Psyllid ID: psy12984

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------18
Protein Sequence
MSKDTEKHLMNKITKREKKKLKILQSKEKSKPAEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQPPTVIKVQTLIF
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHccccccccccccccccHHHHHcccccHHHHHHHHHcccccccHHHHHccccccccccEEEEcccccHHHHHHHHHHHHHHHHcccccccccEEEcccHHHHHHHHHHHHHHHHHccccccEEEEEEEc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHcHHHHcccccccccccccccccccccccccccccccccccccccccccccHHHHcccccHHHHHHHHHcccccccHHHHHccHHHHccccEEEEcccccHHHHHHHHHHHHHHHHccccccccccEEEEEccHHHHHHHHHHHHHHHcccccEEEEEEEEc
Coil and Loop (DISEMBL)
MSKDTEKHLMNKITKREKKKLKILQSkekskpaekdsdanededqtnavevqlpGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQartippllegrdlvgsaktgsgktlAFLVPAVELIynlkfmprngkswqgklrpltnGVYLVACNVfkstqpptvikVQTLIF
Flexible Loop (DISEMBL)
mskdtekhlmnkitkrekkklkilqskekskpaekdsdanededqtnAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNvfkstqpptvikvqtlif
Low Complexity Region (SEG)
MSKDTEKHLMNkitkrekkklkilqskekskPAEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQPPTVIKVQTLIF
Disordered region (IsUnstruct)
********************************************************DVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQPPTVIKVQTL**
Disordered Region (DISOPRED)
******************************************************************QFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQPPTVIKVQTLIF
Disordered Region (DISEMBL)
*********MNKITKREKKKLKIL**********************NAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQPPTVIKVQTLIF
Disordered Region (DISPRO)
**********NKITKRE**********************************************SSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQPPTVIKVQTLIF
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSKDTEKHLMNKITKREKKKLKILQSKEKSKPAEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQPPTVIKVQTLIF
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	178	2.2.26 [Sep-21-2011]
Q9NVP1	670	ATP-dependent RNA helicas	yes	N/A	0.617	0.164	0.537	2e-26
Q9VD51	680	Probable ATP-dependent RN	yes	N/A	0.646	0.169	0.549	6e-26
A4R8B5	587	ATP-dependent RNA helicas	N/A	N/A	0.584	0.177	0.536	9e-25
Q8K363	660	ATP-dependent RNA helicas	yes	N/A	0.634	0.171	0.530	2e-24
Q6BH93	568	ATP-dependent RNA helicas	yes	N/A	0.370	0.116	0.712	7e-24
A1CIQ5	625	ATP-dependent RNA helicas	N/A	N/A	0.601	0.171	0.531	2e-23
Q03532	505	ATP-dependent RNA helicas	yes	N/A	0.516	0.182	0.527	2e-23
A5DID7	569	ATP-dependent RNA helicas	N/A	N/A	0.415	0.130	0.644	6e-23
A5E2Z9	559	ATP-dependent RNA helicas	N/A	N/A	0.477	0.152	0.557	7e-23
Q5AK59	565	ATP-dependent RNA helicas	N/A	N/A	0.359	0.113	0.734	7e-23

>sp|Q9NVP1|DDX18_HUMAN ATP-dependent RNA helicase DDX18 OS=Homo sapiens GN=DDX18 PE=1 SV=2

 Score =  118 bits (296), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 64/119 (53%), Positives = 81/119 (68%), Gaps = 9/119 (7%)

Query: 25  QSKEKSKPAEKD---SDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLK 81
           +S E +K  E +    D +EDE +  ++ + L G+         T F +L   V ENTLK
Sbjct: 139 ESAETTKETENNVEKPDNDEDESEVPSLPLGLTGA------FEDTSFASLCNLVNENTLK 192

Query: 82  AIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
           AI +MGFT MTEIQ ++I PLLEGRDL+ +AKTGSGKTLAFL+PAVELI  L+FMPRNG
Sbjct: 193 AIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNG 251

Probable RNA-dependent helicase.
Homo sapiens (taxid: 9606)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q9VD51|DDX18_DROME Probable ATP-dependent RNA helicase pitchoune OS=Drosophila melanogaster GN=pit PE=2 SV=2

 Score =  117 bits (292), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 67/122 (54%), Positives = 84/122 (68%), Gaps = 7/122 (5%)

Query: 19  KKLKILQSKEKSKPAEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCEN 78
           KK K+L +K K   A+    A +DE  T  VE  L   D          F +LKG V E 
Sbjct: 145 KKTKLLPNKSK---AQNGKPAKDDEPFT--VESSLAALDYRDS--DDRSFASLKGAVSEA 197

Query: 79  TLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPR 138
           TL+AI +MGFT+MTEIQ++++ PLL+GRDLVG+A+TGSGKTLAFL+PAVELI  L+FMPR
Sbjct: 198 TLRAIKEMGFTEMTEIQSKSLTPLLKGRDLVGAAQTGSGKTLAFLIPAVELINKLRFMPR 257

Query: 139 NG 140
           NG
Sbjct: 258 NG 259

Probable RNA-dependent helicase. Functions in cell growth and proliferation. May have a role in ribosome biogenesis and, consequently, in protein biosynthesis.

Drosophila melanogaster (taxid: 7227)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A4R8B5|HAS1_MAGO7 ATP-dependent RNA helicase HAS1 OS=Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) GN=HAS1 PE=3 SV=2

 Score =  112 bits (281), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 59/110 (53%), Positives = 79/110 (71%), Gaps = 6/110 (5%)

Query: 36  DSDANEDEDQTNA----VEVQLPGSDVALEILSSTQFEALKG-KVCENTLKAIADMGFTK 90
           DSD +E +D   A     +  +PG D+ L   + ++ +A     + ENT+KAI +MGFTK
Sbjct: 76  DSDVDEGDDTIAAPAKEADGDIPG-DLTLPTTAESEAQAFSELNLSENTMKAIEEMGFTK 134

Query: 91  MTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
           MTEIQ R IPPLL G+D++G+AKTGSGKTLAFL+PAVE++ +LKF PRNG
Sbjct: 135 MTEIQRRGIPPLLAGKDVLGAAKTGSGKTLAFLIPAVEMLRSLKFKPRNG 184

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) (taxid: 242507)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q8K363|DDX18_MOUSE ATP-dependent RNA helicase DDX18 OS=Mus musculus GN=Ddx18 PE=2 SV=1

 Score =  112 bits (279), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 61/115 (53%), Positives = 76/115 (66%), Gaps = 2/115 (1%)

Query: 28  EKSKPAEKDSDANEDEDQTN-AVEVQLPGSDVALE-ILSSTQFEALKGKVCENTLKAIAD 85
           +K+K  E      E ED    A + ++P   + L      T F +L   V ENTLKAI +
Sbjct: 127 KKAKTEESAEACEEPEDDVKKADDSEVPSLPLGLTGAFEDTSFASLSNLVNENTLKAIEE 186

Query: 86  MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
           MGF +MTEIQ ++I PLLEGRDL+ +AKTGSGKTLAFL+P +ELI  LKFMPRNG
Sbjct: 187 MGFKRMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPVIELIVKLKFMPRNG 241

Probable RNA-dependent helicase.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q6BH93|HAS1_DEBHA ATP-dependent RNA helicase HAS1 OS=Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) GN=HAS1 PE=3 SV=1

 Score =  109 bits (273), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 47/66 (71%), Positives = 61/66 (92%)

Query: 75  VCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLK 134
           + E TLKAI DMGF+KMT++QA+TIPPLL GRD++G+AKTGSGKTLAFL+PA+E++Y+L+
Sbjct: 111 LSEPTLKAIKDMGFSKMTQVQAKTIPPLLAGRDVLGAAKTGSGKTLAFLIPAIEMLYSLR 170

Query: 135 FMPRNG 140
           F PRNG
Sbjct: 171 FKPRNG 176

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) (taxid: 284592)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A1CIQ5|HAS1_ASPCL ATP-dependent RNA helicase has1 OS=Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1) GN=has1 PE=3 SV=1

 Score =  108 bits (270), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 59/111 (53%), Positives = 75/111 (67%), Gaps = 4/111 (3%)

Query: 34  EKDSDANED---EDQTNAVEVQLPGSD-VALEILSSTQFEALKGKVCENTLKAIADMGFT 89
           E+D   NED   ED+ +A    LP  D V L  +     +  +  + E TLKAI +MGF 
Sbjct: 105 EEDGSDNEDGDAEDKNDAEAADLPSMDAVRLPTVDGEPQKFTELGLSEKTLKAINEMGFE 164

Query: 90  KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
            MTEIQ RTIPPLL GRD++G+AKTGSGKTL+FL+PAVE++  L+F PRNG
Sbjct: 165 TMTEIQRRTIPPLLAGRDVLGAAKTGSGKTLSFLIPAVEMLSALRFKPRNG 215

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1) (taxid: 344612)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q03532|HAS1_YEAST ATP-dependent RNA helicase HAS1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=HAS1 PE=1 SV=1

 Score =  108 bits (269), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 58/110 (52%), Positives = 74/110 (67%), Gaps = 18/110 (16%)

Query: 31  KPAEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTK 90
           K   K ++A  + +QT  VE                +FE LK  + + TLKAI  MGFT 
Sbjct: 23  KSTSKQNNAAPEGEQTTCVE----------------KFEELK--LSQPTLKAIEKMGFTT 64

Query: 91  MTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
           MT +QARTIPPLL GRD++G+AKTGSGKTLAFL+PA+EL+++LKF PRNG
Sbjct: 65  MTSVQARTIPPLLAGRDVLGAAKTGSGKTLAFLIPAIELLHSLKFKPRNG 114

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A5DID7|HAS1_PICGU ATP-dependent RNA helicase HAS1 OS=Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) GN=HAS1 PE=3 SV=2

 Score =  106 bits (265), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 49/76 (64%), Positives = 64/76 (84%), Gaps = 2/76 (2%)

Query: 65  STQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLV 124
           S +FE L   + E T++AI DMGF KMT++Q +TIPPLL GRD++G+AKTGSGKTLAFL+
Sbjct: 104 SDKFEDLG--LSEPTMRAIKDMGFEKMTKVQEKTIPPLLAGRDVLGAAKTGSGKTLAFLI 161

Query: 125 PAVELIYNLKFMPRNG 140
           PA+E++Y+LKF PRNG
Sbjct: 162 PAIEMLYSLKFKPRNG 177

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) (taxid: 294746)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A5E2Z9|HAS1_LODEL ATP-dependent RNA helicase HAS1 OS=Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239) GN=HAS1 PE=3 SV=1

 Score =  106 bits (265), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 53/95 (55%), Positives = 67/95 (70%), Gaps = 10/95 (10%)

Query: 46  TNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEG 105
           T+  E   PG + + E          K    E T+KAI +MGF KMT++QA+TIPPLL G
Sbjct: 81  TSEAEADEPGVNYSFE----------KADFSEPTMKAIKEMGFQKMTKVQAKTIPPLLAG 130

Query: 106 RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
           RD++G+AKTGSGKTLAFL+PAVEL+Y+LK  PRNG
Sbjct: 131 RDVLGAAKTGSGKTLAFLLPAVELLYSLKIKPRNG 165

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239) (taxid: 379508)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5AK59|HAS1_CANAL ATP-dependent RNA helicase HAS1 OS=Candida albicans (strain SC5314 / ATCC MYA-2876) GN=HAS1 PE=3 SV=1

 Score =  106 bits (265), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 47/64 (73%), Positives = 59/64 (92%)

Query: 77  ENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFM 136
           E T+KAI +MGFTKMT++QA+TIPPLL GRD++G+AKTGSGKTLAFL+PA+EL+Y+LK  
Sbjct: 117 EPTMKAIKEMGFTKMTKVQAKTIPPLLAGRDVLGAAKTGSGKTLAFLIPAIELLYSLKIK 176

Query: 137 PRNG 140
           PRNG
Sbjct: 177 PRNG 180

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Candida albicans (strain SC5314 / ATCC MYA-2876) (taxid: 237561)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	178
322796780	605	hypothetical protein SINV_02979 [Solenop	0.758	0.223	0.546	2e-37
189234356	695	PREDICTED: similar to pitchoune CG6375-P	0.539	0.138	0.75	1e-36
270001921	629	hypothetical protein TcasGA2_TC000825 [T	0.539	0.152	0.75	1e-36
242022035	636	DEAD box ATP-dependent RNA helicase, put	0.449	0.125	0.8	2e-36
340721973	579	PREDICTED: probable ATP-dependent RNA he	0.651	0.200	0.65	6e-36
383857595	621	PREDICTED: probable ATP-dependent RNA he	0.584	0.167	0.704	2e-35
350412881	578	PREDICTED: probable ATP-dependent RNA he	0.550	0.169	0.734	4e-35
345489122	643	PREDICTED: probable ATP-dependent RNA he	0.584	0.161	0.698	7e-34
193290168	643	pitchoune [Nasonia vitripennis]	0.578	0.160	0.679	7e-34
380011151	607	PREDICTED: probable ATP-dependent RNA he	0.578	0.169	0.663	2e-33

>gi|322796780|gb|EFZ19207.1| hypothetical protein SINV_02979 [Solenopsis invicta]

 Score =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 88/161 (54%), Positives = 105/161 (65%), Gaps = 26/161 (16%)

Query: 6   EKHLMNKITKREKKKLKILQSKEKSK-----PAEKDSDANEDED-------------QTN 47
           EK LM KI KREK KL +L+ +E+ K     P E+++     ED             ++ 
Sbjct: 5   EKVLMRKIKKREKTKLTVLKQREEQKDAIKEPKEEETSQQNTEDSLPKKKIKLKVSKRSE 64

Query: 48  AVEV--------QLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTI 99
             EV         LPG+ +  E+ + T F  L  KVCENTLKAI DMGFT MTEIQA++I
Sbjct: 65  NSEVAEQSPTTENLPGTAIGFEVTNDTNFSVLSEKVCENTLKAIKDMGFTNMTEIQAKSI 124

Query: 100 PPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
           PPLLEGRDLVG+AKTGSGKTLAFL+PAVELIY LKFMPRNG
Sbjct: 125 PPLLEGRDLVGAAKTGSGKTLAFLIPAVELIYKLKFMPRNG 165

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189234356|ref|XP_973872.2| PREDICTED: similar to pitchoune CG6375-PB [Tribolium castaneum]

 Score =  157 bits (398), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 75/100 (75%), Positives = 87/100 (87%), Gaps = 4/100 (4%)

Query: 41  EDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIP 100
           E +D+ N    +LPG++  LEILS+  F++LK KVCENTLKAIADMGFT +TEIQAR+IP
Sbjct: 107 EGDDEQN----KLPGAETTLEILSNCTFDSLKNKVCENTLKAIADMGFTTLTEIQARSIP 162

Query: 101 PLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
           PLLEGRDLVG+AKTGSGKTLAFL+PAVELIY LKFMPRNG
Sbjct: 163 PLLEGRDLVGAAKTGSGKTLAFLIPAVELIYKLKFMPRNG 202

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270001921|gb|EEZ98368.1| hypothetical protein TcasGA2_TC000825 [Tribolium castaneum]

 Score =  157 bits (397), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 75/100 (75%), Positives = 87/100 (87%), Gaps = 4/100 (4%)

Query: 41  EDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIP 100
           E +D+ N    +LPG++  LEILS+  F++LK KVCENTLKAIADMGFT +TEIQAR+IP
Sbjct: 107 EGDDEQN----KLPGAETTLEILSNCTFDSLKNKVCENTLKAIADMGFTTLTEIQARSIP 162

Query: 101 PLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
           PLLEGRDLVG+AKTGSGKTLAFL+PAVELIY LKFMPRNG
Sbjct: 163 PLLEGRDLVGAAKTGSGKTLAFLIPAVELIYKLKFMPRNG 202

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242022035|ref|XP_002431447.1| DEAD box ATP-dependent RNA helicase, putative [Pediculus humanus corporis] gi|212516735|gb|EEB18709.1| DEAD box ATP-dependent RNA helicase, putative [Pediculus humanus corporis]

 Score =  156 bits (395), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 72/90 (80%), Positives = 82/90 (91%)

Query: 51  VQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVG 110
           V++PGS + LEILS T+F +L+GKVCENTLKAI DMGFT MTEIQA++IPPLLEGRDLVG
Sbjct: 126 VKMPGSSLTLEILSDTKFSSLEGKVCENTLKAIVDMGFTTMTEIQAKSIPPLLEGRDLVG 185

Query: 111 SAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
           SAKTGSGKTLAFL+P VELIY LKF+PRNG
Sbjct: 186 SAKTGSGKTLAFLIPVVELIYKLKFLPRNG 215

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340721973|ref|XP_003399387.1| PREDICTED: probable ATP-dependent RNA helicase pitchoune-like [Bombus terrestris]

 Score =  155 bits (392), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 78/120 (65%), Positives = 90/120 (75%), Gaps = 4/120 (3%)

Query: 25  QSKE----KSKPAEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTL 80
           QS+E    K K  + + D    E+ TN+++  LPGS + L I + T F+ L   VCENTL
Sbjct: 58  QSQESVPVKKKRKKIEDDQTSQENNTNSIDENLPGSTMGLTIANDTNFKVLAESVCENTL 117

Query: 81  KAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
           KAI DMGFT MTEIQA+ IPPLLEGRDLVGSAKTGSGKTLAFL+PAVELIY LKFMPRNG
Sbjct: 118 KAIEDMGFTNMTEIQAKAIPPLLEGRDLVGSAKTGSGKTLAFLIPAVELIYKLKFMPRNG 177

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383857595|ref|XP_003704290.1| PREDICTED: probable ATP-dependent RNA helicase pitchoune-like [Megachile rotundata]

 Score =  154 bits (388), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 74/105 (70%), Positives = 87/105 (82%), Gaps = 1/105 (0%)

Query: 37  SDANEDEDQTN-AVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQ 95
           S+++E ++Q + +V V LPGS + LE+   T FE LK  VCENTLKAI DMGF  MTEIQ
Sbjct: 94  SESSETKEQDDDSVAVNLPGSTIGLEVAKDTSFETLKESVCENTLKAIEDMGFKNMTEIQ 153

Query: 96  ARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
           A++IPPLLEGRDLVG+AKTGSGKTLAFL+PAVELIY LKFMPRNG
Sbjct: 154 AKSIPPLLEGRDLVGAAKTGSGKTLAFLIPAVELIYKLKFMPRNG 198

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350412881|ref|XP_003489799.1| PREDICTED: probable ATP-dependent RNA helicase pitchoune-like [Bombus impatiens]

 Score =  152 bits (385), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 72/98 (73%), Positives = 81/98 (82%)

Query: 43  EDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPL 102
           E+ TN+++  LPGS + L I + T F+ L   VCENTLKAI DMGFT MTEIQA+ IPPL
Sbjct: 80  ENNTNSIDENLPGSAMGLTIANDTNFKVLAESVCENTLKAIQDMGFTNMTEIQAKAIPPL 139

Query: 103 LEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
           LEGRDLVGSAKTGSGKTLAFL+PAVELIY LKFMPRNG
Sbjct: 140 LEGRDLVGSAKTGSGKTLAFLIPAVELIYKLKFMPRNG 177

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345489122|ref|XP_001604385.2| PREDICTED: probable ATP-dependent RNA helicase pitchoune-like [Nasonia vitripennis]

 Score =  148 bits (374), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 74/106 (69%), Positives = 85/106 (80%), Gaps = 2/106 (1%)

Query: 35  KDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEI 94
           ++SD+ ED  + NA    LPG+ V LE+     F  LK KVCENTLKAIA+MGFT MTEI
Sbjct: 110 QNSDSAEDT-KDNATS-NLPGTSVGLELTKDRSFSTLKDKVCENTLKAIAEMGFTDMTEI 167

Query: 95  QARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
           QA +IPPLLEGRDLVG+AKTGSGKTL+FL+PAVELIY LKFMPRNG
Sbjct: 168 QAMSIPPLLEGRDLVGAAKTGSGKTLSFLIPAVELIYKLKFMPRNG 213

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193290168|ref|NP_001123270.1| pitchoune [Nasonia vitripennis]

 Score =  148 bits (374), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 70/103 (67%), Positives = 81/103 (78%)

Query: 38  DANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQAR 97
           +++  ED  +     LPG+ V LE+     F  LK KVCENTLKAIA+MGFT MTEIQA 
Sbjct: 111 NSDSAEDTKDKATSSLPGTSVGLELTKDRSFSTLKDKVCENTLKAIAEMGFTDMTEIQAM 170

Query: 98  TIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
           +IPPLLEGRDLVG+AKTGSGKTL+FL+PAVELIY LKFMPRNG
Sbjct: 171 SIPPLLEGRDLVGAAKTGSGKTLSFLIPAVELIYKLKFMPRNG 213

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380011151|ref|XP_003689675.1| PREDICTED: probable ATP-dependent RNA helicase pitchoune-like [Apis florea]

 Score =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 69/104 (66%), Positives = 84/104 (80%), Gaps = 1/104 (0%)

Query: 38  DANED-EDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQA 96
           DAN   ++  + + + LPGS + L++ + T F+ L+  VCENTLKAI DMGFT MTEIQA
Sbjct: 77  DANSTIKNNIDNITINLPGSTIGLKVANDTNFKVLEEIVCENTLKAIKDMGFTNMTEIQA 136

Query: 97  RTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
           + IPPLLEGRDLVG+AKTGSGKTLAFL+PA+ELIY LKFMPRNG
Sbjct: 137 KAIPPLLEGRDLVGAAKTGSGKTLAFLIPAIELIYKLKFMPRNG 180

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	178
UNIPROTKB|F1NEQ3	659	DDX18 "Uncharacterized protein	0.595	0.160	0.560	4e-25
UNIPROTKB|E2RFA3	669	DDX18 "Uncharacterized protein	0.595	0.158	0.585	1.5e-24
UNIPROTKB|F1N533	670	DDX18 "Uncharacterized protein	0.595	0.158	0.585	2.4e-24
UNIPROTKB|F1MSX0	674	F1MSX0 "Uncharacterized protei	0.595	0.157	0.585	2.4e-24
ZFIN|ZDB-GENE-030131-9685	653	ddx18 "DEAD (Asp-Glu-Ala-Asp)	0.567	0.154	0.583	7.8e-24
UNIPROTKB|Q9NVP1	670	DDX18 "ATP-dependent RNA helic	0.595	0.158	0.551	1.1e-23
FB|FBgn0025140	680	pit "pitchoune" [Drosophila me	0.584	0.152	0.564	3e-23
MGI|MGI:1914192	660	Ddx18 "DEAD (Asp-Glu-Ala-Asp)	0.601	0.162	0.536	3.6e-23
UNIPROTKB|I3L840	667	DDX18 "Uncharacterized protein	0.584	0.155	0.577	4.7e-23
UNIPROTKB|F1RY13	671	DDX18 "Uncharacterized protein	0.584	0.154	0.577	4.8e-23

UNIPROTKB|F1NEQ3 DDX18 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 294 (108.6 bits), Expect = 4.0e-25, P = 4.0e-25
 Identities = 60/107 (56%), Positives = 75/107 (70%)

Query:    35 KDSDANEDEDQTNAVEVQLPGSDVALE-ILSSTQFEALKGKVCENTLKAIADMGFTKMTE 93
             +D D  +  ++    E ++P   + L        F +L G V ENTLK I+DMGFT MTE
Sbjct:   132 EDEDGQDTGEKEAEEEDEVPSLPLGLTGAFEDNSFTSLAGLVSENTLKGISDMGFTHMTE 191

Query:    94 IQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
             IQ ++I PLLEGRD++ +AKTGSGKTLAFL+PAVELIY LKFMPRNG
Sbjct:   192 IQHKSIKPLLEGRDILAAAKTGSGKTLAFLIPAVELIYKLKFMPRNG 238

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

UNIPROTKB|E2RFA3 DDX18 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 289 (106.8 bits), Expect = 1.5e-24, P = 1.5e-24
 Identities = 65/111 (58%), Positives = 78/111 (70%)

Query:    32 PAEKDSDANEDEDQTNAVEV-QLP-GSDVALEILSSTQFEALKGKVCENTLKAIADMGFT 89
             P E +++  + +D+    EV  LP G   A E    T F +L   V ENTLKAI +MGFT
Sbjct:   143 PEETENNGEKPDDEEEDSEVPSLPLGLTGAFE---DTSFASLSSLVNENTLKAIKEMGFT 199

Query:    90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
              MTEIQ ++I PLLEGRDL+ +AKTGSGKTLAFL+PAVELI  LKFMPRNG
Sbjct:   200 NMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLKFMPRNG 250

GO:0005524 "ATP binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

UNIPROTKB|F1N533 DDX18 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 287 (106.1 bits), Expect = 2.4e-24, P = 2.4e-24
 Identities = 65/111 (58%), Positives = 78/111 (70%)

Query:    32 PAEKDSDANEDEDQTNAVEV-QLP-GSDVALEILSSTQFEALKGKVCENTLKAIADMGFT 89
             P E ++   + +D+    EV  LP G   A E    T F++L   V ENTLKAI +MGFT
Sbjct:   144 PEETENRVEKPDDEGEDSEVPSLPLGLTGAFE---DTSFDSLTNLVNENTLKAIKEMGFT 200

Query:    90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
              MTEIQ ++I PLLEGRDL+ +AKTGSGKTLAFL+PAVELI  LKFMPRNG
Sbjct:   201 NMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLKFMPRNG 251

GO:0005524 "ATP binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

UNIPROTKB|F1MSX0 F1MSX0 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 287 (106.1 bits), Expect = 2.4e-24, P = 2.4e-24
 Identities = 65/111 (58%), Positives = 78/111 (70%)

Query:    32 PAEKDSDANEDEDQTNAVEV-QLP-GSDVALEILSSTQFEALKGKVCENTLKAIADMGFT 89
             P E ++   + +D+    EV  LP G   A E    T F++L   V ENTLKAI +MGFT
Sbjct:   148 PEETENRVEKPDDEGEDSEVPSLPLGLTGAFE---DTSFDSLTNLVNENTLKAIKEMGFT 204

Query:    90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
              MTEIQ ++I PLLEGRDL+ +AKTGSGKTLAFL+PAVELI  LKFMPRNG
Sbjct:   205 NMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLKFMPRNG 255

GO:0005524 "ATP binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

ZFIN|ZDB-GENE-030131-9685 ddx18 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 18" [Danio rerio (taxid:7955)]

 Score = 282 (104.3 bits), Expect = 7.8e-24, P = 7.8e-24
 Identities = 63/108 (58%), Positives = 75/108 (69%)

Query:    34 EKDSDANEDEDQTNAVEVQLP-GSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMT 92
             EK+  A ED D+      QLP G   A E  S   F +L   V ENTLK + +MGF  MT
Sbjct:   132 EKEGSAEEDSDEDGP---QLPSGLTGAFEDRS---FASLSEVVSENTLKGVKEMGFDTMT 185

Query:    93 EIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
             EIQ +TI PLLEGRD++ +AKTGSGKTLAFL+P++ELIY LKFMPRNG
Sbjct:   186 EIQHKTIRPLLEGRDVLAAAKTGSGKTLAFLIPSIELIYKLKFMPRNG 233

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0004386 "helicase activity" evidence=IEA

GO:0030099 "myeloid cell differentiation" evidence=IMP

GO:0030097 "hemopoiesis" evidence=IMP

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|Q9NVP1 DDX18 "ATP-dependent RNA helicase DDX18" [Homo sapiens (taxid:9606)]

 Score = 281 (104.0 bits), Expect = 1.1e-23, P = 1.1e-23
 Identities = 59/107 (55%), Positives = 76/107 (71%)

Query:    35 KDSDANEDEDQTNAVEVQLPGSDVALE-ILSSTQFEALKGKVCENTLKAIADMGFTKMTE 93
             K+++ N ++   +  E ++P   + L      T F +L   V ENTLKAI +MGFT MTE
Sbjct:   145 KETENNVEKPDNDEDESEVPSLPLGLTGAFEDTSFASLCNLVNENTLKAIKEMGFTNMTE 204

Query:    94 IQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
             IQ ++I PLLEGRDL+ +AKTGSGKTLAFL+PAVELI  L+FMPRNG
Sbjct:   205 IQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNG 251

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

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

FB|FBgn0025140 pit "pitchoune" [Drosophila melanogaster (taxid:7227)]

 Score = 277 (102.6 bits), Expect = 3.0e-23, P = 3.0e-23
 Identities = 61/108 (56%), Positives = 76/108 (70%)

Query:    33 AEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMT 92
             A+    A +DE  T  VE  L   D          F +LKG V E TL+AI +MGFT+MT
Sbjct:   156 AQNGKPAKDDEPFT--VESSLAALDYRDS--DDRSFASLKGAVSEATLRAIKEMGFTEMT 211

Query:    93 EIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
             EIQ++++ PLL+GRDLVG+A+TGSGKTLAFL+PAVELI  L+FMPRNG
Sbjct:   212 EIQSKSLTPLLKGRDLVGAAQTGSGKTLAFLIPAVELINKLRFMPRNG 259

GO:0005730 "nucleolus" evidence=NAS;IDA

GO:0016049 "cell growth" evidence=IMP

GO:0008283 "cell proliferation" evidence=IMP

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

GO:0003724 "RNA helicase activity" evidence=ISS

GO:0005634 "nucleus" evidence=NAS

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

MGI|MGI:1914192 Ddx18 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 18" [Mus musculus (taxid:10090)]

 Score = 276 (102.2 bits), Expect = 3.6e-23, P = 3.6e-23
 Identities = 59/110 (53%), Positives = 77/110 (70%)

Query:    34 EKDSDANED--EDQTNAVEVQLPGSDVALE-ILSSTQFEALKGKVCENTLKAIADMGFTK 90
             E+ ++A E+  +D   A + ++P   + L      T F +L   V ENTLKAI +MGF +
Sbjct:   132 EESAEACEEPEDDVKKADDSEVPSLPLGLTGAFEDTSFASLSNLVNENTLKAIEEMGFKR 191

Query:    91 MTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
             MTEIQ ++I PLLEGRDL+ +AKTGSGKTLAFL+P +ELI  LKFMPRNG
Sbjct:   192 MTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPVIELIVKLKFMPRNG 241

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005730 "nucleolus" evidence=ISO

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

GO:0008150 "biological_process" evidence=ND

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|I3L840 DDX18 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 275 (101.9 bits), Expect = 4.7e-23, P = 4.7e-23
 Identities = 63/109 (57%), Positives = 77/109 (70%)

Query:    34 EKDSDANEDEDQTNAVEV-QLP-GSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKM 91
             E+  ++ E  D+ +  EV  LP G   A E    T F +L   V ENTL+AI +MGFT M
Sbjct:   143 EETENSMEKPDKDDDTEVPSLPLGLTGAFE---DTSFASLTDLVNENTLRAIKEMGFTNM 199

Query:    92 TEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
             TEIQ ++I PLLEGRDL+ +AKTGSGKTLAFL+PAVELI  L+FMPRNG
Sbjct:   200 TEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNG 248

GO:0005524 "ATP binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

UNIPROTKB|F1RY13 DDX18 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 275 (101.9 bits), Expect = 4.8e-23, P = 4.8e-23
 Identities = 63/109 (57%), Positives = 77/109 (70%)

Query:    34 EKDSDANEDEDQTNAVEV-QLP-GSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKM 91
             E+  ++ E  D+ +  EV  LP G   A E    T F +L   V ENTL+AI +MGFT M
Sbjct:   147 EETENSMEKPDKDDDTEVPSLPLGLTGAFE---DTSFASLTDLVNENTLRAIKEMGFTNM 203

Query:    92 TEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
             TEIQ ++I PLLEGRDL+ +AKTGSGKTLAFL+PAVELI  L+FMPRNG
Sbjct:   204 TEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNG 252

GO:0005524 "ATP binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q4IEK8	HAS1_GIBZE	3, ., 6, ., 4, ., 1, 3	0.5145	0.5449	0.1641	yes	N/A
Q8K363	DDX18_MOUSE	3, ., 6, ., 4, ., 1, 3	0.5304	0.6348	0.1712	yes	N/A
Q9NVP1	DDX18_HUMAN	3, ., 6, ., 4, ., 1, 3	0.5378	0.6179	0.1641	yes	N/A
Q9VD51	DDX18_DROME	3, ., 6, ., 4, ., 1, 3	0.5491	0.6460	0.1691	yes	N/A
Q84T03	RH27_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.5232	0.4719	0.1423	yes	N/A
Q03532	HAS1_YEAST	3, ., 6, ., 4, ., 1, 3	0.5272	0.5168	0.1821	yes	N/A
Q9SB89	RH27_ARATH	3, ., 6, ., 4, ., 1, 3	0.5822	0.4325	0.1216	yes	N/A

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	178
cd00268	203	cd00268, DEADc, DEAD-box helicases	2e-25
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	7e-21
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	3e-17
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	2e-14
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	3e-14
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	4e-13
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	6e-12
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	8e-12
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	2e-11
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	6e-11
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	2e-10
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	6e-10
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	8e-09
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	1e-08
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	4e-06
COG1205	851	COG1205, COG1205, Distinct helicase family with a	2e-05
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	3e-04
PRK13767	876	PRK13767, PRK13767, ATP-dependent helicase; Provis	0.003

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

 Score = 96.8 bits (242), Expect = 2e-25
 Identities = 34/67 (50%), Positives = 43/67 (64%), Gaps = 2/67 (2%)

Query: 68  FEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAV 127
           FE L   +    L+ I  +GF K T IQAR IPPLL GRD++G A+TGSGKT AFL+P +
Sbjct: 1   FEELG--LSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPIL 58

Query: 128 ELIYNLK 134
           E +    
Sbjct: 59  EKLDPSP 65

A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region. Length = 203

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

 Score = 88.3 bits (219), Expect = 7e-21
 Identities = 28/67 (41%), Positives = 43/67 (64%), Gaps = 2/67 (2%)

Query: 64  SSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFL 123
           +  +F +L        L+A+ D+GF + T IQ   IP +L GRD++G A+TG+GKT AFL
Sbjct: 27  TPPEFASLGLS--PELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFL 84

Query: 124 VPAVELI 130
           +P ++ I
Sbjct: 85  LPLLQKI 91

Length = 513

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

 Score = 78.1 bits (193), Expect = 3e-17
 Identities = 33/61 (54%), Positives = 45/61 (73%), Gaps = 2/61 (3%)

Query: 66  TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVP 125
           T F  L+  + E+ L+A+ D G+T+ T IQA  IPP L+GRD++GSA TG+GKT AFL+P
Sbjct: 1   TTFSELE--LDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLP 58

Query: 126 A 126
           A
Sbjct: 59  A 59

Length = 434

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

 Score = 69.4 bits (171), Expect = 2e-14
 Identities = 22/43 (51%), Positives = 34/43 (79%)

Query: 80  LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAF 122
           L  + ++G+T+MT IQA+++P +L G+D++  AKTGSGKT AF
Sbjct: 16  LANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAF 58

Length = 460

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

 Score = 66.5 bits (163), Expect = 3e-14
 Identities = 23/47 (48%), Positives = 33/47 (70%)

Query: 92  TEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPR 138
           T IQA+ IP +L G+D++  A TGSGKTLAFL+P ++ +   K  P+
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQ 47

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

 Score = 65.8 bits (161), Expect = 4e-13
 Identities = 27/64 (42%), Positives = 38/64 (59%), Gaps = 6/64 (9%)

Query: 63  LSSTQFE--ALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTL 120
           L+  +F   AL  +V    ++A+   GF   T IQA  +P  L GRD+ G A+TG+GKT+
Sbjct: 5   LTEQKFSDFALHPQV----VEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTM 60

Query: 121 AFLV 124
           AFL 
Sbjct: 61  AFLT 64

Length = 423

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

 Score = 62.6 bits (152), Expect = 6e-12
 Identities = 29/55 (52%), Positives = 40/55 (72%), Gaps = 3/55 (5%)

Query: 80  LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLK 134
           L+A+ D+G+ K + IQA  IP LL GRD++G A+TGSGKT AF +P   L++NL 
Sbjct: 18  LEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLP---LLHNLD 69

Length = 629

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

 Score = 62.1 bits (151), Expect = 8e-12
 Identities = 27/48 (56%), Positives = 37/48 (77%)

Query: 80  LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAV 127
           LK++ + GFT+ T IQ +  P  L GRD++G A+TGSGKTLAFL+PA+
Sbjct: 142 LKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAI 189

Length = 545

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

 Score = 61.0 bits (148), Expect = 2e-11
 Identities = 36/99 (36%), Positives = 56/99 (56%), Gaps = 8/99 (8%)

