcEEEEecccccccch---hhhhhhhhhcCCccc
Confidence            347899999999887665543 4444555555443  344444   455555555666654

>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=91.65  E-value=0.047  Score=37.93  Aligned_cols=21  Identities=29%  Similarity=0.309  Sum_probs=17.3

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ++++++|||+|||..+-..+.
T Consensus        55 ~~lf~Gp~G~GKt~lak~la~   75 (315)
T d1qvra3          55 SFLFLGPTGVGKTELAKTLAA   75 (315)
T ss_dssp             EEEEBSCSSSSHHHHHHHHHH
T ss_pred             EEEEECCCcchHHHHHHHHHH
Confidence            568999999999999865544

>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=91.65  E-value=0.099  Score=32.04  Aligned_cols=28  Identities=25%  Similarity=0.216  Sum_probs=21.1

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCC
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQ  103 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~  103 (138)
                      ++++++-|.|+|||..+. .+++.+...+
T Consensus         2 k~v~ItG~~GtGKTtl~~-~i~~~l~~~~   29 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIH-KASEVLKSSG   29 (189)
T ss_dssp             CCEEEESCCSSCHHHHHH-HHHHHHHHTT
T ss_pred             cEEEEECCCCCcHHHHHH-HHHHHHHHCC
Confidence            578999999999999774 4556665543

>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=91.55  E-value=0.062  Score=34.12  Aligned_cols=21  Identities=19%  Similarity=0.042  Sum_probs=16.6

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      -+++.+|.|||||..+...+-
T Consensus        10 iI~i~GppGSGKsT~a~~La~   30 (196)
T d1ukza_          10 VIFVLGGPGAGKGTQCEKLVK   30 (196)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            457889999999998865544

>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=91.53  E-value=0.062  Score=34.02  Aligned_cols=21  Identities=10%  Similarity=-0.034  Sum_probs=16.8

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      -+++.+|.|||||.++...+-
T Consensus         8 iI~i~G~pGSGKsT~a~~La~   28 (194)
T d1qf9a_           8 VVFVLGGPGSGKGTQCANIVR   28 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            468899999999998855543

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=91.50  E-value=0.036  Score=40.45  Aligned_cols=19  Identities=37%  Similarity=0.396  Sum_probs=17.3

Q ss_pred             cceEEEeecCCCchHhHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEI   93 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~   93 (138)
                      +|+++.-|||+|||+.+--
T Consensus        50 sNILliGPTGvGKTlLAr~   68 (443)
T d1g41a_          50 KNILMIGPTGVGKTEIARR   68 (443)
T ss_dssp             CCEEEECCTTSSHHHHHHH
T ss_pred             ccEEEECCCCCCHHHHHHH
Confidence            8999999999999999853

>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=91.48  E-value=0.074  Score=35.04  Aligned_cols=21  Identities=24%  Similarity=0.264  Sum_probs=17.2

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .+++++|.|+|||..+...+.
T Consensus        36 ~~Ll~Gp~G~GKtt~a~~~~~   56 (239)
T d1njfa_          36 AYLFSGTRGVGKTSIARLLAK   56 (239)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEECCCCCcHHHHHHHHHH
Confidence            479999999999998865444

>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=91.42  E-value=0.047  Score=35.21  Aligned_cols=16  Identities=31%  Similarity=0.150  Sum_probs=13.3

Q ss_pred             EEEccCCcchHHHHHH
Q psy2029           8 VLSIPTSGGKTLVGEI   23 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~   23 (138)
                      -+.+|+|||||.++-.
T Consensus         6 gI~G~~gSGKSTla~~   21 (213)
T d1uj2a_           6 GVSGGTASGKSSVCAK   21 (213)
T ss_dssp             EEECSTTSSHHHHHHH
T ss_pred             EEECCCCCCHHHHHHH
Confidence            4789999999988743

>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=91.32  E-value=0.13  Score=33.02  Aligned_cols=38  Identities=16%  Similarity=0.223  Sum_probs=28.7

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccc
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPY  112 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~  112 (138)
                      .-.++..++|+|||..+.-.+...+...+.+.+|+..-
T Consensus        27 ~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s~e   64 (242)
T d1tf7a1          27 RSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFE   64 (242)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEESS
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCccccccc
Confidence            56679999999999998766666565556677887653

>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=91.27  E-value=0.17  Score=32.79  Aligned_cols=38  Identities=13%  Similarity=0.046  Sum_probs=23.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      +|.-+.+++..|||||.++......-....+..++++-
T Consensus        23 kg~vIwltGlsGsGKTTia~~L~~~l~~~~~~~~~~ld   60 (208)
T d1m7ga_          23 RGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLD   60 (208)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHhcCceEEEEc
Confidence            35567899999999998885444332222344455443

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

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: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=91.26  E-value=0.031  Score=38.82  Aligned_cols=22  Identities=14%  Similarity=0.012  Sum_probs=18.5

Q ss_pred             CCccEEEEccCCcchHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      .++++++.+|.|+|||..+-..
T Consensus        27 ~~h~vLl~G~pG~GKT~lar~~   48 (333)
T d1g8pa_          27 GIGGVLVFGDRGTGKSTAVRAL   48 (333)
T ss_dssp             GGCCEEEECCGGGCTTHHHHHH
T ss_pred             CCCeEEEECCCCccHHHHHHHH
Confidence            4579999999999999887443

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=91.26  E-value=0.068  Score=34.10  Aligned_cols=25  Identities=24%  Similarity=0.101  Sum_probs=19.9

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +.|.-+++++|.|+|||..+...+.
T Consensus        13 ~~g~gvli~G~sG~GKS~lal~l~~   37 (177)
T d1knxa2          13 VFGVGVLLTGRSGIGKSECALDLIN   37 (177)
T ss_dssp             ETTEEEEEEESSSSSHHHHHHHHHT
T ss_pred             ECCEEEEEEcCCCCCHHHHHHHHHH
Confidence            3677899999999999987755443

>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=91.10  E-value=0.17  Score=31.21  Aligned_cols=33  Identities=15%  Similarity=0.005  Sum_probs=21.5

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      +++.++.|+|||..+-..+ ..+..++.++..+.
T Consensus         4 ivi~G~~GsGKTT~~~~La-~~L~~~~~~~~~~~   36 (194)
T d1nksa_           4 GIVTGIPGVGKSTVLAKVK-EILDNQGINNKIIN   36 (194)
T ss_dssp             EEEEECTTSCHHHHHHHHH-HHHHTTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHH-HHHHHcCCCEEEEE
Confidence            4679999999998875443 23444455555443

>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=91.05  E-value=0.18  Score=30.92  Aligned_cols=31  Identities=13%  Similarity=-0.081  Sum_probs=21.4

Q ss_pred             EEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           8 VLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      -|+++.|||||......+- +|.+++.++-++
T Consensus         5 ~I~G~~gSGKTTli~~l~~-~L~~~g~~v~vi   35 (165)
T d1xjca_           5 QVVGYKHSGKTTLMEKWVA-AAVREGWRVGTV   35 (165)
T ss_dssp             EEECCTTSSHHHHHHHHHH-HHHHTTCCEEEE
T ss_pred             EEEeCCCCCHHHHHHHHHH-HHHhCCCeEEEE
Confidence            4899999999987644333 355566666554

>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=90.94  E-value=0.057  Score=34.22  Aligned_cols=18  Identities=22%  Similarity=0.191  Sum_probs=15.3

Q ss_pred             ccEEEEccCCcchHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGE   22 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~   22 (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            457899999999998864

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {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: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=90.88  E-value=0.069  Score=35.70  Aligned_cols=20  Identities=15%  Similarity=0.092  Sum_probs=17.2

Q ss_pred             CCCccEEEEccCCcchHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVG   21 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~   21 (138)
                      -.|+.+.+.+|+|||||...
T Consensus        27 ~~Ge~vaIvG~sGsGKSTLl   46 (241)
T d2pmka1          27 KQGEVIGIVGRSGSGKSTLT   46 (241)
T ss_dssp             ETTCEEEEECSTTSSHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHH
Confidence            35788999999999999765

>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=90.86  E-value=0.091  Score=33.29  Aligned_cols=24  Identities=17%  Similarity=0.109  Sum_probs=18.4

Q ss_pred             CCccEEEEccCCcchHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +..-+++.+|.|||||..+...+-
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~~La~   30 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCEKIVQ   30 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            345678999999999998865433

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC 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: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.57  E-value=0.074  Score=35.76  Aligned_cols=21  Identities=24%  Similarity=0.289  Sum_probs=17.8