Query: 36  DSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQ 95
            S+     +Q  +        D   EI+ S  F+ALK  + E+ L+ I   GF K + IQ
Sbjct: 3   TSEQKNQSEQVASTGTIESNYD---EIVDS--FDALK--LNEDLLRGIYSYGFEKPSAIQ 55

Query: 96  ARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI-YNL 133
            R I P+L+G D +G A++G+GKT  F++ A++LI Y+L
Sbjct: 56  QRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDL 94

Length = 401

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

 Score = 59.4 bits (144), Expect = 6e-11
 Identities = 24/51 (47%), Positives = 38/51 (74%)

Query: 80  LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
           L+A+A+ G+ + T IQ + IP +LEGRDL+ SA+TG+GKT  F +P ++ +
Sbjct: 13  LRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHL 63

Length = 456

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

 Score = 56.7 bits (137), Expect = 2e-10
 Identities = 24/56 (42%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 83  IADMGFTKMTEIQARTIPPLLEG-RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMP 137
           I   GF  +   Q   I  LL G RD++ +A TGSGKTLA L+PA+E +   K   
Sbjct: 1   IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGR 56

Length = 201

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

 Score = 56.9 bits (137), Expect = 6e-10
 Identities = 24/41 (58%), Positives = 30/41 (73%)

Query: 87  GFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAV 127
           GFT+ T IQA T+P  L G D+ G A+TG+GKTLAFLV  +
Sbjct: 28  GFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVM 68

Length = 572

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

 Score = 53.4 bits (128), Expect = 8e-09
 Identities = 28/71 (39%), Positives = 40/71 (56%), Gaps = 3/71 (4%)

Query: 80  LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRN 139
           + AI D+GF   T IQA+ +   L G D +G A+TG+GKT AFL   + +I  L   P  
Sbjct: 99  MHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFL---ISIINQLLQTPPP 155

Query: 140 GKSWQGKLRPL 150
            + + G+ R L
Sbjct: 156 KERYMGEPRAL 166

Length = 475

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

 Score = 52.9 bits (127), Expect = 1e-08
 Identities = 32/88 (36%), Positives = 43/88 (48%), Gaps = 9/88 (10%)

Query: 44  DQTNA----VEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTI 99
            Q       +E+ + G  V   ILS +    L  K+  N    +   G+   T IQ + I
Sbjct: 98  SQAELLRRKLEIHVKGEAVPPPILSFSSC-GLPPKLLLN----LETAGYEFPTPIQMQAI 152

Query: 100 PPLLEGRDLVGSAKTGSGKTLAFLVPAV 127
           P  L GR L+ SA TGSGKT +FLVP +
Sbjct: 153 PAALSGRSLLVSADTGSGKTASFLVPII 180

Length = 518

>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction only]

 Score = 45.7 bits (109), Expect = 4e-06
 Identities = 16/43 (37%), Positives = 24/43 (55%)

Query: 88  FTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
           FT +T  Q   IP +  G +++  A TGSGKT A  +P +  +
Sbjct: 20  FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINEL 62

Length = 814

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

 Score = 43.5 bits (103), Expect = 2e-05
 Identities = 27/132 (20%), Positives = 50/132 (37%), Gaps = 28/132 (21%)

Query: 21  LKILQSKEKSKPAEKDS--DANEDEDQTNAVEVQLPGSDVALEILSSTQF-----EALKG 73
           L ++ S   +     +   D  +D +      ++ P      EI +         E    
Sbjct: 4   LSVVASLRSAFKFITEYLEDEFKDAEGQEGSILRDP------EIEARPGKTSEFPELRDE 57

Query: 74  KVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVE----- 128
            +    +KA    G  ++   Q   +  + EGR++V +  TGSGKT +FL+P ++     
Sbjct: 58  SLKSALVKA----GIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRD 113

Query: 129 ------LIYNLK 134
                 L+Y   
Sbjct: 114 PSARALLLYPTN 125

Length = 851

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

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 17/32 (53%), Positives = 24/32 (75%)

Query: 106 RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMP 137
           RD++ +A TGSGKTLA L+P +EL+ +LK   
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDSLKGGQ 32

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

>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional

 Score = 37.2 bits (87), Expect = 0.003
 Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 13/71 (18%)

Query: 88  FTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTL-AFLVPAVELIYNLKFMPRNGKSWQGK 146
           F   T  Q   IP + EG++++ S+ TGSGKTL AFL     +I  L  + R G+     
Sbjct: 30  FGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLA----IIDELFRLGREGE----- 80

Query: 147 LRPLTNGVYLV 157
              L + VY +
Sbjct: 81  ---LEDKVYCL 88

Length = 876

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	178
KOG0338|consensus	691		99.94
KOG0330|consensus	476		99.92
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.91
KOG0346|consensus	569		99.91
KOG0331|consensus	519		99.91
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.91
KOG0343|consensus	758		99.9
KOG0345|consensus	567		99.9
PTZ00110	545	helicase; Provisional	99.9
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.89
KOG0348|consensus	708		99.89
KOG0340|consensus	442		99.89
KOG0342|consensus	543		99.89
KOG0347|consensus	731		99.88
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.88
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.88
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.87
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.87
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.87
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.85
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.85
KOG0335|consensus	482		99.85
KOG0332|consensus	477		99.85
KOG0333|consensus	673		99.84
KOG0334|consensus	997		99.84
PTZ00424	401	helicase 45; Provisional	99.83
KOG0328|consensus	400		99.83
KOG0341|consensus	610		99.81
KOG0326|consensus	459		99.81
KOG0337|consensus	529		99.8
KOG0339|consensus	731		99.8
KOG0344|consensus	593		99.8
KOG0350|consensus	620		99.78
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.78
KOG0327|consensus	397		99.77
KOG0329|consensus	387		99.76
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.75
PRK02362	737	ski2-like helicase; Provisional	99.75
PRK13767	876	ATP-dependent helicase; Provisional	99.73
PRK00254	720	ski2-like helicase; Provisional	99.72
KOG0336|consensus	629		99.71
COG1205	851	Distinct helicase family with a unique C-terminal	99.68
PRK01172	674	ski2-like helicase; Provisional	99.67
KOG4284|consensus	980		99.65
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.59
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.59
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.58
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.54
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.53
PRK09401	1176	reverse gyrase; Reviewed	99.52
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.51
PRK14701	1638	reverse gyrase; Provisional	99.5
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.5
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.5
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.49
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.48
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.48
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.47
PRK10689	1147	transcription-repair coupling factor; Provisional	99.39
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.29
COG1202	830	Superfamily II helicase, archaea-specific [General	99.29
COG1204	766	Superfamily II helicase [General function predicti	99.28
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.27
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.21
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.19
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.18
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.11
PHA02653	675	RNA helicase NPH-II; Provisional	99.1
KOG0952|consensus	1230		99.09
PHA02558	501	uvsW UvsW helicase; Provisional	99.08
PRK05580	679	primosome assembly protein PriA; Validated	99.06
KOG0349|consensus	725		99.05
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.04
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.0
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	98.97
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	98.96
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	98.93
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	98.82
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	98.82
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	98.78
KOG0352|consensus	641		98.77
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	98.75
PRK12904	830	preprotein translocase subunit SecA; Reviewed	98.74
PRK13766	773	Hef nuclease; Provisional	98.74
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	98.67
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	98.66
PRK13107	908	preprotein translocase subunit SecA; Reviewed	98.61
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	98.59
PRK09694	878	helicase Cas3; Provisional	98.59
KOG0353|consensus	695		98.55
KOG0354|consensus	746		98.55
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	98.51
KOG0951|consensus	1674		98.47
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.41
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.39
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.33
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	98.31
KOG0351|consensus	941		98.31
KOG0947|consensus	1248		98.21
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.18
TIGR00595	505	priA primosomal protein N'. All proteins in this f	98.16
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	98.13
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	98.11
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	98.05
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.02
PRK12326	764	preprotein translocase subunit SecA; Reviewed	98.0
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.97
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	97.91
PF13245	76	AAA_19: Part of AAA domain	97.89
KOG0948|consensus	1041		97.87
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	97.86
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	97.81
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	97.81
CHL00122	870	secA preprotein translocase subunit SecA; Validate	97.78
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	97.68
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	97.66
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	97.62
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	97.28
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	97.28
COG1198	730	PriA Primosomal protein N' (replication factor Y)	97.23
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	96.96
KOG0951|consensus	1674		96.94
PRK11054	684	helD DNA helicase IV; Provisional	96.81
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	96.8
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	96.79
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	96.76
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	96.59
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	96.58
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	96.56
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	96.54
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	96.5
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	96.48
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	96.44
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	96.36
TIGR00376	637	DNA helicase, putative. The gene product may repre	96.36
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	96.29
PRK15483	986	type III restriction-modification system StyLTI en	96.22
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.15
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	96.1
KOG0949|consensus	1330		96.07
PRK05298	652	excinuclease ABC subunit B; Provisional	95.62
PRK04914	956	ATP-dependent helicase HepA; Validated	95.62
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	95.43
COG4096	875	HsdR Type I site-specific restriction-modification	95.32
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	95.26
PRK10536	262	hypothetical protein; Provisional	95.25
COG3587	985	Restriction endonuclease [Defense mechanisms]	95.12
PRK13897	606	type IV secretion system component VirD4; Provisio	94.86
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	94.79
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	94.77
KOG4150|consensus	1034		94.77
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	94.71
KOG1803|consensus	649		94.71
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	94.69
PRK13833	323	conjugal transfer protein TrbB; Provisional	94.68
COG4889	1518	Predicted helicase [General function prediction on	94.59
KOG0950|consensus	1008		94.56
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	94.47
PRK13850	670	type IV secretion system protein VirD4; Provisiona	94.41
KOG0952|consensus	1230		94.41
PRK14873	665	primosome assembly protein PriA; Provisional	94.35
KOG1802|consensus	935		94.31
COG3973	747	Superfamily I DNA and RNA helicases [General funct	94.27
PRK13851	344	type IV secretion system protein VirB11; Provision	94.21
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	94.13
PRK10875	615	recD exonuclease V subunit alpha; Provisional	94.04
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	93.92
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	93.84
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	93.72
PRK13880	636	conjugal transfer coupling protein TraG; Provision	93.58
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	93.54
KOG2340|consensus	698		93.54
KOG1133|consensus	821		93.49
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	93.38
PRK13822	641	conjugal transfer coupling protein TraG; Provision	93.32
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	93.25
KOG1132|consensus	945		93.22
PRK13889	988	conjugal transfer relaxase TraA; Provisional	93.21
PRK13876	663	conjugal transfer coupling protein TraG; Provision	93.17
PF12846	304	AAA_10: AAA-like domain	93.04
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	92.89
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	92.87
KOG0953|consensus	700		92.66
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	92.61
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	92.51
COG1484	254	DnaC DNA replication protein [DNA replication, rec	92.51
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	92.5
PRK13764	602	ATPase; Provisional	92.47
COG0210	655	UvrD Superfamily I DNA and RNA helicases [DNA repl	92.45
smart00382	148	AAA ATPases associated with a variety of cellular	92.44
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	92.31
KOG4150|consensus	1034		92.3
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	92.16
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	92.09
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	92.04
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	91.98
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	91.75
PRK10436	462	hypothetical protein; Provisional	91.6
PRK05973	237	replicative DNA helicase; Provisional	91.6
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	91.48
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	91.29
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	91.04
KOG0390|consensus	776		90.67
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	90.63
TIGR03754	643	conj_TOL_TraD conjugative coupling factor TraD, TO	90.51
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	90.37
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	90.31
COG0610	962	Type I site-specific restriction-modification syst	90.22
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	90.14
KOG0926|consensus	1172		90.02
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	89.97
TIGR02533	486	type_II_gspE general secretory pathway protein E.	89.95
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	89.77
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	89.77
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	89.7
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	89.61
PRK08116	268	hypothetical protein; Validated	89.4
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	89.33
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	89.16
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	89.12
PRK13700	732	conjugal transfer protein TraD; Provisional	89.11
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	88.99
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	88.98
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	88.96
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	88.96
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	88.94
PRK06921	266	hypothetical protein; Provisional	88.93
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	88.9
KOG0745|consensus	564		88.89
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	88.81
PF09439	181	SRPRB: Signal recognition particle receptor beta s	88.79
PRK08181	269	transposase; Validated	88.48
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	88.36
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	88.31
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	88.31
PRK09183	259	transposase/IS protein; Provisional	88.22
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	88.21
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	88.19
PRK04328	249	hypothetical protein; Provisional	88.12
KOG0729|consensus	435		88.11
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	88.1
TIGR02759	566	TraD_Ftype type IV conjugative transfer system cou	87.9
PHA02533	534	17 large terminase protein; Provisional	87.69
PHA00729	226	NTP-binding motif containing protein	87.59
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	87.51
PRK06835	329	DNA replication protein DnaC; Validated	87.5
PRK07952	244	DNA replication protein DnaC; Validated	87.15
PRK13826	1102	Dtr system oriT relaxase; Provisional	86.96
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	86.95
PRK12377	248	putative replication protein; Provisional	86.94
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	86.87
PRK08903	227	DnaA regulatory inactivator Hda; Validated	86.73
PRK06526	254	transposase; Provisional	86.57
PF05729	166	NACHT: NACHT domain	86.45
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	86.41
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	86.4
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	86.24
PF13555	62	AAA_29: P-loop containing region of AAA domain	86.0
COG1125	309	OpuBA ABC-type proline/glycine betaine transport s	85.97
PRK08533	230	flagellar accessory protein FlaH; Reviewed	85.86
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	85.83
PRK08084	235	DNA replication initiation factor; Provisional	85.74
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	85.4
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	85.26
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	85.04
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	84.8
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	84.58
PF00004	132	AAA: ATPase family associated with various cellula	84.54
KOG0924|consensus	1042		84.19
KOG1942|consensus	456		84.12
KOG1131|consensus	755		84.0
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	83.89
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	83.63
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	83.5
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	83.41
PLN03025	319	replication factor C subunit; Provisional	83.26
PTZ00112	1164	origin recognition complex 1 protein; Provisional	83.17
TIGR03744	893	traC_PFL_4706 conjugative transfer ATPase, PFL_470	83.12
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	83.03
PRK00131	175	aroK shikimate kinase; Reviewed	82.95
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	82.91
PRK05642	234	DNA replication initiation factor; Validated	82.89
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	82.81
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	82.75
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	82.66
PRK13531	498	regulatory ATPase RavA; Provisional	82.64
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	82.53
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	82.52
TIGR02237	209	recomb_radB DNA repair and recombination protein R	82.52
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	82.17
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	82.03
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	82.02
COG4185	187	Uncharacterized protein conserved in bacteria [Fun	81.75
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	81.71
PRK06067	234	flagellar accessory protein FlaH; Validated	81.4
PRK12402	337	replication factor C small subunit 2; Reviewed	81.32
KOG0989|consensus	346		80.96
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	80.94
CHL00181	287	cbbX CbbX; Provisional	80.74
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	80.64
PRK14729	300	miaA tRNA delta(2)-isopentenylpyrophosphate transf	80.57
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	80.55
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	80.35
PHA02244	383	ATPase-like protein	80.33
KOG0060|consensus	659		80.32
PRK14530	215	adenylate kinase; Provisional	80.11
PLN02165	334	adenylate isopentenyltransferase	80.1
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	80.1

>KOG0338|consensus

Probab=99.94  E-value=9.7e-28  Score=210.37  Aligned_cols=109  Identities=30%  Similarity=0.350  Sum_probs=100.0

Q ss_pred             ccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHh-ccCCCCCceEE
Q psy12984         65 STQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYN-LKFMPRNGKSW  143 (178)
Q Consensus        65 ~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~-~~~~~~~~~~~  143 (178)
                      ..+|.+|+  |+-.|+++|..+||..|||||..+||.++-|+|+++||-||||||.||+||+|++|+- .+..+..+++|
T Consensus       180 ~~sF~~mN--LSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLV  257 (691)
T KOG0338|consen  180 NESFQSMN--LSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKKVAATRVLV  257 (691)
T ss_pred             hhhHHhcc--cchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCcccCcceeEEE
Confidence            35799998  9999999999999999999999999999999999999999999999999999999864 44566779999


Q ss_pred             EeecHHHHHHHHHHHHHHhhhcCCCCcceEEE
Q psy12984        144 QGKLRPLTNGVYLVACNVFKSTQPPTVIKVQT  175 (178)
Q Consensus       144 l~Ptr~La~qi~~~~~~l~~~~~~~~~~~v~~  175 (178)
                      |+||||||.|++.+.+++.+++...++++|+-
T Consensus       258 L~PTRELaiQv~sV~~qlaqFt~I~~~L~vGG  289 (691)
T KOG0338|consen  258 LVPTRELAIQVHSVTKQLAQFTDITVGLAVGG  289 (691)
T ss_pred             EeccHHHHHHHHHHHHHHHhhccceeeeeecC
Confidence            99999999999999999999999877777754

>KOG0330|consensus

Probab=99.92  E-value=1.6e-25  Score=191.21  Aligned_cols=102  Identities=29%  Similarity=0.294  Sum_probs=92.9

Q ss_pred             CCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceE
Q psy12984         63 LSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKS  142 (178)
Q Consensus        63 ~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~  142 (178)
                      ....+|.+|+  +++++++++.+.||..||+||.++||.++.|+|||+.|.||||||++|+|||+++|...+.  ...++
T Consensus        58 e~~~sf~dLg--v~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~--~~~~l  133 (476)
T KOG0330|consen   58 ESFKSFADLG--VHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPK--LFFAL  133 (476)
T ss_pred             hhhcchhhcC--cCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCC--CceEE
Confidence            4456799998  9999999999999999999999999999999999999999999999999999999988543  36899


Q ss_pred             EEeecHHHHHHHHHHHHHHhhhcCCC
Q psy12984        143 WQGKLRPLTNGVYLVACNVFKSTQPP  168 (178)
Q Consensus       143 ~l~Ptr~La~qi~~~~~~l~~~~~~~  168 (178)
                      |++||||||.||..+|..+++.+|..
T Consensus       134 VLtPtRELA~QI~e~fe~Lg~~iglr  159 (476)
T KOG0330|consen  134 VLTPTRELAQQIAEQFEALGSGIGLR  159 (476)
T ss_pred             EecCcHHHHHHHHHHHHHhccccCeE
Confidence            99999999999999999888665544

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

Probab=99.91  E-value=4.5e-24  Score=191.77  Aligned_cols=99  Identities=31%  Similarity=0.419  Sum_probs=89.0

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      ..|++|+  |++.++++|.++||..|||||..+||.++.|+|++++|+||||||+||++|+|+++..........++|++
T Consensus        29 ~~F~~l~--l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aLil~  106 (513)
T COG0513          29 PEFASLG--LSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILA  106 (513)
T ss_pred             CCHhhcC--CCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccccCCCceEEEC
Confidence            5699998  99999999999999999999999999999999999999999999999999999998742111211289999


Q ss_pred             ecHHHHHHHHHHHHHHhhhcC
Q psy12984        146 KLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      ||||||.|+++++..+..+.+
T Consensus       107 PTRELA~Qi~~~~~~~~~~~~  127 (513)
T COG0513         107 PTRELAVQIAEELRKLGKNLG  127 (513)
T ss_pred             CCHHHHHHHHHHHHHHHhhcC
Confidence            999999999999999999875

>KOG0346|consensus

Probab=99.91  E-value=1.6e-24  Score=187.59  Aligned_cols=101  Identities=33%  Similarity=0.438  Sum_probs=92.9

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccC----CCCCce
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKF----MPRNGK  141 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~----~~~~~~  141 (178)
                      .+|++|+  |++.|++++.++||..||-||..|||.++.|+|+++.|.||||||+||+||+|+.|...+.    ..++.+
T Consensus        19 ktFe~~g--LD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa   96 (569)
T KOG0346|consen   19 KTFEEFG--LDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSA   96 (569)
T ss_pred             ccHHHhC--CCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhccccccccee
Confidence            5799998  9999999999999999999999999999999999999999999999999999999987544    346688


Q ss_pred             EEEeecHHHHHHHHHHHHHHhhhcCCC
Q psy12984        142 SWQGKLRPLTNGVYLVACNVFKSTQPP  168 (178)
Q Consensus       142 ~~l~Ptr~La~qi~~~~~~l~~~~~~~  168 (178)
                      ++|+||||||+|+|.++..+..+.+..
T Consensus        97 ~iLvPTkEL~qQvy~viekL~~~c~k~  123 (569)
T KOG0346|consen   97 VILVPTKELAQQVYKVIEKLVEYCSKD  123 (569)
T ss_pred             EEEechHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999998876643

>KOG0331|consensus

Probab=99.91  E-value=2.8e-24  Score=190.88  Aligned_cols=100  Identities=40%  Similarity=0.442  Sum_probs=91.5

Q ss_pred             ccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhc----cCCCCCc
Q psy12984         65 STQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNL----KFMPRNG  140 (178)
Q Consensus        65 ~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~----~~~~~~~  140 (178)
                      +..|++++  |++++..++...||..|||||+.+||.++.|+|+++.|.|||||||+|+||+|.++...    ....++.
T Consensus        90 ~~~f~~~~--ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~  167 (519)
T KOG0331|consen   90 SAAFQELG--LSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPI  167 (519)
T ss_pred             chhhhccc--ccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCe
Confidence            34799998  99999999999999999999999999999999999999999999999999999999862    2345778


Q ss_pred             eEEEeecHHHHHHHHHHHHHHhhhcC
Q psy12984        141 KSWQGKLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus       141 ~~~l~Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      +++|+||||||.||+.++..+...+.
T Consensus       168 vLVL~PTRELA~QV~~~~~~~~~~~~  193 (519)
T KOG0331|consen  168 VLVLAPTRELAVQVQAEAREFGKSLR  193 (519)
T ss_pred             EEEEcCcHHHHHHHHHHHHHHcCCCC
Confidence            99999999999999999999887766

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.91  E-value=4.2e-24  Score=187.16  Aligned_cols=103  Identities=26%  Similarity=0.378  Sum_probs=92.4

Q ss_pred             CccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccC-----CCC
Q psy12984         64 SSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKF-----MPR  138 (178)
Q Consensus        64 ~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~-----~~~  138 (178)
                      ...+|++|+  |+++++++|.++||..|||+|.+|||.++.|+|++++||||||||++|++|+++.+.....     ...
T Consensus         6 ~~~~f~~~~--l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~   83 (423)
T PRK04837          6 TEQKFSDFA--LHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQ   83 (423)
T ss_pred             CCCCHhhCC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCC
Confidence            446899998  9999999999999999999999999999999999999999999999999999999975432     234


Q ss_pred             CceEEEeecHHHHHHHHHHHHHHhhhcCCC
Q psy12984        139 NGKSWQGKLRPLTNGVYLVACNVFKSTQPP  168 (178)
Q Consensus       139 ~~~~~l~Ptr~La~qi~~~~~~l~~~~~~~  168 (178)
                      .+++||+|||+||.|+++++..+...++..
T Consensus        84 ~~~lil~PtreLa~Qi~~~~~~l~~~~~~~  113 (423)
T PRK04837         84 PRALIMAPTRELAVQIHADAEPLAQATGLK  113 (423)
T ss_pred             ceEEEECCcHHHHHHHHHHHHHHhccCCce
Confidence            689999999999999999999998776543

>KOG0343|consensus

Probab=99.90  E-value=2.3e-24  Score=190.60  Aligned_cols=111  Identities=40%  Similarity=0.552  Sum_probs=101.2

Q ss_pred             CCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCC--CC
Q psy12984         62 ILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMP--RN  139 (178)
Q Consensus        62 ~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~--~~  139 (178)
                      +.....|++|+  |+..++++|.+.+|..||.||+.+||..|.|+|||++|.|||||||||++|+|++|++.++.+  +.
T Consensus        65 ~~~~~kF~dlp--ls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGl  142 (758)
T KOG0343|consen   65 STTIKKFADLP--LSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGL  142 (758)
T ss_pred             hhhhhhHHhCC--CchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCCCCCCc
Confidence            34557899998  999999999999999999999999999999999999999999999999999999999988754  77


Q ss_pred             ceEEEeecHHHHHHHHHHHHHHhhhcCCCCcceEE
Q psy12984        140 GKSWQGKLRPLTNGVYLVACNVFKSTQPPTVIKVQ  174 (178)
Q Consensus       140 ~~~~l~Ptr~La~qi~~~~~~l~~~~~~~~~~~v~  174 (178)
                      +++||+||||||.|++.++.++++...-..++-++
T Consensus       143 GalIISPTRELA~QtFevL~kvgk~h~fSaGLiiG  177 (758)
T KOG0343|consen  143 GALIISPTRELALQTFEVLNKVGKHHDFSAGLIIG  177 (758)
T ss_pred             eeEEecchHHHHHHHHHHHHHHhhccccccceeec
Confidence            89999999999999999999999887776665543

>KOG0345|consensus

Probab=99.90  E-value=1.7e-23  Score=182.21  Aligned_cols=101  Identities=39%  Similarity=0.540  Sum_probs=91.3

Q ss_pred             ccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccC-CC--CCce
Q psy12984         65 STQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKF-MP--RNGK  141 (178)
Q Consensus        65 ~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~-~~--~~~~  141 (178)
                      ...|+++..+|+++++.++..+||...||+|..|||.++.++||++.|+||||||+||++|+++.+++... .+  ..++
T Consensus         3 ~~~~~~l~~~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vga   82 (567)
T KOG0345|consen    3 PKSFSSLAPPLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGA   82 (567)
T ss_pred             CcchhhcCCCccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeE
Confidence            35799999889999999999999999999999999999999999999999999999999999999966432 22  2478


Q ss_pred             EEEeecHHHHHHHHHHHHHHhhhc
Q psy12984        142 SWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus       142 ~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      +||+||||||.||+.++..+...+
T Consensus        83 lIIsPTRELa~QI~~V~~~F~~~l  106 (567)
T KOG0345|consen   83 LIISPTRELARQIREVAQPFLEHL  106 (567)
T ss_pred             EEecCcHHHHHHHHHHHHHHHHhh
Confidence            999999999999999999998884

>PTZ00110 helicase; Provisional

Probab=99.90  E-value=1.8e-23  Score=189.01  Aligned_cols=108  Identities=32%  Similarity=0.413  Sum_probs=93.9

Q ss_pred             CCCCCCcCCCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhc
Q psy12984         54 PGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNL  133 (178)
Q Consensus        54 ~~~~~~~~~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~  133 (178)
                      .+.+.|.++   .+|++++  |++.++++|.++||..||+||..|||.++.|+|+|++|+||||||++|++|++.++...
T Consensus       121 ~g~~~p~p~---~~f~~~~--l~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~  195 (545)
T PTZ00110        121 AGENVPKPV---VSFEYTS--FPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQ  195 (545)
T ss_pred             cCCCCCccc---CCHhhcC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhc
Confidence            456666555   4599987  99999999999999999999999999999999999999999999999999999988753


Q ss_pred             c---CCCCCceEEEeecHHHHHHHHHHHHHHhhhcC
Q psy12984        134 K---FMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus       134 ~---~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      .   ...++.++||+||||||.|++..+..+...++
T Consensus       196 ~~~~~~~gp~~LIL~PTreLa~Qi~~~~~~~~~~~~  231 (545)
T PTZ00110        196 PLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASSK  231 (545)
T ss_pred             ccccCCCCcEEEEECChHHHHHHHHHHHHHHhcccC
Confidence            2   23356789999999999999999999876543

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

Probab=99.89  E-value=1.8e-23  Score=187.90  Aligned_cols=116  Identities=30%  Similarity=0.323  Sum_probs=99.0

Q ss_pred             ccccccccCCCCCCcCCCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHH
Q psy12984         46 TNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVP  125 (178)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp  125 (178)
                      .....+...|.+.|.|+.+   |++++  |++.++++|..+||..|||+|.+|||.++.|+|+|++|+||||||++|++|
T Consensus       104 r~~~~i~~~g~~~p~pi~~---f~~~~--l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllP  178 (518)
T PLN00206        104 RRKLEIHVKGEAVPPPILS---FSSCG--LPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVP  178 (518)
T ss_pred             HHHCCCEecCCCCCchhcC---HHhCC--CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHH
Confidence            3445556677777766655   99988  999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcc-----CCCCCceEEEeecHHHHHHHHHHHHHHhhhcC
Q psy12984        126 AVELIYNLK-----FMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus       126 ~l~~l~~~~-----~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      ++.++....     ....+.++||+||||||.|++..+..+.+.++
T Consensus       179 il~~l~~~~~~~~~~~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~~  224 (518)
T PLN00206        179 IISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLP  224 (518)
T ss_pred             HHHHHHhhccccccccCCceEEEEeCCHHHHHHHHHHHHHHhCCCC
Confidence            999886421     12456899999999999999999988876553

>KOG0348|consensus

Probab=99.89  E-value=2.7e-23  Score=183.28  Aligned_cols=105  Identities=29%  Similarity=0.364  Sum_probs=94.9

Q ss_pred             CCCCccchHhhcccCCHHHHHHHHH-CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhcc----C
Q psy12984         61 EILSSTQFEALKGKVCENTLKAIAD-MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLK----F  135 (178)
Q Consensus        61 ~~~~~~~f~~l~~~l~~~ll~~l~~-~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~----~  135 (178)
                      -+.....|..|+  |++.+...|.. +++..||.||..|||.++.|+|++|.|+||||||+||++|+++.|....    .
T Consensus       131 ~~fts~~f~~LG--L~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~R  208 (708)
T KOG0348|consen  131 APFTSAAFASLG--LHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQR  208 (708)
T ss_pred             cccccccchhcC--CCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccccc
Confidence            346678899998  99999999976 9999999999999999999999999999999999999999999998632    3


Q ss_pred             CCCCceEEEeecHHHHHHHHHHHHHHhhhcCC
Q psy12984        136 MPRNGKSWQGKLRPLTNGVYLVACNVFKSTQP  167 (178)
Q Consensus       136 ~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~~  167 (178)
                      ..+..++||+||||||.|+|++++++++.+.+
T Consensus       209 s~G~~ALVivPTREL~~Q~y~~~qKLl~~~hW  240 (708)
T KOG0348|consen  209 SDGPYALVIVPTRELALQIYETVQKLLKPFHW  240 (708)
T ss_pred             cCCceEEEEechHHHHHHHHHHHHHHhcCceE
Confidence            55778999999999999999999999987654

>KOG0340|consensus

Probab=99.89  E-value=1.6e-23  Score=177.50  Aligned_cols=101  Identities=29%  Similarity=0.288  Sum_probs=91.4

Q ss_pred             ccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEE
Q psy12984         65 STQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQ  144 (178)
Q Consensus        65 ~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l  144 (178)
                      ...|+.|+  |++|+.+.|..+|+..|||||..|||.++.|+|+|++|.||||||++|.+|+++++...  ..+..++++
T Consensus         6 ~~~F~~LG--l~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsed--P~giFalvl   81 (442)
T KOG0340|consen    6 AKPFSILG--LSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSED--PYGIFALVL   81 (442)
T ss_pred             cCchhhcC--ccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccC--CCcceEEEe
Confidence            46799998  99999999999999999999999999999999999999999999999999999999764  445688999


Q ss_pred             eecHHHHHHHHHHHHHHhhhcCCCC
Q psy12984        145 GKLRPLTNGVYLVACNVFKSTQPPT  169 (178)
Q Consensus       145 ~Ptr~La~qi~~~~~~l~~~~~~~~  169 (178)
                      +||||||.|+.+.|..+++.++..+
T Consensus        82 TPTrELA~QiaEQF~alGk~l~lK~  106 (442)
T KOG0340|consen   82 TPTRELALQIAEQFIALGKLLNLKV  106 (442)
T ss_pred             cchHHHHHHHHHHHHHhcccccceE
Confidence            9999999999999888776655543

>KOG0342|consensus

Probab=99.89  E-value=7.2e-23  Score=178.91  Aligned_cols=102  Identities=46%  Similarity=0.701  Sum_probs=93.6

Q ss_pred             CCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCC--CC
Q psy12984         62 ILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMP--RN  139 (178)
Q Consensus        62 ~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~--~~  139 (178)
                      +.....|+++.  |++.++++|.++||..+|+||+.+||.++.|+|+++.|.||||||+||+||+++++...+..+  ..
T Consensus        78 ~~~~~~f~~~~--LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~  155 (543)
T KOG0342|consen   78 ITTTFRFEEGS--LSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGT  155 (543)
T ss_pred             hhhhhHhhccc--cCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCCCCCe
Confidence            45567788887  999999999999999999999999999999999999999999999999999999998876544  44


Q ss_pred             ceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984        140 GKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus       140 ~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      .++||+||||||.|++.+++.++.+.
T Consensus       156 ~vlIi~PTRELA~Q~~~eak~Ll~~h  181 (543)
T KOG0342|consen  156 GVLIICPTRELAMQIFAEAKELLKYH  181 (543)
T ss_pred             eEEEecccHHHHHHHHHHHHHHHhhC
Confidence            77889999999999999999999987

>KOG0347|consensus

Probab=99.88  E-value=4.2e-23  Score=182.57  Aligned_cols=107  Identities=31%  Similarity=0.438  Sum_probs=89.6

Q ss_pred             CccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCC-CcEEEEccCCCchhhHhHHHHHHHHHh---------c
Q psy12984         64 SSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEG-RDLVGSAKTGSGKTLAFLVPAVELIYN---------L  133 (178)
Q Consensus        64 ~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g-~dvi~~a~TGsGKTlaf~lp~l~~l~~---------~  133 (178)
                      +...|.+|.  |+.++|++|..+||.+||+||..+||++..| .||++.|.|||||||||.||+++.+..         .
T Consensus       179 DvsAW~~l~--lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~  256 (731)
T KOG0347|consen  179 DVSAWKNLF--LPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELSN  256 (731)
T ss_pred             ChHHHhcCC--CCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhhhh
Confidence            335588886  9999999999999999999999999999999 899999999999999999999995543         2


Q ss_pred             c--CCCCCceEEEeecHHHHHHHHHHHHHHhhhcCCCCcceEEEe
Q psy12984        134 K--FMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQPPTVIKVQTL  176 (178)
Q Consensus       134 ~--~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~~~~~~~v~~~  176 (178)
                      -  ....+.++|++||||||.||...+..++.+++    |+|.++
T Consensus       257 ~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~----i~v~si  297 (731)
T KOG0347|consen  257 TSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQ----IRVASI  297 (731)
T ss_pred             HHhccCcceeEEecChHHHHHHHHHHHHHhccccC----eEEEEe
Confidence            1  12233489999999999999999999887544    555544

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.88  E-value=2.7e-22  Score=177.65  Aligned_cols=98  Identities=30%  Similarity=0.417  Sum_probs=88.4

Q ss_pred             chHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccC----CCCCceE
Q psy12984         67 QFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKF----MPRNGKS  142 (178)
Q Consensus        67 ~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~----~~~~~~~  142 (178)
                      +|++|+  |+++++++|.++||..||++|..|||.++.|+|+|++||||||||++|++|+++.+.....    ....+++
T Consensus         2 ~f~~l~--l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aL   79 (456)
T PRK10590          2 SFDSLG--LSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRAL   79 (456)
T ss_pred             CHHHcC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEE
Confidence            599998  9999999999999999999999999999999999999999999999999999999865322    1234789


Q ss_pred             EEeecHHHHHHHHHHHHHHhhhcC
Q psy12984        143 WQGKLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus       143 ~l~Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      ||+|||+||.|++.++..+.+.++
T Consensus        80 il~PtreLa~Qi~~~~~~~~~~~~  103 (456)
T PRK10590         80 ILTPTRELAAQIGENVRDYSKYLN  103 (456)
T ss_pred             EEeCcHHHHHHHHHHHHHHhccCC
Confidence            999999999999999999887654

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.88  E-value=1.8e-22  Score=183.45  Aligned_cols=99  Identities=29%  Similarity=0.352  Sum_probs=88.9

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhcc-----CCCCCc
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLK-----FMPRNG  140 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~-----~~~~~~  140 (178)
                      .+|++|+  |++.++++|.++||..|||||..+||.++.|+|++++||||||||++|++|+++++....     .....+
T Consensus         9 ~~f~~l~--l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~r   86 (572)
T PRK04537          9 LTFSSFD--LHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPR   86 (572)
T ss_pred             CChhhcC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCce
Confidence            4699998  999999999999999999999999999999999999999999999999999999986532     122468


Q ss_pred             eEEEeecHHHHHHHHHHHHHHhhhcC
Q psy12984        141 KSWQGKLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus       141 ~~~l~Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      ++||+||||||.|++..+..++..++
T Consensus        87 aLIl~PTreLa~Qi~~~~~~l~~~~~  112 (572)
T PRK04537         87 ALILAPTRELAIQIHKDAVKFGADLG  112 (572)
T ss_pred             EEEEeCcHHHHHHHHHHHHHHhccCC
Confidence            99999999999999999998876654