Q ss_pred             CCCccEEEEccCCcchHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGE   22 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~   22 (138)
                      -.|+.+.+.+|+|||||...-
T Consensus        38 ~~Ge~vaivG~sGsGKSTLl~   58 (251)
T d1jj7a_          38 RPGEVTALVGPNGSGKSTVAA   58 (251)
T ss_dssp             CTTCEEEEECSTTSSHHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHHH
Confidence            367889999999999997763

>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=90.53  E-value=0.45  Score=30.92  Aligned_cols=54  Identities=15%  Similarity=0.065  Sum_probs=28.1

Q ss_pred             eEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEcc--chhHHHHHHHHHHHHhhhcCcee
Q psy2029          77 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP--YISLVHEKYQSLAKAAEEFKFYL  134 (138)
Q Consensus        77 ~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P--~~~l~~q~~~~~~~~~~~~~~~v  134 (138)
                      +.+.-|||.|||....=.+.+ +...+.++.++.-  +|.=+.++.   +.++...|+.+
T Consensus        15 i~lvGptGvGKTTTiAKLA~~-~~~~g~kV~lit~Dt~R~ga~eQL---~~~a~~l~v~~   70 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLAYF-YKKKGFKVGLVGADVYRPAALEQL---QQLGQQIGVPV   70 (211)
T ss_dssp             EEEECSCCC----HHHHHHHH-HHHTTCCEEEEECCCSSHHHHHHH---HHHHHHHTCCE
T ss_pred             EEEECCCCCCHHHHHHHHHHH-HHHCCCceEEEEeeccccchhHHH---HHhccccCcce
Confidence            346899999999887655543 4444555444433  455555544   44444455554

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=90.50  E-value=0.069  Score=35.95  Aligned_cols=22  Identities=18%  Similarity=0.285  Sum_probs=18.1

Q ss_pred             CCCccEEEEccCCcchHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      -.|+.+.+.+|+|||||...-+
T Consensus        39 ~~Ge~iaivG~sGsGKSTLl~l   60 (253)
T d3b60a1          39 PAGKTVALVGRSGSGKSTIASL   60 (253)
T ss_dssp             CTTCEEEEEECTTSSHHHHHHH
T ss_pred             cCCCEEEEECCCCChHHHHHHH
Confidence            3678899999999999977633

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

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: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=90.44  E-value=0.1  Score=36.42  Aligned_cols=22  Identities=18%  Similarity=0.071  Sum_probs=17.6

Q ss_pred             cEEEEccCCcchHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      ++++.+|.|+|||+++...+..
T Consensus       125 ~~l~~G~pG~GKT~la~ala~~  146 (321)
T d1w44a_         125 MVIVTGKGNSGKTPLVHALGEA  146 (321)
T ss_dssp             EEEEECSSSSCHHHHHHHHHHH
T ss_pred             eEEEECCCCccHHHHHHHHHHH
Confidence            4566899999999999766554

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

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: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=90.42  E-value=0.066  Score=36.11  Aligned_cols=20  Identities=15%  Similarity=0.197  Sum_probs=17.3

Q ss_pred             CCCccEEEEccCCcchHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVG   21 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~   21 (138)
                      -.|+.+.+++|+|||||...
T Consensus        42 ~~Ge~vaivG~sGsGKSTLl   61 (255)
T d2hyda1          42 EKGETVAFVGMSGGGKSTLI   61 (255)
T ss_dssp             CTTCEEEEECSTTSSHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHH
Confidence            36788999999999999775

>d1l2ta_ c.37.1.12 (A:) MJ0796 {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: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=90.39  E-value=0.068  Score=35.53  Aligned_cols=20  Identities=15%  Similarity=0.194  Sum_probs=17.1

Q ss_pred             CCCccEEEEccCCcchHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVG   21 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~   21 (138)
                      -+|+.+-+.+|+|||||...
T Consensus        29 ~~Ge~~~iiG~sGsGKSTLl   48 (230)
T d1l2ta_          29 KEGEFVSIMGPSGSGKSTML   48 (230)
T ss_dssp             CTTCEEEEECSTTSSHHHHH
T ss_pred             cCCCEEEEECCCCCCcchhh
Confidence            36888999999999999664

>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=90.26  E-value=0.096  Score=33.30  Aligned_cols=22  Identities=14%  Similarity=0.104  Sum_probs=17.8

Q ss_pred             ccEEEEccCCcchHHHHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ..+++.+|.|||||..+...+-
T Consensus         7 mrIiliG~PGSGKtT~a~~La~   28 (189)
T d2ak3a1           7 LRAAIMGAPGSGKGTVSSRITK   28 (189)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             eeEEEECCCCCCHHHHHHHHHH
Confidence            4678999999999999865443

>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=90.10  E-value=0.1  Score=32.91  Aligned_cols=20  Identities=10%  Similarity=0.004  Sum_probs=16.2

Q ss_pred             EEEEccCCcchHHHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +++.+|.|||||..|...+-
T Consensus         4 I~i~GppGSGKsT~a~~La~   23 (194)
T d1teva_           4 VFVLGGPGAGKGTQCARIVE   23 (194)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67899999999999855443

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

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: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=90.09  E-value=0.073  Score=35.57  Aligned_cols=21  Identities=24%  Similarity=0.338  Sum_probs=17.4

Q ss_pred             CCCccEEEEccCCcchHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGE   22 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~   22 (138)
                      -.|+.+.+.+|+|||||...-
T Consensus        26 ~~Ge~vaivG~sGsGKSTLl~   46 (242)
T d1mv5a_          26 QPNSIIAFAGPSGGGKSTIFS   46 (242)
T ss_dssp             CTTEEEEEECCTTSSHHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHHH
Confidence            357788999999999997653

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=90.08  E-value=0.1  Score=33.19  Aligned_cols=25  Identities=12%  Similarity=0.125  Sum_probs=19.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +.|+-+++++|.|+|||..+...+.
T Consensus        12 ~~g~gvl~~G~sG~GKStlal~l~~   36 (176)
T d1kkma_          12 IYGLGVLITGDSGVGKSETALELVQ   36 (176)
T ss_dssp             ETTEEEEEECCTTSCHHHHHHHHHH
T ss_pred             ECCEEEEEEeCCCCCHHHHHHHHHH
Confidence            3677889999999999987754443

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {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: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=90.07  E-value=0.13  Score=33.65  Aligned_cols=21  Identities=14%  Similarity=-0.035  Sum_probs=16.9

Q ss_pred             CccEEEEccCCcchHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      +..+++.+|.|+|||......
T Consensus        29 ~~~i~i~G~~G~GKTsLl~~~   49 (283)
T d2fnaa2          29 APITLVLGLRRTGKSSIIKIG   49 (283)
T ss_dssp             SSEEEEEESTTSSHHHHHHHH
T ss_pred             CCEEEEEcCCCCcHHHHHHHH
Confidence            467889999999999776443

>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=90.07  E-value=0.23  Score=31.22  Aligned_cols=32  Identities=19%  Similarity=0.087  Sum_probs=21.8

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      ++++++.|||||..|-..+. .+...+.++-.+
T Consensus         5 i~l~GlpgsGKSTla~~L~~-~l~~~~~~~~~~   36 (213)
T d1bifa1           5 IVMVGLPARGKTYISKKLTR-YLNFIGVPTREF   36 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHH-HHHHTTCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHH-HHHhcCCCCeEE
Confidence            57899999999998855543 344445555444

>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=90.02  E-value=0.21  Score=32.39  Aligned_cols=36  Identities=19%  Similarity=0.150  Sum_probs=27.0

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEcc
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP  111 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P  111 (138)
                      .-.++..|+|+|||..+.-.+.. +..++.+++|+.-
T Consensus        27 sl~li~G~pGsGKT~l~~qia~~-~~~~~~~~~~is~   62 (242)
T d1tf7a2          27 SIILATGATGTGKTLLVSRFVEN-ACANKERAILFAY   62 (242)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHH-HHTTTCCEEEEES
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHH-HHHhccccceeec
Confidence            56679999999999999665554 4445677788764

>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=89.99  E-value=0.2  Score=31.68  Aligned_cols=35  Identities=20%  Similarity=0.114  Sum_probs=24.7