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.87  E-value=4e-22  Score=177.16  Aligned_cols=101  Identities=29%  Similarity=0.360  Sum_probs=90.6

Q ss_pred             ccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCC-----CCC
Q psy12984         65 STQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFM-----PRN  139 (178)
Q Consensus        65 ~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~-----~~~  139 (178)
                      ...|.+++  |++.++++|.++||..||+||.+||+.++.|+|+|++|+||||||++|++|+++.+......     ...
T Consensus        86 ~~~f~~~~--l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~  163 (475)
T PRK01297         86 KTRFHDFN--LAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEP  163 (475)
T ss_pred             CCCHhHCC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCc
Confidence            45799998  99999999999999999999999999999999999999999999999999999998764321     246


Q ss_pred             ceEEEeecHHHHHHHHHHHHHHhhhcCC
Q psy12984        140 GKSWQGKLRPLTNGVYLVACNVFKSTQP  167 (178)
Q Consensus       140 ~~~~l~Ptr~La~qi~~~~~~l~~~~~~  167 (178)
                      +++||+|||+||.|++..+..+.+.++.
T Consensus       164 ~aLil~PtreLa~Q~~~~~~~l~~~~~~  191 (475)
T PRK01297        164 RALIIAPTRELVVQIAKDAAALTKYTGL  191 (475)
T ss_pred             eEEEEeCcHHHHHHHHHHHHHhhccCCC
Confidence            8899999999999999999998876653

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.87  E-value=6.8e-22  Score=174.88  Aligned_cols=96  Identities=30%  Similarity=0.383  Sum_probs=87.8

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      .+|++|+  |++.++++|..+||..|||+|.+|||.++.|+|++++||||||||++|++|+++++...  ....+++|++
T Consensus         4 ~~f~~l~--l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~--~~~~~~lil~   79 (460)
T PRK11776          4 TAFSTLP--LPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVK--RFRVQALVLC   79 (460)
T ss_pred             CChhhcC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhc--cCCceEEEEe
Confidence            4699998  99999999999999999999999999999999999999999999999999999998643  2345789999


Q ss_pred             ecHHHHHHHHHHHHHHhhhc
Q psy12984        146 KLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~~~~  165 (178)
                      |||+||.|++..++.+....
T Consensus        80 PtreLa~Q~~~~~~~~~~~~   99 (460)
T PRK11776         80 PTRELADQVAKEIRRLARFI   99 (460)
T ss_pred             CCHHHHHHHHHHHHHHHhhC
Confidence            99999999999999987654

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.87  E-value=5.2e-22  Score=174.27  Aligned_cols=100  Identities=38%  Similarity=0.502  Sum_probs=90.2

Q ss_pred             chHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhcc--CCCCCceEEE
Q psy12984         67 QFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLK--FMPRNGKSWQ  144 (178)
Q Consensus        67 ~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~--~~~~~~~~~l  144 (178)
                      +|++|+  |++.++++|.++||..||++|.+|||+++.|+|++++||||+|||++|++|+++++....  .....+++|+
T Consensus         2 ~f~~l~--l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil   79 (434)
T PRK11192          2 TFSELE--LDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILIL   79 (434)
T ss_pred             CHhhcC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEE
Confidence            699998  999999999999999999999999999999999999999999999999999999987532  1234588999


Q ss_pred             eecHHHHHHHHHHHHHHhhhcCCC
Q psy12984        145 GKLRPLTNGVYLVACNVFKSTQPP  168 (178)
Q Consensus       145 ~Ptr~La~qi~~~~~~l~~~~~~~  168 (178)
                      +||++||.|+++++..+...++..
T Consensus        80 ~Pt~eLa~Q~~~~~~~l~~~~~~~  103 (434)
T PRK11192         80 TPTRELAMQVADQARELAKHTHLD  103 (434)
T ss_pred             CCcHHHHHHHHHHHHHHHccCCcE
Confidence            999999999999999998776543

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.85  E-value=3.8e-21  Score=176.42  Aligned_cols=96  Identities=34%  Similarity=0.438  Sum_probs=88.2

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      ..|++|+  |++.++++|.++||..|||+|.++||.++.|+|+|++||||||||++|++|+++.+...  ...++++||+
T Consensus         6 ~~f~~l~--L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~--~~~~~~LIL~   81 (629)
T PRK11634          6 TTFADLG--LKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPE--LKAPQILVLA   81 (629)
T ss_pred             CCHhhcC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhc--cCCCeEEEEe
Confidence            4699998  99999999999999999999999999999999999999999999999999999988643  2345889999


Q ss_pred             ecHHHHHHHHHHHHHHhhhc
Q psy12984        146 KLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~~~~  165 (178)
                      |||+||.|++..+..+.+.+
T Consensus        82 PTreLa~Qv~~~l~~~~~~~  101 (629)
T PRK11634         82 PTRELAVQVAEAMTDFSKHM  101 (629)
T ss_pred             CcHHHHHHHHHHHHHHHhhc
Confidence            99999999999999987765

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

Probab=99.85  E-value=2.6e-21  Score=180.32  Aligned_cols=92  Identities=20%  Similarity=0.254  Sum_probs=84.5

Q ss_pred             hHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeec
Q psy12984         68 FEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKL  147 (178)
Q Consensus        68 f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Pt  147 (178)
                      |..++.+|++.+.++|.++||..||+||..|||.++.|+|++++||||||||+||++|+|+.+..   .+..+++||+||
T Consensus        14 ~~~~~~~l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~---~~~~~aL~l~Pt   90 (742)
T TIGR03817        14 TAPWPAWAHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALAD---DPRATALYLAPT   90 (742)
T ss_pred             cCCCCCcCCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhh---CCCcEEEEEcCh
Confidence            44555569999999999999999999999999999999999999999999999999999999976   345689999999


Q ss_pred             HHHHHHHHHHHHHHh
Q psy12984        148 RPLTNGVYLVACNVF  162 (178)
Q Consensus       148 r~La~qi~~~~~~l~  162 (178)
                      ||||+|++..++.+.
T Consensus        91 raLa~q~~~~l~~l~  105 (742)
T TIGR03817        91 KALAADQLRAVRELT  105 (742)
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999886

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.

>KOG0335|consensus

Probab=99.85  E-value=1.4e-21  Score=171.79  Aligned_cols=126  Identities=29%  Similarity=0.348  Sum_probs=108.4

Q ss_pred             CCCccccccccccccccCCCCCCcCCCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCC
Q psy12984         37 SDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGS  116 (178)
Q Consensus        37 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGs  116 (178)
                      .+.....+..+.+.++..+.+.|.++.   .|++-.  +.+.+..++...||..|||||+.+||.+..|+|+++||+|||
T Consensus        48 ~~~~~nfd~~~~i~v~~~G~~~p~~i~---~f~~~~--l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGs  122 (482)
T KOG0335|consen   48 ISTGINFDKYNDIPVKVSGRDVPPHIP---TFDEAI--LGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGS  122 (482)
T ss_pred             cchhhccCCccceeeeccCCccCCCcc---cccccc--hhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCC
Confidence            345556677788889999999988877   476554  889999999999999999999999999999999999999999


Q ss_pred             chhhHhHHHHHHHHHhccCC--------CCCceEEEeecHHHHHHHHHHHHHHhhhcCC
Q psy12984        117 GKTLAFLVPAVELIYNLKFM--------PRNGKSWQGKLRPLTNGVYLVACNVFKSTQP  167 (178)
Q Consensus       117 GKTlaf~lp~l~~l~~~~~~--------~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~~  167 (178)
                      |||.||++|++.+++.....        ..++++|++||||||.|+|+..+++......
T Consensus       123 GKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~lIlapTReL~~Qi~nea~k~~~~s~~  181 (482)
T KOG0335|consen  123 GKTAAFLIPIISYLLDEGPEDRGESGGGVYPRALILAPTRELVDQIYNEARKFSYLSGM  181 (482)
T ss_pred             cchHHHHHHHHHHHHhcCcccCcccCCCCCCceEEEeCcHHHhhHHHHHHHhhcccccc
Confidence            99999999999999875331        2578999999999999999999988755443

>KOG0332|consensus

Probab=99.85  E-value=9.6e-22  Score=167.59  Aligned_cols=106  Identities=25%  Similarity=0.310  Sum_probs=98.4

Q ss_pred             CCCcCCCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCC--CcEEEEccCCCchhhHhHHHHHHHHHhcc
Q psy12984         57 DVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEG--RDLVGSAKTGSGKTLAFLVPAVELIYNLK  134 (178)
Q Consensus        57 ~~~~~~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g--~dvi~~a~TGsGKTlaf~lp~l~~l~~~~  134 (178)
                      ++..|+++..+|++|.  |.|+++++|+.++|.+|+.||..|+|.++..  +|+|+++.+|+|||.||+|.+|.++... 
T Consensus        81 dpnsPlyS~ksFeeL~--LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~-  157 (477)
T KOG0332|consen   81 DPNSPLYSAKSFEELR--LKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPD-  157 (477)
T ss_pred             CCCCCccccccHHhhC--CCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCcc-
Confidence            5778999999999998  9999999999999999999999999999976  8999999999999999999999988653 


Q ss_pred             CCCCCceEEEeecHHHHHHHHHHHHHHhhhcC
Q psy12984        135 FMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus       135 ~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~  166 (178)
                       ...+++++|+|||+||.|+.+++..++++.+
T Consensus       158 -~~~PQ~iCLaPtrELA~Q~~eVv~eMGKf~~  188 (477)
T KOG0332|consen  158 -VVVPQCICLAPTRELAPQTGEVVEEMGKFTE  188 (477)
T ss_pred             -ccCCCceeeCchHHHHHHHHHHHHHhcCcee
Confidence             4566999999999999999999999999873

>KOG0333|consensus

Probab=99.84  E-value=6.3e-21  Score=168.11  Aligned_cols=122  Identities=26%  Similarity=0.317  Sum_probs=106.5

Q ss_pred             cccccccCCCCCCcCCCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHH
Q psy12984         47 NAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPA  126 (178)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~  126 (178)
                      ....++..|...+.|+-+   |++.+  |+.++++.+...||..|||||+.|||..+..+|+|+.|.||||||+||++|+
T Consensus       229 edynis~kg~~lpnplrn---wEE~~--~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsGktaaf~ipL  303 (673)
T KOG0333|consen  229 EDYNISIKGGRLPNPLRN---WEESG--FPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPL  303 (673)
T ss_pred             cceeeeecCCCCCccccC---hhhcC--CCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccCCccccchhhH
Confidence            345566778888888877   99998  9999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhccC-------CCCCceEEEeecHHHHHHHHHHHHHHhhhcCCCCcceEEEee
Q psy12984        127 VELIYNLKF-------MPRNGKSWQGKLRPLTNGVYLVACNVFKSTQPPTVIKVQTLI  177 (178)
Q Consensus       127 l~~l~~~~~-------~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~~~~~~~v~~~i  177 (178)
                      +.+|.+.+.       ..++.+++++|||+||+||...-.++++.++    +++.++|
T Consensus       304 l~~IsslP~~~~~en~~~gpyaiilaptReLaqqIeeEt~kf~~~lg----~r~vsvi  357 (673)
T KOG0333|consen  304 LIWISSLPPMARLENNIEGPYAIILAPTRELAQQIEEETNKFGKPLG----IRTVSVI  357 (673)
T ss_pred             HHHHHcCCCcchhhhcccCceeeeechHHHHHHHHHHHHHHhccccc----ceEEEEe
Confidence            999987542       3467899999999999999999888776665    5666554

>KOG0334|consensus

Probab=99.84  E-value=1e-20  Score=176.62  Aligned_cols=111  Identities=29%  Similarity=0.432  Sum_probs=97.9

Q ss_pred             cccCCCCCCcCCCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHH
Q psy12984         51 VQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI  130 (178)
Q Consensus        51 ~~~~~~~~~~~~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l  130 (178)
                      ++..+...+.|+.+   |...+  ++..++..++++||..|++||..|||+++.|+|||+.|.||||||++|+||++.++
T Consensus       353 i~v~g~~~pkpv~s---W~q~g--l~~~il~tlkkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi  427 (997)
T KOG0334|consen  353 IKVKGKECPKPVTS---WTQCG--LSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHI  427 (997)
T ss_pred             eeeccCCCCcccch---HhhCC--chHHHHHHHHHhcCCCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhh
Confidence            55667777777766   88887  99999999999999999999999999999999999999999999999999999888


Q ss_pred             HhccC---CCCCceEEEeecHHHHHHHHHHHHHHhhhcC
Q psy12984        131 YNLKF---MPRNGKSWQGKLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus       131 ~~~~~---~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      ...+.   ..++.++|++|||+||.||++.+..|++.++
T Consensus       428 ~dQr~~~~gdGPi~li~aPtrela~QI~r~~~kf~k~l~  466 (997)
T KOG0334|consen  428 KDQRPLEEGDGPIALILAPTRELAMQIHREVRKFLKLLG  466 (997)
T ss_pred             hcCCChhhCCCceEEEEcCCHHHHHHHHHHHHHHHhhcC
Confidence            65432   3477889999999999999999999987733

>PTZ00424 helicase 45; Provisional

Probab=99.83  E-value=2.8e-20  Score=161.03  Aligned_cols=98  Identities=32%  Similarity=0.463  Sum_probs=88.3

Q ss_pred             ccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEE
Q psy12984         65 STQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQ  144 (178)
Q Consensus        65 ~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l  144 (178)
                      ..+|++++  |++.++++|...||..|+|+|..||+.++.|+|++++||||||||++|++|++..+...  ....++++|
T Consensus        27 ~~~~~~l~--l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~--~~~~~~lil  102 (401)
T PTZ00424         27 VDSFDALK--LNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYD--LNACQALIL  102 (401)
T ss_pred             cCCHhhCC--CCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCC--CCCceEEEE
Confidence            35799998  99999999999999999999999999999999999999999999999999999987532  234578999


Q ss_pred             eecHHHHHHHHHHHHHHhhhcC
Q psy12984        145 GKLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus       145 ~Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      +|||+||.|++..+..++...+
T Consensus       103 ~Pt~~L~~Q~~~~~~~~~~~~~  124 (401)
T PTZ00424        103 APTRELAQQIQKVVLALGDYLK  124 (401)
T ss_pred             CCCHHHHHHHHHHHHHHhhhcC
Confidence            9999999999999998876544

>KOG0328|consensus

Probab=99.83  E-value=2.9e-21  Score=160.09  Aligned_cols=104  Identities=24%  Similarity=0.365  Sum_probs=91.8

Q ss_pred             CCCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCc
Q psy12984         61 EILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG  140 (178)
Q Consensus        61 ~~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~  140 (178)
                      .+....+|++++  |.++++++++++||+.|+.||+.|||.++.|+|||++|.+|+|||.+|.+.+++.+.-.  ....+
T Consensus        22 ~~~v~~~F~~Mg--l~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~--~r~tQ   97 (400)
T KOG0328|consen   22 KVKVIPTFDDMG--LKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDIS--VRETQ   97 (400)
T ss_pred             CcccccchhhcC--chHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccc--cceee
Confidence            344556899999  99999999999999999999999999999999999999999999999999999877542  22358


Q ss_pred             eEEEeecHHHHHHHHHHHHHHhhhcCCC
Q psy12984        141 KSWQGKLRPLTNGVYLVACNVFKSTQPP  168 (178)
Q Consensus       141 ~~~l~Ptr~La~qi~~~~~~l~~~~~~~  168 (178)
                      +++++||||||.|+..++..++..++..
T Consensus        98 ~lilsPTRELa~Qi~~vi~alg~~mnvq  125 (400)
T KOG0328|consen   98 ALILSPTRELAVQIQKVILALGDYMNVQ  125 (400)
T ss_pred             EEEecChHHHHHHHHHHHHHhcccccce
Confidence            9999999999999999998887666544

>KOG0341|consensus

Probab=99.81  E-value=3.1e-20  Score=159.43  Aligned_cols=116  Identities=26%  Similarity=0.351  Sum_probs=100.6

Q ss_pred             ccccccccCCCCCCcCCCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHH
Q psy12984         46 TNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVP  125 (178)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp  125 (178)
                      +....+...|.++|+|+.+   |.++.  ++..+++.|++.|+.+|||||.+-||.+++|||+|+.|.||||||+.|+||
T Consensus       153 Rk~~~I~veGd~ipPPIks---F~eMK--FP~~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP  227 (610)
T KOG0341|consen  153 RKQLHILVEGDDIPPPIKS---FKEMK--FPKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLP  227 (610)
T ss_pred             HHhheEEeeCCCCCCchhh---hhhcc--CCHHHHHHHHhcCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHH
Confidence            3444556678888888876   98997  999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhc------cCCCCCceEEEeecHHHHHHHHHHHHHHhhhcC
Q psy12984        126 AVELIYNL------KFMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus       126 ~l~~l~~~------~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      +|...+..      ....++..+||||+||||.|+++.+..++..+.
T Consensus       228 ~imf~LeqE~~lPf~~~EGP~gLiicPSRELArQt~~iie~~~~~L~  274 (610)
T KOG0341|consen  228 VIMFALEQEMMLPFARGEGPYGLIICPSRELARQTHDIIEQYVAALQ  274 (610)
T ss_pred             HHHHHHHHHhcCccccCCCCeeEEEcCcHHHHHHHHHHHHHHHHHHH
Confidence            99876642      224577889999999999999999888876554

>KOG0326|consensus

Probab=99.81  E-value=1.2e-20  Score=158.54  Aligned_cols=98  Identities=30%  Similarity=0.329  Sum_probs=90.4

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      ..|+++.  |..+++..+.+.||+.|+|||.++||.++.|+|+++.|..|+|||.||++|+|+++...  ....++++++
T Consensus        85 ~efEd~~--Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~--~~~IQ~~ilV  160 (459)
T KOG0326|consen   85 NEFEDYC--LKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPK--KNVIQAIILV  160 (459)
T ss_pred             ccHHHhh--hhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCcc--ccceeEEEEe
Confidence            4599998  99999999999999999999999999999999999999999999999999999998654  4456889999


Q ss_pred             ecHHHHHHHHHHHHHHhhhcCC
Q psy12984        146 KLRPLTNGVYLVACNVFKSTQP  167 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~~~~~~  167 (178)
                      ||||||.|+..++..+.+.++.
T Consensus       161 PtrelALQtSqvc~~lskh~~i  182 (459)
T KOG0326|consen  161 PTRELALQTSQVCKELSKHLGI  182 (459)
T ss_pred             ecchhhHHHHHHHHHHhcccCe
Confidence            9999999999999999887764

>KOG0337|consensus

Probab=99.80  E-value=5.2e-20  Score=158.90  Aligned_cols=105  Identities=34%  Similarity=0.441  Sum_probs=96.6

Q ss_pred             ccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEE
Q psy12984         65 STQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQ  144 (178)
Q Consensus        65 ~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l  144 (178)
                      ...|..++  |+..++++|.+.||..|||||+++||.++.|+|+++.|.||||||+||++|+++++.... ..+.+++++
T Consensus        20 ~g~fqsmg--L~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s-~~g~Ralil   96 (529)
T KOG0337|consen   20 SGGFQSMG--LDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHS-QTGLRALIL   96 (529)
T ss_pred             CCCccccC--CCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhcc-ccccceeec
Confidence            45699998  999999999999999999999999999999999999999999999999999999998765 566799999


Q ss_pred             eecHHHHHHHHHHHHHHhhhcCCCCcce
Q psy12984        145 GKLRPLTNGVYLVACNVFKSTQPPTVIK  172 (178)
Q Consensus       145 ~Ptr~La~qi~~~~~~l~~~~~~~~~~~  172 (178)
                      +|||+||.|..+++..+++++++...+.
T Consensus        97 sptreLa~qtlkvvkdlgrgt~lr~s~~  124 (529)
T KOG0337|consen   97 SPTRELALQTLKVVKDLGRGTKLRQSLL  124 (529)
T ss_pred             cCcHHHHHHHHHHHHHhccccchhhhhh
Confidence            9999999999999999999888765543

>KOG0339|consensus

Probab=99.80  E-value=1.4e-19  Score=159.42  Aligned_cols=115  Identities=29%  Similarity=0.343  Sum_probs=100.1

Q ss_pred             cccccCCCCCCcCCCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHH
Q psy12984         49 VEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVE  128 (178)
Q Consensus        49 ~~~~~~~~~~~~~~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~  128 (178)
                      ....+.+..++.|+.+   |++++  +++.|+.+++...|+.|||||..++|..+.|+||+.+|.||||||.||++|.+.
T Consensus       209 Lnlrv~g~s~~rpvts---feh~g--fDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~  283 (731)
T KOG0339|consen  209 LNLRVSGSSPPRPVTS---FEHFG--FDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIV  283 (731)
T ss_pred             hcceeccCCCCCCcch---hhhcC--chHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHH
Confidence            3444566666666555   88887  999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhcc---CCCCCceEEEeecHHHHHHHHHHHHHHhhhcCCC
Q psy12984        129 LIYNLK---FMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQPP  168 (178)
Q Consensus       129 ~l~~~~---~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~~~  168 (178)
                      +++..+   ...++..+|+||||+||.||+.++++|++.++++
T Consensus       284 himdq~eL~~g~gPi~vilvPTrela~Qi~~eaKkf~K~ygl~  326 (731)
T KOG0339|consen  284 HIMDQPELKPGEGPIGVILVPTRELASQIFSEAKKFGKAYGLR  326 (731)
T ss_pred             HhcchhhhcCCCCCeEEEEeccHHHHHHHHHHHHHhhhhccce
Confidence            998643   3567788999999999999999999988777665

>KOG0344|consensus

Probab=99.80  E-value=1.3e-19  Score=161.13  Aligned_cols=111  Identities=29%  Similarity=0.404  Sum_probs=95.5

Q ss_pred             cccccCCCCCCcCCCCccchHhhcc--cCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHH
Q psy12984         49 VEVQLPGSDVALEILSSTQFEALKG--KVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPA  126 (178)
Q Consensus        49 ~~~~~~~~~~~~~~~~~~~f~~l~~--~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~  126 (178)
                      ......|.+.++++.+   |++|..  ..++.+++++...||..|||+|+.|||.++.++|+++|||||||||++|++|+
T Consensus       118 ~k~~v~G~~~~~~l~~---f~~lt~~~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pi  194 (593)
T KOG0344|consen  118 NKINVDGFHLPPPLLS---FSDLTYDYSMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPI  194 (593)
T ss_pred             ceeeccCCCCCCcccc---ccccchhhhhcHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHH
Confidence            3445567777777776   555431  38899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhccC---CCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984        127 VELIYNLKF---MPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus       127 l~~l~~~~~---~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      +++|.....   ..+.+++|++|||+||.|+|..+..+.
T Consensus       195 l~~L~~~~~~~~~~gl~a~Il~ptreLa~Qi~re~~k~~  233 (593)
T KOG0344|consen  195 LQHLKDLSQEKHKVGLRALILSPTRELAAQIYREMRKYS  233 (593)
T ss_pred             HHHHHHhhcccCccceEEEEecchHHHHHHHHHHHHhcC
Confidence            999976542   556788999999999999999999988

>KOG0350|consensus

Probab=99.78  E-value=3.7e-19  Score=156.21  Aligned_cols=93  Identities=26%  Similarity=0.298  Sum_probs=80.4

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHhhccc---------cCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         75 VCENTLKAIADMGFTKMTEIQARTIPPL---------LEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        75 l~~~ll~~l~~~g~~~pt~iQ~~aip~~---------l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      |...+.+++..+++.+.+|+|...+|.+         ..++||.|.||||||||+||.|||++.+..+ ..++.+++||+
T Consensus       144 lea~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R-~v~~LRavViv  222 (620)
T KOG0350|consen  144 LEATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSR-PVKRLRAVVIV  222 (620)
T ss_pred             HHHHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHHHccC-CccceEEEEEe
Confidence            3344667799999999999999988765         3478999999999999999999999987653 36679999999


Q ss_pred             ecHHHHHHHHHHHHHHhhhcCCC
Q psy12984        146 KLRPLTNGVYLVACNVFKSTQPP  168 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~~~~~~~  168 (178)
                      |||+|+.|+|++|..++.+.+..
T Consensus       223 Ptr~L~~QV~~~f~~~~~~tgL~  245 (620)
T KOG0350|consen  223 PTRELALQVYDTFKRLNSGTGLA  245 (620)
T ss_pred             eHHHHHHHHHHHHHHhccCCceE
Confidence            99999999999999999887765

>cd00268 DEADc DEAD-box helicases

Probab=99.78  E-value=1.3e-18  Score=137.28  Aligned_cols=96  Identities=42%  Similarity=0.538  Sum_probs=86.9

Q ss_pred             hHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeec
Q psy12984         68 FEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKL  147 (178)
Q Consensus        68 f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Pt  147 (178)
                      |++++  +++.+.+.+.+.||..|+++|.++|+.++.|+|++++++||+|||++|++|+++.+.......+.+++|++|+
T Consensus         1 ~~~~~--~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~   78 (203)
T cd00268           1 FEELG--LSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPT   78 (203)
T ss_pred             CCcCC--CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCC
Confidence            56777  9999999999999999999999999999999999999999999999999999999887533356689999999


Q ss_pred             HHHHHHHHHHHHHHhhhc
Q psy12984        148 RPLTNGVYLVACNVFKST  165 (178)
Q Consensus       148 r~La~qi~~~~~~l~~~~  165 (178)
                      ++|+.|+...+..+....
T Consensus        79 ~~L~~q~~~~~~~~~~~~   96 (203)
T cd00268          79 RELALQIAEVARKLGKHT   96 (203)
T ss_pred             HHHHHHHHHHHHHHhccC
Confidence            999999999999887653

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.

>KOG0327|consensus

Probab=99.77  E-value=1.8e-19  Score=153.72  Aligned_cols=103  Identities=25%  Similarity=0.367  Sum_probs=90.8

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      .+|++++  |.++||++++.+||..|+.||+.||+++..|.|+++++++|+|||.+|++++++++.-.  .....+++++
T Consensus        26 dsfddm~--L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~--~ke~qalila  101 (397)
T KOG0327|consen   26 DSFDDMN--LKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMS--VKETQALILA  101 (397)
T ss_pred             hhhhhcC--CCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcc--hHHHHHHHhc
Confidence            3799999  99999999999999999999999999999999999999999999999999999998543  2344888999


Q ss_pred             ecHHHHHHHHHHHHHHhhhcCCCCcce
Q psy12984        146 KLRPLTNGVYLVACNVFKSTQPPTVIK  172 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~~~~~~~~~~~  172 (178)
                      |||+||.|+..++..++...+-.+..+
T Consensus       102 PtreLa~qi~~v~~~lg~~~~~~v~~~  128 (397)
T KOG0327|consen  102 PTRELAQQIQKVVRALGDHMDVSVHAC  128 (397)
T ss_pred             chHHHHHHHHHHHHhhhcccceeeeee
Confidence            999999999999888887665544333

>KOG0329|consensus

Probab=99.76  E-value=9.4e-19  Score=143.66  Aligned_cols=102  Identities=25%  Similarity=0.290  Sum_probs=91.7

Q ss_pred             CCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCce
Q psy12984         62 ILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGK  141 (178)
Q Consensus        62 ~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~  141 (178)
                      ..+++.|.++-  |.|++++++-++||.+|+.+|..|||...-|.||+++|.+|-|||..|++..|++|...  .....+
T Consensus        38 ~ihssgfrdfl--lkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv--~g~vsv  113 (387)
T KOG0329|consen   38 SIHSSGFRDFL--LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPV--DGQVSV  113 (387)
T ss_pred             EEeccchhhhh--cCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCC--CCeEEE
Confidence            44567899998  99999999999999999999999999999999999999999999999999999988653  334577


Q ss_pred             EEEeecHHHHHHHHHHHHHHhhhcCC
Q psy12984        142 SWQGKLRPLTNGVYLVACNVFKSTQP  167 (178)
Q Consensus       142 ~~l~Ptr~La~qi~~~~~~l~~~~~~  167 (178)
                      +++|.|||||.||.+.+.++.+++..
T Consensus       114 lvmchtrelafqi~~ey~rfskymP~  139 (387)
T KOG0329|consen  114 LVMCHTRELAFQISKEYERFSKYMPS  139 (387)
T ss_pred             EEEeccHHHHHHHHHHHHHHHhhCCC
Confidence            88999999999999999999888754

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

Probab=99.75  E-value=4.1e-18  Score=158.61  Aligned_cols=97  Identities=21%  Similarity=0.242  Sum_probs=89.0

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhcc---CCCCCceEEEeecHHHH
Q psy12984         75 VCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLK---FMPRNGKSWQGKLRPLT  151 (178)
Q Consensus        75 l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~---~~~~~~~~~l~Ptr~La  151 (178)
                      |++.+.++|.+. |..||++|.+|||.+..|+|++++||||||||+|.+||+++.|....   ...+..++||+|+|||+
T Consensus         8 l~~~v~~~~~~~-~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkALn   86 (814)
T COG1201           8 LDPRVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKALN   86 (814)
T ss_pred             cCHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHHH
Confidence            899999999997 99999999999999999999999999999999999999999998762   23357899999999999


Q ss_pred             HHHHHHHHHHhhhcCCCCcce
Q psy12984        152 NGVYLVACNVFKSTQPPTVIK  172 (178)
Q Consensus       152 ~qi~~~~~~l~~~~~~~~~~~  172 (178)
                      +++...+..++..+|.++.++
T Consensus        87 ~Di~~rL~~~~~~~G~~v~vR  107 (814)
T COG1201          87 NDIRRRLEEPLRELGIEVAVR  107 (814)
T ss_pred             HHHHHHHHHHHHHcCCcccee
Confidence            999999999999999887554

>PRK02362 ski2-like helicase; Provisional

Probab=99.75  E-value=7.6e-18  Score=157.13  Aligned_cols=89  Identities=21%  Similarity=0.262  Sum_probs=82.3

Q ss_pred             chHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhcc-ccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         67 QFEALKGKVCENTLKAIADMGFTKMTEIQARTIPP-LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        67 ~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~-~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      .|++++  |++.+++++.+.||..|+|+|.+||+. ++.|+|++++||||||||++|.+|+++.+..     +.+++|++
T Consensus         2 ~~~~l~--lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~-----~~kal~i~   74 (737)
T PRK02362          2 KIAELP--LPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIAR-----GGKALYIV   74 (737)
T ss_pred             ChhhcC--CCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhc-----CCcEEEEe
Confidence            588998  999999999999999999999999998 7899999999999999999999999998853     45899999


Q ss_pred             ecHHHHHHHHHHHHHHh
Q psy12984        146 KLRPLTNGVYLVACNVF  162 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~  162 (178)
                      |||+||.|++..++.+.
T Consensus        75 P~raLa~q~~~~~~~~~   91 (737)
T PRK02362         75 PLRALASEKFEEFERFE   91 (737)
T ss_pred             ChHHHHHHHHHHHHHhh
Confidence            99999999999998764

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.73  E-value=2.1e-17  Score=156.67  Aligned_cols=85  Identities=25%  Similarity=0.292  Sum_probs=74.7

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccC----CCCCceEEEeecHHH
Q psy12984         75 VCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKF----MPRNGKSWQGKLRPL  150 (178)
Q Consensus        75 l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~----~~~~~~~~l~Ptr~L  150 (178)
                      |++.+.+++.. +|..|||+|..|||.++.|+|++++||||||||++|++|+++++.....    ..+.+++||+|||+|
T Consensus        18 l~~~v~~~~~~-~~~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtraL   96 (876)
T PRK13767         18 LRPYVREWFKE-KFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRAL   96 (876)
T ss_pred             cCHHHHHHHHH-ccCCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHHHH
Confidence            78888888776 8999999999999999999999999999999999999999999875321    235678999999999


Q ss_pred             HHHHHHHHHH
Q psy12984        151 TNGVYLVACN  160 (178)
Q Consensus       151 a~qi~~~~~~  160 (178)
                      |+|++..+..
T Consensus        97 a~di~~~L~~  106 (876)
T PRK13767         97 NNDIHRNLEE  106 (876)
T ss_pred             HHHHHHHHHH
Confidence            9999987664

>PRK00254 ski2-like helicase; Provisional

Probab=99.72  E-value=2.8e-17  Score=152.96  Aligned_cols=89  Identities=24%  Similarity=0.312  Sum_probs=82.0

Q ss_pred             chHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhcc-ccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         67 QFEALKGKVCENTLKAIADMGFTKMTEIQARTIPP-LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        67 ~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~-~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      +|++++  +++.+.+.|.+.||..|+|+|.+||+. ++.|+|++++||||||||++|.+|+++++..    .+.+++||+
T Consensus         2 ~~~~l~--l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~----~~~~~l~l~   75 (720)
T PRK00254          2 KVDELR--VDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLR----EGGKAVYLV   75 (720)
T ss_pred             cHHHcC--CCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHh----cCCeEEEEe
Confidence            588888  999999999999999999999999986 7899999999999999999999999998864    245899999


Q ss_pred             ecHHHHHHHHHHHHHH
Q psy12984        146 KLRPLTNGVYLVACNV  161 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l  161 (178)
                      |+|+||.|++..+..+
T Consensus        76 P~~aLa~q~~~~~~~~   91 (720)
T PRK00254         76 PLKALAEEKYREFKDW   91 (720)
T ss_pred             ChHHHHHHHHHHHHHH
Confidence            9999999999998875

>KOG0336|consensus

Probab=99.71  E-value=1.2e-17  Score=144.35  Aligned_cols=95  Identities=32%  Similarity=0.381  Sum_probs=82.2

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhc----cCCCCCce
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNL----KFMPRNGK  141 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~----~~~~~~~~  141 (178)
                      .+|++-- .-.++++..+.+.||..|||||.+|||.+|.|.|+++.|.||+|||++|++|.+-++...    ...++++.
T Consensus       219 ctFddAF-q~~pevmenIkK~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~  297 (629)
T KOG0336|consen  219 CTFDDAF-QCYPEVMENIKKTGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGV  297 (629)
T ss_pred             CcHHHHH-hhhHHHHHHHHhccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhccCCCce
Confidence            4476543 267899999999999999999999999999999999999999999999999998887542    34567789


Q ss_pred             EEEeecHHHHHHHHHHHHHH
Q psy12984        142 SWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus       142 ~~l~Ptr~La~qi~~~~~~l  161 (178)
                      ++++|||+||.|+.-.+..+
T Consensus       298 lvl~ptreLalqie~e~~ky  317 (629)
T KOG0336|consen  298 LVLTPTRELALQIEGEVKKY  317 (629)
T ss_pred             EEEeccHHHHHHHHhHHhHh
Confidence            99999999999999877654

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

Probab=99.68  E-value=1.1e-16  Score=150.93  Aligned_cols=91  Identities=22%  Similarity=0.261  Sum_probs=83.9

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHH
Q psy12984         75 VCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGV  154 (178)
Q Consensus        75 l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi  154 (178)
                      ....+..+|...|+..+++||..|+..+..|+||||+++||||||++|++||++++.+   .+..++++|.||+|||++|
T Consensus        55 ~~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~---~~~a~AL~lYPtnALa~DQ  131 (851)
T COG1205          55 RDESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLR---DPSARALLLYPTNALANDQ  131 (851)
T ss_pred             hhhHHHHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhh---CcCccEEEEechhhhHhhH
Confidence            5666788888899999999999999999999999999999999999999999999998   4455899999999999999


Q ss_pred             HHHHHHHhhhcCCC
Q psy12984        155 YLVACNVFKSTQPP  168 (178)
Q Consensus       155 ~~~~~~l~~~~~~~  168 (178)
                      ...|.++...++.+
T Consensus       132 ~~rl~~~~~~~~~~  145 (851)
T COG1205         132 AERLRELISDLPGK  145 (851)
T ss_pred             HHHHHHHHHhCCCc
Confidence            99999999998874

>PRK01172 ski2-like helicase; Provisional

Probab=99.67  E-value=3.9e-16  Score=144.31  Aligned_cols=88  Identities=20%  Similarity=0.202  Sum_probs=80.9

Q ss_pred             chHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEee
Q psy12984         67 QFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGK  146 (178)
Q Consensus        67 ~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~P  146 (178)
                      .|++|+  |++.+++.+...||. ++++|.+|++.++.|+|++++||||||||++|.+++++.+..     +.+++|++|
T Consensus         2 ~~~~~~--l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~-----~~k~v~i~P   73 (674)
T PRK01172          2 KISDLG--YDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLA-----GLKSIYIVP   73 (674)
T ss_pred             cHhhcC--CCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHh-----CCcEEEEec
Confidence            588898  999999999999996 999999999999999999999999999999999999998764     347899999


Q ss_pred             cHHHHHHHHHHHHHHh
Q psy12984        147 LRPLTNGVYLVACNVF  162 (178)
Q Consensus       147 tr~La~qi~~~~~~l~  162 (178)
                      +|+||.|+++.++++.
T Consensus        74 ~raLa~q~~~~~~~l~   89 (674)
T PRK01172         74 LRSLAMEKYEELSRLR   89 (674)
T ss_pred             hHHHHHHHHHHHHHHh
Confidence            9999999999998753

>KOG4284|consensus

Probab=99.65  E-value=5.8e-17  Score=146.15  Aligned_cols=97  Identities=30%  Similarity=0.323  Sum_probs=88.5

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      ..|++|.  |..+++..|++.||..||+||..|||+++.+.|+||+|.+|+|||+.|.+-+++.+...  ....+.+|++
T Consensus        25 ~~fe~l~--l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~--~~~~q~~Iv~  100 (980)
T KOG4284|consen   25 PGFEQLA--LWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSR--SSHIQKVIVT  100 (980)
T ss_pred             CCHHHHH--HHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcc--cCcceeEEEe
Confidence            5699997  99999999999999999999999999999999999999999999999999999987653  4566889999


Q ss_pred             ecHHHHHHHHHHHHHHhhhcC
Q psy12984        146 KLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      ||||||.||..++..++..+.
T Consensus       101 PTREiaVQI~~tv~~v~~sf~  121 (980)
T KOG4284|consen  101 PTREIAVQIKETVRKVAPSFT  121 (980)
T ss_pred             cchhhhhHHHHHHHHhccccc
Confidence            999999999999999887543

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.59  E-value=7.8e-15  Score=137.82  Aligned_cols=89  Identities=15%  Similarity=0.125  Sum_probs=79.5

Q ss_pred             CCHHHHHHHH-----HCCCCCC---cHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEee
Q psy12984         75 VCENTLKAIA-----DMGFTKM---TEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGK  146 (178)
Q Consensus        75 l~~~ll~~l~-----~~g~~~p---t~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~P  146 (178)
                      +..++.+.+.     .+||..|   +|+|.++||.++.++|+|++++||+|||++|++|++..+...     ..+++|+|
T Consensus        69 l~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g-----~~v~IVTp  143 (970)
T PRK12899         69 VVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTG-----KPVHLVTV  143 (970)
T ss_pred             CCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhc-----CCeEEEeC
Confidence            8888887776     7899999   999999999999999999999999999999999999888642     24788999


Q ss_pred             cHHHHHHHHHHHHHHhhhcCCC
Q psy12984        147 LRPLTNGVYLVACNVFKSTQPP  168 (178)
Q Consensus       147 tr~La~qi~~~~~~l~~~~~~~  168 (178)
                      ||+||.|+..++..+.++++..
T Consensus       144 TrELA~Qdae~m~~L~k~lGLs  165 (970)
T PRK12899        144 NDYLAQRDCEWVGSVLRWLGLT  165 (970)
T ss_pred             CHHHHHHHHHHHHHHHhhcCCe
Confidence            9999999999999999876633

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.59  E-value=2.2e-15  Score=134.15  Aligned_cols=68  Identities=25%  Similarity=0.297  Sum_probs=61.8

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      +||..|+|+|.+||+.++.|+|+++++|||||||++|++|++..        ...++||+|||+|+.|++..+..+
T Consensus         7 ~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~--------~~~~lVi~P~~~L~~dq~~~l~~~   74 (470)
T TIGR00614         7 FGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCS--------DGITLVISPLISLMEDQVLQLKAS   74 (470)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHc--------CCcEEEEecHHHHHHHHHHHHHHc
Confidence            69999999999999999999999999999999999999999751        236899999999999999888753

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

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

Probab=99.58  E-value=9.5e-15  Score=111.33  Aligned_cols=70  Identities=27%  Similarity=0.378  Sum_probs=63.2

Q ss_pred             cHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984         92 TEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus        92 t~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      ||+|.++|+.+..|+|+++.||||+|||++|++|++..+...   ....+++++|+++|+.|++..+..++..
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~---~~~~~lii~P~~~l~~q~~~~~~~~~~~   70 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEG---KDARVLIIVPTRALAEQQFERLRKFFSN   70 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTT---SSSEEEEEESSHHHHHHHHHHHHHHTTT
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccC---CCceEEEEeecccccccccccccccccc
Confidence            799999999999999999999999999999999999988763   2338899999999999999999988876

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 ....

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

Probab=99.54  E-value=3e-14  Score=136.18  Aligned_cols=87  Identities=16%  Similarity=0.131  Sum_probs=70.2

Q ss_pred             cchHhhcccCCHHHHHHHHH-CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEE
Q psy12984         66 TQFEALKGKVCENTLKAIAD-MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQ  144 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~-~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l  144 (178)
                      ..|+....+....+...+.. +||..++|+|.++|++++.|+|+|+++|||+|||+||+||+|..        ...++||
T Consensus       435 ~~W~~~~fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~--------~GiTLVI  506 (1195)
T PLN03137        435 KKWSSRNFPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC--------PGITLVI  506 (1195)
T ss_pred             ccccccCCCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc--------CCcEEEE
Confidence            34554333355666666655 89999999999999999999999999999999999999999852        2368999


Q ss_pred             eecHHHHHHHHHHHHH
Q psy12984        145 GKLRPLTNGVYLVACN  160 (178)
Q Consensus       145 ~Ptr~La~qi~~~~~~  160 (178)
                      +||++|++|+...+..
T Consensus       507 SPLiSLmqDQV~~L~~  522 (1195)
T PLN03137        507 SPLVSLIQDQIMNLLQ  522 (1195)
T ss_pred             eCHHHHHHHHHHHHHh
Confidence            9999999976655543

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.53  E-value=2.3e-14  Score=131.34  Aligned_cols=75  Identities=23%  Similarity=0.301  Sum_probs=64.8

Q ss_pred             HHHHHHH-CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHH
Q psy12984         79 TLKAIAD-MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLV  157 (178)
Q Consensus        79 ll~~l~~-~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~  157 (178)
                      ....|.+ .||..|+|+|..+|+.++.|+|+++++|||+|||++|++|++..        ...+++|+||++|+.|+...
T Consensus        13 ~~~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~--------~g~tlVisPl~sL~~dqv~~   84 (607)
T PRK11057         13 AKQVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL--------DGLTLVVSPLISLMKDQVDQ   84 (607)
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc--------CCCEEEEecHHHHHHHHHHH
Confidence            3344444 79999999999999999999999999999999999999999852        23679999999999999988


Q ss_pred             HHHH
Q psy12984        158 ACNV  161 (178)
Q Consensus       158 ~~~l  161 (178)
                      +..+
T Consensus        85 l~~~   88 (607)
T PRK11057         85 LLAN   88 (607)
T ss_pred             HHHc
Confidence            8764

>PRK09401 reverse gyrase; Reviewed

Probab=99.52  E-value=4.8e-14  Score=136.88  Aligned_cols=84  Identities=20%  Similarity=0.011  Sum_probs=69.5

Q ss_pred             HHHHHHH-CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHH
Q psy12984         79 TLKAIAD-MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLV  157 (178)
Q Consensus        79 ll~~l~~-~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~  157 (178)
                      +.+.+.+ .|+ .||++|+.++|.++.|+|++++||||||||+ |++|++..+..    .+.+++||+|||+||.|++..
T Consensus        69 ~~~~f~~~~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~~----~g~~alIL~PTreLa~Qi~~~  142 (1176)
T PRK09401         69 FEKFFKKKTGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLAK----KGKKSYIIFPTRLLVEQVVEK  142 (1176)
T ss_pred             HHHHHHHhcCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHHh----cCCeEEEEeccHHHHHHHHHH
Confidence            3444544 588 8999999999999999999999999999996 66776665543    356899999999999999999


Q ss_pred             HHHHhhhcCCC
Q psy12984        158 ACNVFKSTQPP  168 (178)
Q Consensus       158 ~~~l~~~~~~~  168 (178)
                      ++.++...+..
T Consensus       143 l~~l~~~~~~~  153 (1176)
T PRK09401        143 LEKFGEKVGCG  153 (1176)
T ss_pred             HHHHhhhcCce
Confidence            99998765543

>TIGR01054 rgy reverse gyrase

Probab=99.51  E-value=5.5e-14  Score=136.50  Aligned_cols=86  Identities=15%  Similarity=-0.022  Sum_probs=71.7

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHH
Q psy12984         77 ENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYL  156 (178)
Q Consensus        77 ~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~  156 (178)
                      .++.+.+.+....+||++|+.++|.++.|+|++++||||||||+ |++|++..+..    .+.++++|+|||+||.|++.
T Consensus        65 ~~f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~----~g~~vLIL~PTreLa~Qi~~  139 (1171)
T TIGR01054        65 KEFEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAK----KGKRCYIILPTTLLVIQVAE  139 (1171)
T ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHh----cCCeEEEEeCHHHHHHHHHH
Confidence            34555666544448999999999999999999999999999997 77888776643    24689999999999999999


Q ss_pred             HHHHHhhhcCC
Q psy12984        157 VACNVFKSTQP  167 (178)
Q Consensus       157 ~~~~l~~~~~~  167 (178)
                      .+..++..++.
T Consensus       140 ~l~~l~~~~~i  150 (1171)
T TIGR01054       140 KISSLAEKAGV  150 (1171)
T ss_pred             HHHHHHHhcCC
Confidence            99999887653

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.

>PRK14701 reverse gyrase; Provisional

Probab=99.50  E-value=7.2e-14  Score=138.72  Aligned_cols=85  Identities=16%  Similarity=0.036  Sum_probs=71.3

Q ss_pred             HHHHHHHH-CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHH
Q psy12984         78 NTLKAIAD-MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYL  156 (178)
Q Consensus        78 ~ll~~l~~-~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~  156 (178)
                      ++.+.|.+ .|| .||++|..+||.++.|+|++++||||||||++++++.+....     .+.++++|+|||+|+.|++.
T Consensus        67 ~~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~~-----~g~~aLVl~PTreLa~Qi~~  140 (1638)
T PRK14701         67 EFEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLAL-----KGKKCYIILPTTLLVKQTVE  140 (1638)
T ss_pred             HHHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHh-----cCCeEEEEECHHHHHHHHHH
Confidence            45566766 899 699999999999999999999999999999976666654322     34578999999999999999


Q ss_pred             HHHHHhhhcCCC
Q psy12984        157 VACNVFKSTQPP  168 (178)
Q Consensus       157 ~~~~l~~~~~~~  168 (178)
                      .++.++..++..
T Consensus       141 ~l~~l~~~~~~~  152 (1638)
T PRK14701        141 KIESFCEKANLD  152 (1638)
T ss_pred             HHHHHHhhcCCc
Confidence            999998876543

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.50  E-value=5.7e-14  Score=129.25  Aligned_cols=83  Identities=22%  Similarity=0.226  Sum_probs=71.8

Q ss_pred             HHHHHHHCCCCCCcHHHHHhhccccCC------CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHH
Q psy12984         79 TLKAIADMGFTKMTEIQARTIPPLLEG------RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTN  152 (178)
Q Consensus        79 ll~~l~~~g~~~pt~iQ~~aip~~l~g------~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~  152 (178)
                      +.+.+..++| .||++|..||+.++.+      .+.+++++||||||++|++|++..+..     +.++++++||++||.
T Consensus       225 ~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~-----g~qvlilaPT~~LA~  298 (630)
T TIGR00643       225 LTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEA-----GYQVALMAPTEILAE  298 (630)
T ss_pred             HHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHc-----CCcEEEECCHHHHHH
Confidence            3445677899 7999999999999876      368999999999999999999998753     458999999999999


Q ss_pred             HHHHHHHHHhhhcCC
Q psy12984        153 GVYLVACNVFKSTQP  167 (178)
Q Consensus       153 qi~~~~~~l~~~~~~  167 (178)
                      |++..++.++..++.
T Consensus       299 Q~~~~~~~l~~~~gi  313 (630)
T TIGR00643       299 QHYNSLRNLLAPLGI  313 (630)
T ss_pred             HHHHHHHHHhcccCc
Confidence            999999999876543

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.50  E-value=6.4e-14  Score=129.96  Aligned_cols=83  Identities=20%  Similarity=0.235  Sum_probs=71.4

Q ss_pred             HHHH-HHHCCCCCCcHHHHHhhccccCC------CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHH
Q psy12984         79 TLKA-IADMGFTKMTEIQARTIPPLLEG------RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLT  151 (178)
Q Consensus        79 ll~~-l~~~g~~~pt~iQ~~aip~~l~g------~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La  151 (178)
                      +.+. +..++| .||++|..||+.+..+      ++++++|+||||||++|++|++..+..     +.++++++||++||
T Consensus       250 ~~~~~~~~l~f-~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~-----g~q~lilaPT~~LA  323 (681)
T PRK10917        250 LLKKFLASLPF-ELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEA-----GYQAALMAPTEILA  323 (681)
T ss_pred             HHHHHHHhCCC-CCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHc-----CCeEEEEeccHHHH
Confidence            3344 455788 6999999999999876      489999999999999999999998753     55899999999999


Q ss_pred             HHHHHHHHHHhhhcCC
Q psy12984        152 NGVYLVACNVFKSTQP  167 (178)
Q Consensus       152 ~qi~~~~~~l~~~~~~  167 (178)
                      .|++..++.++..++.
T Consensus       324 ~Q~~~~l~~l~~~~~i  339 (681)
T PRK10917        324 EQHYENLKKLLEPLGI  339 (681)
T ss_pred             HHHHHHHHHHHhhcCc
Confidence            9999999999877653

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.49  E-value=9.5e-14  Score=132.18  Aligned_cols=86  Identities=15%  Similarity=0.074  Sum_probs=73.5

Q ss_pred             CCHHHHHHHHH-CCCCCCcHHHHHhhccccCC------CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeec
Q psy12984         75 VCENTLKAIAD-MGFTKMTEIQARTIPPLLEG------RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKL  147 (178)
Q Consensus        75 l~~~ll~~l~~-~g~~~pt~iQ~~aip~~l~g------~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Pt  147 (178)
                      .+..+.+.+.+ .+| .||++|..||+.++.+      +|++++|+||||||++|++|++..+..     +.++++++||
T Consensus       436 ~~~~~~~~~~~~~~f-~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~-----g~qvlvLvPT  509 (926)
T TIGR00580       436 PDLEWQQEFEDSFPF-EETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLD-----GKQVAVLVPT  509 (926)
T ss_pred             CCHHHHHHHHHhCCC-CCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHh-----CCeEEEEeCc
Confidence            34456666655 689 5999999999999875      799999999999999999999998864     3589999999


Q ss_pred             HHHHHHHHHHHHHHhhhcC
Q psy12984        148 RPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus       148 r~La~qi~~~~~~l~~~~~  166 (178)
                      ++||.|++..|+.++..++
T Consensus       510 ~~LA~Q~~~~f~~~~~~~~  528 (926)
T TIGR00580       510 TLLAQQHFETFKERFANFP  528 (926)
T ss_pred             HHHHHHHHHHHHHHhccCC
Confidence            9999999999999887654

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.

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.48  E-value=6.4e-14  Score=127.84  Aligned_cols=72  Identities=25%  Similarity=0.342  Sum_probs=63.5

Q ss_pred             HHHH-CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHH
Q psy12984         82 AIAD-MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACN  160 (178)
Q Consensus        82 ~l~~-~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~  160 (178)
                      .|.+ +||..++|+|..+|++++.|+|+++++|||+|||++|++|++..        ...++||+|+++|+.|++..+..
T Consensus         4 ~l~~~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~--------~g~~lVisPl~sL~~dq~~~l~~   75 (591)
T TIGR01389         4 VLKRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL--------KGLTVVISPLISLMKDQVDQLRA   75 (591)
T ss_pred             HHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc--------CCcEEEEcCCHHHHHHHHHHHHH
Confidence            3444 89999999999999999999999999999999999999999741        23578999999999999998876


Q ss_pred             H
Q psy12984        161 V  161 (178)
Q Consensus       161 l  161 (178)
                      +
T Consensus        76 ~   76 (591)
T TIGR01389        76 A   76 (591)
T ss_pred             c
Confidence            4

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.

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

Probab=99.48  E-value=1.2e-13  Score=129.49  Aligned_cols=77  Identities=16%  Similarity=0.012  Sum_probs=62.2

Q ss_pred             CCCCCCcHHHHHhhccccCCC-cEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEE-EeecHHHHHHHHHHHHHHhh
Q psy12984         86 MGFTKMTEIQARTIPPLLEGR-DLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSW-QGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~-dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~-l~Ptr~La~qi~~~~~~l~~  163 (178)
                      .||. |||+|.++||.++.|+ ++++++|||||||++|.++++.. ..  ....++.++ ++|||+||.|++..+..+++
T Consensus        12 ~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~-~~--~~~~~~rLv~~vPtReLa~Qi~~~~~~~~k   87 (844)
T TIGR02621        12 HGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAV-EI--GAKVPRRLVYVVNRRTVVDQVTEEAEKIGE   87 (844)
T ss_pred             hCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccc-cc--cccccceEEEeCchHHHHHHHHHHHHHHHH
Confidence            5997 9999999999999998 68888999999999776555532 11  133445555 66999999999999999999


Q ss_pred             hcC
Q psy12984        164 STQ  166 (178)
Q Consensus       164 ~~~  166 (178)
                      .+.
T Consensus        88 ~l~   90 (844)
T TIGR02621        88 RLP   90 (844)
T ss_pred             Hhc
Confidence            873

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.

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.47  E-value=2e-13  Score=125.39  Aligned_cols=75  Identities=20%  Similarity=0.151  Sum_probs=68.0

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      .|. +||++|..++|+++.|+  |+.+.||+|||++|++|++.....     +.++.+++||++||.|.+.++..++.++
T Consensus       100 lg~-~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al~-----G~~v~VvTptreLA~qdae~~~~l~~~l  171 (656)
T PRK12898        100 LGQ-RHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAALA-----GLPVHVITVNDYLAERDAELMRPLYEAL  171 (656)
T ss_pred             hCC-CCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhc-----CCeEEEEcCcHHHHHHHHHHHHHHHhhc
Confidence            677 89999999999999999  899999999999999999987654     4589999999999999999999999886


Q ss_pred             CCC
Q psy12984        166 QPP  168 (178)
Q Consensus       166 ~~~  168 (178)
                      +..
T Consensus       172 Gls  174 (656)
T PRK12898        172 GLT  174 (656)
T ss_pred             CCE
Confidence            643

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.39  E-value=9.8e-13  Score=127.62  Aligned_cols=81  Identities=19%  Similarity=0.067  Sum_probs=69.3

Q ss_pred             HHHHHHHCCCCCCcHHHHHhhccccCC------CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHH
Q psy12984         79 TLKAIADMGFTKMTEIQARTIPPLLEG------RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTN  152 (178)
Q Consensus        79 ll~~l~~~g~~~pt~iQ~~aip~~l~g------~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~  152 (178)
                      ..+.....+| .||++|..||+.++.+      +|++++++||||||.+|+.++...+.     .+.++++|+||++||.
T Consensus       590 ~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~-----~g~qvlvLvPT~eLA~  663 (1147)
T PRK10689        590 YQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE-----NHKQVAVLVPTTLLAQ  663 (1147)
T ss_pred             HHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHH-----cCCeEEEEeCcHHHHH
Confidence            3344566888 7999999999999887      89999999999999999988877654     2458999999999999


Q ss_pred             HHHHHHHHHhhhc
Q psy12984        153 GVYLVACNVFKST  165 (178)
Q Consensus       153 qi~~~~~~l~~~~  165 (178)
                      |++..|+..+..+
T Consensus       664 Q~~~~f~~~~~~~  676 (1147)
T PRK10689        664 QHYDNFRDRFANW  676 (1147)
T ss_pred             HHHHHHHHhhccC
Confidence            9999999876654

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.29  E-value=9.9e-12  Score=116.38  Aligned_cols=79  Identities=19%  Similarity=0.159  Sum_probs=69.6

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      .|. +|+++|..++++++.|+  |+.+.||+|||++|++|++...+.     +.++.+++||++||.|.+..+..+..++
T Consensus        75 ~g~-~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al~-----G~~v~VvTpt~~LA~qd~e~~~~l~~~l  146 (790)
T PRK09200         75 LGM-RPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNALE-----GKGVHLITVNDYLAKRDAEEMGQVYEFL  146 (790)
T ss_pred             hCC-CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHc-----CCCeEEEeCCHHHHHHHHHHHHHHHhhc
Confidence            687 99999999999999887  899999999999999999866554     5588999999999999999999999998


Q ss_pred             CCCCcce
Q psy12984        166 QPPTVIK  172 (178)
Q Consensus       166 ~~~~~~~  172 (178)
                      +..+++.
T Consensus       147 Gl~v~~i  153 (790)
T PRK09200        147 GLTVGLN  153 (790)
T ss_pred             CCeEEEE
Confidence            7655443

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

Probab=99.29  E-value=6.2e-12  Score=112.91  Aligned_cols=103  Identities=20%  Similarity=0.238  Sum_probs=92.8

Q ss_pred             chHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhcc-ccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         67 QFEALKGKVCENTLKAIADMGFTKMTEIQARTIPP-LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        67 ~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~-~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      +.++|.  +++++.+.|...|++.+.|+|..|+.+ ++.|.|.+|.+.|+|||||.--+.-|..++.    .+...++++
T Consensus       195 ~vdeLd--ipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~----~g~KmlfLv  268 (830)
T COG1202         195 PVDELD--IPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLS----GGKKMLFLV  268 (830)
T ss_pred             cccccC--CcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHh----CCCeEEEEe
Confidence            355676  999999999999999999999999987 6799999999999999999999999888875    345789999


Q ss_pred             ecHHHHHHHHHHHHHHhhhcCCCCcceEEE
Q psy12984        146 KLRPLTNGVYLVACNVFKSTQPPTVIKVQT  175 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~~~~~~~~~~~v~~  175 (178)
                      |+-+||+|-|..|+.-...++..+.|+|++
T Consensus       269 PLVALANQKy~dF~~rYs~LglkvairVG~  298 (830)
T COG1202         269 PLVALANQKYEDFKERYSKLGLKVAIRVGM  298 (830)
T ss_pred             hhHHhhcchHHHHHHHhhcccceEEEEech
Confidence            999999999999999999999998888875

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.28  E-value=9.3e-12  Score=116.66  Aligned_cols=89  Identities=19%  Similarity=0.206  Sum_probs=74.7

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHhhccc-cCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHH
Q psy12984         75 VCENTLKAIADMGFTKMTEIQARTIPPL-LEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNG  153 (178)
Q Consensus        75 l~~~ll~~l~~~g~~~pt~iQ~~aip~~-l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~q  153 (178)
                      +++.++..+...|+...++.|+.++... +.|.|+|+|+|||||||+...+.+++.+...    +..++||||+|+||.+
T Consensus        16 ~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~----~~k~vYivPlkALa~E   91 (766)
T COG1204          16 LDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG----GGKVVYIVPLKALAEE   91 (766)
T ss_pred             ccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc----CCcEEEEeChHHHHHH
Confidence            6778888888889988888888887664 5669999999999999999999999999763    5588999999999999


Q ss_pred             HHHHHHHHhhhcCCC
Q psy12984        154 VYLVACNVFKSTQPP  168 (178)
Q Consensus       154 i~~~~~~l~~~~~~~  168 (178)
                      ++..|+ -...+|..
T Consensus        92 k~~~~~-~~~~~Gir  105 (766)
T COG1204          92 KYEEFS-RLEELGIR  105 (766)
T ss_pred             HHHHhh-hHHhcCCE
Confidence            999999 34444433

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.27  E-value=1.5e-11  Score=106.18  Aligned_cols=72  Identities=22%  Similarity=0.224  Sum_probs=60.1

Q ss_pred             HHHHhhccccCCCc--EEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhcCCCCcc
Q psy12984         94 IQARTIPPLLEGRD--LVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQPPTVI  171 (178)
Q Consensus        94 iQ~~aip~~l~g~d--vi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~~~~~~  171 (178)
                      +|.++++.+..+.+  ++++||||||||++|++|++..        ...+++++|+++|++|+++.+..++..+....++
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~~--------~~~~~~~~P~~aL~~~~~~~~~~~~~~~~~~~~~   72 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLHG--------ENDTIALYPTNALIEDQTEAIKEFVDVFKPERDV   72 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHHc--------CCCEEEEeChHHHHHHHHHHHHHHHHhcCCCCCc
Confidence            69999999998875  7889999999999999999841        2367999999999999999999998776544344


Q ss_pred             eE
Q psy12984        172 KV  173 (178)
Q Consensus       172 ~v  173 (178)
                      .+
T Consensus        73 ~v   74 (357)
T TIGR03158        73 NL   74 (357)
T ss_pred             eE
Confidence            33

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.

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.21  E-value=4.5e-11  Score=110.97  Aligned_cols=77  Identities=21%  Similarity=0.158  Sum_probs=65.8

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      +|. +|+++|..+.++++.|+  |+.++||+|||++|++|++-....     +.++.+++||++||.|.+.++..+.+++
T Consensus        53 lg~-~p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~-----G~~V~VvTpt~~LA~qdae~~~~l~~~L  124 (745)
T TIGR00963        53 LGM-RPFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALT-----GKGVHVVTVNDYLAQRDAEWMGQVYRFL  124 (745)
T ss_pred             hCC-CccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHh-----CCCEEEEcCCHHHHHHHHHHHHHHhccC
Confidence            677 89999999999998887  899999999999999999543333     3368899999999999999999999887


Q ss_pred             CCCCc
Q psy12984        166 QPPTV  170 (178)
Q Consensus       166 ~~~~~  170 (178)
                      +..++
T Consensus       125 GLsv~  129 (745)
T TIGR00963       125 GLSVG  129 (745)
T ss_pred             CCeEE
Confidence            65443

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.

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

Probab=99.19  E-value=1.2e-10  Score=110.61  Aligned_cols=88  Identities=18%  Similarity=0.148  Sum_probs=71.7

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHhhc----cccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHH
Q psy12984         75 VCENTLKAIADMGFTKMTEIQARTIP----PLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPL  150 (178)
Q Consensus        75 l~~~ll~~l~~~g~~~pt~iQ~~aip----~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~L  150 (178)
                      +++.+.+.+...||. +.+.|...+.    .+..|+++++.|+||+|||++|++|++.+..     ...+++|.+||++|
T Consensus       231 ~~~~~~~~~~~~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~-----~~~~vvi~t~t~~L  304 (850)
T TIGR01407       231 LSSLFSKNIDRLGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI-----TEKPVVISTNTKVL  304 (850)
T ss_pred             ccHHHHHhhhhcCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc-----CCCeEEEEeCcHHH
Confidence            556777788889995 8899998665    5567899999999999999999999988765     22378889999999


Q ss_pred             HHHHHH-HHHHHhhhcCCC
Q psy12984        151 TNGVYL-VACNVFKSTQPP  168 (178)
Q Consensus       151 a~qi~~-~~~~l~~~~~~~  168 (178)
                      +.|+.. .+..+.+.++.+
T Consensus       305 q~Ql~~~~~~~l~~~~~~~  323 (850)
T TIGR01407       305 QSQLLEKDIPLLNEILNFK  323 (850)
T ss_pred             HHHHHHHHHHHHHHHcCCC
Confidence            999965 677777666655

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.

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.18  E-value=8.1e-11  Score=109.73  Aligned_cols=79  Identities=19%  Similarity=0.125  Sum_probs=67.8

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      .|. +|+++|..+..++..|  .|+.++||+|||++|++|++...+.     +.+++|++|+++||.|...++..+.+++
T Consensus        67 lgl-rpydVQlig~l~l~~G--~Iaem~TGeGKTLta~Lpa~l~aL~-----g~~V~VVTpn~yLA~Rdae~m~~l~~~L  138 (762)
T TIGR03714        67 LGM-FPYDVQVLGAIVLHQG--NIAEMKTGEGKTLTATMPLYLNALT-----GKGAMLVTTNDYLAKRDAEEMGPVYEWL  138 (762)
T ss_pred             cCC-CccHHHHHHHHHhcCC--ceeEecCCcchHHHHHHHHHHHhhc-----CCceEEeCCCHHHHHHHHHHHHHHHhhc
Confidence            677 8999999988887777  5999999999999999998776654     3468999999999999999999999998


Q ss_pred             CCCCcce
Q psy12984        166 QPPTVIK  172 (178)
Q Consensus       166 ~~~~~~~  172 (178)
                      |..+++.
T Consensus       139 GLsv~~~  145 (762)
T TIGR03714       139 GLTVSLG  145 (762)
T ss_pred             CCcEEEE
Confidence            8775543

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.

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.11  E-value=2.6e-10  Score=87.07  Aligned_cols=77  Identities=32%  Similarity=0.324  Sum_probs=67.4

Q ss_pred             HCCCCCCcHHHHHhhccccCC-CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984         85 DMGFTKMTEIQARTIPPLLEG-RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus        85 ~~g~~~pt~iQ~~aip~~l~g-~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      ..++..|+++|..++..++.+ ++++++++||||||.+++.+++..+...   ....+++++|++.++.|++..+..++.
T Consensus         3 ~~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~---~~~~~l~~~p~~~~~~~~~~~~~~~~~   79 (201)
T smart00487        3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRG---KGKRVLVLVPTRELAEQWAEELKKLGP   79 (201)
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhccc---CCCcEEEEeCCHHHHHHHHHHHHHHhc
Confidence            346789999999999999988 9999999999999999999999988653   234789999999999999999888775


Q ss_pred             h
Q psy12984        164 S  164 (178)
Q Consensus       164 ~  164 (178)
                      .
T Consensus        80 ~   80 (201)
T smart00487       80 S   80 (201)
T ss_pred             c
Confidence            4

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.10  E-value=1.2e-10  Score=107.89  Aligned_cols=71  Identities=13%  Similarity=0.092  Sum_probs=59.4

Q ss_pred             HHHHhhccccCCCcEEEEccCCCchhhH---------hHHHHHHHHHhcc-CCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984         94 IQARTIPPLLEGRDLVGSAKTGSGKTLA---------FLVPAVELIYNLK-FMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus        94 iQ~~aip~~l~g~dvi~~a~TGsGKTla---------f~lp~l~~l~~~~-~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      +|.++++.++.|+|+|++|+||||||.+         |++|.+..+.... ......+++++|||+||.|+...+...++
T Consensus       168 iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~~vg  247 (675)
T PHA02653        168 VQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLKSLG  247 (675)
T ss_pred             HHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHHHhC
Confidence            9999999999999999999999999997         6677777664322 23345788899999999999999888776


Q ss_pred             h
Q psy12984        164 S  164 (178)
Q Consensus       164 ~  164 (178)
                      +
T Consensus       248 ~  248 (675)
T PHA02653        248 F  248 (675)
T ss_pred             c
Confidence            5

>KOG0952|consensus

Probab=99.09  E-value=2.6e-10  Score=107.69  Aligned_cols=80  Identities=16%  Similarity=0.173  Sum_probs=66.9

Q ss_pred             CCCCCCcHHHHHhhccccC-CCcEEEEccCCCchhhHhHHHHHHHHHhc-----cCCCCCceEEEeecHHHHHHHHHHHH
Q psy12984         86 MGFTKMTEIQARTIPPLLE-GRDLVGSAKTGSGKTLAFLVPAVELIYNL-----KFMPRNGKSWQGKLRPLTNGVYLVAC  159 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~-g~dvi~~a~TGsGKTlaf~lp~l~~l~~~-----~~~~~~~~~~l~Ptr~La~qi~~~~~  159 (178)
                      .+|..+..+|..++|.+.+ .-|+|||||||||||..|+|.||+.|...     -.......+||+|+++||..+++.+.
T Consensus       106 f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~~~~  185 (1230)
T KOG0952|consen  106 FSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDKFS  185 (1230)
T ss_pred             ccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHHHHh
Confidence            5788899999999998874 57999999999999999999999999751     12345588999999999999998877


Q ss_pred             HHhhhc
Q psy12984        160 NVFKST  165 (178)
Q Consensus       160 ~l~~~~  165 (178)
                      +-+..+
T Consensus       186 kkl~~~  191 (1230)
T KOG0952|consen  186 KKLAPL  191 (1230)
T ss_pred             hhcccc
Confidence            766433

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.08  E-value=3.2e-10  Score=101.91  Aligned_cols=72  Identities=10%  Similarity=-0.111  Sum_probs=58.5

Q ss_pred             CCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984         88 FTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus        88 ~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      ...|+++|..|++.++.+.++++++|||+|||+++..-+ ..+..   ....++++|+||++|+.|++..+..++.
T Consensus       112 ~~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~-~~~~~---~~~~~vLilvpt~eL~~Q~~~~l~~~~~  183 (501)
T PHA02558        112 KIEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLS-RYYLE---NYEGKVLIIVPTTSLVTQMIDDFVDYRL  183 (501)
T ss_pred             cCCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHH-HHHHh---cCCCeEEEEECcHHHHHHHHHHHHHhcc
Confidence            458999999999999999999999999999999865422 22222   1233889999999999999999988763

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.06  E-value=6.9e-10  Score=103.22  Aligned_cols=68  Identities=19%  Similarity=0.141  Sum_probs=59.4

Q ss_pred             CCcHHHHHhhccccCC---CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         90 KMTEIQARTIPPLLEG---RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g---~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      .+|+.|..++..+..+   +++++.++||||||.+|+.++...+..     +.++++|+||++|+.|++..++..+
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~-----g~~vLvLvPt~~L~~Q~~~~l~~~f  214 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQ-----GKQALVLVPEIALTPQMLARFRARF  214 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHc-----CCeEEEEeCcHHHHHHHHHHHHHHh
Confidence            4799999999999874   899999999999999999888776643     3478999999999999999998754

>KOG0349|consensus

Probab=99.05  E-value=1e-10  Score=102.40  Aligned_cols=65  Identities=37%  Similarity=0.578  Sum_probs=60.9

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHh
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYN  132 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~  132 (178)
                      +.|++++  +-|+|-.+..++.|.-||.+|+++||.++.|-||+.+|.||||||-||++|+|+.+..
T Consensus         2 ~af~e~g--v~pel~~a~~e~dw~lptdvqaeaiplilgggdvlmaaetgsgktgaf~lpilqiv~e   66 (725)
T KOG0349|consen    2 TAFEEFG--VLPELGMATDELDWTLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPILQIVWE   66 (725)
T ss_pred             cchHhhC--cchHhhhhhhhhccccccccccccccEEecCCcEEEEeccCCCCccceehhhHHHHHH
Confidence            3589998  9999999999999999999999999999999999999999999999999999997653

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.04  E-value=4.7e-10  Score=95.97  Aligned_cols=54  Identities=31%  Similarity=0.198  Sum_probs=47.4

Q ss_pred             cEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984        107 DLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus       107 dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      |++++||||||||++|++|++..+..   ....++++++|+|+|+.|+++.+..+++
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~---~~~~~ii~v~P~~~L~~q~~~~l~~~f~   54 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKS---QKADRVIIALPTRATINAMYRRAKELFG   54 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhh---CCCCeEEEEeehHHHHHHHHHHHHHHhC
Confidence            68999999999999999999988654   3455889999999999999999998754

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.

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

Probab=99.00  E-value=1.1e-09  Score=100.77  Aligned_cols=65  Identities=22%  Similarity=0.219  Sum_probs=54.4

Q ss_pred             cccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh-hhcCCC
Q psy12984        101 PLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF-KSTQPP  168 (178)
Q Consensus       101 ~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~-~~~~~~  168 (178)
                      ++..++.+++.|+||+|||++|++|++..+..   ....+++|++||++|+.|+++.+..+. +.++.+
T Consensus        12 al~~~~~lliEA~TGtGKTlAYLlpal~~~~~---~~~~rvlIstpT~~Lq~Ql~~~l~~l~~~~l~~~   77 (636)
T TIGR03117        12 SLRQKRIGMLEASTGVGKTLAMIMAALTMLKE---RPDQKIAIAVPTLALMGQLWSELERLTAEGLAGP   77 (636)
T ss_pred             HHhcCCeEEEEcCCCCcHHHHHHHHHHHHHHh---ccCceEEEECCcHHHHHHHHHHHHHHHHhhcCCC
Confidence            34567899999999999999999999998763   234688999999999999999998887 555544

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.