Q ss_pred             ceEEEee-cCCCchHhHHHHHHHHHHhCCCeEEEEcc
Q psy2029          76 NCVLSIP-TSGGKTLVGEILIMKELKIKQKSAIFILP  111 (138)
Q Consensus        76 ~~ii~~p-tg~GKt~~~~~~~l~~~~~~~~~~~~i~P  111 (138)
                      +++++.. ||.|||.++...+. .+.+.+.|++++-|
T Consensus         3 ~~~i~gt~~GVGKTtvs~~La~-aLa~~G~rVl~id~   38 (224)
T d1byia_           3 RYFVTGTDTEVGKTVASCALLQ-AAKAAGYRTAGYKP   38 (224)
T ss_dssp             EEEEEESSTTSCHHHHHHHHHH-HHHHTTCCEEEECS
T ss_pred             eEEEEECCCCccHHHHHHHHHH-HHHHCCCeEEEECc
Confidence            3444444 69999999966554 45667888888865

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=89.88  E-value=0.1  Score=33.02  Aligned_cols=25  Identities=20%  Similarity=0.125  Sum_probs=19.7

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      ++|.-+++++|.|+|||..+...+.
T Consensus        13 ~~g~gvli~G~sg~GKS~la~~l~~   37 (169)
T d1ko7a2          13 VYGVGVLITGDSGIGKSETALELIK   37 (169)
T ss_dssp             ETTEEEEEEESTTSSHHHHHHHHHH
T ss_pred             ECCEEEEEEeCCCCCHHHHHHHHHH
Confidence            3677899999999999977755443

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding 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: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.57  E-value=0.11  Score=35.40  Aligned_cols=20  Identities=20%  Similarity=0.147  Sum_probs=17.1

Q ss_pred             CCCccEEEEccCCcchHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVG   21 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~   21 (138)
                      -+|+-+.+.+|+|||||...
T Consensus        60 ~~Ge~vaivG~nGsGKSTLl   79 (281)
T d1r0wa_          60 EKGEMLAITGSTGSGKTSLL   79 (281)
T ss_dssp             CTTCEEEEEESTTSSHHHHH
T ss_pred             cCCCEEEEECCCCChHHHHH
Confidence            46788899999999999764

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=89.56  E-value=0.097  Score=34.92  Aligned_cols=22  Identities=14%  Similarity=0.276  Sum_probs=18.2

Q ss_pred             CCccEEEEccCCcchHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~   24 (138)
                      .+..+++.+++|+||+.+|-..
T Consensus        22 ~~~pvlI~Ge~GtGK~~~A~~i   43 (247)
T d1ny5a2          22 AECPVLITGESGVGKEVVARLI   43 (247)
T ss_dssp             CCSCEEEECSTTSSHHHHHHHH
T ss_pred             CCCCEEEECCCCcCHHHHHHHH
Confidence            4568999999999999887544

>d1c9ka_ c.37.1.11 (A:) Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU
species: Salmonella typhimurium [TaxId: 90371]

Probab=89.14  E-value=0.14  Score=32.60  Aligned_cols=45  Identities=16%  Similarity=0.115  Sum_probs=28.3

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKA   56 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~   56 (138)
                      ++|.++.+|||+..|+-.     ....++++|+....+.-.+..+++..-
T Consensus         2 iLVtGGarSGKS~~AE~l-----~~~~~~~~YiAT~~~~D~em~~RI~~H   46 (180)
T d1c9ka_           2 ILVTGGARSGKSRHAEAL-----IGDAPQVLYIATSQILDDEMAARIQHH   46 (180)
T ss_dssp             EEEEECTTSSHHHHHHHH-----HCSCSSEEEEECCCC------CHHHHH
T ss_pred             EEEECCCCccHHHHHHHH-----HhcCCCcEEEEccCCCCHHHHHHHHHH
Confidence            589999999999888642     345678899887666554444444443

>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=89.09  E-value=0.38  Score=31.09  Aligned_cols=21  Identities=29%  Similarity=0.438  Sum_probs=18.0

Q ss_pred             cceEEEeecCCCchHhHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILI   95 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~   95 (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            689999999999999996543

>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=88.97  E-value=0.14  Score=31.98  Aligned_cols=21  Identities=29%  Similarity=0.197  Sum_probs=17.0

Q ss_pred             cEEEEccCCcchHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~   26 (138)
                      .+++.+|.|||||..+-..+-
T Consensus         4 rIvl~G~pGSGKtT~a~~La~   24 (180)
T d1akya1           4 RMVLIGPPGAGKGTQAPNLQE   24 (180)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            568889999999999855544

>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=88.97  E-value=0.75  Score=32.82  Aligned_cols=51  Identities=18%  Similarity=0.132  Sum_probs=39.0

Q ss_pred             ceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHHHHHHHHhhhc
Q psy2029          76 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAAEEF  130 (138)
Q Consensus        76 ~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~~~~~~~~~~~  130 (138)
                      ...+...+|++|+++..- +.+   ..++++++|+|....|.+.+++++.++.+.
T Consensus        30 ~~~L~GlsgS~ka~~~A~-l~~---~~~rp~LvVt~~~~~A~~l~~dL~~~l~~~   80 (408)
T d1c4oa1          30 FVTLLGATGTGKTVTMAK-VIE---ALGRPALVLAPNKILAAQLAAEFRELFPEN   80 (408)
T ss_dssp             EEEEEECTTSCHHHHHHH-HHH---HHTCCEEEEESSHHHHHHHHHHHHHHCTTS
T ss_pred             cEEEecCCCCHHHHHHHH-HHH---HhCCCEEEEeCCHHHHHHHHHHHHHhcCcc
Confidence            356777899999965532 222   236689999999999999999999997543

>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=88.95  E-value=0.59  Score=33.39  Aligned_cols=48  Identities=17%  Similarity=0.131  Sum_probs=36.9

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEcchhhhHHHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKYQSLAKAA   57 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~P~~aL~~q~~~~l~~~~   57 (138)
                      ...+.+-+||+|+++.... ..   ..++.+++|+|......+.++++..+.
T Consensus        30 ~~~L~GlsgS~ka~~~A~l-~~---~~~rp~LvVt~~~~~A~~l~~dL~~~l   77 (408)
T d1c4oa1          30 FVTLLGATGTGKTVTMAKV-IE---ALGRPALVLAPNKILAAQLAAEFRELF   77 (408)
T ss_dssp             EEEEEECTTSCHHHHHHHH-HH---HHTCCEEEEESSHHHHHHHHHHHHHHC
T ss_pred             cEEEecCCCCHHHHHHHHH-HH---HhCCCEEEEeCCHHHHHHHHHHHHHhc
Confidence            3688999999999764322 22   236688999999999999999998873

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=88.91  E-value=1.8  Score=27.41  Aligned_cols=53  Identities=9%  Similarity=-0.030  Sum_probs=32.9

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhh---cCCeEEEEcchh-hhHHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKI---KQKSAIFILPYI-SLVHEKYQSLAKA   56 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~---~~~~~l~v~P~~-aL~~q~~~~l~~~   56 (138)
                      .+.++++++|.|+|||..+...+-. +..   .-...+++.|-. ...-+..+++.++
T Consensus        14 ~~~~~l~~G~~g~gk~~~a~~l~~~-i~~~~~~h~D~~~i~~~~~~I~Id~IR~i~~~   70 (198)
T d2gnoa2          14 EGISILINGEDLSYPREVSLELPEY-VEKFPPKASDVLEIDPEGENIGIDDIRTIKDF   70 (198)
T ss_dssp             SSEEEEEECSSSSHHHHHHHHHHHH-HHTSCCCTTTEEEECCSSSCBCHHHHHHHHHH
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHH-HhccccCCCCEEEEeCCcCCCCHHHHHHHHHH
Confidence            3568899999999999998665543 222   123578887743 2223334445444

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {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: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=88.89  E-value=0.12  Score=34.56  Aligned_cols=20  Identities=10%  Similarity=-0.017  Sum_probs=17.0

Q ss_pred             CCCccEEEEccCCcchHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVG   21 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~   21 (138)
                      -+|+-+-+.+|+|||||...
T Consensus        29 ~~Ge~~~iiG~sGsGKSTLl   48 (240)
T d3dhwc1          29 PAGQIYGVIGASGAGKSTLI   48 (240)
T ss_dssp             CSSCEEEEEESTTSSHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHH
Confidence            36788899999999999664

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

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: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=88.73  E-value=0.16  Score=33.80  Aligned_cols=19  Identities=26%  Similarity=0.232  Sum_probs=16.6

Q ss_pred             CCccEEEEccCCcchHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVG   21 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~   21 (138)
                      +|+-+-+.+|+|||||...
T Consensus        28 ~Ge~~~liG~sGaGKSTll   46 (240)
T d1g2912          28 DGEFMILLGPSGCGKTTTL   46 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCChHHHHH
Confidence            5788899999999999765