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=98.97  E-value=1.1e-09  Score=108.12  Aligned_cols=54  Identities=24%  Similarity=0.173  Sum_probs=45.4

Q ss_pred             EEccCCCchhhHhHHHHHHHHHhccC--------CCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984        110 GSAKTGSGKTLAFLVPAVELIYNLKF--------MPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus       110 ~~a~TGsGKTlaf~lp~l~~l~~~~~--------~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      |+||||||||+||+||+|+.+.....        ....+++||+|||+|++|+++.++..+.
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~~~~~~~~~~~~~~~raLYISPLKALa~Dv~~~L~~pl~   62 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIPLK   62 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhcccccccccccCCCCEEEEEeChHHHHHHHHHHHHHHHH
Confidence            57999999999999999999976421        2356899999999999999999887544

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=98.96  E-value=1.7e-09  Score=102.03  Aligned_cols=77  Identities=19%  Similarity=0.140  Sum_probs=64.2

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      .|. +|+++|...--++..|+  |+.++||+|||++|.+|++..+..     +.++.+++||++||.|.+.++..+..++
T Consensus        79 lg~-~~ydvQliGg~~Lh~G~--Iaem~TGeGKTL~a~Lpa~~~al~-----G~~V~VvTpn~yLA~qd~e~m~~l~~~l  150 (896)
T PRK13104         79 LGL-RHFDVQLIGGMVLHEGN--IAEMRTGEGKTLVATLPAYLNAIS-----GRGVHIVTVNDYLAKRDSQWMKPIYEFL  150 (896)
T ss_pred             cCC-CcchHHHhhhhhhccCc--cccccCCCCchHHHHHHHHHHHhc-----CCCEEEEcCCHHHHHHHHHHHHHHhccc
Confidence            566 89999987665666665  789999999999999999987754     3468899999999999999999999887


Q ss_pred             CCCCc
Q psy12984        166 QPPTV  170 (178)
Q Consensus       166 ~~~~~  170 (178)
                      +..++
T Consensus       151 GLtv~  155 (896)
T PRK13104        151 GLTVG  155 (896)
T ss_pred             CceEE
Confidence            65443

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

Probab=98.93  E-value=2.9e-09  Score=100.86  Aligned_cols=78  Identities=17%  Similarity=0.128  Sum_probs=60.6

Q ss_pred             HHCCCCCCcHHHHHhhc----cccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHH-HHHH
Q psy12984         84 ADMGFTKMTEIQARTIP----PLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGV-YLVA  158 (178)
Q Consensus        84 ~~~g~~~pt~iQ~~aip----~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi-~~~~  158 (178)
                      .-.|| .+.+-|..-..    ++..+.++++.|+||+|||++|++|++...      ....++|++|||+|+.|+ ...+
T Consensus       240 ~~~~~-e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~------~~~~vvI~t~T~~Lq~Ql~~~~i  312 (820)
T PRK07246        240 ALLGL-EERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS------DQRQIIVSVPTKILQDQIMAEEV  312 (820)
T ss_pred             ccCCC-ccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc------CCCcEEEEeCcHHHHHHHHHHHH
Confidence            33466 67888877332    345678999999999999999999988754      235789999999999999 4778


Q ss_pred             HHHhhhcCCC
Q psy12984        159 CNVFKSTQPP  168 (178)
Q Consensus       159 ~~l~~~~~~~  168 (178)
                      ..+.+.++.+
T Consensus       313 ~~l~~~~~~~  322 (820)
T PRK07246        313 KAIQEVFHID  322 (820)
T ss_pred             HHHHHhcCCc
Confidence            8877775543

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=98.82  E-value=1.2e-08  Score=85.86  Aligned_cols=73  Identities=15%  Similarity=0.071  Sum_probs=57.7

Q ss_pred             CCcHHHHH----hhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCC-CCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         90 KMTEIQAR----TIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFM-PRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        90 ~pt~iQ~~----aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~-~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      .|+|.|..    .+..+..|.++++.||||+|||++|++|++.++...... .....+|.++|..+..|....++++.
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~~   85 (289)
T smart00488        8 EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKLM   85 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhcc
Confidence            46899998    444566789999999999999999999999887653221 23477889999999888877777653

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=98.82  E-value=1.2e-08  Score=85.86  Aligned_cols=73  Identities=15%  Similarity=0.071  Sum_probs=57.7

Q ss_pred             CCcHHHHH----hhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCC-CCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         90 KMTEIQAR----TIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFM-PRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        90 ~pt~iQ~~----aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~-~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      .|+|.|..    .+..+..|.++++.||||+|||++|++|++.++...... .....+|.++|..+..|....++++.
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~~   85 (289)
T smart00489        8 EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKLM   85 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhcc
Confidence            46899998    444566789999999999999999999999887653221 23477889999999888877777653

>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=98.78  E-value=1.5e-08  Score=77.41  Aligned_cols=65  Identities=25%  Similarity=0.191  Sum_probs=52.9

Q ss_pred             CCcHHHHHhhccccC-------CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         90 KMTEIQARTIPPLLE-------GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~-------g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      .+++.|..|+..+..       .+++++.++||||||.+.+..+.... .       .+++++|++.|+.|.+..+..+.
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~-~-------~~l~~~p~~~l~~Q~~~~~~~~~   74 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELA-R-------KVLIVAPNISLLEQWYDEFDDFG   74 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHH-C-------EEEEEESSHHHHHHHHHHHHHHS
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhccc-c-------ceeEecCHHHHHHHHHHHHHHhh
Confidence            578999999988763       68999999999999999886554433 2       78999999999999999985544

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 ....

>KOG0352|consensus

Probab=98.77  E-value=1.2e-08  Score=89.48  Aligned_cols=75  Identities=21%  Similarity=0.255  Sum_probs=61.6

Q ss_pred             HHHHHHH-CCCCCC-cHHHHHhhccccCC-CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHH
Q psy12984         79 TLKAIAD-MGFTKM-TEIQARTIPPLLEG-RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVY  155 (178)
Q Consensus        79 ll~~l~~-~g~~~p-t~iQ~~aip~~l~g-~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~  155 (178)
                      +..+|++ .|+... |+.|..|+..+..+ .||.|+.|||+||+|||.||.|-        .....++++|+.+|.+++.
T Consensus         7 VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~--------~~gITIV~SPLiALIkDQi   78 (641)
T KOG0352|consen    7 VREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALV--------HGGITIVISPLIALIKDQI   78 (641)
T ss_pred             HHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHH--------hCCeEEEehHHHHHHHHHH
Confidence            3445544 687765 88999999987665 79999999999999999999975        2237788999999999999


Q ss_pred             HHHHHH
Q psy12984        156 LVACNV  161 (178)
Q Consensus       156 ~~~~~l  161 (178)
                      +.+..|
T Consensus        79 DHL~~L   84 (641)
T KOG0352|consen   79 DHLKRL   84 (641)
T ss_pred             HHHHhc
Confidence            987764

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

Probab=98.75  E-value=1.7e-08  Score=91.90  Aligned_cols=74  Identities=23%  Similarity=0.270  Sum_probs=65.0

Q ss_pred             HHHHH-CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHH
Q psy12984         81 KAIAD-MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVAC  159 (178)
Q Consensus        81 ~~l~~-~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~  159 (178)
                      ..|++ +||....+-|..+|..+++|+|+++.-|||.||++||.+|.+-.       .+ -+++|+|+.+|..++.+.+.
T Consensus         7 ~~L~~~fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~-------~G-~TLVVSPLiSLM~DQV~~l~   78 (590)
T COG0514           7 QVLKQVFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL-------EG-LTLVVSPLISLMKDQVDQLE   78 (590)
T ss_pred             HHHHHHhCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc-------CC-CEEEECchHHHHHHHHHHHH
Confidence            44555 79999999999999999999999999999999999999999752       23 56889999999999999988


Q ss_pred             HHh
Q psy12984        160 NVF  162 (178)
Q Consensus       160 ~l~  162 (178)
                      ..+
T Consensus        79 ~~G   81 (590)
T COG0514          79 AAG   81 (590)
T ss_pred             HcC
Confidence            755

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=98.74  E-value=2.4e-08  Score=94.06  Aligned_cols=78  Identities=21%  Similarity=0.184  Sum_probs=64.8

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHH-HHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAV-ELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l-~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      +|. +|+++|...--++..|+  |+.++||+|||+++.+|++ +.+ .     +.++-+++||+.||.|.+..+..+..+
T Consensus        78 lg~-~~~dvQlig~l~L~~G~--Iaem~TGeGKTLva~lpa~l~aL-~-----G~~V~IvTpn~yLA~rd~e~~~~l~~~  148 (830)
T PRK12904         78 LGM-RHFDVQLIGGMVLHEGK--IAEMKTGEGKTLVATLPAYLNAL-T-----GKGVHVVTVNDYLAKRDAEWMGPLYEF  148 (830)
T ss_pred             hCC-CCCccHHHhhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHH-c-----CCCEEEEecCHHHHHHHHHHHHHHHhh
Confidence            677 89999998887777775  8899999999999999996 544 2     225668999999999999999999988


Q ss_pred             cCCCCcce
Q psy12984        165 TQPPTVIK  172 (178)
Q Consensus       165 ~~~~~~~~  172 (178)
                      +|..+++.
T Consensus       149 LGlsv~~i  156 (830)
T PRK12904        149 LGLSVGVI  156 (830)
T ss_pred             cCCeEEEE
Confidence            87765443

>PRK13766 Hef nuclease; Provisional

Probab=98.74  E-value=2.7e-08  Score=93.45  Aligned_cols=71  Identities=15%  Similarity=0.033  Sum_probs=61.1

Q ss_pred             CCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984         88 FTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus        88 ~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      ...|.+.|...+..++.+ |+|+++|||+|||+++++++...+.    .+...+++|+||++|+.|+...+..++.
T Consensus        13 ~~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~----~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~   83 (773)
T PRK13766         13 TIEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLH----KKGGKVLILAPTKPLVEQHAEFFRKFLN   83 (773)
T ss_pred             cCCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHH----hCCCeEEEEeCcHHHHHHHHHHHHHHhC
Confidence            347888999988878877 9999999999999999999998773    3445889999999999999999988764

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

Probab=98.67  E-value=5.1e-08  Score=93.33  Aligned_cols=78  Identities=19%  Similarity=0.239  Sum_probs=66.1

Q ss_pred             HHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984         82 AIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus        82 ~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      .....|| .+-++|+.|+-.+..|..|+||||||+|||+.--+.+-..+.+     +.+++|.+|++||.+|.|+.+...
T Consensus       112 ~~~~~~F-~LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~-----~qrviYTsPIKALsNQKyrdl~~~  185 (1041)
T COG4581         112 PAREYPF-ELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRD-----GQRVIYTSPIKALSNQKYRDLLAK  185 (1041)
T ss_pred             HHHhCCC-CcCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHc-----CCceEeccchhhhhhhHHHHHHHH
Confidence            3566789 7899999999999999999999999999999976666555544     225899999999999999998887


Q ss_pred             hhhc
Q psy12984        162 FKST  165 (178)
Q Consensus       162 ~~~~  165 (178)
                      .+..
T Consensus       186 fgdv  189 (1041)
T COG4581         186 FGDV  189 (1041)
T ss_pred             hhhh
Confidence            7755

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=98.66  E-value=3.6e-08  Score=93.36  Aligned_cols=55  Identities=15%  Similarity=0.007  Sum_probs=46.0

Q ss_pred             cccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHH
Q psy12984        101 PLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACN  160 (178)
Q Consensus       101 ~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~  160 (178)
                      .+..+++++++|+||||||.+|.+|+++...     ...+++++.|+|++|.|++..+..
T Consensus        16 ~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~-----~~~~ilvlqPrR~aA~qia~rva~   70 (812)
T PRK11664         16 ALKTAPQVLLKAPTGAGKSTWLPLQLLQHGG-----INGKIIMLEPRRLAARNVAQRLAE   70 (812)
T ss_pred             HHHhCCCEEEEcCCCCCHHHHHHHHHHHcCC-----cCCeEEEECChHHHHHHHHHHHHH
Confidence            4456889999999999999999999997532     224788999999999999988754

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=98.61  E-value=1.3e-07  Score=89.58  Aligned_cols=77  Identities=18%  Similarity=0.071  Sum_probs=63.7

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      .|. +|+++|...=-++..|+  |+.++||+|||++|.+|++...+.     +.++.|++|+++||.+...++..+..++
T Consensus        79 lgm-~~ydVQliGgl~L~~G~--IaEm~TGEGKTL~a~lp~~l~al~-----g~~VhIvT~ndyLA~RD~e~m~~l~~~l  150 (908)
T PRK13107         79 FEM-RHFDVQLLGGMVLDSNR--IAEMRTGEGKTLTATLPAYLNALT-----GKGVHVITVNDYLARRDAENNRPLFEFL  150 (908)
T ss_pred             hCC-CcCchHHhcchHhcCCc--cccccCCCCchHHHHHHHHHHHhc-----CCCEEEEeCCHHHHHHHHHHHHHHHHhc
Confidence            566 89999976654555554  789999999999999999877754     3468899999999999999999999997


Q ss_pred             CCCCc
Q psy12984        166 QPPTV  170 (178)
Q Consensus       166 ~~~~~  170 (178)
                      |..++
T Consensus       151 Glsv~  155 (908)
T PRK13107        151 GLTVG  155 (908)
T ss_pred             CCeEE
Confidence            66544

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=98.59  E-value=1.9e-07  Score=88.57  Aligned_cols=56  Identities=14%  Similarity=0.014  Sum_probs=47.3

Q ss_pred             ccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHH
Q psy12984        100 PPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACN  160 (178)
Q Consensus       100 p~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~  160 (178)
                      ..+..+.++|++|+||||||.+|.+|+++...     ...+++++.|+|++|.|+...+..
T Consensus        12 ~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~-----~~~~ilvlqPrR~aA~qiA~rva~   67 (819)
T TIGR01970        12 DALAAHPQVVLEAPPGAGKSTAVPLALLDAPG-----IGGKIIMLEPRRLAARSAAQRLAS   67 (819)
T ss_pred             HHHHcCCcEEEECCCCCCHHHHHHHHHHHhhc-----cCCeEEEEeCcHHHHHHHHHHHHH
Confidence            34556789999999999999999999998762     234789999999999999998753

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.

>PRK09694 helicase Cas3; Provisional

Probab=98.59  E-value=2.5e-07  Score=88.19  Aligned_cols=73  Identities=21%  Similarity=0.043  Sum_probs=56.7

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      .|+|+|..+......+.-+|+.||||+|||.+.++.+...+..   ....+.++..||+++++|+|..+..+.+.+
T Consensus       286 ~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~~~---~~~~gi~~aLPT~Atan~m~~Rl~~~~~~~  358 (878)
T PRK09694        286 QPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLIDQ---GLADSIIFALPTQATANAMLSRLEALASKL  358 (878)
T ss_pred             CChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHHHh---CCCCeEEEECcHHHHHHHHHHHHHHHHHHh
Confidence            7999999876544456678999999999999977665543332   234577888999999999999998876654

>KOG0353|consensus

Probab=98.55  E-value=1.5e-07  Score=81.83  Aligned_cols=80  Identities=19%  Similarity=0.195  Sum_probs=65.4

Q ss_pred             CCHHHHHHHHH-CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHH
Q psy12984         75 VCENTLKAIAD-MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNG  153 (178)
Q Consensus        75 l~~~ll~~l~~-~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~q  153 (178)
                      .+.+....|++ .......|.|..+|.+.+.|.|+++.-|||.||+|||.+|+|-       . ..-+++|+|+..|..+
T Consensus        78 ws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~-------a-dg~alvi~plislmed  149 (695)
T KOG0353|consen   78 WSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALC-------A-DGFALVICPLISLMED  149 (695)
T ss_pred             CchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHh-------c-CCceEeechhHHHHHH
Confidence            44444555544 3456778999999999999999999999999999999999975       2 2367899999999999


Q ss_pred             HHHHHHHHh
Q psy12984        154 VYLVACNVF  162 (178)
Q Consensus       154 i~~~~~~l~  162 (178)
                      +.-+++.++
T Consensus       150 qil~lkqlg  158 (695)
T KOG0353|consen  150 QILQLKQLG  158 (695)
T ss_pred             HHHHHHHhC
Confidence            988887764

>KOG0354|consensus

Probab=98.55  E-value=1.4e-07  Score=87.54  Aligned_cols=69  Identities=23%  Similarity=0.282  Sum_probs=59.5

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      .+...|......+| |+|+||++|||+|||.+.++-+++++.-   .+...+++++||+-|..|+...++.++
T Consensus        62 ~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw---~p~~KiVF~aP~~pLv~QQ~a~~~~~~  130 (746)
T KOG0354|consen   62 ELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEW---RPKGKVVFLAPTRPLVNQQIACFSIYL  130 (746)
T ss_pred             cccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhc---CCcceEEEeeCCchHHHHHHHHHhhcc
Confidence            66778888888888 9999999999999999999999998866   445788999999999999996666655

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=98.51  E-value=7.3e-07  Score=63.98  Aligned_cols=56  Identities=36%  Similarity=0.395  Sum_probs=47.2

Q ss_pred             CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984        106 RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      +++++.++||+|||..++..+......   .....+++++|++.|+.|....+......
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~---~~~~~~lv~~p~~~l~~~~~~~~~~~~~~   56 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDS---LKGGQVLVLAPTRELANQVAERLKELFGE   56 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhc---ccCCCEEEEcCcHHHHHHHHHHHHHHhhC
Confidence            468999999999999999888886654   34558899999999999999988887754

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

>KOG0951|consensus

Probab=98.47  E-value=6.2e-07  Score=86.71  Aligned_cols=91  Identities=15%  Similarity=0.143  Sum_probs=73.3

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHhhccccCC-CcEEEEccCCCchhhHhHHHHHHHHHhccC------CCCCceEEEeec
Q psy12984         75 VCENTLKAIADMGFTKMTEIQARTIPPLLEG-RDLVGSAKTGSGKTLAFLVPAVELIYNLKF------MPRNGKSWQGKL  147 (178)
Q Consensus        75 l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g-~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~------~~~~~~~~l~Pt  147 (178)
                      ++.|-..++.  |+..+..||...-++++.+ .++++|||||+|||...++-+|+.+.+...      ......+||+|+
T Consensus       296 lP~Wnq~aF~--g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPm  373 (1674)
T KOG0951|consen  296 LPKWNQPAFF--GKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPM  373 (1674)
T ss_pred             Ccchhhhhcc--cchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeH
Confidence            6666666663  5667999999999988877 699999999999999999999999977543      223367899999


Q ss_pred             HHHHHHHHHHHHHHhhhcCC
Q psy12984        148 RPLTNGVYLVACNVFKSTQP  167 (178)
Q Consensus       148 r~La~qi~~~~~~l~~~~~~  167 (178)
                      ++|++.+...|++-+..++.
T Consensus       374 KaLvqE~VgsfSkRla~~GI  393 (1674)
T KOG0951|consen  374 KALVQEMVGSFSKRLAPLGI  393 (1674)
T ss_pred             HHHHHHHHHHHHhhccccCc
Confidence            99999999988887755443

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

Probab=98.41  E-value=1.8e-06  Score=82.23  Aligned_cols=82  Identities=20%  Similarity=0.082  Sum_probs=65.7

Q ss_pred             HHHHHHH-CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHH
Q psy12984         79 TLKAIAD-MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLV  157 (178)
Q Consensus        79 ll~~l~~-~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~  157 (178)
                      +.+.+.+ .|| .|+..|+.....+..|+++-+.||||.|||..-++-.+-.-.     .+.++.+|+||..|+.|+++.
T Consensus        71 ~~~fF~k~~G~-~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~a~-----kgkr~yii~PT~~Lv~Q~~~k  144 (1187)
T COG1110          71 FEEFFKKATGF-RPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLAK-----KGKRVYIIVPTTTLVRQVYER  144 (1187)
T ss_pred             HHHHHHHhhCC-CchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHHHHh-----cCCeEEEEecCHHHHHHHHHH
Confidence            3344555 466 999999998899999999999999999999865444333222     235889999999999999999


Q ss_pred             HHHHhhhcC
Q psy12984        158 ACNVFKSTQ  166 (178)
Q Consensus       158 ~~~l~~~~~  166 (178)
                      +..+....+
T Consensus       145 l~~~~e~~~  153 (1187)
T COG1110         145 LKKFAEDAG  153 (1187)
T ss_pred             HHHHHhhcC
Confidence            999998877

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

Probab=98.39  E-value=1.3e-06  Score=84.05  Aligned_cols=77  Identities=21%  Similarity=0.175  Sum_probs=57.7

Q ss_pred             CCCCCcHHHHHhhcc----ccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHH-HHHH
Q psy12984         87 GFTKMTEIQARTIPP----LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLV-ACNV  161 (178)
Q Consensus        87 g~~~pt~iQ~~aip~----~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~-~~~l  161 (178)
                      || .+.+-|..-+..    +..+.++++-|+||+|||++|++|++.+...    .+..++|-++|+.|..|+... +-.+
T Consensus       255 ~~-e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~----~~~~vvIsT~T~~LQ~Ql~~kDiP~L  329 (928)
T PRK08074        255 KY-EKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKK----KEEPVVISTYTIQLQQQLLEKDIPLL  329 (928)
T ss_pred             CC-cCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhc----cCCeEEEEcCCHHHHHHHHHhhHHHH
Confidence            56 788888874433    3467899999999999999999999876643    334677789999999998763 4444


Q ss_pred             hhhcCCC
Q psy12984        162 FKSTQPP  168 (178)
Q Consensus       162 ~~~~~~~  168 (178)
                      .+-++.+
T Consensus       330 ~~~~~~~  336 (928)
T PRK08074        330 QKIFPFP  336 (928)
T ss_pred             HHHcCCC
Confidence            5555444

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.33  E-value=3.1e-06  Score=79.19  Aligned_cols=78  Identities=24%  Similarity=0.233  Sum_probs=56.3

Q ss_pred             CCCCCcHHHHHhhccc---cC------CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHH-
Q psy12984         87 GFTKMTEIQARTIPPL---LE------GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYL-  156 (178)
Q Consensus        87 g~~~pt~iQ~~aip~~---l~------g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~-  156 (178)
                      || .+.+-|..-+..+   +.      ++.++|-|+||+|||+||++|++-+...    ...+++|=+.|+.|-.|+.. 
T Consensus        23 ~~-e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~----~~k~vVIST~T~~LQeQL~~k   97 (697)
T PRK11747         23 GF-IPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARA----EKKKLVISTATVALQEQLVSK   97 (697)
T ss_pred             CC-CcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHH----cCCeEEEEcCCHHHHHHHHhh
Confidence            66 6778887744333   33      3678999999999999999999876653    23356667899999999964 


Q ss_pred             HHHHHhhhcCCCC
Q psy12984        157 VACNVFKSTQPPT  169 (178)
Q Consensus       157 ~~~~l~~~~~~~~  169 (178)
                      .+-.+.+-++.++
T Consensus        98 DlP~l~~~l~~~~  110 (697)
T PRK11747         98 DLPLLLKISGLDF  110 (697)
T ss_pred             hhhHHHHHcCCCc
Confidence            4555555555553

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

Probab=98.31  E-value=1.2e-06  Score=77.94  Aligned_cols=66  Identities=17%  Similarity=0.096  Sum_probs=53.5

Q ss_pred             CCcHHHHHhhccccC----CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984         90 KMTEIQARTIPPLLE----GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~----g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      .|.+.|.+|+..+..    ++..+++.|||+|||..++.-+-. +..       .++||||+++|+.|.++.+...+.
T Consensus        36 ~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~-~~~-------~~Lvlv~~~~L~~Qw~~~~~~~~~  105 (442)
T COG1061          36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAE-LKR-------STLVLVPTKELLDQWAEALKKFLL  105 (442)
T ss_pred             CCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHH-hcC-------CEEEEECcHHHHHHHHHHHHHhcC
Confidence            689999999999887    899999999999999988654433 211       389999999999999866555443

>KOG0351|consensus

Probab=98.31  E-value=5.2e-07  Score=86.35  Aligned_cols=72  Identities=22%  Similarity=0.212  Sum_probs=61.7

Q ss_pred             HHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHH
Q psy12984         79 TLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVA  158 (178)
Q Consensus        79 ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~  158 (178)
                      ........|+....+-|.++|.+.+.|+|+++..|||.||.+||.||++-       .++ ..++|.|+.+|.+++...+
T Consensus       253 ~~~l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l-------~~g-itvVISPL~SLm~DQv~~L  324 (941)
T KOG0351|consen  253 ELLLKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALL-------LGG-VTVVISPLISLMQDQVTHL  324 (941)
T ss_pred             HHHHHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeeccccc-------cCC-ceEEeccHHHHHHHHHHhh
Confidence            33334558999999999999999999999999999999999999999863       222 6788999999999888776

>KOG0947|consensus

Probab=98.21  E-value=1.9e-06  Score=81.60  Aligned_cols=77  Identities=17%  Similarity=0.154  Sum_probs=62.6

Q ss_pred             HCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984         85 DMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus        85 ~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      ..+| +|-.+|+.||-.+..|..|+|+|+|.+|||+..-+.+.-.-     ....+++|-+|.++|.+|-|+.|+.-++.
T Consensus       293 ~~pF-elD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq-----~h~TR~iYTSPIKALSNQKfRDFk~tF~D  366 (1248)
T KOG0947|consen  293 IYPF-ELDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQ-----KHMTRTIYTSPIKALSNQKFRDFKETFGD  366 (1248)
T ss_pred             hCCC-CccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHH-----hhccceEecchhhhhccchHHHHHHhccc
Confidence            3566 67789999999999999999999999999998444332211     23458899999999999999999988877


Q ss_pred             cCC
Q psy12984        165 TQP  167 (178)
Q Consensus       165 ~~~  167 (178)
                      .|+
T Consensus       367 vgL  369 (1248)
T KOG0947|consen  367 VGL  369 (1248)
T ss_pred             cce
Confidence            654

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

Probab=98.18  E-value=5.6e-06  Score=76.58  Aligned_cols=71  Identities=23%  Similarity=0.211  Sum_probs=57.8

Q ss_pred             CCCCCcHHHHHhhcc----ccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984         87 GFTKMTEIQARTIPP----LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus        87 g~~~pt~iQ~~aip~----~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      ....|.+.|...+..    +..|+.+++.||||+|||++|++|+|......    ...+++.++|+.|-.|++.....+
T Consensus        12 ~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~----~~~viist~t~~lq~q~~~~~~~~   86 (654)
T COG1199          12 PGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREE----GKKVIISTRTKALQEQLLEEDLPI   86 (654)
T ss_pred             CCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHc----CCcEEEECCCHHHHHHHHHhhcch
Confidence            444899999988854    34566799999999999999999999987653    257788899999999999886654

>TIGR00595 priA primosomal protein N'

Probab=98.16  E-value=2.8e-06  Score=76.81  Aligned_cols=49  Identities=20%  Similarity=0.029  Sum_probs=39.2

Q ss_pred             EEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984        109 VGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus       109 i~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      ++.++||||||.+|+..+...+..     +.++++++|+++|+.|++..|+..+
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~-----g~~vLvlvP~i~L~~Q~~~~l~~~f   49 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLAL-----GKSVLVLVPEIALTPQMIQRFKYRF   49 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHc-----CCeEEEEeCcHHHHHHHHHHHHHHh
Confidence            357999999999997665444432     4478999999999999999998754

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).

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

Probab=98.13  E-value=6.1e-06  Score=80.75  Aligned_cols=69  Identities=16%  Similarity=0.110  Sum_probs=54.7

Q ss_pred             CCcHHHHHhhcccc----CC-CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984         90 KMTEIQARTIPPLL----EG-RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus        90 ~pt~iQ~~aip~~l----~g-~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      .+.+.|..||..+.    .| +.++++.+||||||... +.++.++.+.  ....++++|+|+++|+.|....|..+
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~ta-i~li~~L~~~--~~~~rVLfLvDR~~L~~Qa~~~F~~~  486 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTA-IALMYRLLKA--KRFRRILFLVDRSALGEQAEDAFKDT  486 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHH-HHHHHHHHhc--CccCeEEEEecHHHHHHHHHHHHHhc
Confidence            58999999998764    33 68999999999999884 3455555543  22348899999999999999998876

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=98.11  E-value=9.6e-06  Score=76.50  Aligned_cols=78  Identities=19%  Similarity=0.161  Sum_probs=67.3

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      .|. +|+++|..+--++..|+  |+.-.||+|||++..+|++-..+.     +.++-+++||-.||.|=+..+..+..++
T Consensus        77 ~g~-~~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~-----G~~v~vvT~neyLA~Rd~e~~~~~~~~L  148 (796)
T PRK12906         77 LGL-RPFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALT-----GKGVHVVTVNEYLSSRDATEMGELYRWL  148 (796)
T ss_pred             hCC-CCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHc-----CCCeEEEeccHHHHHhhHHHHHHHHHhc
Confidence            676 89999998877777777  889999999999999999887765     5578889999999999999999999998


Q ss_pred             CCCCcc
Q psy12984        166 QPPTVI  171 (178)
Q Consensus       166 ~~~~~~  171 (178)
                      |..+++
T Consensus       149 Gl~vg~  154 (796)
T PRK12906        149 GLTVGL  154 (796)
T ss_pred             CCeEEE
Confidence            866554

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

Probab=98.05  E-value=8.6e-06  Score=75.05  Aligned_cols=90  Identities=20%  Similarity=0.204  Sum_probs=73.2

Q ss_pred             CCHHHHHH-HHHCCCCCCcHHHHHhhccccCC------CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeec
Q psy12984         75 VCENTLKA-IADMGFTKMTEIQARTIPPLLEG------RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKL  147 (178)
Q Consensus        75 l~~~ll~~-l~~~g~~~pt~iQ~~aip~~l~g------~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Pt  147 (178)
                      .+..+++. +..+.| .+|.-|..+|..++..      .+=++++--|||||+..++.++..+..     +-++..++||
T Consensus       247 ~~~~l~~~~~~~LPF-~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~-----G~Q~ALMAPT  320 (677)
T COG1200         247 ANGELLAKFLAALPF-KLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEA-----GYQAALMAPT  320 (677)
T ss_pred             ccHHHHHHHHHhCCC-CccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHc-----CCeeEEeccH
Confidence            33444544 467899 8999999999988653      355788999999999999999998854     5588889999


Q ss_pred             HHHHHHHHHHHHHHhhhcCCCCc
Q psy12984        148 RPLTNGVYLVACNVFKSTQPPTV  170 (178)
Q Consensus       148 r~La~qi~~~~~~l~~~~~~~~~  170 (178)
                      --||.|=|..+.+++..++..+.
T Consensus       321 EILA~QH~~~~~~~l~~~~i~V~  343 (677)
T COG1200         321 EILAEQHYESLRKWLEPLGIRVA  343 (677)
T ss_pred             HHHHHHHHHHHHHHhhhcCCeEE
Confidence            99999999999999987774433

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.02  E-value=2.5e-05  Score=73.21  Aligned_cols=74  Identities=12%  Similarity=0.117  Sum_probs=59.9

Q ss_pred             CCCCCcHHHHHhhcc----ccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         87 GFTKMTEIQARTIPP----LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        87 g~~~pt~iQ~~aip~----~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      -|..++|.|.+.+..    +..|.++++.||||+|||++-+.|+|.++....  ...+.+|.+.|..=-.|+.+.++++.
T Consensus         7 Py~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~--~~~kIiy~sRThsQl~q~i~Elk~~~   84 (705)
T TIGR00604         7 PYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKP--EVRKIIYASRTHSQLEQATEELRKLM   84 (705)
T ss_pred             CCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhcc--ccccEEEEcccchHHHHHHHHHHhhh
Confidence            365668999887754    457899999999999999999999999876432  23477889999998888888988864

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).

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=98.00  E-value=2.4e-05  Score=73.08  Aligned_cols=77  Identities=19%  Similarity=0.099  Sum_probs=66.4

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      .|. +|+.+|..+.-.++.|+  |+...||+|||++..+|++-..+.     +.++-+++|+-.||.+-+.++..+..++
T Consensus        75 lg~-r~ydvQlig~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL~-----G~~VhvvT~NdyLA~RDae~m~~ly~~L  146 (764)
T PRK12326         75 LGL-RPFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYALQ-----GRRVHVITVNDYLARRDAEWMGPLYEAL  146 (764)
T ss_pred             cCC-CcchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHHc-----CCCeEEEcCCHHHHHHHHHHHHHHHHhc
Confidence            677 89999999998888874  678999999999999999876654     5578889999999999999999999997


Q ss_pred             CCCCc
Q psy12984        166 QPPTV  170 (178)
Q Consensus       166 ~~~~~  170 (178)
                      |..++
T Consensus       147 GLsvg  151 (764)
T PRK12326        147 GLTVG  151 (764)
T ss_pred             CCEEE
Confidence            76544

>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=97.97  E-value=3.8e-05  Score=63.49  Aligned_cols=73  Identities=22%  Similarity=0.196  Sum_probs=57.1

Q ss_pred             CcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhcC
Q psy12984         91 MTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus        91 pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      +|+-|..+|..  ...+++|.|..|||||.+.+--++..+.... .+..+.+++++|+..|..+...+...+....
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~-~~~~~Il~lTft~~aa~e~~~ri~~~l~~~~   73 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGG-VPPERILVLTFTNAAAQEMRERIRELLEEEQ   73 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSS-STGGGEEEEESSHHHHHHHHHHHHHHHHHCC
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhcccc-CChHHheecccCHHHHHHHHHHHHHhcCccc
Confidence            46789898876  6778999999999999998877777776543 4445788999999999999999998876653

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 ....

>TIGR00603 rad25 DNA repair helicase rad25

Probab=97.91  E-value=2.7e-05  Score=73.07  Aligned_cols=65  Identities=12%  Similarity=0.040  Sum_probs=52.1

Q ss_pred             CCcHHHHHhhcccc-CC--CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         90 KMTEIQARTIPPLL-EG--RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        90 ~pt~iQ~~aip~~l-~g--~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      .+.|.|..|+..++ .|  +..+++.|||+|||+..+..+ ..+       ...++||||+..|+.|....|..+.
T Consensus       255 ~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa-~~l-------~k~tLILvps~~Lv~QW~~ef~~~~  322 (732)
T TIGR00603       255 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAA-CTV-------KKSCLVLCTSAVSVEQWKQQFKMWS  322 (732)
T ss_pred             CcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHH-HHh-------CCCEEEEeCcHHHHHHHHHHHHHhc
Confidence            57889999998876 34  467889999999999976433 333       2368999999999999999998874

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).

>PF13245 AAA_19: Part of AAA domain

Probab=97.89  E-value=4.4e-05  Score=51.95  Aligned_cols=52  Identities=15%  Similarity=0.028  Sum_probs=37.9

Q ss_pred             CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHH
Q psy12984        106 RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVA  158 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~  158 (178)
                      .-+++.++.|||||...+--+...+...... ..++++++||+..+..+.+.+
T Consensus        11 ~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~-~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen   11 PLFVVQGPPGTGKTTTLAARIAELLAARADP-GKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHHhcCC-CCeEEEECCCHHHHHHHHHHH
Confidence            3355599999999976655555544332223 568899999999999888877

>KOG0948|consensus

Probab=97.87  E-value=2.4e-05  Score=72.88  Aligned_cols=75  Identities=20%  Similarity=0.234  Sum_probs=64.6

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhcCCCC
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQPPT  169 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~~~~  169 (178)
                      .+-|+|..||..+-.+..|+|+|.|.+|||.+.-+.|...+..     .-+++|-+|.++|.+|-|+.+..=++..|+-+
T Consensus       129 ~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~-----kQRVIYTSPIKALSNQKYREl~~EF~DVGLMT  203 (1041)
T KOG0948|consen  129 TLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLRE-----KQRVIYTSPIKALSNQKYRELLEEFKDVGLMT  203 (1041)
T ss_pred             ccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHh-----cCeEEeeChhhhhcchhHHHHHHHhcccceee
Confidence            4567999999999999999999999999999988888877754     33888999999999999999988877776643

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

Probab=97.86  E-value=3.6e-05  Score=68.86  Aligned_cols=70  Identities=14%  Similarity=0.008  Sum_probs=54.2

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      .|...|......++. +|++|+.|||-|||...++-+...+..   .++ .+++++||+.|+.|....|.++++-
T Consensus        15 e~R~YQ~~i~a~al~-~NtLvvlPTGLGKT~IA~~V~~~~l~~---~~~-kvlfLAPTKPLV~Qh~~~~~~v~~i   84 (542)
T COG1111          15 EPRLYQLNIAAKALF-KNTLVVLPTGLGKTFIAAMVIANRLRW---FGG-KVLFLAPTKPLVLQHAEFCRKVTGI   84 (542)
T ss_pred             cHHHHHHHHHHHHhh-cCeEEEecCCccHHHHHHHHHHHHHHh---cCC-eEEEecCCchHHHHHHHHHHHHhCC
Confidence            444555554444453 499999999999999998888877755   444 7899999999999999988877644

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

Probab=97.81  E-value=3.4e-05  Score=71.94  Aligned_cols=70  Identities=20%  Similarity=0.179  Sum_probs=53.2

Q ss_pred             CcHHHHHhhcccc----C------CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHH
Q psy12984         91 MTEIQARTIPPLL----E------GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACN  160 (178)
Q Consensus        91 pt~iQ~~aip~~l----~------g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~  160 (178)
                      |..+|..|+..+.    .      .+..++..+||||||+..+.-+...+ .  .....++++|+|.++|..|....|..
T Consensus       239 ~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~-~--~~~~~~vl~lvdR~~L~~Q~~~~f~~  315 (667)
T TIGR00348       239 QRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKAL-E--LLKNPKVFFVVDRRELDYQLMKEFQS  315 (667)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHH-h--hcCCCeEEEEECcHHHHHHHHHHHHh
Confidence            5668999887652    2      25788999999999998665554433 2  13455888999999999999999998


Q ss_pred             Hhh
Q psy12984        161 VFK  163 (178)
Q Consensus       161 l~~  163 (178)
                      +..
T Consensus       316 ~~~  318 (667)
T TIGR00348       316 LQK  318 (667)
T ss_pred             hCC
Confidence            763

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

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=97.81  E-value=7.4e-05  Score=71.24  Aligned_cols=78  Identities=19%  Similarity=0.095  Sum_probs=63.7

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      +|. +|+++|...=-++..|  -|+...||+|||++..+|++-..+.     +.++-+++|+-.||.+-+..|..+..++
T Consensus        79 lGm-~~ydVQliGg~~Lh~G--~iaEM~TGEGKTLvA~l~a~l~al~-----G~~VhvvT~ndyLA~RD~e~m~~l~~~l  150 (913)
T PRK13103         79 MGM-RHFDVQLIGGMTLHEG--KIAEMRTGEGKTLVGTLAVYLNALS-----GKGVHVVTVNDYLARRDANWMRPLYEFL  150 (913)
T ss_pred             hCC-CcchhHHHhhhHhccC--ccccccCCCCChHHHHHHHHHHHHc-----CCCEEEEeCCHHHHHHHHHHHHHHhccc
Confidence            575 8999998765555555  4678999999999999999876654     5578889999999999999999999988


Q ss_pred             CCCCcc
Q psy12984        166 QPPTVI  171 (178)
Q Consensus       166 ~~~~~~  171 (178)
                      |..+++
T Consensus       151 Gl~v~~  156 (913)
T PRK13103        151 GLSVGI  156 (913)
T ss_pred             CCEEEE
Confidence            766543

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=97.78  E-value=9.8e-05  Score=70.12  Aligned_cols=78  Identities=18%  Similarity=0.120  Sum_probs=64.1

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      .|. +|+++|..+--++..  .-|+...||.|||+++.+|+.-..+     .+.++-+++++..||.+-+.++..+.+++
T Consensus        73 lG~-r~ydvQlig~l~L~~--G~IaEm~TGEGKTL~a~l~ayl~aL-----~G~~VhVvT~NdyLA~RD~e~m~pvy~~L  144 (870)
T CHL00122         73 LGL-RHFDVQLIGGLVLND--GKIAEMKTGEGKTLVATLPAYLNAL-----TGKGVHIVTVNDYLAKRDQEWMGQIYRFL  144 (870)
T ss_pred             hCC-CCCchHhhhhHhhcC--CccccccCCCCchHHHHHHHHHHHh-----cCCceEEEeCCHHHHHHHHHHHHHHHHHc
Confidence            677 799999887644544  4678999999999999999964333     35577889999999999999999999999


Q ss_pred             CCCCcc
Q psy12984        166 QPPTVI  171 (178)
Q Consensus       166 ~~~~~~  171 (178)
                      |..+++
T Consensus       145 GLsvg~  150 (870)
T CHL00122        145 GLTVGL  150 (870)
T ss_pred             CCceee
Confidence            987664

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=97.68  E-value=0.00011  Score=69.25  Aligned_cols=78  Identities=23%  Similarity=0.183  Sum_probs=62.5

Q ss_pred             CcHHHHHhhccccCC---C-cEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhcC
Q psy12984         91 MTEIQARTIPPLLEG---R-DLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus        91 pt~iQ~~aip~~l~g---~-dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      +++.|..++..++.+   . .+++.||||.|||.+.+++++..+.... ....+.+++.|+|.+..++++.+....+..+
T Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~~-~~~~r~i~vlP~~t~ie~~~~r~~~~~~~~~  274 (733)
T COG1203         196 GYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKI-KLKSRVIYVLPFRTIIEDMYRRAKEIFGLFS  274 (733)
T ss_pred             hhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhccc-cccceEEEEccHHHHHHHHHHHHHhhhcccc
Confidence            377888888766532   4 7889999999999999999998887632 2556888899999999999999998877665


Q ss_pred             CCC
Q psy12984        167 PPT  169 (178)
Q Consensus       167 ~~~  169 (178)
                      ...
T Consensus       275 ~~~  277 (733)
T COG1203         275 VIG  277 (733)
T ss_pred             ccc
Confidence            543

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

Probab=97.66  E-value=0.00024  Score=55.93  Aligned_cols=69  Identities=12%  Similarity=0.072  Sum_probs=48.5

Q ss_pred             CcHHHHHhhccccCCCc-EEEEccCCCchhhHhHHHHHHHHHh----ccCCCCCceEEEeecHHHHHHHHHHHHH
Q psy12984         91 MTEIQARTIPPLLEGRD-LVGSAKTGSGKTLAFLVPAVELIYN----LKFMPRNGKSWQGKLRPLTNGVYLVACN  160 (178)
Q Consensus        91 pt~iQ~~aip~~l~g~d-vi~~a~TGsGKTlaf~lp~l~~l~~----~~~~~~~~~~~l~Ptr~La~qi~~~~~~  160 (178)
                      +.+-|..|+..++...+ .+|.+|+|||||..-. -++..+..    .........++++|+..-+..+...+..
T Consensus         2 ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~-~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    2 LNESQREAIQSALSSNGITLIQGPPGTGKTTTLA-SIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             --HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHH-HHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHH-HHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            56789999999998888 9999999999995433 34444421    1124555778899999988888887776

>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=97.62  E-value=0.00044  Score=57.82  Aligned_cols=80  Identities=21%  Similarity=0.167  Sum_probs=61.5

Q ss_pred             HCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984         85 DMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus        85 ~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      ..|+ .|+++|..++=++..|+  |+.-.||-|||++..+|++-..+.     +..+=+++....||..=+..+..+...
T Consensus        73 ~~g~-~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~-----G~~V~vvT~NdyLA~RD~~~~~~~y~~  144 (266)
T PF07517_consen   73 TLGL-RPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQ-----GKGVHVVTSNDYLAKRDAEEMRPFYEF  144 (266)
T ss_dssp             HTS-----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTT-----SS-EEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             HcCC-cccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHh-----cCCcEEEeccHHHhhccHHHHHHHHHH
Confidence            3566 89999999997777777  889999999999988888766654     446677899999999999999999999


Q ss_pred             cCCCCcce
Q psy12984        165 TQPPTVIK  172 (178)
Q Consensus       165 ~~~~~~~~  172 (178)
                      +|..+++.
T Consensus       145 LGlsv~~~  152 (266)
T PF07517_consen  145 LGLSVGII  152 (266)
T ss_dssp             TT--EEEE
T ss_pred             hhhccccC
Confidence            98876654

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 ....

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

Probab=97.28  E-value=0.00028  Score=63.84  Aligned_cols=65  Identities=25%  Similarity=0.269  Sum_probs=49.3

Q ss_pred             CCcHHHHHhhccccCC-----CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         90 KMTEIQARTIPPLLEG-----RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g-----~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      .|+.-|-.||..+..|     ++-...+-||||||.... -+|..+.      + -+++|+|.+-||-|+|..|+.++
T Consensus        12 ~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~A-nVI~~~~------r-PtLV~AhNKTLAaQLy~Efk~fF   81 (663)
T COG0556          12 KPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTMA-NVIAKVQ------R-PTLVLAHNKTLAAQLYSEFKEFF   81 (663)
T ss_pred             CCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHHH-HHHHHhC------C-CeEEEecchhHHHHHHHHHHHhC
Confidence            6777888888766543     567778999999998754 2333232      2 45899999999999999999886

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=97.28  E-value=0.0014  Score=62.78  Aligned_cols=78  Identities=21%  Similarity=0.125  Sum_probs=64.9

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      .|. +|+++|...--++..|  -|+...||-||||+..+|+.-..+.     +.++-+++++..||..-..++..+.+++
T Consensus        82 lG~-r~ydVQliGgl~Lh~G--~IAEM~TGEGKTL~atlpaylnAL~-----GkgVhVVTvNdYLA~RDae~m~~vy~~L  153 (939)
T PRK12902         82 LGM-RHFDVQLIGGMVLHEG--QIAEMKTGEGKTLVATLPSYLNALT-----GKGVHVVTVNDYLARRDAEWMGQVHRFL  153 (939)
T ss_pred             hCC-CcchhHHHhhhhhcCC--ceeeecCCCChhHHHHHHHHHHhhc-----CCCeEEEeCCHHHHHhHHHHHHHHHHHh
Confidence            577 8999998766556555  4689999999999999998765543     4577889999999999999999999999


Q ss_pred             CCCCcc
Q psy12984        166 QPPTVI  171 (178)
Q Consensus       166 ~~~~~~  171 (178)
                      |..+++
T Consensus       154 GLtvg~  159 (939)
T PRK12902        154 GLSVGL  159 (939)
T ss_pred             CCeEEE
Confidence            887664

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

Probab=97.23  E-value=0.00067  Score=63.83  Aligned_cols=69  Identities=17%  Similarity=0.136  Sum_probs=55.4

Q ss_pred             CCcHHHHHhhccccCC----CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984         90 KMTEIQARTIPPLLEG----RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g----~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      .+++-|..|+..+...    .-.++.+.||||||-+|+--+-..|..     +.++++|+|-.+|..|+...|...++
T Consensus       198 ~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~-----GkqvLvLVPEI~Ltpq~~~rf~~rFg  270 (730)
T COG1198         198 ALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQ-----GKQVLVLVPEIALTPQLLARFKARFG  270 (730)
T ss_pred             ccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHc-----CCEEEEEeccccchHHHHHHHHHHhC
Confidence            5567888888877544    678999999999999997555555533     45899999999999999999887665

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

Probab=96.96  E-value=0.0024  Score=50.67  Aligned_cols=63  Identities=16%  Similarity=0.104  Sum_probs=43.2

Q ss_pred             CCcHHHHHhhccccCC--CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHH
Q psy12984         90 KMTEIQARTIPPLLEG--RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLV  157 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g--~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~  157 (178)
                      ++++-|..++..++..  +-++++++.|+|||.+. -.+...+..    .+..+++++||..-+..+...
T Consensus         1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l-~~~~~~~~~----~g~~v~~~apT~~Aa~~L~~~   65 (196)
T PF13604_consen    1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLL-KALAEALEA----AGKRVIGLAPTNKAAKELREK   65 (196)
T ss_dssp             -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHH-HHHHHHHHH----TT--EEEEESSHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHH-HHHHHHHHh----CCCeEEEECCcHHHHHHHHHh
Confidence            3678899999988644  34778899999999753 334444443    245788899998887776655

>KOG0951|consensus

Probab=96.94  E-value=0.0012  Score=64.67  Aligned_cols=69  Identities=19%  Similarity=0.236  Sum_probs=54.6

Q ss_pred             CCCCcHHHHHhhccccC-CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         88 FTKMTEIQARTIPPLLE-GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        88 ~~~pt~iQ~~aip~~l~-g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      |....|+|...++.+.. ..+|+++||+|||||.+..+.++.      ..+..++++|.|.-+.+.-++..+.+-+
T Consensus      1141 f~~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~------~~~~~~~vyi~p~~~i~~~~~~~w~~~f 1210 (1674)
T KOG0951|consen 1141 FQDFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR------PDTIGRAVYIAPLEEIADEQYRDWEKKF 1210 (1674)
T ss_pred             ccccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC------CccceEEEEecchHHHHHHHHHHHHHhh
Confidence            33447899999998764 578999999999999998888866      2556689999999999987776654433

>PRK11054 helD DNA helicase IV; Provisional

Probab=96.81  E-value=0.011  Score=55.62  Aligned_cols=72  Identities=18%  Similarity=0.057  Sum_probs=53.9

Q ss_pred             CCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984         89 TKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus        89 ~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      ..+++-|+.|+-.  ...+++|.|..|||||.+.+--+...+.... ....+.++++.||..|..+...+...++
T Consensus       195 ~~L~~~Q~~av~~--~~~~~lV~agaGSGKT~vl~~r~ayLl~~~~-~~~~~IL~ltft~~AA~em~eRL~~~lg  266 (684)
T PRK11054        195 SPLNPSQARAVVN--GEDSLLVLAGAGSGKTSVLVARAGWLLARGQ-AQPEQILLLAFGRQAAEEMDERIRERLG  266 (684)
T ss_pred             CCCCHHHHHHHhC--CCCCeEEEEeCCCCHHHHHHHHHHHHHHhCC-CCHHHeEEEeccHHHHHHHHHHHHHhcC
Confidence            4689999998843  3356889999999999987665555454322 3345888999999999999988877654

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

Probab=96.80  E-value=0.0028  Score=48.47  Aligned_cols=54  Identities=20%  Similarity=0.132  Sum_probs=38.1

Q ss_pred             CCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984        104 EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      .|.--++-..+|+|||--.+--++.....    .+.++|+|.|||.+|..++..++..
T Consensus         3 kg~~~~~d~hpGaGKTr~vlp~~~~~~i~----~~~rvLvL~PTRvva~em~~aL~~~   56 (148)
T PF07652_consen    3 KGELTVLDLHPGAGKTRRVLPEIVREAIK----RRLRVLVLAPTRVVAEEMYEALKGL   56 (148)
T ss_dssp             TTEEEEEE--TTSSTTTTHHHHHHHHHHH----TT--EEEEESSHHHHHHHHHHTTTS
T ss_pred             CCceeEEecCCCCCCcccccHHHHHHHHH----ccCeEEEecccHHHHHHHHHHHhcC
Confidence            35555678899999999876655554443    3668999999999999999887643

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 ....

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

Probab=96.79  E-value=0.0049  Score=60.20  Aligned_cols=85  Identities=15%  Similarity=0.084  Sum_probs=65.9

Q ss_pred             HHHHHHHHH-CCCCCCcHHHHHhhccccC----C--CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHH
Q psy12984         77 ENTLKAIAD-MGFTKMTEIQARTIPPLLE----G--RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRP  149 (178)
Q Consensus        77 ~~ll~~l~~-~g~~~pt~iQ~~aip~~l~----g--~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~  149 (178)
                      .+....+.+ .+| ..|+-|..||..+..    +  +|=++|+--|-|||-..+=.+.-.+.     .+.++.++|||--
T Consensus       581 ~~~q~~F~~~FPy-eET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~-----~GKQVAvLVPTTl  654 (1139)
T COG1197         581 TEWQEEFEASFPY-EETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVM-----DGKQVAVLVPTTL  654 (1139)
T ss_pred             hHHHHHHHhcCCC-cCCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhc-----CCCeEEEEcccHH
Confidence            334444433 566 679999999998753    3  68899999999999988777766664     3568999999999


Q ss_pred             HHHHHHHHHHHHhhhcCC
Q psy12984        150 LTNGVYLVACNVFKSTQP  167 (178)
Q Consensus       150 La~qi~~~~~~l~~~~~~  167 (178)
                      ||+|=|+.|+.=+++++-
T Consensus       655 LA~QHy~tFkeRF~~fPV  672 (1139)
T COG1197         655 LAQQHYETFKERFAGFPV  672 (1139)
T ss_pred             hHHHHHHHHHHHhcCCCe
Confidence            999999999976655443

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=96.76  E-value=0.0065  Score=56.89  Aligned_cols=71  Identities=13%  Similarity=0.009  Sum_probs=54.1

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      .+++-|+.|+-..  ...++|.|..|||||.+...-+...+.... .+..+.++|+-|+.-|..+...+..+++
T Consensus         2 ~Ln~~Q~~av~~~--~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~-v~p~~IL~lTFT~kAA~em~~Rl~~~l~   72 (672)
T PRK10919          2 RLNPGQQQAVEFV--TGPCLVLAGAGSGKTRVITNKIAHLIRGCG-YQARHIAAVTFTNKAAREMKERVAQTLG   72 (672)
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHhcC-CCHHHeeeEechHHHHHHHHHHHHHHhC
Confidence            4678899988542  456788899999999997776666664322 3344788999999999999988887764

>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=96.59  E-value=0.0031  Score=50.87  Aligned_cols=57  Identities=21%  Similarity=0.176  Sum_probs=39.3

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHH
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRP  149 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~  149 (178)
                      ..|+-|..++.+++...-+++.++.|||||+..+.-.++.+..   ....+.++.-|+-+
T Consensus         4 p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~---g~~~kiii~Rp~v~   60 (205)
T PF02562_consen    4 PKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKE---GEYDKIIITRPPVE   60 (205)
T ss_dssp             --SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHT---TS-SEEEEEE-S--
T ss_pred             CCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHh---CCCcEEEEEecCCC
Confidence            4578999999999988889999999999999999999988876   33335455555443

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

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

Probab=96.58  E-value=0.008  Score=49.35  Aligned_cols=59  Identities=14%  Similarity=-0.047  Sum_probs=35.6

Q ss_pred             cCCCcEEEEccCCCchhhHhHHHHHHHHHhc-cCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984        103 LEGRDLVGSAKTGSGKTLAFLVPAVELIYNL-KFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~-~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      ...+.+|++-..|+|||+..+.-+. .+... +......++|++|. .|..|....+..++.
T Consensus        23 ~~~~g~lL~de~GlGKT~~~i~~~~-~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~~~~   82 (299)
T PF00176_consen   23 SPPRGGLLADEMGLGKTITAIALIS-YLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEKWFD   82 (299)
T ss_dssp             TTT-EEEE---TTSSHHHHHHHHHH-HHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHHHSG
T ss_pred             cCCCCEEEEECCCCCchhhhhhhhh-hhhhccccccccceeEeecc-chhhhhhhhhccccc
Confidence            4457899999999999987654443 33332 21222358999999 777788888877774

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.

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=96.56  E-value=0.0053  Score=57.41  Aligned_cols=65  Identities=22%  Similarity=0.243  Sum_probs=50.4

Q ss_pred             CCcHHHHHhhccccCC-----CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         90 KMTEIQARTIPPLLEG-----RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g-----~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      .|+..|..+|..+..|     ++.++.+-||||||+...- ++..+      + ..+++|+|.+.+|.|+|..|+.++
T Consensus         9 ~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~a~-~~~~~------~-~p~Lvi~~n~~~A~ql~~el~~f~   78 (655)
T TIGR00631         9 QPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMAN-VIAQV------N-RPTLVIAHNKTLAAQLYNEFKEFF   78 (655)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHHHH-HHHHh------C-CCEEEEECCHHHHHHHHHHHHHhC
Confidence            7888999999876443     3667899999999987542 33322      1 246899999999999999998886

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

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=96.54  E-value=0.011  Score=55.68  Aligned_cols=72  Identities=11%  Similarity=-0.014  Sum_probs=55.3

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      .+++-|+.|+-..  ...++|.|..|||||.+...=+...+... ..+..+.++|+-|+.-|..+...+..+++.
T Consensus         9 ~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~vl~~Ria~Li~~~-~v~p~~IL~lTFT~kAA~Em~~Rl~~~~~~   80 (721)
T PRK11773          9 SLNDKQREAVAAP--LGNMLVLAGAGSGKTRVLVHRIAWLMQVE-NASPYSIMAVTFTNKAAAEMRHRIEQLLGT   80 (721)
T ss_pred             hcCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHcC-CCChhHeEeeeccHHHHHHHHHHHHHHhcc
Confidence            5889999988533  35788999999999998766666555332 234457889999999999999999888764

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=96.50  E-value=0.014  Score=54.19  Aligned_cols=71  Identities=14%  Similarity=-0.001  Sum_probs=53.7

Q ss_pred             CcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984         91 MTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus        91 pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      +++-|..++-.  .+.+++|.|..|||||.+.+--+...+.... .+....++++.|+.-|.++...+...++.
T Consensus         2 Ln~~Q~~av~~--~~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~-~~p~~IL~vTFt~~Aa~em~~Rl~~~l~~   72 (664)
T TIGR01074         2 LNPQQQEAVEY--VTGPCLVLAGAGSGKTRVITNKIAYLIQNCG-YKARNIAAVTFTNKAAREMKERVAKTLGK   72 (664)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcC-CCHHHeEEEeccHHHHHHHHHHHHHHhCc
Confidence            57889888743  3458999999999999988777776664322 23347788899999999999888776653

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

>TIGR01075 uvrD DNA helicase II

Probab=96.48  E-value=0.012  Score=55.32  Aligned_cols=73  Identities=12%  Similarity=0.006  Sum_probs=55.8

Q ss_pred             CCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984         89 TKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus        89 ~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      ..+++-|+.|+-.  ....++|.|..|||||.+...=+...+... ..+..+.++++-|+.-|..+...+..+++.
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~L~~Ria~Li~~~-~v~p~~IL~lTFTnkAA~em~~Rl~~~~~~   75 (715)
T TIGR01075         3 DGLNDKQREAVAA--PPGNLLVLAGAGSGKTRVLTHRIAWLLSVE-NASPHSIMAVTFTNKAAAEMRHRIGALLGT   75 (715)
T ss_pred             cccCHHHHHHHcC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcC-CCCHHHeEeeeccHHHHHHHHHHHHHHhcc
Confidence            3578999998854  345789999999999998766665555432 234457888999999999999998888764

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

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=96.44  E-value=0.014  Score=56.00  Aligned_cols=80  Identities=21%  Similarity=0.101  Sum_probs=65.1

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      +|. +|+++|...--++..|+  |+...||-||||+..+|+.-..+.     +.++=+++..--||.-=..++..+..++
T Consensus        75 lG~-r~ydVQliGglvLh~G~--IAEMkTGEGKTLvAtLpayLnAL~-----GkgVhVVTvNdYLA~RDae~mg~vy~fL  146 (925)
T PRK12903         75 LGK-RPYDVQIIGGIILDLGS--VAEMKTGEGKTITSIAPVYLNALT-----GKGVIVSTVNEYLAERDAEEMGKVFNFL  146 (925)
T ss_pred             hCC-CcCchHHHHHHHHhcCC--eeeecCCCCccHHHHHHHHHHHhc-----CCceEEEecchhhhhhhHHHHHHHHHHh
Confidence            577 89999998876667674  689999999999999998644433     4466678888999999999999999999


Q ss_pred             CCCCcceE
Q psy12984        166 QPPTVIKV  173 (178)
Q Consensus       166 ~~~~~~~v  173 (178)
                      |..+++.+
T Consensus       147 GLsvG~i~  154 (925)
T PRK12903        147 GLSVGINK  154 (925)
T ss_pred             CCceeeeC
Confidence            99877544

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=96.36  E-value=0.014  Score=58.14  Aligned_cols=69  Identities=17%  Similarity=0.111  Sum_probs=54.8

Q ss_pred             CcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984         91 MTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus        91 pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      .|+-|..||-  ..|.+++|.|..|||||.+.+--++..+...  ....+.++++=|++-|..+...+..-+.
T Consensus         2 ~t~~Q~~ai~--~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~--~~~~~il~~tFt~~aa~e~~~ri~~~l~   70 (1232)
T TIGR02785         2 WTDEQWQAIY--TRGQNILVSASAGSGKTAVLVERIIKKILRG--VDIDRLLVVTFTNAAAREMKERIEEALQ   70 (1232)
T ss_pred             CCHHHHHHHh--CCCCCEEEEecCCCcHHHHHHHHHHHHHhcC--CCHhhEEEEeccHHHHHHHHHHHHHHHH
Confidence            5889999995  4689999999999999999888888877653  2224678899999999887777665443

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.

>TIGR00376 DNA helicase, putative

Probab=96.36  E-value=0.013  Score=54.64  Aligned_cols=65  Identities=12%  Similarity=0.042  Sum_probs=47.8

Q ss_pred             CcHHHHHhhccccCC-CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHH
Q psy12984         91 MTEIQARTIPPLLEG-RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACN  160 (178)
Q Consensus        91 pt~iQ~~aip~~l~g-~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~  160 (178)
                      +.+.|..|+..++.. ..+++.+|+|||||....--+.+.+..     +.++++++||..=+.++...+..
T Consensus       158 ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~~~-----g~~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       158 LNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLVKR-----GLRVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHHHc-----CCCEEEEcCcHHHHHHHHHHHHh
Confidence            477999999888766 678899999999997554333333322     33788899998888777776654

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.

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=96.29  E-value=0.0078  Score=59.91  Aligned_cols=56  Identities=20%  Similarity=0.169  Sum_probs=35.5

Q ss_pred             ccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe-e----cHHHHHHHHHHHHH
Q psy12984        100 PPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG-K----LRPLTNGVYLVACN  160 (178)
Q Consensus       100 p~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~-P----tr~La~qi~~~~~~  160 (178)
                      ..+..+..++++|+||||||.  .+|.+-....  ... .+.++++ |    +++||.+|...+..
T Consensus        84 ~ai~~~~VviI~GeTGSGKTT--qlPq~lle~g--~g~-~g~I~~TQPRRlAArsLA~RVA~El~~  144 (1294)
T PRK11131         84 EAIRDHQVVIVAGETGSGKTT--QLPKICLELG--RGV-KGLIGHTQPRRLAARTVANRIAEELET  144 (1294)
T ss_pred             HHHHhCCeEEEECCCCCCHHH--HHHHHHHHcC--CCC-CCceeeCCCcHHHHHHHHHHHHHHHhh
Confidence            344456678889999999999  5785432221  111 1122221 3    68999999998875

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

Probab=96.22  E-value=0.016  Score=56.28  Aligned_cols=51  Identities=16%  Similarity=0.021  Sum_probs=41.2

Q ss_pred             CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHH
Q psy12984        106 RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVAC  159 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~  159 (178)
                      .++.+..+||||||.+|+--++.....   ......+++||+.+.-..++.-+.
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~~~---~~~~~fii~vp~~aI~egv~~~l~  110 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELHQK---YGLFKFIIVVPTPAIKEGTRNFIQ  110 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHH---cCCcEEEEEeCCHHHHHHHHHHhh
Confidence            589999999999999998887775544   345678899999998888876655

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.15  E-value=0.014  Score=50.04  Aligned_cols=48  Identities=27%  Similarity=0.391  Sum_probs=32.6

Q ss_pred             HHHHHHCCCCCCcHHHHHhhcc-ccCCCcEEEEccCCCchhhHhHHHHHHHH
Q psy12984         80 LKAIADMGFTKMTEIQARTIPP-LLEGRDLVGSAKTGSGKTLAFLVPAVELI  130 (178)
Q Consensus        80 l~~l~~~g~~~pt~iQ~~aip~-~l~g~dvi~~a~TGsGKTlaf~lp~l~~l  130 (178)
                      +..|...|+  +++.|...+.. +..+.+++++++|||||| .++-.++..+
T Consensus       124 l~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKT-Tll~aL~~~~  172 (319)
T PRK13894        124 LDQYVERGI--MTAAQREAIIAAVRAHRNILVIGGTGSGKT-TLVNAIINEM  172 (319)
T ss_pred             HHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHH-HHHHHHHHhh
Confidence            344555565  34566666654 457789999999999999 4555555544

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=96.10  E-value=0.027  Score=53.12  Aligned_cols=72  Identities=14%  Similarity=0.016  Sum_probs=55.3

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      .+++-|..|+-..  ..+++|.|..|||||.+...=+...+.... ....+.++++-|+.-|..+...+..+++.
T Consensus         4 ~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~l~~ria~Li~~~~-i~P~~IL~lTFT~kAA~em~~Rl~~~~~~   75 (726)
T TIGR01073         4 HLNPEQREAVKTT--EGPLLIMAGAGSGKTRVLTHRIAHLIAEKN-VAPWNILAITFTNKAAREMKERVEKLLGP   75 (726)
T ss_pred             ccCHHHHHHHhCC--CCCEEEEeCCCCCHHHHHHHHHHHHHHcCC-CCHHHeeeeeccHHHHHHHHHHHHHHhcc
Confidence            5789999988543  457899999999999988777766664322 23347788999999999999888877653

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

>KOG0949|consensus

Probab=96.07  E-value=0.016  Score=56.01  Aligned_cols=70  Identities=20%  Similarity=0.120  Sum_probs=52.8

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      .|-..|.+.+-.+-.+...++.|||-+|||.+ .+-+++...+.  ....-+++.+||++|.+|+...+....
T Consensus       511 ~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfi-sfY~iEKVLRe--sD~~VVIyvaPtKaLVnQvsa~VyaRF  580 (1330)
T KOG0949|consen  511 CPDEWQRELLDSVDRNESAVIVAPTSAGKTFI-SFYAIEKVLRE--SDSDVVIYVAPTKALVNQVSANVYARF  580 (1330)
T ss_pred             CCcHHHHHHhhhhhcccceEEEeeccCCceec-cHHHHHHHHhh--cCCCEEEEecchHHHhhhhhHHHHHhh
Confidence            46678888888888889999999999999986 23455655553  223355678999999999987766554

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=95.62  E-value=0.027  Score=52.70  Aligned_cols=67  Identities=22%  Similarity=0.272  Sum_probs=51.6

Q ss_pred             CCCCCcHHHHHhhccccCC-----CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984         87 GFTKMTEIQARTIPPLLEG-----RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus        87 g~~~pt~iQ~~aip~~l~g-----~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      .| .|++.|..+|..+..+     +..++.+.+|||||+... .++...       ....++|+|+..+|.|++..+..+
T Consensus        10 ~~-~~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~lia-~l~~~~-------~r~vLIVt~~~~~A~~l~~dL~~~   80 (652)
T PRK05298         10 PY-KPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMA-NVIARL-------QRPTLVLAHNKTLAAQLYSEFKEF   80 (652)
T ss_pred             CC-CCChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHHH-HHHHHh-------CCCEEEEECCHHHHHHHHHHHHHh
Confidence            45 7999999999877533     256789999999998754 233221       225799999999999999999887


Q ss_pred             h
Q psy12984        162 F  162 (178)
Q Consensus       162 ~  162 (178)
                      +
T Consensus        81 ~   81 (652)
T PRK05298         81 F   81 (652)
T ss_pred             c
Confidence            6

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=95.62  E-value=0.044  Score=53.39  Aligned_cols=67  Identities=9%  Similarity=-0.058  Sum_probs=50.2

Q ss_pred             CCcHHHHHhhccccC--CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHH
Q psy12984         90 KMTEIQARTIPPLLE--GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACN  160 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~--g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~  160 (178)
                      .|.|+|..+.-.++.  ...+|++-..|-|||+-..+-+-..+..   ....+++|+||. .|..|....+.+
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~---g~~~rvLIVvP~-sL~~QW~~El~~  220 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLT---GRAERVLILVPE-TLQHQWLVEMLR  220 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHc---CCCCcEEEEcCH-HHHHHHHHHHHH
Confidence            599999998766543  3468889999999999876665554444   233478999997 899888877754

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=95.43  E-value=0.012  Score=51.10  Aligned_cols=48  Identities=15%  Similarity=-0.008  Sum_probs=36.2

Q ss_pred             cEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984        107 DLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus       107 dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      ++++.|+||||||.+|++|-+-.       ....+++.-|--+|........+.+
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~-------~~~s~vv~D~Kge~~~~t~~~r~~~   48 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLT-------WPGSVVVLDPKGENFELTSEHRRAL   48 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhc-------CCCCEEEEccchhHHHHHHHHHHHc
Confidence            57899999999999999987642       1246677788888887766555543

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.

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

Probab=95.32  E-value=0.024  Score=53.83  Aligned_cols=70  Identities=14%  Similarity=0.155  Sum_probs=54.2

Q ss_pred             CCcHHHHHhhccc----cCC-CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         90 KMTEIQARTIPPL----LEG-RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        90 ~pt~iQ~~aip~~----l~g-~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      .|...|..||..+    -.| +-+|+...||+|||-.. +.++.+|.+....  .++|.|+-.++|..|.+..+..+.
T Consensus       165 ~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTA-iaii~rL~r~~~~--KRVLFLaDR~~Lv~QA~~af~~~~  239 (875)
T COG4096         165 GPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTA-IAIIDRLIKSGWV--KRVLFLADRNALVDQAYGAFEDFL  239 (875)
T ss_pred             cchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeH-HHHHHHHHhcchh--heeeEEechHHHHHHHHHHHHHhC
Confidence            4666888888754    344 45899999999999875 4677777765433  388999999999999998887765

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=95.26  E-value=0.02  Score=50.96  Aligned_cols=49  Identities=22%  Similarity=0.209  Sum_probs=36.9

Q ss_pred             CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984        106 RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      .++++.|+||||||.+|++|.|-   .   .++ .+++.-|-.||.......+++.
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll---~---~~~-s~iV~D~KgEl~~~t~~~r~~~   93 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLL---N---YPG-SMIVTDPKGELYEKTAGYRKKR   93 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHH---h---ccC-CEEEEECCCcHHHHHHHHHHHC
Confidence            47999999999999999999762   2   122 6677788888887766655543

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

>PRK10536 hypothetical protein; Provisional

Probab=95.25  E-value=0.039  Score=46.12  Aligned_cols=46  Identities=20%  Similarity=0.224  Sum_probs=37.3

Q ss_pred             CCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHh
Q psy12984         87 GFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYN  132 (178)
Q Consensus        87 g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~  132 (178)
                      ++.--+..|...+-++..+.-+++.+++|||||+..+.-.++.+..
T Consensus        56 ~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~  101 (262)
T PRK10536         56 PILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIH  101 (262)
T ss_pred             cccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            4555577888888888888889999999999999877777766644

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=95.12  E-value=0.05  Score=51.96  Aligned_cols=57  Identities=19%  Similarity=0.108  Sum_probs=40.9

Q ss_pred             CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984        106 RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      -++=|...||+|||.+|+--+.+.-.   +-.....+++||+.+.-..++..+...-..|
T Consensus        75 lNiDI~METGTGKTy~YlrtmfeLhk---~YG~~KFIivVPs~AIkeGv~~~s~~~~ehF  131 (985)
T COG3587          75 LNIDILMETGTGKTYTYLRTMFELHK---KYGLFKFIIVVPSLAIKEGVFLTSKETTEHF  131 (985)
T ss_pred             ceeeEEEecCCCceeeHHHHHHHHHH---HhCceeEEEEeccHHHHhhhHHHHHHHHHHH
Confidence            46667899999999999866655222   2344577889999998777776666655555

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=94.86  E-value=0.031  Score=51.95  Aligned_cols=49  Identities=16%  Similarity=0.059  Sum_probs=38.5

Q ss_pred             CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984        106 RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      .++++.||||||||.+|++|-|-..       ...++++-|--||........+++
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~~-------~~S~VV~DpKGEl~~~Ta~~R~~~  207 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLFW-------EDSVVVHDIKLENYELTSGWREKQ  207 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHhC-------CCCEEEEeCcHHHHHHHHHHHHHC
Confidence            5899999999999999999987532       236677788888887777665553

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=94.79  E-value=0.12  Score=51.68  Aligned_cols=43  Identities=23%  Similarity=0.421  Sum_probs=28.4

Q ss_pred             HHCCCCCCcHHHH--Hhhc-cccCCCcEEEEccCCCchhhHhHHHHHH
Q psy12984         84 ADMGFTKMTEIQA--RTIP-PLLEGRDLVGSAKTGSGKTLAFLVPAVE  128 (178)
Q Consensus        84 ~~~g~~~pt~iQ~--~aip-~~l~g~dvi~~a~TGsGKTlaf~lp~l~  128 (178)
                      ....|....||..  ..|. .+..+..+|++|+||||||.  .+|.+-
T Consensus        58 ~~~~~~~~LPi~~~~~~Il~~l~~~~vvii~g~TGSGKTT--qlPq~l  103 (1283)
T TIGR01967        58 PEIRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTT--QLPKIC  103 (1283)
T ss_pred             ccccCCCCCCHHHHHHHHHHHHHhCceEEEeCCCCCCcHH--HHHHHH
Confidence            3456666666654  2333 34455678899999999999  567654

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.