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, 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: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=88.60  E-value=0.17  Score=33.55  Aligned_cols=20  Identities=20%  Similarity=0.219  Sum_probs=16.9

Q ss_pred             CCCccEEEEccCCcchHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVG   21 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~   21 (138)
                      -+|+-+.+.+|.|||||...
T Consensus        24 ~~Gei~~liGpsGsGKSTLl   43 (232)
T d2awna2          24 HEGEFVVFVGPSGCGKSTLL   43 (232)
T ss_dssp             CTTCEEEEECCTTSSHHHHH
T ss_pred             cCCCEEEEECCCCChHHHHH
Confidence            36788899999999999664

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=88.53  E-value=0.16  Score=32.75  Aligned_cols=22  Identities=9%  Similarity=-0.073  Sum_probs=18.1

Q ss_pred             cEEEEccCCcchHHHHHHHHHH
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      ..++.+|.|+|||..+...+..
T Consensus        26 ~lLl~Gp~G~GKtt~a~~~a~~   47 (207)
T d1a5ta2          26 ALLIQALPGMGDDALIYALSRY   47 (207)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHHh
Confidence            4799999999999988665543

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {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: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=88.45  E-value=0.13  Score=33.16  Aligned_cols=21  Identities=19%  Similarity=0.139  Sum_probs=17.4

Q ss_pred             CCccEEEEccCCcchHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~   23 (138)
                      +|+-+.+.+|.|||||...-.
T Consensus        26 ~Gei~~l~G~NGsGKSTLl~~   46 (200)
T d1sgwa_          26 KGNVVNFHGPNGIGKTTLLKT   46 (200)
T ss_dssp             TTCCEEEECCTTSSHHHHHHH
T ss_pred             CCCEEEEECCCCChHHHHHHH
Confidence            577788999999999987633

>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=88.09  E-value=0.1  Score=35.94  Aligned_cols=19  Identities=37%  Similarity=0.396  Sum_probs=17.0

Q ss_pred             cceEEEeecCCCchHhHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEI   93 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~   93 (138)
                      +++++.-|||+|||..|-.
T Consensus        50 ~~iLl~GPpG~GKT~lAka   68 (309)
T d1ofha_          50 KNILMIGPTGVGKTEIARR   68 (309)
T ss_dssp             CCEEEECCTTSSHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            7889999999999999943

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

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: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=87.89  E-value=0.14  Score=33.88  Aligned_cols=20  Identities=35%  Similarity=0.340  Sum_probs=17.1

Q ss_pred             CCCccEEEEccCCcchHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVG   21 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~   21 (138)
                      -+|+-+.+.+|+|||||...
T Consensus        24 ~~Ge~~~liGpsGaGKSTll   43 (229)
T d3d31a2          24 ESGEYFVILGPTGAGKTLFL   43 (229)
T ss_dssp             CTTCEEEEECCCTHHHHHHH
T ss_pred             CCCCEEEEECCCCCcHHHHH
Confidence            36778899999999999765

>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=87.56  E-value=0.27  Score=31.66  Aligned_cols=25  Identities=32%  Similarity=0.202  Sum_probs=20.3

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      ...|+++.+|.|.|||.+..-.+..
T Consensus        42 ~k~n~lLvG~pGVGKTalv~~LA~r   66 (195)
T d1jbka_          42 TKNNPVLIGEPGVGKTAIVEGLAQR   66 (195)
T ss_dssp             SSCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCCCeEEEecCCcccHHHHHHHHHH
Confidence            3469999999999999888666554

>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=87.46  E-value=0.77  Score=29.64  Aligned_cols=51  Identities=14%  Similarity=0.010  Sum_probs=33.0

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEcc--chhHHHHHHHHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILP--YISLVHEKYQSLAKA  126 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P--~~~l~~q~~~~~~~~  126 (138)
                      +-+.+.-|||+|||....=.+.+ +...+.++.++.-  +|+=+.|+.+.+.+.
T Consensus         7 ~vi~lvGptGvGKTTTiaKLA~~-~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~   59 (207)
T d1okkd2           7 RVVLVVGVNGVGKTTTIAKLGRY-YQNLGKKVMFCAGDTFRAAGGTQLSEWGKR   59 (207)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHH-HHTTTCCEEEECCCCSSTTHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH-HHHCCCcEEEEEeccccccchhhHhhcccc
Confidence            33467899999999887655543 4444556554443  567776666666554

>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=87.00  E-value=0.19  Score=29.98  Aligned_cols=21  Identities=33%  Similarity=0.529  Sum_probs=17.5

Q ss_pred             cceEEEeecCCCchHhHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILI   95 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~   95 (138)
                      ++++++-|.|+|||.++-..+
T Consensus         3 k~I~l~G~~GsGKSTvak~La   23 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLA   23 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHH
Confidence            688999999999999885443

>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=86.96  E-value=0.53  Score=33.06  Aligned_cols=19  Identities=42%  Similarity=0.574  Sum_probs=17.0

Q ss_pred             cceEEEeecCCCchHhHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEI   93 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~   93 (138)
                      .|+++.-|||.|||..+-.
T Consensus        69 ~niLfiGPTGvGKTElAk~   87 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMAQT   87 (364)
T ss_dssp             CCEEEECCTTSSHHHHHHH
T ss_pred             cceeeeCCCCccHHHHHHH
Confidence            8899999999999998843

>d1w1wa_ c.37.1.12 (A:) Smc head 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: ABC transporter ATPase domain-like
domain: Smc head domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.90  E-value=0.21  Score=34.88  Aligned_cols=18  Identities=17%  Similarity=0.279  Sum_probs=14.6

Q ss_pred             EEEEccCCcchHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~   24 (138)
                      .++.+|+|||||.+....
T Consensus        28 ~~i~G~NGsGKS~ileAi   45 (427)
T d1w1wa_          28 TSIIGPNGSGKSNMMDAI   45 (427)
T ss_dssp             EEEECSTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            478899999999886543

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

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: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=86.89  E-value=0.22  Score=33.13  Aligned_cols=20  Identities=30%  Similarity=0.187  Sum_probs=17.2

Q ss_pred             CCCccEEEEccCCcchHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVG   21 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~   21 (138)
                      -+|+-+.+.+|.|||||...
T Consensus        30 ~~Ge~~~liGpsGaGKSTLl   49 (239)
T d1v43a3          30 KDGEFLVLLGPSGCGKTTTL   49 (239)
T ss_dssp             CTTCEEEEECCTTSSHHHHH
T ss_pred             CCCCEEEEECCCCChHHHHH
Confidence            36788899999999999775

>d1bg2a_ c.37.1.9 (A:) Kinesin {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: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.77  E-value=0.14  Score=35.37  Aligned_cols=20  Identities=30%  Similarity=0.134  Sum_probs=15.4

Q ss_pred             CCCccE--EEEccCCcchHHHH
Q psy2029           2 VQNKNC--VLSIPTSGGKTLVG   21 (138)
Q Consensus         2 ~~~~~~--~~~~ptg~GKt~~~   21 (138)
                      ++|.|+  +..++||||||..-
T Consensus        72 l~G~n~~i~aYGqtgSGKTyT~   93 (323)
T d1bg2a_          72 LEGYNGTIFAYGQTSSGKTHTM   93 (323)
T ss_dssp             HTTCCEEEEEECSTTSSHHHHH
T ss_pred             HcCCCcceeeecccCCCCceec
Confidence            356544  88999999999764

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon 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: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=86.73  E-value=0.14  Score=34.23  Aligned_cols=21  Identities=19%  Similarity=0.173  Sum_probs=17.8

Q ss_pred             CCCccEEEEccCCcchHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGE   22 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~   22 (138)
                      -+|+.+.+.+|+|||||...-
T Consensus        29 ~~Ge~~~iiG~sGsGKSTll~   49 (242)
T d1oxxk2          29 ENGERFGILGPSGAGKTTFMR   49 (242)
T ss_dssp             CTTCEEEEECSCHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCcHHHHHH
Confidence            367889999999999998753

>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=86.61  E-value=0.49  Score=31.39  Aligned_cols=34  Identities=15%  Similarity=0.148  Sum_probs=25.6

Q ss_pred             cEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEEc
Q psy2029           6 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL   40 (138)
Q Consensus         6 ~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v~   40 (138)
                      -+++++.=|.|||.++...+.. +.++|.|++.+-
T Consensus        10 ~i~~sGKGGVGKTTvaa~lA~~-lA~~G~rVLlvD   43 (296)
T d1ihua1          10 YLFFTGKGGVGKTSISCATAIR-LAEQGKRVLLVS   43 (296)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH-HHHTTCCEEEEE
T ss_pred             EEEEECCCcChHHHHHHHHHHH-HHHCCCCEEEEe
Confidence            4578889999999988665554 556788888764