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=94.77  E-value=0.1  Score=44.23  Aligned_cols=48  Identities=27%  Similarity=0.352  Sum_probs=29.3

Q ss_pred             HHHHHHCCCCCCcHHHHHhhcc-ccCCCcEEEEccCCCchhhHhHHHHHHHH
Q psy12984         80 LKAIADMGFTKMTEIQARTIPP-LLEGRDLVGSAKTGSGKTLAFLVPAVELI  130 (178)
Q Consensus        80 l~~l~~~g~~~pt~iQ~~aip~-~l~g~dvi~~a~TGsGKTlaf~lp~l~~l  130 (178)
                      +..|...|.  .++-|...+.. +..+.+++++++||||||... -.++..+
T Consensus       108 l~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll-~al~~~i  156 (299)
T TIGR02782       108 LDDYVEAGI--MTAAQRDVLREAVLARKNILVVGGTGSGKTTLA-NALLAEI  156 (299)
T ss_pred             HHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHh
Confidence            334444454  33444444443 456789999999999999753 3344444

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.

>KOG4150|consensus

Probab=94.77  E-value=0.018  Score=53.04  Aligned_cols=72  Identities=10%  Similarity=-0.095  Sum_probs=59.0

Q ss_pred             HHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHH
Q psy12984         84 ADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVA  158 (178)
Q Consensus        84 ~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~  158 (178)
                      ..+.-.....||..+|..+-.|+++++...|.+||.++|.+..+..+..   .+....+++.||.+|+++..+.+
T Consensus       280 ~~~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~---~~~s~~~~~~~~~~~~~~~~~~~  351 (1034)
T KOG4150|consen  280 NKNTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTL---CHATNSLLPSEMVEHLRNGSKGQ  351 (1034)
T ss_pred             hcccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhc---CcccceecchhHHHHhhccCCce
Confidence            4455666778999999999999999999999999999999988886655   34446688999999998765543

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

Probab=94.71  E-value=0.2  Score=41.09  Aligned_cols=83  Identities=16%  Similarity=0.132  Sum_probs=56.6

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHhhcccc---CCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHH
Q psy12984         75 VCENTLKAIADMGFTKMTEIQARTIPPLL---EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLT  151 (178)
Q Consensus        75 l~~~ll~~l~~~g~~~pt~iQ~~aip~~l---~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La  151 (178)
                      -+.+++=-+ +.++ -..+.|......+.   .|.|.+.+...|.|||-+- +|++..+...   .. +.+.++=.++|.
T Consensus        10 ~P~wLl~E~-e~~i-liR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsVI-~Pmla~~LAd---g~-~LvrviVpk~Ll   82 (229)
T PF12340_consen   10 YPDWLLFEI-ESNI-LIRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSVI-VPMLALALAD---GS-RLVRVIVPKALL   82 (229)
T ss_pred             ChHHHHHHH-HcCc-eeeHHHHHHHHHHhCCCCCCCeEeeecccCCccchH-HHHHHHHHcC---CC-cEEEEEcCHHHH
Confidence            344444333 2344 67788887776665   4689999999999999875 5888877652   22 333343348899


Q ss_pred             HHHHHHHHHHhhh
Q psy12984        152 NGVYLVACNVFKS  164 (178)
Q Consensus       152 ~qi~~~~~~l~~~  164 (178)
                      .|.+..++.-+++
T Consensus        83 ~q~~~~L~~~lg~   95 (229)
T PF12340_consen   83 EQMRQMLRSRLGG   95 (229)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999998876654

There are two conserved sequence motifs: LLE and NMG.

>KOG1803|consensus

Probab=94.71  E-value=0.077  Score=48.98  Aligned_cols=62  Identities=13%  Similarity=0.156  Sum_probs=46.5

Q ss_pred             CcHHHHHhhccccCCCc-EEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHH
Q psy12984         91 MTEIQARTIPPLLEGRD-LVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLV  157 (178)
Q Consensus        91 pt~iQ~~aip~~l~g~d-vi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~  157 (178)
                      .-+-|..|+..+.+.++ .++.+|+|+|||.....-|.+.+.+     ..++++.+||.+=..-+.+.
T Consensus       186 ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk~-----~k~VLVcaPSn~AVdNiver  248 (649)
T KOG1803|consen  186 LNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQ-----KKRVLVCAPSNVAVDNIVER  248 (649)
T ss_pred             ccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHHc-----CCeEEEEcCchHHHHHHHHH
Confidence            45688899988887755 5778999999999887766666654     35888999998755555553

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

Probab=94.69  E-value=0.054  Score=47.13  Aligned_cols=69  Identities=19%  Similarity=0.151  Sum_probs=52.3

Q ss_pred             CCcHHHHHhhccc----cCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984         90 KMTEIQARTIPPL----LEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus        90 ~pt~iQ~~aip~~----l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      .+|+.|+.+-..+    ....|.|+.|-||+|||-- +++.++...+    .+.++++.+|--..+..+|..++.-+.
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEM-if~~i~~al~----~G~~vciASPRvDVclEl~~Rlk~aF~  169 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEM-IFQGIEQALN----QGGRVCIASPRVDVCLELYPRLKQAFS  169 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhh-hHHHHHHHHh----cCCeEEEecCcccchHHHHHHHHHhhc
Confidence            5788888776554    3568999999999999985 4567776664    455667778988888888888877654

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=94.68  E-value=0.086  Score=45.34  Aligned_cols=45  Identities=33%  Similarity=0.287  Sum_probs=29.6

Q ss_pred             HHHCCCCCCcHHHHHhhcc-ccCCCcEEEEccCCCchhhHhHHHHHHHH
Q psy12984         83 IADMGFTKMTEIQARTIPP-LLEGRDLVGSAKTGSGKTLAFLVPAVELI  130 (178)
Q Consensus        83 l~~~g~~~pt~iQ~~aip~-~l~g~dvi~~a~TGsGKTlaf~lp~l~~l  130 (178)
                      +...|.  .++.|...|-. +..+.+++++++||||||... -.++..+
T Consensus       123 lv~~g~--~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTll-~aL~~~i  168 (323)
T PRK13833        123 YVTSKI--MTEAQASVIRSAIDSRLNIVISGGTGSGKTTLA-NAVIAEI  168 (323)
T ss_pred             HHHcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHH
Confidence            445554  44566655543 456789999999999999753 3444444

>COG4889 Predicted helicase [General function prediction only]

Probab=94.59  E-value=0.049  Score=52.58  Aligned_cols=74  Identities=19%  Similarity=0.049  Sum_probs=52.2

Q ss_pred             HHHHHHHHCCCCCCcHHHHHhhccccCC-----CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHH
Q psy12984         78 NTLKAIADMGFTKMTEIQARTIPPLLEG-----RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTN  152 (178)
Q Consensus        78 ~ll~~l~~~g~~~pt~iQ~~aip~~l~g-----~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~  152 (178)
                      ++..+|.-+.-..|.|+|+.||.+++.|     |.=++-| .|+|||..-+ -+.+.+..      .+.++|+|...|-.
T Consensus       149 e~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLIMA-cGTGKTfTsL-kisEala~------~~iL~LvPSIsLLs  220 (1518)
T COG4889         149 ELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLIMA-CGTGKTFTSL-KISEALAA------ARILFLVPSISLLS  220 (1518)
T ss_pred             ccccccccCCCCCCChhHHHHHHHHHhhcccccCCcEEEe-cCCCccchHH-HHHHHHhh------hheEeecchHHHHH
Confidence            4555555556678999999999988755     3334333 4999998753 44444432      47899999999999


Q ss_pred             HHHHHHH
Q psy12984        153 GVYLVAC  159 (178)
Q Consensus       153 qi~~~~~  159 (178)
                      |..+...
T Consensus       221 QTlrew~  227 (1518)
T COG4889         221 QTLREWT  227 (1518)
T ss_pred             HHHHHHh
Confidence            8876644

>KOG0950|consensus

Probab=94.56  E-value=0.073  Score=51.30  Aligned_cols=88  Identities=19%  Similarity=0.147  Sum_probs=60.0

Q ss_pred             CCHHHHHH-HHHCCCCCCcHHHHHhh--ccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHH
Q psy12984         75 VCENTLKA-IADMGFTKMTEIQARTI--PPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLT  151 (178)
Q Consensus        75 l~~~ll~~-l~~~g~~~pt~iQ~~ai--p~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La  151 (178)
                      +++.+... ....|....+..|..|+  |.++.++++|-.+||+.|||++.-+=++..+...+    ..++.+.|--+.+
T Consensus       207 ~~~k~~~~~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~r----r~~llilp~vsiv  282 (1008)
T KOG0950|consen  207 LPTKVSHLYAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCRR----RNVLLILPYVSIV  282 (1008)
T ss_pred             CchHHHHHHHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHHh----hceeEecceeehh
Confidence            55555444 45579999999999988  56889999999999999999998888877766532    2334455544444


Q ss_pred             HHHHHHHHHHhhhcC
Q psy12984        152 NGVYLVACNVFKSTQ  166 (178)
Q Consensus       152 ~qi~~~~~~l~~~~~  166 (178)
                      +.-...+..+...+|
T Consensus       283 ~Ek~~~l~~~~~~~G  297 (1008)
T KOG0950|consen  283 QEKISALSPFSIDLG  297 (1008)
T ss_pred             HHHHhhhhhhccccC
Confidence            444444444443333

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=94.47  E-value=0.045  Score=47.40  Aligned_cols=36  Identities=31%  Similarity=0.320  Sum_probs=30.3

Q ss_pred             CCCCCCcHHHHHhhccccCCC-cEEEEccCCCchhhH
Q psy12984         86 MGFTKMTEIQARTIPPLLEGR-DLVGSAKTGSGKTLA  121 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~-dvi~~a~TGsGKTla  121 (178)
                      ..|...++-|...+-.+..++ ++++++.||||||..
T Consensus       153 i~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTl  189 (355)
T COG4962         153 IIFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTL  189 (355)
T ss_pred             HHcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHH
Confidence            357788999998888777665 999999999999964

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=94.41  E-value=0.05  Score=51.11  Aligned_cols=48  Identities=13%  Similarity=0.019  Sum_probs=36.4

Q ss_pred             CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHH
Q psy12984        106 RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACN  160 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~  160 (178)
                      .++++.|+||||||.+|++|-|-..       ...++|+=|--|+..........
T Consensus       140 ~hvlviApTgSGKgvg~VIPnLL~~-------~gS~VV~DpKGE~~~~Ta~~R~~  187 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIPTLLTF-------KGSVIALDVKGELFELTSRARKA  187 (670)
T ss_pred             ceEEEEecCCCCceeeehHhHHhcC-------CCCEEEEeCCchHHHHHHHHHHh
Confidence            4899999999999999999986421       23667778888887766555444

>KOG0952|consensus

Probab=94.41  E-value=0.025  Score=55.02  Aligned_cols=69  Identities=17%  Similarity=0.150  Sum_probs=52.4

Q ss_pred             CCCCcHHHHHhhccccC-CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHH
Q psy12984         88 FTKMTEIQARTIPPLLE-GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVAC  159 (178)
Q Consensus        88 ~~~pt~iQ~~aip~~l~-g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~  159 (178)
                      +....|+|...+-.+.+ ..++++-+|||+|||++|-+.+..-+..   .+...++||+|.++|...-.+...
T Consensus       925 ~~~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~---~p~~kvvyIap~kalvker~~Dw~  994 (1230)
T KOG0952|consen  925 YKYFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSY---YPGSKVVYIAPDKALVKERSDDWS  994 (1230)
T ss_pred             hcccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhcc---CCCccEEEEcCCchhhcccccchh
Confidence            33555677776655543 4688999999999999999999887665   566789999999999886555443

>PRK14873 primosome assembly protein PriA; Provisional

Probab=94.35  E-value=0.061  Score=50.51  Aligned_cols=48  Identities=8%  Similarity=-0.059  Sum_probs=37.6

Q ss_pred             EccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984        111 SAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus       111 ~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      .+.+|||||..|+--+-..+..     +.++++|+|...|+.|+...|...++
T Consensus       166 ~~~~GSGKTevyl~~i~~~l~~-----Gk~vLvLvPEi~lt~q~~~rl~~~f~  213 (665)
T PRK14873        166 QALPGEDWARRLAAAAAATLRA-----GRGALVVVPDQRDVDRLEAALRALLG  213 (665)
T ss_pred             hcCCCCcHHHHHHHHHHHHHHc-----CCeEEEEecchhhHHHHHHHHHHHcC
Confidence            3346999999998666555533     44799999999999999999987654

>KOG1802|consensus

Probab=94.31  E-value=0.12  Score=48.55  Aligned_cols=73  Identities=11%  Similarity=0.010  Sum_probs=52.8

Q ss_pred             HHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHH
Q psy12984         83 IADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVAC  159 (178)
Q Consensus        83 l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~  159 (178)
                      +...|+..+..-|..|+..+|...=-|+++|+|+|||..-.--+++.+..    ....+++.+|..-=.-|+..-+.
T Consensus       403 ~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~----~~~~VLvcApSNiAVDqLaeKIh  475 (935)
T KOG1802|consen  403 FSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ----HAGPVLVCAPSNIAVDQLAEKIH  475 (935)
T ss_pred             hcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHh----cCCceEEEcccchhHHHHHHHHH
Confidence            44456667778999999999988888999999999999866555554433    34466778887665555555444

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=94.27  E-value=0.12  Score=47.98  Aligned_cols=88  Identities=19%  Similarity=0.132  Sum_probs=57.1

Q ss_pred             CCHH-HHHHHHHCCCCCCcH----HHHHhhcccc--CCCcEEEEccCCCchhhHhHHHHHHHHHhccC-CCCCceEEEee
Q psy12984         75 VCEN-TLKAIADMGFTKMTE----IQARTIPPLL--EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKF-MPRNGKSWQGK  146 (178)
Q Consensus        75 l~~~-ll~~l~~~g~~~pt~----iQ~~aip~~l--~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~-~~~~~~~~l~P  146 (178)
                      +.++ |.++|.+.-=.++..    ||.+==..+.  .+.=++|++..|||||.+.+--+...++..+. .....++++.|
T Consensus       189 ~~dEvL~~~Lek~ss~~mrdIV~TIQkEQneIIR~ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~P  268 (747)
T COG3973         189 GRDEVLQRVLEKNSSAKMRDIVETIQKEQNEIIRFEKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGP  268 (747)
T ss_pred             hHHHHHHHHHHhccchhHHHHHHHhhHhHHHHHhccCCCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEEEcC
Confidence            4444 445566543333332    4443333333  45678999999999999887777666766432 22335889999


Q ss_pred             cHHHHHHHHHHHHHHh
Q psy12984        147 LRPLTNGVYLVACNVF  162 (178)
Q Consensus       147 tr~La~qi~~~~~~l~  162 (178)
                      .|-+..-+.+++=.|+
T Consensus       269 N~vFleYis~VLPeLG  284 (747)
T COG3973         269 NRVFLEYISRVLPELG  284 (747)
T ss_pred             cHHHHHHHHHhchhhc
Confidence            9999988888876654

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=94.21  E-value=0.04  Score=47.77  Aligned_cols=21  Identities=29%  Similarity=0.292  Sum_probs=18.1

Q ss_pred             cccCCCcEEEEccCCCchhhH
Q psy12984        101 PLLEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       101 ~~l~g~dvi~~a~TGsGKTla  121 (178)
                      ++..+.+++++++||||||..
T Consensus       158 ~v~~~~nilI~G~tGSGKTTl  178 (344)
T PRK13851        158 CVVGRLTMLLCGPTGSGKTTM  178 (344)
T ss_pred             HHHcCCeEEEECCCCccHHHH
Confidence            345789999999999999975

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=94.13  E-value=0.27  Score=46.83  Aligned_cols=64  Identities=14%  Similarity=0.093  Sum_probs=44.5

Q ss_pred             CCCCCCcHHHHHhhccccCC-CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHH
Q psy12984         86 MGFTKMTEIQARTIPPLLEG-RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVY  155 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g-~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~  155 (178)
                      .++ .+++-|..|+..++.+ +-++++++.|+|||...- .++..+..    .+..++.++||---|..+.
T Consensus       349 ~~~-~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll~-~i~~~~~~----~g~~V~~~ApTg~Aa~~L~  413 (744)
T TIGR02768       349 QHY-RLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTMLK-AAREAWEA----AGYRVIGAALSGKAAEGLQ  413 (744)
T ss_pred             ccC-CCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHHH-HHHHHHHh----CCCeEEEEeCcHHHHHHHH
Confidence            344 6899999999988764 667899999999986532 23333322    2446777899976665554

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=94.04  E-value=0.34  Score=45.21  Aligned_cols=63  Identities=19%  Similarity=0.047  Sum_probs=42.6

Q ss_pred             cHHHHHhhccccCCCcEEEEccCCCchhhHh--HHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHH
Q psy12984         92 TEIQARTIPPLLEGRDLVGSAKTGSGKTLAF--LVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLV  157 (178)
Q Consensus        92 t~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf--~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~  157 (178)
                      .+.|+.|+-..+..+-+++.+++|+|||..-  ++-.+..+.   ......+.+.+||.-=|..+.+.
T Consensus       154 ~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~~ll~~l~~~~---~~~~~~i~l~APTgkAA~rL~e~  218 (615)
T PRK10875        154 VDWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQLA---DGERCRIRLAAPTGKAAARLTES  218 (615)
T ss_pred             CHHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhc---CCCCcEEEEECCcHHHHHHHHHH
Confidence            4789999999999999999999999999763  333332221   12234556679996555544443

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=93.92  E-value=0.28  Score=46.51  Aligned_cols=67  Identities=13%  Similarity=0.075  Sum_probs=46.6

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHH
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYL  156 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~  156 (178)
                      .++ .+++-|+.|+..+..++-+++++..|||||.... .++..+...  .+...+++++||.--|..+..
T Consensus       320 ~~~-~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l~-~i~~~~~~~--~~~~~v~l~ApTg~AA~~L~e  386 (720)
T TIGR01448       320 LRK-GLSEEQKQALDTAIQHKVVILTGGPGTGKTTITR-AIIELAEEL--GGLLPVGLAAPTGRAAKRLGE  386 (720)
T ss_pred             cCC-CCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHHH-HHHHHHHHc--CCCceEEEEeCchHHHHHHHH
Confidence            455 7899999999999888899999999999997532 333333221  111355667999666655543

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=93.84  E-value=0.22  Score=42.74  Aligned_cols=24  Identities=25%  Similarity=0.476  Sum_probs=18.9

Q ss_pred             EEEEccCCCchhhHhHHHHHHHHHh
Q psy12984        108 LVGSAKTGSGKTLAFLVPAVELIYN  132 (178)
Q Consensus       108 vi~~a~TGsGKTlaf~lp~l~~l~~  132 (178)
                      |+|.+|||||||.... .+|+++.+
T Consensus       128 ILVTGpTGSGKSTTlA-amId~iN~  151 (353)
T COG2805         128 ILVTGPTGSGKSTTLA-AMIDYINK  151 (353)
T ss_pred             EEEeCCCCCcHHHHHH-HHHHHHhc
Confidence            8899999999987643 66676654

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=93.72  E-value=0.28  Score=45.44  Aligned_cols=62  Identities=13%  Similarity=-0.020  Sum_probs=42.2

Q ss_pred             HHHHHhhccccCCCcEEEEccCCCchhhH--hHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHH
Q psy12984         93 EIQARTIPPLLEGRDLVGSAKTGSGKTLA--FLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYL  156 (178)
Q Consensus        93 ~iQ~~aip~~l~g~dvi~~a~TGsGKTla--f~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~  156 (178)
                      ..|+.|+-.++..+-++++++.|||||..  .++-++.....  .....+.++.+||.-=|..+.+
T Consensus       148 ~~Qk~A~~~al~~~~~vitGgpGTGKTt~v~~ll~~l~~~~~--~~~~~~I~l~APTGkAA~rL~e  211 (586)
T TIGR01447       148 NWQKVAVALALKSNFSLITGGPGTGKTTTVARLLLALVKQSP--KQGKLRIALAAPTGKAAARLAE  211 (586)
T ss_pred             HHHHHHHHHHhhCCeEEEEcCCCCCHHHHHHHHHHHHHHhcc--ccCCCcEEEECCcHHHHHHHHH
Confidence            68999999999999999999999999976  33333332221  1112467778999554444443

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=93.58  E-value=0.067  Score=49.96  Aligned_cols=45  Identities=18%  Similarity=0.033  Sum_probs=34.4

Q ss_pred             CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHH
Q psy12984        106 RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLV  157 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~  157 (178)
                      .++++.|+||||||.+|++|.|-.       ....++++-|-.|+..-....
T Consensus       176 ~HvlviapTgSGKgvg~ViPnLL~-------~~~S~VV~D~KGE~~~~Tag~  220 (636)
T PRK13880        176 EHVLTYAPTRSGKGVGLVVPTLLS-------WGHSSVITDLKGELWALTAGW  220 (636)
T ss_pred             ceEEEEecCCCCCceEEEccchhh-------CCCCEEEEeCcHHHHHHHHHH
Confidence            689999999999999999998742       233677788888886544433

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

Probab=93.54  E-value=0.2  Score=43.09  Aligned_cols=52  Identities=15%  Similarity=0.138  Sum_probs=36.6

Q ss_pred             EEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984        108 LVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus       108 vi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      ++|.+..|||||+..+- ++..+.  ........+++++..+|...++..+..-.
T Consensus         4 ~~I~G~aGTGKTvla~~-l~~~l~--~~~~~~~~~~l~~n~~l~~~l~~~l~~~~   55 (352)
T PF09848_consen    4 ILITGGAGTGKTVLALN-LAKELQ--NSEEGKKVLYLCGNHPLRNKLREQLAKKY   55 (352)
T ss_pred             EEEEecCCcCHHHHHHH-HHHHhh--ccccCCceEEEEecchHHHHHHHHHhhhc
Confidence            68899999999997542 223231  11345577899999999998887775543

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

>KOG2340|consensus

Probab=93.54  E-value=0.2  Score=45.86  Aligned_cols=78  Identities=13%  Similarity=0.162  Sum_probs=59.0

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccC-CCch--hhHhHHHHHHHHHhcc--------------------------CCCCCc
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKT-GSGK--TLAFLVPAVELIYNLK--------------------------FMPRNG  140 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~T-GsGK--Tlaf~lp~l~~l~~~~--------------------------~~~~~~  140 (178)
                      .+|+.|.+-+..+..-+|++....| +.|+  +-.|++-+|+|+++.+                          ...++.
T Consensus       216 pltalQ~~L~~~m~~YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~~IL~Nn~r~~Sqk~g~~~~~~frDQG~tRpk  295 (698)
T KOG2340|consen  216 PLTALQKELFKIMFNYRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRDLILGNNRRLASQKEGENPDESFRDQGFTRPK  295 (698)
T ss_pred             cchHHHHHHHHHHHhhhhhccccccccccchhhhhHHHHHHHHHHHHHHHHhcchHhhhhhhcCCCCchhhhhcCCCCce
Confidence            4688999988888889999755443 3455  4569999999987511                          123678


Q ss_pred             eEEEeecHHHHHHHHHHHHHHhhhcCC
Q psy12984        141 KSWQGKLRPLTNGVYLVACNVFKSTQP  167 (178)
Q Consensus       141 ~~~l~Ptr~La~qi~~~~~~l~~~~~~  167 (178)
                      ++++||+|+-|..+.+.+..++.+...
T Consensus       296 VLivvpfRe~A~riVn~lis~l~G~~q  322 (698)
T KOG2340|consen  296 VLIVVPFRESAYRIVNLLISLLSGDDQ  322 (698)
T ss_pred             EEEEecchHHHHHHHHHHHHHhcCccc
Confidence            899999999999999988888655544

>KOG1133|consensus

Probab=93.49  E-value=0.077  Score=49.75  Aligned_cols=44  Identities=25%  Similarity=0.379  Sum_probs=36.2

Q ss_pred             CCcHHHHHhhccc----cCCCcEEEEccCCCchhhHhHHHHHHHHHhc
Q psy12984         90 KMTEIQARTIPPL----LEGRDLVGSAKTGSGKTLAFLVPAVELIYNL  133 (178)
Q Consensus        90 ~pt~iQ~~aip~~----l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~  133 (178)
                      .|+.||..-+..+    -.|+=-|.-+|||+||||..+=..+.+|...
T Consensus        15 ~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL~~~   62 (821)
T KOG1133|consen   15 TPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWLRDF   62 (821)
T ss_pred             CchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHHHHh
Confidence            6888998777644    4688778899999999999998999988653

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=93.38  E-value=0.19  Score=43.36  Aligned_cols=28  Identities=25%  Similarity=0.316  Sum_probs=20.7

Q ss_pred             ccCCCcEEEEccCCCchhhHhHHHHHHHH
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAFLVPAVELI  130 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf~lp~l~~l  130 (178)
                      +..+.+++++++||||||... -.++..+
T Consensus       157 v~~~~nili~G~tgSGKTTll-~aL~~~i  184 (332)
T PRK13900        157 VISKKNIIISGGTSTGKTTFT-NAALREI  184 (332)
T ss_pred             HHcCCcEEEECCCCCCHHHHH-HHHHhhC
Confidence            456899999999999999753 3344444

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=93.32  E-value=0.12  Score=48.49  Aligned_cols=49  Identities=14%  Similarity=-0.066  Sum_probs=36.6

Q ss_pred             CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHH
Q psy12984        105 GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACN  160 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~  160 (178)
                      ..++++.|+||||||.++++|-+-   .    ....++++-|-.|++.-+....++
T Consensus       224 ~~H~Lv~ApTgsGKt~g~VIPnLL---~----~~gS~VV~DpKgEl~~~Ta~~R~~  272 (641)
T PRK13822        224 STHGLVFAGSGGFKTTSVVVPTAL---K----WGGPLVVLDPSTEVAPMVSEHRRD  272 (641)
T ss_pred             CceEEEEeCCCCCccceEehhhhh---c----CCCCEEEEeCcHHHHHHHHHHHHH
Confidence            368999999999999999999753   2    233667777888887766655433

>TIGR02767 TraG-Ti Ti-type conjugative transfer system protien TraG

Probab=93.25  E-value=0.13  Score=48.07  Aligned_cols=49  Identities=14%  Similarity=0.019  Sum_probs=37.0

Q ss_pred             CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984        106 RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      .++++.|+||||||.++++|-+   +.    ....++++-|-.|++.-....-++.
T Consensus       212 ~H~lv~ApTgsGKgvg~VIPnL---L~----~~gS~VV~DpKgE~~~~Ta~~R~~~  260 (623)
T TIGR02767       212 THMIFFAGSGGFKTTSVVVPTA---LK----YGGPLVCLDPSTEVAPMVCEHRRQA  260 (623)
T ss_pred             ceEEEEeCCCCCccceeehhhh---hc----CCCCEEEEEChHHHHHHHHHHHHHc
Confidence            6999999999999999999963   22    2336677888888877666554433

This protein is found in the Agrobacterium tumefaciens Ti plasmid tra region responsible for conjugative transfer of the entire plasmid among Agrobacterium strains. The protein is distantly related to the F-type conjugation system TraG protein. Both of these systems are examples of type IV secretion systems.

>KOG1132|consensus

Probab=93.22  E-value=0.051  Score=51.97  Aligned_cols=43  Identities=19%  Similarity=0.247  Sum_probs=34.2

Q ss_pred             CCcHHHHHhhcccc----CCCcEEEEccCCCchhhHhHHHHHHHHHh
Q psy12984         90 KMTEIQARTIPPLL----EGRDLVGSAKTGSGKTLAFLVPAVELIYN  132 (178)
Q Consensus        90 ~pt~iQ~~aip~~l----~g~dvi~~a~TGsGKTlaf~lp~l~~l~~  132 (178)
                      .|++.|...+-.++    .+.+.++-+||||||||+.+=..|-+...
T Consensus        21 qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~   67 (945)
T KOG1132|consen   21 QPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQH   67 (945)
T ss_pred             CcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHH
Confidence            68889987776554    45788999999999999988777776654

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=93.21  E-value=0.4  Score=47.03  Aligned_cols=63  Identities=21%  Similarity=0.144  Sum_probs=45.0

Q ss_pred             CCCCCCcHHHHHhhccccCCCc-EEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHH
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRD-LVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGV  154 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~d-vi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi  154 (178)
                      .|+ .+++-|..|+..++.+.+ +++++..|+|||.. +-.++..+..    .+..++.++||---|..+
T Consensus       343 ~g~-~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~-l~~~~~~~e~----~G~~V~~~ApTGkAA~~L  406 (988)
T PRK13889        343 RGL-VLSGEQADALAHVTDGRDLGVVVGYAGTGKSAM-LGVAREAWEA----AGYEVRGAALSGIAAENL  406 (988)
T ss_pred             cCC-CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH-HHHHHHHHHH----cCCeEEEecCcHHHHHHH
Confidence            455 789999999999888665 68899999999985 3334443322    244677789996655444

>PRK13876 conjugal transfer coupling protein TraG; Provisional

Probab=93.17  E-value=0.1  Score=48.99  Aligned_cols=45  Identities=16%  Similarity=0.013  Sum_probs=33.9

Q ss_pred             CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHH
Q psy12984        106 RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLV  157 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~  157 (178)
                      .++++.||||||||.+|++|-|-..       ...++|+-|--||.......
T Consensus       145 ~hvLviApTrSGKgvg~VIPnLL~~-------~~S~VV~D~KGEl~~~Ta~~  189 (663)
T PRK13876        145 EHVLCFAPTRSGKGVGLVVPTLLTW-------PGSAIVHDIKGENWQLTAGF  189 (663)
T ss_pred             ceEEEEecCCCCcceeEehhhHHhC-------CCCEEEEeCcchHHHHHHHH
Confidence            6899999999999999999986532       23666677777776655444

>PF12846 AAA_10: AAA-like domain

Probab=93.04  E-value=0.19  Score=40.96  Aligned_cols=42  Identities=19%  Similarity=0.063  Sum_probs=27.3

Q ss_pred             CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHH
Q psy12984        106 RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTN  152 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~  152 (178)
                      +++++.+.||||||.... .++..+..    .+...+++=|..+...
T Consensus         2 ~h~~i~G~tGsGKT~~~~-~l~~~~~~----~g~~~~i~D~~g~~~~   43 (304)
T PF12846_consen    2 PHTLILGKTGSGKTTLLK-NLLEQLIR----RGPRVVIFDPKGDYSP   43 (304)
T ss_pred             CeEEEECCCCCcHHHHHH-HHHHHHHH----cCCCEEEEcCCchHHH
Confidence            589999999999997766 55554443    2335555555544443

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=92.89  E-value=0.17  Score=44.56  Aligned_cols=52  Identities=15%  Similarity=0.068  Sum_probs=35.1

Q ss_pred             hhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHH
Q psy12984         98 TIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGV  154 (178)
Q Consensus        98 aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi  154 (178)
                      .+|.-...+++++.++||||||.. +..++..+...    +.+++++=|..++....
T Consensus        35 ~~~~~~~~~h~~i~g~tGsGKt~~-i~~l~~~~~~~----~~~~vi~D~kg~~~~~~   86 (410)
T cd01127          35 PFPKDAEEAHTMIIGTTGTGKTTQ-IRELLASIRAR----GDRAIIYDPNGGFVSKF   86 (410)
T ss_pred             eCCcchhhccEEEEcCCCCCHHHH-HHHHHHHHHhc----CCCEEEEeCCcchhHhh
Confidence            355556678999999999999985 44455555432    33666677777765543

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.

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=92.87  E-value=0.11  Score=40.63  Aligned_cols=31  Identities=29%  Similarity=0.320  Sum_probs=22.3

Q ss_pred             cHHHHHhhcc-ccCCCcEEEEccCCCchhhHh
Q psy12984         92 TEIQARTIPP-LLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus        92 t~iQ~~aip~-~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      ++-|...+.. +..|..++++++||||||..+
T Consensus        11 ~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll   42 (186)
T cd01130          11 SPLQAAYLWLAVEARKNILISGGTGSGKTTLL   42 (186)
T ss_pred             CHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH
Confidence            3444444443 456899999999999999754

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.

>KOG0953|consensus

Probab=92.66  E-value=0.15  Score=46.91  Aligned_cols=47  Identities=26%  Similarity=0.259  Sum_probs=36.7

Q ss_pred             cEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984        107 DLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus       107 dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      =++-++||.||||..    +|+++..     ....++-.|+|-||..||+.+++.+
T Consensus       193 Ii~H~GPTNSGKTy~----ALqrl~~-----aksGvycGPLrLLA~EV~~r~na~g  239 (700)
T KOG0953|consen  193 IIMHVGPTNSGKTYR----ALQRLKS-----AKSGVYCGPLRLLAHEVYDRLNALG  239 (700)
T ss_pred             EEEEeCCCCCchhHH----HHHHHhh-----hccceecchHHHHHHHHHHHhhhcC
Confidence            466789999999975    4565543     3356889999999999999987654

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

Probab=92.61  E-value=0.45  Score=37.17  Aligned_cols=49  Identities=14%  Similarity=0.091  Sum_probs=28.7

Q ss_pred             ccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHH
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYL  156 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~  156 (178)
                      +-.+.++++.+++|+|||.... .+...+..    .+.. +..+++.+|...+..
T Consensus        44 ~~~~~~l~l~G~~G~GKThLa~-ai~~~~~~----~g~~-v~f~~~~~L~~~l~~   92 (178)
T PF01695_consen   44 IENGENLILYGPPGTGKTHLAV-AIANEAIR----KGYS-VLFITASDLLDELKQ   92 (178)
T ss_dssp             -SC--EEEEEESTTSSHHHHHH-HHHHHHHH----TT---EEEEEHHHHHHHHHC
T ss_pred             cccCeEEEEEhhHhHHHHHHHH-HHHHHhcc----CCcc-eeEeecCceeccccc
Confidence            4468899999999999998644 33333433    1223 445666777766543

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.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=92.51  E-value=0.35  Score=39.25  Aligned_cols=53  Identities=13%  Similarity=-0.025  Sum_probs=34.0

Q ss_pred             cCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984        103 LEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      ..|.-+++.+++|+|||...+--+.+.+.+     +..++|++ +-+-..|+.+.+..+
T Consensus        19 ~~gs~~lI~G~pGsGKT~la~~~l~~~~~~-----ge~~lyvs-~ee~~~~i~~~~~~~   71 (237)
T TIGR03877        19 PERNVVLLSGGPGTGKSIFSQQFLWNGLQM-----GEPGIYVA-LEEHPVQVRRNMAQF   71 (237)
T ss_pred             cCCeEEEEEcCCCCCHHHHHHHHHHHHHHc-----CCcEEEEE-eeCCHHHHHHHHHHh
Confidence            347889999999999998544334444422     33556655 555566666665544

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.

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

Probab=92.51  E-value=0.28  Score=40.59  Aligned_cols=51  Identities=20%  Similarity=0.089  Sum_probs=36.9

Q ss_pred             CCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHH
Q psy12984        104 EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACN  160 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~  160 (178)
                      .+.++++.+++|+|||.-...-....+ .     ...-++.+++.+|..++...+..
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~-~-----~g~sv~f~~~~el~~~Lk~~~~~  154 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELL-K-----AGISVLFITAPDLLSKLKAAFDE  154 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHH-H-----cCCeEEEEEHHHHHHHHHHHHhc
Confidence            688999999999999976543333333 2     12336688999999998887664

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=92.50  E-value=0.28  Score=47.87  Aligned_cols=75  Identities=19%  Similarity=0.070  Sum_probs=59.1

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhcCCCC
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQPPT  169 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~~~~  169 (178)
                      .|+++|...=-++..|+  |+-..||-||||+..+|+.=..+.     +.++=+++..--||.-=..++..+..++|..+
T Consensus       138 ~~ydVQLiGgivLh~G~--IAEM~TGEGKTLvatlp~yLnAL~-----G~gVHvVTvNDYLA~RDaewm~p~y~flGLtV  210 (1025)
T PRK12900        138 VPYDVQLIGGIVLHSGK--ISEMATGEGKTLVSTLPTFLNALT-----GRGVHVVTVNDYLAQRDKEWMNPVFEFHGLSV  210 (1025)
T ss_pred             cccchHHhhhHHhhcCC--ccccCCCCCcchHhHHHHHHHHHc-----CCCcEEEeechHhhhhhHHHHHHHHHHhCCee
Confidence            68999977554555554  678899999999999998655543     44666778888999999999999999988876


Q ss_pred             cc
Q psy12984        170 VI  171 (178)
Q Consensus       170 ~~  171 (178)
                      +.
T Consensus       211 g~  212 (1025)
T PRK12900        211 GV  212 (1025)
T ss_pred             ee
Confidence            53

>PRK13764 ATPase; Provisional

Probab=92.47  E-value=0.24  Score=46.05  Aligned_cols=27  Identities=15%  Similarity=0.217  Sum_probs=20.3

Q ss_pred             CCCcEEEEccCCCchhhHhHHHHHHHHH
Q psy12984        104 EGRDLVGSAKTGSGKTLAFLVPAVELIY  131 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~lp~l~~l~  131 (178)
                      .+.+++++++||||||.. +-.++..+.
T Consensus       256 ~~~~ILIsG~TGSGKTTl-l~AL~~~i~  282 (602)
T PRK13764        256 RAEGILIAGAPGAGKSTF-AQALAEFYA  282 (602)
T ss_pred             cCCEEEEECCCCCCHHHH-HHHHHHHHh
Confidence            467899999999999974 345555554

>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]

Probab=92.45  E-value=0.71  Score=42.90  Aligned_cols=72  Identities=17%  Similarity=-0.005  Sum_probs=54.4

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      .+++-|..|+...  .-.++|.|..|||||-+-.--+.+.+....-.+. ..++++=|+--|..+...+..+++.
T Consensus         2 ~Ln~~Q~~av~~~--~gp~lV~AGaGsGKT~vlt~Ria~li~~~~v~p~-~Il~vTFTnkAA~em~~Rl~~~~~~   73 (655)
T COG0210           2 KLNPEQREAVLHP--DGPLLVLAGAGSGKTRVLTERIAYLIAAGGVDPE-QILAITFTNKAAAEMRERLLKLLGL   73 (655)
T ss_pred             CCCHHHHHHHhcC--CCCeEEEECCCCCchhhHHHHHHHHHHcCCcChH-HeeeeechHHHHHHHHHHHHHHhCc
Confidence            5678899888555  4567778888999999887777776655433333 5677888899999998888888764

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=92.44  E-value=0.095  Score=36.81  Aligned_cols=18  Identities=33%  Similarity=0.362  Sum_probs=15.7

Q ss_pred             CCcEEEEccCCCchhhHh
Q psy12984        105 GRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf  122 (178)
                      +..+++.+|+|+|||...
T Consensus         2 ~~~~~l~G~~G~GKTtl~   19 (148)
T smart00382        2 GEVILIVGPPGSGKTTLA   19 (148)
T ss_pred             CCEEEEECCCCCcHHHHH
Confidence            567899999999999864

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.