>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=86.52  E-value=1.2  Score=31.30  Aligned_cols=54  Identities=11%  Similarity=0.042  Sum_probs=39.5

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhC-----------CCeEEEEccchhHHHHHHHHHHHHhh
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIK-----------QKSAIFILPYISLVHEKYQSLAKAAE  128 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~-----------~~~~~~i~P~~~l~~q~~~~~~~~~~  128 (138)
                      .+.+|.++-|+|||.+-.-.+++-+...           ..+++.|+=|+.=+.|.-+.+.+.+.
T Consensus        17 g~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~~L~   81 (485)
T d1w36b1          17 GERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSNIH   81 (485)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHHHHH
Confidence            6778999999999998888777765431           12577777777777777777665543

>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=86.51  E-value=0.18  Score=31.67  Aligned_cols=17  Identities=24%  Similarity=0.325  Sum_probs=14.1

Q ss_pred             EEEccCCcchHHHHHHH
Q psy2029           8 VLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~~   24 (138)
                      -++++.|||||.++.+.
T Consensus         7 gitG~~gSGKstva~~l   23 (191)
T d1uf9a_           7 GITGNIGSGKSTVAALL   23 (191)
T ss_dssp             EEEECTTSCHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHH
Confidence            36799999999998653

>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=86.37  E-value=0.24  Score=31.44  Aligned_cols=21  Identities=14%  Similarity=0.238  Sum_probs=16.1

Q ss_pred             EEEEccCCcchHHHHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      +.|.+|.||||+..+-..+-+
T Consensus         6 I~I~GppGSGKgT~ak~La~~   26 (225)
T d1ckea_           6 ITIDGPSGAGKGTLCKAMAEA   26 (225)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            356699999999998665544

>d1r6bx2 c.37.1.20 (X:169-436) 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=86.34  E-value=0.32  Score=32.84  Aligned_cols=24  Identities=29%  Similarity=0.271  Sum_probs=20.0

Q ss_pred             CccEEEEccCCcchHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      .+|+++.+|.|.|||.+..-.+..
T Consensus        39 k~n~lLVG~~GvGKTalv~~la~r   62 (268)
T d1r6bx2          39 KNNPLLVGESGVGKTAIAEGLAWR   62 (268)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cCCcEEECCCCCcHHHHHHHHHHH
Confidence            468999999999999888666554

>d1nn5a_ c.37.1.1 (A:) Thymidylate 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: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.28  E-value=0.65  Score=29.74  Aligned_cols=39  Identities=21%  Similarity=0.205  Sum_probs=26.6

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE-cch
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI-LPY   42 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v-~P~   42 (138)
                      +|.=+.+.+|-|||||..+... .+.+.+++.++.++ .|.
T Consensus         2 rG~lI~ieG~dGsGKsT~~~~L-~~~L~~~g~~v~~~~~p~   41 (209)
T d1nn5a_           2 RGALIVLEGVDRAGKSTQSRKL-VEALCAAGHRAELLRFPE   41 (209)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHH-HHHHHHTTCCEEEEESSC
T ss_pred             CeeEEEEECCCCCCHHHHHHHH-HHHHHHCCCcEEEEeCCC
Confidence            4666677899999999887543 33455566666654 453

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=85.78  E-value=0.2  Score=33.71  Aligned_cols=21  Identities=10%  Similarity=-0.002  Sum_probs=17.6

Q ss_pred             CCCccEEEEccCCcchHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGE   22 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~   22 (138)
                      -+|+-+-+.+|.|||||..+-
T Consensus        26 ~~GEi~~iiG~sGsGKSTLl~   46 (258)
T d1b0ua_          26 RAGDVISIIGSSGSGKSTFLR   46 (258)
T ss_dssp             CTTCEEEEECCTTSSHHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHHH
Confidence            367888999999999997753

>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=85.67  E-value=0.59  Score=30.84  Aligned_cols=32  Identities=16%  Similarity=0.070  Sum_probs=23.6

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      +++++.=|.|||.++...+.. +.+++.|++++
T Consensus        23 ii~sGKGGVGKTT~a~nLA~~-lA~~G~rVllv   54 (279)
T d1ihua2          23 IMLMGKGGVGKTTMAAAIAVR-LADMGFDVHLT   54 (279)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH-HHHTTCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHH-HHHCCCcEEEE
Confidence            467799999999888665553 44567788775

>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=85.44  E-value=0.38  Score=34.25  Aligned_cols=25  Identities=24%  Similarity=0.238  Sum_probs=17.9

Q ss_pred             ceEEEeecCCCchHhHHHHHHHHHHh
Q psy2029          76 NCVLSIPTSGGKTLVGEILIMKELKI  101 (138)
Q Consensus        76 ~~ii~~ptg~GKt~~~~~~~l~~~~~  101 (138)
                      =++++-|||+|||-.. ..+++++..
T Consensus       160 liLvtGpTGSGKSTTl-~~~l~~~~~  184 (401)
T d1p9ra_         160 IILVTGPTGSGKSTTL-YAGLQELNS  184 (401)
T ss_dssp             EEEEECSTTSCHHHHH-HHHHHHHCC
T ss_pred             eEEEEcCCCCCccHHH-HHHhhhhcC
Confidence            3568999999998766 445566644

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {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: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=85.19  E-value=0.23  Score=31.78  Aligned_cols=17  Identities=24%  Similarity=0.327  Sum_probs=13.9

Q ss_pred             EEEccCCcchHHHHHHH
Q psy2029           8 VLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~~   24 (138)
                      -++++.|||||.++.+.
T Consensus         6 gITG~igSGKStv~~~l   22 (205)
T d1jjva_           6 GLTGGIGSGKTTIANLF   22 (205)
T ss_dssp             EEECSTTSCHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHH
Confidence            36999999999987543

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

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: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=85.14  E-value=0.25  Score=32.78  Aligned_cols=19  Identities=21%  Similarity=0.118  Sum_probs=16.7

Q ss_pred             CCccEEEEccCCcchHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVG   21 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~   21 (138)
                      +|+-+-+.+|.|||||...
T Consensus        31 ~Gei~~liGpnGaGKSTl~   49 (240)
T d1ji0a_          31 RGQIVTLIGANGAGKTTTL   49 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHH
Confidence            5778899999999999775

>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=85.06  E-value=0.3  Score=33.39  Aligned_cols=32  Identities=13%  Similarity=0.113  Sum_probs=17.2

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      +-|++++|||||.++....- .+...+.++.++
T Consensus         7 IgIaG~SGSGKTTva~~l~~-i~~~~~v~~~iI   38 (288)
T d1a7ja_           7 ISVTGSSGAGTSTVKHTFDQ-IFRREGVKAVSI   38 (288)
T ss_dssp             EEEESCC---CCTHHHHHHH-HHHHHTCCEEEE
T ss_pred             EEEECCCCCcHHHHHHHHHH-HHhhcCCCeEEE
Confidence            46899999999998744322 233345555444

>d1sdma_ c.37.1.9 (A:) Kinesin heavy chain-like protein {Potato (Solanum tuberosum) [TaxId: 4113]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin heavy chain-like protein
species: Potato (Solanum tuberosum) [TaxId: 4113]

Probab=84.81  E-value=0.2  Score=35.27  Aligned_cols=20  Identities=30%  Similarity=0.199  Sum_probs=15.1

Q ss_pred             CCCccE--EEEccCCcchHHHH
Q psy2029           2 VQNKNC--VLSIPTSGGKTLVG   21 (138)
Q Consensus         2 ~~~~~~--~~~~ptg~GKt~~~   21 (138)
                      ++|.|+  +..++||||||..-
T Consensus        71 l~G~n~~i~aYGqTGSGKTyTm   92 (364)
T d1sdma_          71 VDGYNVCIFAYGQTGSGKTFTI   92 (364)
T ss_dssp             HTTCEEEEEEECSTTSSHHHHH
T ss_pred             hcCCceeeeccccCCCCccccc
Confidence            456554  77899999999773

>d1goja_ c.37.1.9 (A:) Kinesin {Neurospora crassa [TaxId: 5141]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Neurospora crassa [TaxId: 5141]

Probab=84.75  E-value=0.25  Score=34.57  Aligned_cols=19  Identities=21%  Similarity=0.170  Sum_probs=14.9

Q ss_pred             CCCccE--EEEccCCcchHHH
Q psy2029           2 VQNKNC--VLSIPTSGGKTLV   20 (138)
Q Consensus         2 ~~~~~~--~~~~ptg~GKt~~   20 (138)
                      ++|.|+  +..++||||||..
T Consensus        76 l~G~n~ti~aYG~tgSGKT~T   96 (354)
T d1goja_          76 LNGYNGTVFAYGQTGAGKSYT   96 (354)
T ss_dssp             TTTCCEEEEEECSTTSSHHHH
T ss_pred             hccCceeEEecccCCCCccee
Confidence            466654  7789999999966

>d1v8ka_ c.37.1.9 (A:) Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif2c [TaxId: 10090]

Probab=84.70  E-value=0.2  Score=35.24  Aligned_cols=20  Identities=20%  Similarity=0.084  Sum_probs=14.7

Q ss_pred             CCCccE--EEEccCCcchHHHH
Q psy2029           2 VQNKNC--VLSIPTSGGKTLVG   21 (138)
Q Consensus         2 ~~~~~~--~~~~ptg~GKt~~~   21 (138)
                      ++|.|+  +..++||||||..-
T Consensus       110 l~G~n~tifaYGqTGSGKTyTm  131 (362)
T d1v8ka_         110 FEGGKATCFAYGQTGSGKTHTM  131 (362)
T ss_dssp             HTTCEEEEEEEESTTSSHHHHH
T ss_pred             HhccCceEEeeccCCCCCceee
Confidence            456655  56799999999653

>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=84.51  E-value=0.4  Score=30.50  Aligned_cols=20  Identities=30%  Similarity=0.473  Sum_probs=15.5

Q ss_pred             EEEEccCCcchHHHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEILIM   26 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~   26 (138)
                      +.|.+|.|||||..|-..+-
T Consensus         6 IaIdGp~GsGKgT~ak~La~   25 (223)
T d1q3ta_           6 IAIDGPASSGKSTVAKIIAK   25 (223)
T ss_dssp             EEEECSSCSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            44669999999999865544

>d1x88a1 c.37.1.9 (A:18-362) Kinesin {Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]

Probab=84.50  E-value=0.16  Score=35.40  Aligned_cols=19  Identities=32%  Similarity=0.424  Sum_probs=14.8

Q ss_pred             CCCccE--EEEccCCcchHHH
Q psy2029           2 VQNKNC--VLSIPTSGGKTLV   20 (138)
Q Consensus         2 ~~~~~~--~~~~ptg~GKt~~   20 (138)
                      ++|.|+  +..++||||||..
T Consensus        77 l~G~n~~i~aYGqtgSGKTyT   97 (345)
T d1x88a1          77 IMGYNCTIFAYGQTGTGKTFT   97 (345)
T ss_dssp             HTTCEEEEEEEECTTSSHHHH
T ss_pred             hccCCceEEeeeeccccceEE
Confidence            456554  7889999999965

>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=84.43  E-value=0.29  Score=29.56  Aligned_cols=21  Identities=33%  Similarity=0.371  Sum_probs=17.2

Q ss_pred             cceEEEeecCCCchHhHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILI   95 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~   95 (138)
                      .+++++-|.|+|||.++-..+
T Consensus         5 ~~I~i~G~pGsGKTTia~~La   25 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELA   25 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHH
Confidence            578899999999999885544

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA 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: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=84.31  E-value=0.32  Score=31.12  Aligned_cols=17  Identities=24%  Similarity=0.309  Sum_probs=14.2

Q ss_pred             EEEccCCcchHHHHHHH
Q psy2029           8 VLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~~   24 (138)
                      -++++.|||||.++-+.
T Consensus         7 gitG~igSGKStv~~~l   23 (208)
T d1vhta_           7 ALTGGIGSGKSTVANAF   23 (208)
T ss_dssp             EEECCTTSCHHHHHHHH
T ss_pred             EEECCCcCCHHHHHHHH
Confidence            37999999999998643

>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=84.15  E-value=0.29  Score=31.71  Aligned_cols=21  Identities=24%  Similarity=0.349  Sum_probs=18.0

Q ss_pred             cceEEEeecCCCchHhHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILI   95 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~   95 (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            789999999999999986543

>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=83.99  E-value=0.082  Score=32.88  Aligned_cols=18  Identities=22%  Similarity=0.163  Sum_probs=13.8

Q ss_pred             EEEEccCCcchHHHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGEIL   24 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~   24 (138)
                      .++.+|+|||||.+....
T Consensus        27 tvi~G~NGsGKStil~Ai   44 (222)
T d1qhla_          27 TTLSGGNGAGKSTTMAAF   44 (222)
T ss_dssp             HHHHSCCSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            367899999999776443

>d1f9va_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]

Probab=83.96  E-value=0.24  Score=34.50  Aligned_cols=20  Identities=25%  Similarity=0.189  Sum_probs=15.3

Q ss_pred             CCCccE--EEEccCCcchHHHH
Q psy2029           2 VQNKNC--VLSIPTSGGKTLVG   21 (138)
Q Consensus         2 ~~~~~~--~~~~ptg~GKt~~~   21 (138)
                      ++|.|+  +..++||||||..-
T Consensus        79 l~G~n~~i~aYGqtgSGKT~T~  100 (342)
T d1f9va_          79 LDGYNVCIFAYGQTGSGKTFTM  100 (342)
T ss_dssp             GGTCCEEEEEECCTTSSHHHHH
T ss_pred             hcccccceeeeeccCCcccccc
Confidence            456654  67899999999664

>d2ncda_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=83.78  E-value=0.18  Score=35.52  Aligned_cols=19  Identities=26%  Similarity=0.205  Sum_probs=14.6

Q ss_pred             CCCcc--EEEEccCCcchHHH
Q psy2029           2 VQNKN--CVLSIPTSGGKTLV   20 (138)
Q Consensus         2 ~~~~~--~~~~~ptg~GKt~~   20 (138)
                      ++|.|  ++..++||||||..
T Consensus       121 l~G~n~ti~aYGqtGSGKT~T  141 (368)
T d2ncda_         121 LDGYNICIFAYGQTGSGKTYT  141 (368)
T ss_dssp             HTTCEEEEEEECSTTSSHHHH
T ss_pred             hcccceeEEeeccCCCccceE
Confidence            35554  47889999999976

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

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 protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=83.68  E-value=0.35  Score=31.38  Aligned_cols=19  Identities=26%  Similarity=0.364  Sum_probs=16.3

Q ss_pred             ccEEEEccCCcchHHHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVGEI   23 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~~~   23 (138)
                      +.+++.+|.++|||+.+..
T Consensus        54 n~i~~~GP~~TGKS~f~~s   72 (205)
T d1tuea_          54 NCLVFCGPANTGKSYFGMS   72 (205)
T ss_dssp             SEEEEESCGGGCHHHHHHH
T ss_pred             eEEEEECCCCccHHHHHHH
Confidence            5678999999999999854

>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=83.56  E-value=0.81  Score=27.35  Aligned_cols=33  Identities=18%  Similarity=0.099  Sum_probs=22.5

Q ss_pred             eEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEc
Q psy2029          77 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFIL  110 (138)
Q Consensus        77 ~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~  110 (138)
                      +.++-+.|+|||..+.-. ++++..++.++.++.
T Consensus         5 i~itG~~GSGKTTL~~~L-~~~l~~~g~~v~v~~   37 (170)
T d1np6a_           5 LAFAAWSGTGKTTLLKKL-IPALCARGIRPGLIK   37 (170)
T ss_dssp             EEEECCTTSCHHHHHHHH-HHHHHHTTCCEEEEE
T ss_pred             EEEEcCCCCCHHHHHHHH-HHHHHHCCCeEEEec
Confidence            458889999999888543 345555566655543

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

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: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=83.37  E-value=0.3  Score=30.60  Aligned_cols=16  Identities=19%  Similarity=0.127  Sum_probs=13.8

Q ss_pred             EEEEccCCcchHHHHH
Q psy2029           7 CVLSIPTSGGKTLVGE   22 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~   22 (138)
                      +.+.++.|||||..+-
T Consensus        12 I~ieG~~GsGKTTl~~   27 (197)
T d2vp4a1          12 VLIEGNIGSGKTTYLN   27 (197)
T ss_dssp             EEEECSTTSCHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6789999999998764

>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=83.23  E-value=1.9  Score=27.56  Aligned_cols=44  Identities=14%  Similarity=0.046  Sum_probs=28.3

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEKY  120 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~~  120 (138)
                      ..+++.-|.|+|||-... ++.+++...+.+++|+ +...+..+..
T Consensus        37 n~l~l~G~~G~GKTHLl~-A~~~~~~~~~~~~~~~-~~~~~~~~~~   80 (213)
T d1l8qa2          37 NPIFIYGSVGTGKTHLLQ-AAGNEAKKRGYRVIYS-SADDFAQAMV   80 (213)
T ss_dssp             SSEEEECSSSSSHHHHHH-HHHHHHHHTTCCEEEE-EHHHHHHHHH
T ss_pred             CcEEEECCCCCcHHHHHH-HHHHHhccCccceEEe-chHHHHHHHH
Confidence            347899999999997774 4445555556666665 5544544433

>d2zfia1 c.37.1.9 (A:4-352) Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif1a [TaxId: 10090]

Probab=83.12  E-value=0.24  Score=34.53  Aligned_cols=20  Identities=20%  Similarity=0.107  Sum_probs=15.2

Q ss_pred             CCCcc--EEEEccCCcchHHHH
Q psy2029           2 VQNKN--CVLSIPTSGGKTLVG   21 (138)
Q Consensus         2 ~~~~~--~~~~~ptg~GKt~~~   21 (138)
                      ++|.|  ++..++||||||..-
T Consensus        83 l~G~n~ti~aYGqTgSGKT~Tm  104 (349)
T d2zfia1          83 FEGYNVCIFAYGQTGAGKSYTM  104 (349)
T ss_dssp             HTTCCEEEEEECSTTSSHHHHH
T ss_pred             HhccCceeeeeccCCCCCceee
Confidence            35554  478899999999764

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {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: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=83.00  E-value=0.25  Score=32.55  Aligned_cols=20  Identities=20%  Similarity=0.135  Sum_probs=16.8

Q ss_pred             CCCccEEEEccCCcchHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVG   21 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~   21 (138)
                      .+|+-+-+.+|.|||||...
T Consensus        23 ~~Gei~~iiG~nGaGKSTLl   42 (231)
T d1l7vc_          23 RAGEILHLVGPNGAGKSTLL   42 (231)
T ss_dssp             ETTCEEECBCCTTSSHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHH
Confidence            36788889999999999764

>d4tmka_ c.37.1.1 (A:) Thymidylate 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: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=82.97  E-value=1.6  Score=27.42  Aligned_cols=33  Identities=18%  Similarity=0.216  Sum_probs=22.7

Q ss_pred             CCccEEEEccCCcchHHHHHHHHHHHHhhcCCeE
Q psy2029           3 QNKNCVLSIPTSGGKTLVGEILIMKELKIKQKSA   36 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~   36 (138)
                      +|+=+++.++-|||||..+.... +++...+.+.
T Consensus         1 rgkfIviEG~dGsGKsT~~~~L~-~~L~~~g~~~   33 (210)
T d4tmka_           1 RSKYIVIEGLEGAGKTTARNVVV-ETLEQLGIRD   33 (210)
T ss_dssp             CCCEEEEEECTTSCHHHHHHHHH-HHHHHTTCCC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHH-HHHHhCCCCe
Confidence            36667889999999998885543 3354555443

>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=82.62  E-value=1.1  Score=29.43  Aligned_cols=34  Identities=24%  Similarity=0.173  Sum_probs=24.0

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccc
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPY  112 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~  112 (138)
                      +.+++.-|.|+|||..+-..+ ++   -+.+.+++.+.
T Consensus        43 ~giLl~GppGtGKT~la~aia-~~---~~~~~~~i~~~   76 (247)
T d1ixza_          43 KGVLLVGPPGVGKTHLARAVA-GE---ARVPFITASGS   76 (247)
T ss_dssp             SEEEEECCTTSSHHHHHHHHH-HH---TTCCEEEEEHH
T ss_pred             ceEEEecCCCCChhHHHHHHH-HH---cCCCEEEEEhH
Confidence            668999999999999985544 32   24566666543

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {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: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=82.36  E-value=0.49  Score=31.38  Aligned_cols=17  Identities=41%  Similarity=0.612  Sum_probs=13.9

Q ss_pred             ccEEEEccCCcchHHHH
Q psy2029           5 KNCVLSIPTSGGKTLVG   21 (138)
Q Consensus         5 ~~~~~~~ptg~GKt~~~   21 (138)
                      +-+.+.+|.|||||...
T Consensus        25 e~~~liGpnGaGKSTll   41 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFL   41 (240)
T ss_dssp             SEEEEECCTTSSHHHHH
T ss_pred             EEEEEECCCCChHHHHH
Confidence            45668899999999764

>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=82.08  E-value=0.33  Score=33.61  Aligned_cols=42  Identities=29%  Similarity=0.130  Sum_probs=25.8

Q ss_pred             hhhc-cceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchh
Q psy2029          71 MIQN-KNCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYIS  114 (138)
Q Consensus        71 ~~~~-~~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~  114 (138)
                      .+.. .|++++-|||+|||-.- -.++..+ ....+++.+=...+
T Consensus       162 ~v~~~~nili~G~tgSGKTT~l-~al~~~i-~~~~rivtiEd~~E  204 (323)
T d1g6oa_         162 GIAIGKNVIVCGGTGSGKTTYI-KSIMEFI-PKEERIISIEDTEE  204 (323)
T ss_dssp             HHHHTCCEEEEESTTSSHHHHH-HHHGGGS-CTTCCEEEEESSCC
T ss_pred             HHHhCCCEEEEeeccccchHHH-HHHhhhc-ccccceeeccchhh
Confidence            3444 89999999999999764 2333322 23455555544433

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, 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: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=82.06  E-value=1.3  Score=30.13  Aligned_cols=26  Identities=15%  Similarity=0.284  Sum_probs=20.3

Q ss_pred             CCCccEEEEccCCcchHHHHHHHHHH
Q psy2029           2 VQNKNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         2 ~~~~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      -+|-...+.+|.|+|||......+.+
T Consensus        41 grGQr~~I~g~~g~GKT~l~~~i~~~   66 (289)
T d1xpua3          41 GRGQRGLIVAPPKAGKTMLLQNIAQS   66 (289)
T ss_dssp             BTTCEEEEEECSSSSHHHHHHHHHHH
T ss_pred             cCCCeeeEeCCCCCCHHHHHHHHHHH
Confidence            46788999999999999886444443

>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=81.72  E-value=0.55  Score=30.44  Aligned_cols=21  Identities=24%  Similarity=0.343  Sum_probs=17.3

Q ss_pred             cceEEEeecCCCchHhHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILI   95 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~   95 (138)
                      .++++.-|.|+|||..+...+
T Consensus        53 ~~lll~GPpG~GKTt~a~~la   73 (253)
T d1sxja2          53 RAAMLYGPPGIGKTTAAHLVA   73 (253)
T ss_dssp             SEEEEECSTTSSHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHH
Confidence            678899999999998885433

>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=81.55  E-value=0.31  Score=29.66  Aligned_cols=21  Identities=24%  Similarity=0.232  Sum_probs=17.7

Q ss_pred             cceEEEeecCCCchHhHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILI   95 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~   95 (138)
                      +++++.-|+|+|||..+-..+
T Consensus         8 K~I~i~G~~GsGKTTla~~La   28 (192)
T d1lw7a2           8 KTVAILGGESSGKSVLVNKLA   28 (192)
T ss_dssp             EEEEEECCTTSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            788999999999998885433

>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=81.51  E-value=1.1  Score=28.59  Aligned_cols=31  Identities=16%  Similarity=0.217  Sum_probs=19.8

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      +++.+|.|||||...... ++++. .++++..+
T Consensus         3 i~v~G~~GsGKTTLl~~l-l~~~~-~~~~~~iv   33 (244)
T d1yrba1           3 VVFVGTAGSGKTTLTGEF-GRYLE-DNYKVAYV   33 (244)
T ss_dssp             EEEECSTTSSHHHHHHHH-HHHHT-TTSCEEEE
T ss_pred             EEEEcCCCCcHHHHHHHH-HHHHh-hCCeEEEE
Confidence            578999999999775433 33333 34455544

>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=81.50  E-value=0.96  Score=28.74  Aligned_cols=31  Identities=23%  Similarity=0.232  Sum_probs=22.6

Q ss_pred             EEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           8 VLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         8 ~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      +.+.--|.|||.++.-.+.. +.+++.+++++
T Consensus         7 v~~~kGGvGKTtia~nLA~~-la~~g~~Vlli   37 (237)
T d1g3qa_           7 IVSGKGGTGKTTVTANLSVA-LGDRGRKVLAV   37 (237)
T ss_dssp             EECSSTTSSHHHHHHHHHHH-HHHTTCCEEEE
T ss_pred             EECCCCCCcHHHHHHHHHHH-HHhCCCCEEEE
Confidence            45577899999888555443 55677888887

>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=81.48  E-value=0.4  Score=29.02  Aligned_cols=21  Identities=24%  Similarity=0.352  Sum_probs=17.7

Q ss_pred             cceEEEeecCCCchHhHHHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEILI   95 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~   95 (138)
                      .+++++-|.|+|||.++-...
T Consensus         6 ~~I~i~G~~GsGKTT~~~~La   26 (174)
T d1y63a_           6 INILITGTPGTGKTSMAEMIA   26 (174)
T ss_dssp             CEEEEECSTTSSHHHHHHHHH
T ss_pred             CEEEEEeCCCCCHHHHHHHHH
Confidence            578899999999999986554

>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=81.42  E-value=0.9  Score=29.29  Aligned_cols=34  Identities=21%  Similarity=0.133  Sum_probs=22.9

Q ss_pred             cceEEEeecCCCchHhHHHHHHHHHHhC-CCeEEEE
Q psy2029          75 KNCVLSIPTSGGKTLVGEILIMKELKIK-QKSAIFI  109 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~~~l~~~~~~-~~~~~~i  109 (138)
                      .++++.-|+|+|||.++ -.+.+.+... ..+.+++
T Consensus        44 ~~lll~GppGtGKT~l~-~~l~~~l~~~~~~~~~~~   78 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTL-RKLWELYKDKTTARFVYI   78 (276)
T ss_dssp             CEEEEECCTTSSHHHHH-HHHHHHHTTSCCCEEEEE
T ss_pred             CceEEECCCCCCHHHHH-HHHHHHHhcccCCcEEEe
Confidence            67899999999999887 3355555432 3344443

>d1gsia_ c.37.1.1 (A:) Thymidylate 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: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=81.27  E-value=1.2  Score=27.70  Aligned_cols=34  Identities=18%  Similarity=0.226  Sum_probs=23.0

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE-cc
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI-LP   41 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v-~P   41 (138)
                      +.+.++-|||||..+.... +.+.+++..+.++ .|
T Consensus         3 I~ieG~dGsGKST~~~~L~-~~l~~~g~~v~~~~~P   37 (208)
T d1gsia_           3 IAIEGVDGAGKRTLVEKLS-GAFRAAGRSVATLAFP   37 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHH-HHHHHTTCCEEEEESS
T ss_pred             EEEECCCCCCHHHHHHHHH-HHHHHCCCCEEEEecC
Confidence            5678999999998875544 3354556666554 45

>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=81.12  E-value=1.2  Score=28.20  Aligned_cols=32  Identities=22%  Similarity=0.119  Sum_probs=23.7

Q ss_pred             EEEEccCCcchHHHHHHHHHHHHhhcCCeEEEE
Q psy2029           7 CVLSIPTSGGKTLVGEILIMKELKIKQKSAIFI   39 (138)
Q Consensus         7 ~~~~~ptg~GKt~~~~~~~~~~~~~~~~~~l~v   39 (138)
                      .+.++-=|.|||.++.-.+.. +.+++.+++++
T Consensus         5 av~s~KGGvGKTtia~nlA~~-la~~g~~Vlli   36 (232)
T d1hyqa_           5 TVASGKGGTGKTTITANLGVA-LAQLGHDVTIV   36 (232)
T ss_dssp             EEEESSSCSCHHHHHHHHHHH-HHHTTCCEEEE
T ss_pred             EEECCCCCChHHHHHHHHHHH-HHhCCCCEEEE
Confidence            356678899999998655553 55678888887

>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=80.92  E-value=0.42  Score=31.21  Aligned_cols=19  Identities=21%  Similarity=0.209  Sum_probs=16.1

Q ss_pred             cceEEEeecCCCchHhHHH
Q psy2029          75 KNCVLSIPTSGGKTLVGEI   93 (138)
Q Consensus        75 ~~~ii~~ptg~GKt~~~~~   93 (138)
                      +.+++.-|+|+|||..+-.
T Consensus        33 ~~ilL~GpPGtGKT~la~~   51 (273)
T d1gvnb_          33 TAFLLGGQPGSGKTSLRSA   51 (273)
T ss_dssp             EEEEEECCTTSCTHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHH
Confidence            5678999999999998843

>d1g6ha_ c.37.1.12 (A:) MJ1267 {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: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=80.88  E-value=0.46  Score=31.66  Aligned_cols=19  Identities=16%  Similarity=0.251  Sum_probs=16.3

Q ss_pred             CCccEEEEccCCcchHHHH
Q psy2029           3 QNKNCVLSIPTSGGKTLVG   21 (138)
Q Consensus         3 ~~~~~~~~~ptg~GKt~~~   21 (138)
                      .|+-+-+.+|.|||||...
T Consensus        29 ~Gei~~liG~nGaGKSTLl   47 (254)
T d1g6ha_          29 KGDVTLIIGPNGSGKSTLI   47 (254)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHH
Confidence            5777889999999999765

>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=80.47  E-value=1.2  Score=29.86  Aligned_cols=43  Identities=23%  Similarity=0.118  Sum_probs=30.2

Q ss_pred             ceEEEeecCCCchHhHHHHHHHHHHhCCCeEEEEccchhHHHHH
Q psy2029          76 NCVLSIPTSGGKTLVGEILIMKELKIKQKSAIFILPYISLVHEK  119 (138)
Q Consensus        76 ~~ii~~ptg~GKt~~~~~~~l~~~~~~~~~~~~i~P~~~l~~q~  119 (138)
                      -..+.-|.|+|||..++..+. .....+.+++||..-.++-.+.
T Consensus        62 i~e~~G~~~~GKT~l~l~~~~-~~q~~g~~~vyIDtE~~~~~e~  104 (269)
T d1mo6a1          62 VIEIYGPESSGKTTVALHAVA-NAQAAGGVAAFIDAEHALDPDY  104 (269)
T ss_dssp             EEEEECSSSSSHHHHHHHHHH-HHHHTTCEEEEEESSCCCCHHH
T ss_pred             eEEEecCCCcHHHHHHHHHHH-HHhcCCCEEEEEECCccCCHHH
Confidence            335888999999999965554 4445567788877766665443

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, 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: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=80.24  E-value=0.93  Score=29.29  Aligned_cols=14  Identities=29%  Similarity=0.261  Sum_probs=12.2

Q ss_pred             EEEEccCCcchHHH
Q psy2029           7 CVLSIPTSGGKTLV   20 (138)
Q Consensus         7 ~~~~~ptg~GKt~~   20 (138)
                      .++++.-|||||..
T Consensus         6 ~iitGFLGaGKTTl   19 (222)
T d1nija1           6 TLLTGFLGAGKTTL   19 (222)
T ss_dssp             EEEEESSSSSCHHH
T ss_pred             EEEeeCCCCCHHHH
Confidence            47899999999975

>d1qvra2 c.37.1.20 (A:149-535) 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=80.15  E-value=1.6  Score=30.83  Aligned_cols=24  Identities=33%  Similarity=0.210  Sum_probs=19.7

Q ss_pred             CccEEEEccCCcchHHHHHHHHHH
Q psy2029           4 NKNCVLSIPTSGGKTLVGEILIMK   27 (138)
Q Consensus         4 ~~~~~~~~ptg~GKt~~~~~~~~~   27 (138)
                      .+|.++.+|.|.|||.+..-.+..
T Consensus        43 k~n~llvG~~GvGKtaiv~~la~~   66 (387)
T d1qvra2          43 KNNPVLIGEPGVGKTAIVEGLAQR   66 (387)
T ss_dssp             CCCCEEEECTTSCHHHHHHHHHHH
T ss_pred             CCCCeEECCCCCCHHHHHHHHHHH
Confidence            468999999999999988765554

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=80.12  E-value=0.83  Score=29.14  Aligned_cols=34  Identities=12%  Similarity=0.042  Sum_probs=23.1

Q ss_pred             hhhhhHHHhhh----hc---cc-eEEEeecCCCchHhHHHHH
Q psy2029          62 FYLEGKCLEMI----QN---KN-CVLSIPTSGGKTLVGEILI   95 (138)
Q Consensus        62 ~~~Q~~~~~~~----~~---~~-~ii~~ptg~GKt~~~~~~~   95 (138)
                      +|||......+    ..   .+ +++..|.|.|||..+...+
T Consensus         4 yPw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~a   45 (207)
T d1a5ta2           4 YPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALS   45 (207)
T ss_dssp             CGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHH
T ss_pred             CcccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHHH
Confidence            46776665322    22   33 7899999999999985544