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=92.31  E-value=0.35  Score=47.46  Aligned_cols=75  Identities=17%  Similarity=0.064  Sum_probs=59.3

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhcCCCC
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQPPT  169 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~~~~  169 (178)
                      +|+.+|...=-++..|+  |+-..||-||||+..+|+.-..+.     +.++-+++..--||.-=..++..+..++|..+
T Consensus       169 ~~yDVQliGgivLh~G~--IAEM~TGEGKTLvAtlp~yLnAL~-----GkgVHvVTVNDYLA~RDaewmgply~fLGLsv  241 (1112)
T PRK12901        169 VHYDVQLIGGVVLHQGK--IAEMATGEGKTLVATLPVYLNALT-----GNGVHVVTVNDYLAKRDSEWMGPLYEFHGLSV  241 (1112)
T ss_pred             cccchHHhhhhhhcCCc--eeeecCCCCchhHHHHHHHHHHHc-----CCCcEEEEechhhhhccHHHHHHHHHHhCCce
Confidence            68889876554455554  678999999999999998765544     44666788889999999999999999999887


Q ss_pred             cc
Q psy12984        170 VI  171 (178)
Q Consensus       170 ~~  171 (178)
                      ++
T Consensus       242 g~  243 (1112)
T PRK12901        242 DC  243 (1112)
T ss_pred             ee
Confidence            64

>KOG4150|consensus

Probab=92.30  E-value=0.28  Score=45.53  Aligned_cols=87  Identities=20%  Similarity=0.241  Sum_probs=68.9

Q ss_pred             cCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHH
Q psy12984         74 KVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNG  153 (178)
Q Consensus        74 ~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~q  153 (178)
                      ++++...+++.+.|....+.+|..++.+++.             |.++|-.|+.+.+..   ....-.+|+.|+.+|+..
T Consensus       371 ~~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~-------------~~~~~~~~~~~~~~~---~~~~~~~Y~~~~~~~~~~  434 (1034)
T KOG4150|consen  371 KLSETTKSALKRIGLNTLYSHQAEAISAALA-------------KSLCYNVPVFEELCK---DTNSCALYLFPTKALAQD  434 (1034)
T ss_pred             CCCchhHHHHHhcCcceeecCHHHHHHHHhh-------------hccccccHHHHHHHh---cccceeeeecchhhHHHH
Confidence            4667777888888888888888888877763             346788888886654   233356899999999999


Q ss_pred             HHHHHHHHhhhcCCCCcceEEEe
Q psy12984        154 VYLVACNVFKSTQPPTVIKVQTL  176 (178)
Q Consensus       154 i~~~~~~l~~~~~~~~~~~v~~~  176 (178)
                      +.+.+..+++.+-.+.++-+..+
T Consensus       435 ~~R~L~~L~~~F~~~~~~~~~~~  457 (1034)
T KOG4150|consen  435 QLRALSDLIKGFEASINMGVYDG  457 (1034)
T ss_pred             HHHHHHHHHHHHHhhcCcceEeC
Confidence            99999999999988888777654

>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=92.16  E-value=0.3  Score=42.81  Aligned_cols=53  Identities=23%  Similarity=0.206  Sum_probs=33.1

Q ss_pred             hccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHH
Q psy12984         99 IPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYL  156 (178)
Q Consensus        99 ip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~  156 (178)
                      ||.-...+++++.+.||||||. ++-+++..+...    +.+++|.=|.-+.....|+
T Consensus         9 l~~~~e~~~~li~G~~GsGKT~-~i~~ll~~~~~~----g~~~iI~D~kg~~~~~f~~   61 (386)
T PF10412_consen    9 LPKDSENRHILIIGATGSGKTQ-AIRHLLDQIRAR----GDRAIIYDPKGEFTERFYR   61 (386)
T ss_dssp             E-GGGGGG-EEEEE-TTSSHHH-HHHHHHHHHHHT----T-EEEEEEETTHHHHHH--
T ss_pred             cccchhhCcEEEECCCCCCHHH-HHHHHHHHHHHc----CCEEEEEECCchHHHHhcC
Confidence            3445667899999999999997 445777776542    3356666677776655444

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.

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

Probab=92.09  E-value=0.37  Score=45.08  Aligned_cols=54  Identities=13%  Similarity=-0.105  Sum_probs=36.3

Q ss_pred             CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecH--HHHHHHHHHHHHHhh
Q psy12984        105 GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLR--PLTNGVYLVACNVFK  163 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr--~La~qi~~~~~~l~~  163 (178)
                      ..|++|.++||+|||..+.+ ++....+.    +..++++=|-.  +|...++..++..+.
T Consensus       176 ~~H~lv~G~TGsGKT~l~~~-l~~q~i~~----g~~viv~DpKgD~~l~~~~~~~~~~~G~  231 (634)
T TIGR03743       176 VGHTLVLGTTGVGKTRLAEL-LITQDIRR----GDVVIVIDPKGDADLKRRMRAEAKRAGR  231 (634)
T ss_pred             CCcEEEECCCCCCHHHHHHH-HHHHHHHc----CCeEEEEeCCCchHHHHHHHHHHHHhCC
Confidence            46899999999999987744 44444331    23566676764  477777777666543

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.

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=92.04  E-value=0.51  Score=46.54  Aligned_cols=70  Identities=14%  Similarity=0.072  Sum_probs=47.1

Q ss_pred             CCcHHHHHhhcccc----CCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         90 KMTEIQARTIPPLL----EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        90 ~pt~iQ~~aip~~l----~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      .+.++|..++.-++    .|.+.|++-..|.|||+-- +.++..+.... ......+||||. .|..+....+..++
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQa-IalL~~L~~~~-~~~gp~LIVvP~-SlL~nW~~Ei~kw~  242 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQT-ISLLGYLHEYR-GITGPHMVVAPK-STLGNWMNEIRRFC  242 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHH-HHHHHHHHHhc-CCCCCEEEEeCh-HHHHHHHHHHHHHC
Confidence            56778888876553    6788999999999999863 34444443322 223356899995 55566666666654

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=91.98  E-value=0.7  Score=40.21  Aligned_cols=59  Identities=17%  Similarity=0.172  Sum_probs=45.6

Q ss_pred             cEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHH-HHHHHHHHHHHHhhhcCC
Q psy12984        107 DLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRP-LTNGVYLVACNVFKSTQP  167 (178)
Q Consensus       107 dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~-La~qi~~~~~~l~~~~~~  167 (178)
                      -.++.+..|||||.+.++-++..+...  .+....+++.++.. |..-++..+...+..++.
T Consensus         3 ~~i~~GgrgSGKS~~~~~~~~~~~~~~--~~~~~~~~~r~~~~sl~~sv~~~l~~~i~~~g~   62 (396)
T TIGR01547         3 EIIAKGGRRSGKTFAIALKLVEKLAIN--KKQQNILAARKVQNSIRDSVFKDIENLLSIEGI   62 (396)
T ss_pred             eEEEeCCCCcccHHHHHHHHHHHHHhc--CCCcEEEEEehhhhHHHHHHHHHHHHHHHHcCC
Confidence            357789999999999998888887764  13457777888854 888888888877776654

This model detects members of a highly divergent family of the large subunit of phage terminase. All members are encoded by phage genomes or within prophage regions of bacterial genomes. This is a distinct family from pfam03354.

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=91.75  E-value=0.098  Score=45.25  Aligned_cols=60  Identities=18%  Similarity=0.133  Sum_probs=34.3

Q ss_pred             cCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEE----EeecHHHHHHHHHHHHHHhhhcCCCC
Q psy12984        103 LEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSW----QGKLRPLTNGVYLVACNVFKSTQPPT  169 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~----l~Ptr~La~qi~~~~~~l~~~~~~~~  169 (178)
                      +...|++..+|||||||+-.  -.|.++++-+     .++.    |+----...++.+.+.++++.-.-++
T Consensus        95 L~KSNILLiGPTGsGKTlLA--qTLAk~LnVP-----FaiADATtLTEAGYVGEDVENillkLlqaadydV  158 (408)
T COG1219          95 LSKSNILLIGPTGSGKTLLA--QTLAKILNVP-----FAIADATTLTEAGYVGEDVENILLKLLQAADYDV  158 (408)
T ss_pred             eeeccEEEECCCCCcHHHHH--HHHHHHhCCC-----eeeccccchhhccccchhHHHHHHHHHHHcccCH
Confidence            44568999999999999853  3444444421     1111    11111134577777777777655443

>PRK10436 hypothetical protein; Provisional

Probab=91.60  E-value=0.22  Score=44.84  Aligned_cols=25  Identities=28%  Similarity=0.414  Sum_probs=19.0

Q ss_pred             CcEEEEccCCCchhhHhHHHHHHHHH
Q psy12984        106 RDLVGSAKTGSGKTLAFLVPAVELIY  131 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~lp~l~~l~  131 (178)
                      --+++++|||||||... ..+|..+.
T Consensus       219 GliLvtGpTGSGKTTtL-~a~l~~~~  243 (462)
T PRK10436        219 GLILVTGPTGSGKTVTL-YSALQTLN  243 (462)
T ss_pred             CeEEEECCCCCChHHHH-HHHHHhhC
Confidence            45889999999999865 34666653

>PRK05973 replicative DNA helicase; Provisional

Probab=91.60  E-value=0.73  Score=37.93  Aligned_cols=39  Identities=33%  Similarity=0.297  Sum_probs=25.3

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHH
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVEL  129 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~  129 (178)
                      .+||... .+.-+..|.-+++.|++|+|||..-+--+.+.
T Consensus        50 ~~~p~~~-l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~   88 (237)
T PRK05973         50 ATTPAEE-LFSQLKPGDLVLLGARPGHGKTLLGLELAVEA   88 (237)
T ss_pred             CCCCHHH-hcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHH
Confidence            3455332 33455677889999999999998644333333

>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=91.48  E-value=0.53  Score=35.95  Aligned_cols=48  Identities=17%  Similarity=0.016  Sum_probs=28.5

Q ss_pred             EEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984        108 LVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus       108 vi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      +++.+++|+|||..-+--+...+.     .+..++|+ .+-+-..++...+..+
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~-----~g~~v~~~-s~e~~~~~~~~~~~~~   49 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLA-----RGEPGLYV-TLEESPEELIENAESL   49 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHH-----CCCcEEEE-ECCCCHHHHHHHHHHc
Confidence            688999999999854323333332     23355555 4455566666655544

A related protein is found in archaea.

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

Probab=91.29  E-value=0.46  Score=45.46  Aligned_cols=52  Identities=21%  Similarity=0.125  Sum_probs=38.7

Q ss_pred             CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984        106 RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      .=.++.||.|||||.+..-++-+.+.    .+..++++|+.-|.|+.++...|+.-
T Consensus        50 ~V~vVRSpMGTGKTtaLi~wLk~~l~----~~~~~VLvVShRrSL~~sL~~rf~~~  101 (824)
T PF02399_consen   50 GVLVVRSPMGTGKTTALIRWLKDALK----NPDKSVLVVSHRRSLTKSLAERFKKA  101 (824)
T ss_pred             CeEEEECCCCCCcHHHHHHHHHHhcc----CCCCeEEEEEhHHHHHHHHHHHHhhc
Confidence            34578999999999877443333222    35568899999999999999998643

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

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=91.04  E-value=0.62  Score=46.43  Aligned_cols=56  Identities=13%  Similarity=0.081  Sum_probs=40.7

Q ss_pred             cCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHH
Q psy12984        103 LEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVA  158 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~  158 (178)
                      -.+.+++|.|..|||||.+...=+|..|.......-...++++-|++=|..+...+
T Consensus        14 ~~~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~~v~~ILvvTFT~aAa~Emk~RI   69 (1139)
T COG1074          14 PPGQSVLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERI   69 (1139)
T ss_pred             CCCCcEEEEEcCCCCchhHHHHHHHHHHhhcCCCChhHeeeeeccHHHHHHHHHHH
Confidence            34679999999999999999988888887742123347788888866554444443

>KOG0390|consensus

Probab=90.67  E-value=0.73  Score=43.99  Aligned_cols=71  Identities=17%  Similarity=0.132  Sum_probs=49.3

Q ss_pred             CCcHHHHHhhcccc---CC-------CcEEEEccCCCchhhHhHHHHHHHHHhccCCCC-----CceEEEeecHHHHHHH
Q psy12984         90 KMTEIQARTIPPLL---EG-------RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPR-----NGKSWQGKLRPLTNGV  154 (178)
Q Consensus        90 ~pt~iQ~~aip~~l---~g-------~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~-----~~~~~l~Ptr~La~qi  154 (178)
                      .+.|||.+.+..+.   .|       -.+|++-..|+|||+-. ++.|+.+++.  .+.     ..++|++| ..|.+-.
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~-IsflwtlLrq--~P~~~~~~~k~lVV~P-~sLv~nW  313 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQC-ISFIWTLLRQ--FPQAKPLINKPLVVAP-SSLVNNW  313 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHH-HHHHHHHHHh--CcCccccccccEEEcc-HHHHHHH
Confidence            67899999997553   22       34667777899999854 4555555442  344     57889999 6677777


Q ss_pred             HHHHHHHhhh
Q psy12984        155 YLVACNVFKS  164 (178)
Q Consensus       155 ~~~~~~l~~~  164 (178)
                      ++.|.++...
T Consensus       314 kkEF~KWl~~  323 (776)
T KOG0390|consen  314 KKEFGKWLGN  323 (776)
T ss_pred             HHHHHHhccc
Confidence            7777776654

>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=90.63  E-value=0.28  Score=41.93  Aligned_cols=34  Identities=21%  Similarity=0.216  Sum_probs=25.3

Q ss_pred             CCCCcHHHHHh-hccccCCCcEEEEccCCCchhhH
Q psy12984         88 FTKMTEIQART-IPPLLEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus        88 ~~~pt~iQ~~a-ip~~l~g~dvi~~a~TGsGKTla  121 (178)
                      +..+++.|..- |-++..+++++++++||||||..
T Consensus       125 ~gt~~~~~~ayL~~~ie~~~siii~G~t~sGKTt~  159 (312)
T COG0630         125 YGTISPEQAAYLWLAIEARKSIIICGGTASGKTTL  159 (312)
T ss_pred             cCCCCHHHHHHHHHHHHcCCcEEEECCCCCCHHHH
Confidence            44556666554 44566889999999999999964

>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family

Probab=90.51  E-value=1  Score=42.28  Aligned_cols=54  Identities=15%  Similarity=-0.082  Sum_probs=39.0

Q ss_pred             CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecH--HHHHHHHHHHHHHhh
Q psy12984        105 GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLR--PLTNGVYLVACNVFK  163 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr--~La~qi~~~~~~l~~  163 (178)
                      ..+.+|.++||+|||..+.+=+.+.+..     +.+++++=|-.  +|..-++..++.+++
T Consensus       180 ~gHtlV~GtTGsGKT~l~~~li~q~i~~-----g~~vi~fDpkgD~el~~~~~~~~~~~GR  235 (643)
T TIGR03754       180 VGHTLVLGTTRVGKTRLAELLITQDIRR-----GDVVIVFDPKGDADLLKRMYAEAKRAGR  235 (643)
T ss_pred             cCceEEECCCCCCHHHHHHHHHHHHHHc-----CCeEEEEeCCCCHHHHHHHHHHHHHhCC
Confidence            4688999999999999877656565543     33667777774  577777777666554

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.

>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=90.37  E-value=0.24  Score=40.72  Aligned_cols=30  Identities=30%  Similarity=0.266  Sum_probs=21.9

Q ss_pred             ccCCCcEEEEccCCCchhhHhHHHHHHHHHh
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAFLVPAVELIYN  132 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~  132 (178)
                      +..+.+++++++||||||... -.++..+..
T Consensus       124 v~~~~~ili~G~tGSGKTT~l-~all~~i~~  153 (270)
T PF00437_consen  124 VRGRGNILISGPTGSGKTTLL-NALLEEIPP  153 (270)
T ss_dssp             HHTTEEEEEEESTTSSHHHHH-HHHHHHCHT
T ss_pred             cccceEEEEECCCccccchHH-HHHhhhccc
Confidence            356789999999999999864 344554443

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 ....

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=90.31  E-value=0.33  Score=44.68  Aligned_cols=45  Identities=24%  Similarity=0.374  Sum_probs=28.9

Q ss_pred             HHHCCCCCCcHHHHHhhccccC--CCcEEEEccCCCchhhHhHHHHHHHHH
Q psy12984         83 IADMGFTKMTEIQARTIPPLLE--GRDLVGSAKTGSGKTLAFLVPAVELIY  131 (178)
Q Consensus        83 l~~~g~~~pt~iQ~~aip~~l~--g~dvi~~a~TGsGKTlaf~lp~l~~l~  131 (178)
                      |.++||.   +-|...|..++.  .--+++++|||||||... ..++..+.
T Consensus       295 l~~lg~~---~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl-~a~l~~~~  341 (564)
T TIGR02538       295 IDKLGFE---PDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL-YTALNILN  341 (564)
T ss_pred             HHHcCCC---HHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHHhhC
Confidence            5566663   445555544433  235789999999999874 45666653

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.

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

Probab=90.22  E-value=0.95  Score=44.40  Aligned_cols=59  Identities=19%  Similarity=0.013  Sum_probs=43.4

Q ss_pred             CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhcCC
Q psy12984        106 RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQP  167 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~~  167 (178)
                      +.-+|.--+|||||+.-+..+-..+ ..  ...+.+++|+--++|-.|+.+.|..+......
T Consensus       274 ~~G~IWHtqGSGKTlTm~~~A~~l~-~~--~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~~  332 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMFKLARLLL-EL--PKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFN  332 (962)
T ss_pred             CceEEEeecCCchHHHHHHHHHHHH-hc--cCCCeEEEEechHHHHHHHHHHHHHHHHhhhh
Confidence            5678889999999998444332222 22  44557888999999999999999988765443

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=90.14  E-value=0.65  Score=40.73  Aligned_cols=26  Identities=19%  Similarity=0.019  Sum_probs=19.1

Q ss_pred             CCcEEEEccCCCchhhHhHHHHHHHHH
Q psy12984        105 GRDLVGSAKTGSGKTLAFLVPAVELIY  131 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf~lp~l~~l~  131 (178)
                      +..++++++||||||... ..++.++.
T Consensus       149 ~GlilI~G~TGSGKTT~l-~al~~~i~  174 (372)
T TIGR02525       149 AGLGLICGETGSGKSTLA-ASIYQHCG  174 (372)
T ss_pred             CCEEEEECCCCCCHHHHH-HHHHHHHH
Confidence            346899999999999754 44556554

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).

>KOG0926|consensus

Probab=90.02  E-value=0.85  Score=43.91  Aligned_cols=34  Identities=32%  Similarity=0.466  Sum_probs=24.1

Q ss_pred             CCCCcHHHHHhh--c----------cccCCCcEEEEccCCCchhhH
Q psy12984         88 FTKMTEIQARTI--P----------PLLEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus        88 ~~~pt~iQ~~ai--p----------~~l~g~dvi~~a~TGsGKTla  121 (178)
                      +.+|..||..-+  |          ++...-=||||+.||||||.-
T Consensus       242 V~R~~EIQ~sR~~LPI~aeEq~IMEaIn~n~vvIIcGeTGsGKTTQ  287 (1172)
T KOG0926|consen  242 VSRPAEIQESRLDLPIVAEEQRIMEAINENPVVIICGETGSGKTTQ  287 (1172)
T ss_pred             ecCcHHHHHHHhcCchhHHHHHHHHHhhcCCeEEEecCCCCCcccc
Confidence            346788886543  3          333455689999999999974

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=89.97  E-value=1  Score=44.88  Aligned_cols=57  Identities=18%  Similarity=0.113  Sum_probs=43.2

Q ss_pred             CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984        105 GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      .++++|.|..|||||....--++..+...  ......++|+-|+.=|..+...+...+.
T Consensus        10 ~~~~~~~a~agsgkt~~l~~~~~~~~~~~--~~~~~i~~~t~t~~aa~em~~Ri~~~L~   66 (1141)
T TIGR02784        10 KTSAWVSANAGSGKTHVLTQRVIRLLLNG--VPPSKILCLTYTKAAAAEMQNRVFDRLG   66 (1141)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHHcC--CCCCeEEEEecCHHHHHHHHHHHHHHHH
Confidence            46899999999999999888888777653  2234778899998877777666555554

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species.

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=89.95  E-value=0.3  Score=44.24  Aligned_cols=44  Identities=20%  Similarity=0.329  Sum_probs=26.9

Q ss_pred             HHHCCCCCCcHHHHHhhccccCC-C-cEEEEccCCCchhhHhHHHHHHHH
Q psy12984         83 IADMGFTKMTEIQARTIPPLLEG-R-DLVGSAKTGSGKTLAFLVPAVELI  130 (178)
Q Consensus        83 l~~~g~~~pt~iQ~~aip~~l~g-~-dvi~~a~TGsGKTlaf~lp~l~~l  130 (178)
                      |.++||   ++-|...|..++.. . =+++++|||||||... ..++..+
T Consensus       221 l~~Lg~---~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL-~a~L~~l  266 (486)
T TIGR02533       221 LETLGM---SPELLSRFERLIRRPHGIILVTGPTGSGKTTTL-YAALSRL  266 (486)
T ss_pred             HHHcCC---CHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH-HHHHhcc
Confidence            455565   34455555444432 3 3789999999999864 2345544

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.

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

Probab=89.77  E-value=0.78  Score=37.53  Aligned_cols=46  Identities=20%  Similarity=0.145  Sum_probs=27.4

Q ss_pred             HHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhH
Q psy12984         78 NTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFL  123 (178)
Q Consensus        78 ~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~  123 (178)
                      +++++|...|.....+-=-..+.-+..|.-+++.|++|+|||...+
T Consensus         3 ~~~~~~~~~~~~tg~~~Ld~~~gG~~~g~~~~i~g~~G~GKT~l~~   48 (271)
T cd01122           3 EIREALSNEEVWWPFPVLNKLTKGLRKGELIILTAGTGVGKTTFLR   48 (271)
T ss_pred             hhhccccccCCCCCcceeeeeeEEEcCCcEEEEEcCCCCCHHHHHH
Confidence            4555555444433222111222445667889999999999997543

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

>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=89.77  E-value=0.71  Score=36.24  Aligned_cols=27  Identities=26%  Similarity=0.298  Sum_probs=18.4

Q ss_pred             CCcEEEEccCCCchhhHhHHHHHHHHH
Q psy12984        105 GRDLVGSAKTGSGKTLAFLVPAVELIY  131 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf~lp~l~~l~  131 (178)
                      ..++++.+.||||||.+...-+...+.
T Consensus        38 ~~h~li~G~tgsGKS~~l~~ll~~l~~   64 (205)
T PF01580_consen   38 NPHLLIAGATGSGKSTLLRTLLLSLAL   64 (205)
T ss_dssp             S-SEEEE--TTSSHHHHHHHHHHHHHT
T ss_pred             CceEEEEcCCCCCccHHHHHHHHHHHH
Confidence            459999999999999986655555444

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.

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

Probab=89.70  E-value=0.82  Score=36.47  Aligned_cols=55  Identities=16%  Similarity=0.085  Sum_probs=31.3

Q ss_pred             ccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      +-.|.-+++.+++|+|||.--+--+.+.+.+.    +..+++++ +-+-..++...+..+
T Consensus        16 ip~gs~~li~G~~GsGKT~l~~q~l~~~~~~~----ge~vlyvs-~ee~~~~l~~~~~s~   70 (226)
T PF06745_consen   16 IPKGSVVLISGPPGSGKTTLALQFLYNGLKNF----GEKVLYVS-FEEPPEELIENMKSF   70 (226)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHHHHHH----T--EEEEE-SSS-HHHHHHHHHTT
T ss_pred             CCCCcEEEEEeCCCCCcHHHHHHHHHHhhhhc----CCcEEEEE-ecCCHHHHHHHHHHc
Confidence            34578899999999999986443344444320    22555554 444445555555443

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 ....

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=89.61  E-value=0.23  Score=45.01  Aligned_cols=39  Identities=26%  Similarity=0.293  Sum_probs=24.9

Q ss_pred             HHHHHhhccccCCC--cEEEEccCCCchhhHhHHHHHHHHHh
Q psy12984         93 EIQARTIPPLLEGR--DLVGSAKTGSGKTLAFLVPAVELIYN  132 (178)
Q Consensus        93 ~iQ~~aip~~l~g~--dvi~~a~TGsGKTlaf~lp~l~~l~~  132 (178)
                      +.|...+-.++...  =+++.+|||||||... +.+|+.+..
T Consensus       244 ~~~~~~~~~~~~~p~GliLvTGPTGSGKTTTL-Y~~L~~ln~  284 (500)
T COG2804         244 PFQLARLLRLLNRPQGLILVTGPTGSGKTTTL-YAALSELNT  284 (500)
T ss_pred             HHHHHHHHHHHhCCCeEEEEeCCCCCCHHHHH-HHHHHHhcC
Confidence            45555554444332  2788999999999873 456665543

>PRK08116 hypothetical protein; Validated

Probab=89.40  E-value=2.7  Score=35.02  Aligned_cols=47  Identities=15%  Similarity=0.007  Sum_probs=30.4

Q ss_pred             CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHH
Q psy12984        105 GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLV  157 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~  157 (178)
                      +..+++.+++|+|||.... .+.+.+...    + ..++..+..+|...+...
T Consensus       114 ~~gl~l~G~~GtGKThLa~-aia~~l~~~----~-~~v~~~~~~~ll~~i~~~  160 (268)
T PRK08116        114 NVGLLLWGSVGTGKTYLAA-CIANELIEK----G-VPVIFVNFPQLLNRIKST  160 (268)
T ss_pred             CceEEEECCCCCCHHHHHH-HHHHHHHHc----C-CeEEEEEHHHHHHHHHHH
Confidence            3459999999999997543 455655542    2 234455667777666544

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=89.33  E-value=0.25  Score=40.82  Aligned_cols=25  Identities=24%  Similarity=0.227  Sum_probs=20.3

Q ss_pred             hhccccCCCcEEEEccCCCchhhHh
Q psy12984         98 TIPPLLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus        98 aip~~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      ++..+..|+++++.+++|+|||...
T Consensus        14 ~l~~l~~g~~vLL~G~~GtGKT~lA   38 (262)
T TIGR02640        14 ALRYLKSGYPVHLRGPAGTGKTTLA   38 (262)
T ss_pred             HHHHHhcCCeEEEEcCCCCCHHHHH
Confidence            3445667899999999999999763

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).

>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=89.16  E-value=0.37  Score=34.14  Aligned_cols=18  Identities=28%  Similarity=0.375  Sum_probs=15.6

Q ss_pred             CCCcEEEEccCCCchhhH
Q psy12984        104 EGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTla  121 (178)
                      .+..+++.+++|+|||..
T Consensus        18 ~~~~v~i~G~~G~GKT~l   35 (151)
T cd00009          18 PPKNLLLYGPPGTGKTTL   35 (151)
T ss_pred             CCCeEEEECCCCCCHHHH
Confidence            367899999999999963

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.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=89.12  E-value=0.51  Score=37.30  Aligned_cols=23  Identities=26%  Similarity=0.489  Sum_probs=16.8

Q ss_pred             EEEEccCCCchhhHhHHHHHHHHH
Q psy12984        108 LVGSAKTGSGKTLAFLVPAVELIY  131 (178)
Q Consensus       108 vi~~a~TGsGKTlaf~lp~l~~l~  131 (178)
                      +++++|||||||... ..++..+.
T Consensus         4 ilI~GptGSGKTTll-~~ll~~~~   26 (198)
T cd01131           4 VLVTGPTGSGKSTTL-AAMIDYIN   26 (198)
T ss_pred             EEEECCCCCCHHHHH-HHHHHHhh
Confidence            688999999999874 33455443

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.

>PRK13700 conjugal transfer protein TraD; Provisional

Probab=89.11  E-value=0.41  Score=45.38  Aligned_cols=71  Identities=10%  Similarity=0.026  Sum_probs=43.6

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHH
Q psy12984         77 ENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTN  152 (178)
Q Consensus        77 ~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~  152 (178)
                      .++.+.+++.|-..+..|--.-||.-...+++++.+-||||||.++ .-+|..+..    .+.+++|.=|+.+...
T Consensus       157 ~~l~k~lk~~~~~s~i~I~gvPip~~~E~~H~li~GttGSGKS~~i-~~LL~~ir~----RGdrAIIyD~~GeFv~  227 (732)
T PRK13700        157 KDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVI-RRLANYARQ----RGDMVVIYDRSGEFVK  227 (732)
T ss_pred             HHHHHHHHhcCCCCCeeEccccCCcchhhcceEEeCCCCCCHHHHH-HHHHHHHHH----cCCeEEEEeCCCchHH
Confidence            3455667776654554443333444556799999999999999965 355555533    2335555555555544

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=88.99  E-value=0.8  Score=39.58  Aligned_cols=41  Identities=27%  Similarity=0.250  Sum_probs=27.0

Q ss_pred             HHHHHHCCCCCCcHHHHHhhcc-ccCCCcEEEEccCCCchhhHh
Q psy12984         80 LKAIADMGFTKMTEIQARTIPP-LLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus        80 l~~l~~~g~~~pt~iQ~~aip~-~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      +..+.+.|+-  ++.+...+.. +..+.+++++++||||||..+
T Consensus       154 l~~l~~~g~~--~~~~~~~L~~~v~~~~~ili~G~tGsGKTTll  195 (340)
T TIGR03819       154 LDELVASGTF--PPGVARLLRAIVAARLAFLISGGTGSGKTTLL  195 (340)
T ss_pred             HHHHHHcCCC--CHHHHHHHHHHHhCCCeEEEECCCCCCHHHHH
Confidence            4445566653  3444444443 446789999999999998754

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.

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=88.98  E-value=0.72  Score=36.46  Aligned_cols=20  Identities=30%  Similarity=0.248  Sum_probs=16.4

Q ss_pred             cCCCcEEEEccCCCchhhHh
Q psy12984        103 LEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTlaf  122 (178)
                      ..+..+++.+++|+|||...
T Consensus        36 ~~~~~lll~G~~G~GKT~la   55 (226)
T TIGR03420        36 KGDRFLYLWGESGSGKSHLL   55 (226)
T ss_pred             CCCCeEEEECCCCCCHHHHH
Confidence            34678999999999999653

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.

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=88.96  E-value=0.26  Score=35.40  Aligned_cols=20  Identities=45%  Similarity=0.380  Sum_probs=13.1

Q ss_pred             CCCcEEEEccCCCchhhHhH
Q psy12984        104 EGRDLVGSAKTGSGKTLAFL  123 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~  123 (178)
                      .++.+++.+++|+|||....
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~   22 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIK   22 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHH
Confidence            45678999999999998743

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=88.96  E-value=0.78  Score=36.77  Aligned_cols=40  Identities=20%  Similarity=0.121  Sum_probs=24.5

Q ss_pred             ccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      +..|.-++++|++|+|||..-+--+.+.+..    .+..+++++
T Consensus        10 l~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~----~g~~vly~s   49 (242)
T cd00984          10 LQPGDLIIIAARPSMGKTAFALNIAENIAKK----QGKPVLFFS   49 (242)
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHHHHHHHHHh----CCCceEEEe
Confidence            4457788999999999996433233333322    133556653

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.

>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=88.94  E-value=0.22  Score=41.71  Aligned_cols=21  Identities=33%  Similarity=0.495  Sum_probs=18.2

Q ss_pred             ccCCCcEEEEccCCCchhhHh
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      +..++.+++++++|+|||...
T Consensus        30 ~~~~~pvLl~G~~GtGKT~li   50 (272)
T PF12775_consen   30 LSNGRPVLLVGPSGTGKTSLI   50 (272)
T ss_dssp             HHCTEEEEEESSTTSSHHHHH
T ss_pred             HHcCCcEEEECCCCCchhHHH
Confidence            457899999999999999853

>PRK06921 hypothetical protein; Provisional

Probab=88.93  E-value=1.9  Score=35.83  Aligned_cols=50  Identities=12%  Similarity=-0.076  Sum_probs=29.3

Q ss_pred             CCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHH
Q psy12984        104 EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVA  158 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~  158 (178)
                      .+..+++.+++|+|||... ..+...+..   ..+..++ -++..+|..++...+
T Consensus       116 ~~~~l~l~G~~G~GKThLa-~aia~~l~~---~~g~~v~-y~~~~~l~~~l~~~~  165 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLL-TAAANELMR---KKGVPVL-YFPFVEGFGDLKDDF  165 (266)
T ss_pred             CCCeEEEECCCCCcHHHHH-HHHHHHHhh---hcCceEE-EEEHHHHHHHHHHHH
Confidence            4678999999999999643 233444433   1123334 445566655554443

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=88.90  E-value=0.56  Score=42.03  Aligned_cols=47  Identities=17%  Similarity=0.242  Sum_probs=30.4

Q ss_pred             CHHHHHHHHHCCCCCCcHH-------HHHhh-ccccCCCcEEEEccCCCchhhHhH
Q psy12984         76 CENTLKAIADMGFTKMTEI-------QARTI-PPLLEGRDLVGSAKTGSGKTLAFL  123 (178)
Q Consensus        76 ~~~ll~~l~~~g~~~pt~i-------Q~~ai-p~~l~g~dvi~~a~TGsGKTlaf~  123 (178)
                      .+|+---|...||. |+..       +...+ |.+-.+.|++..+|+|+|||-.|.
T Consensus       173 dEWid~LlrSiG~~-P~~~~~r~k~~~L~rl~~fve~~~Nli~lGp~GTGKThla~  227 (449)
T TIGR02688       173 EEWIDVLIRSIGYE-PEGFEARQKLLLLARLLPLVEPNYNLIELGPKGTGKSYIYN  227 (449)
T ss_pred             HHHHHHHHHhcCCC-cccCChHHHHHHHHhhHHHHhcCCcEEEECCCCCCHHHHHH
Confidence            33444445668884 4331       11222 556678999999999999995554

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>KOG0745|consensus

Probab=88.89  E-value=0.32  Score=43.77  Aligned_cols=61  Identities=20%  Similarity=0.179  Sum_probs=36.1

Q ss_pred             cCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeec----HHHHHHHHHHHHHHhhhcCCCCc
Q psy12984        103 LEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKL----RPLTNGVYLVACNVFKSTQPPTV  170 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Pt----r~La~qi~~~~~~l~~~~~~~~~  170 (178)
                      |...|||+.+|||||||+..  -.|.++++   .+  .++.=|-|    --...++..++.+|+..-+-++.
T Consensus       224 LeKSNvLllGPtGsGKTlla--qTLAr~ld---VP--faIcDcTtLTQAGYVGeDVEsvi~KLl~~A~~nVe  288 (564)
T KOG0745|consen  224 LEKSNVLLLGPTGSGKTLLA--QTLARVLD---VP--FAICDCTTLTQAGYVGEDVESVIQKLLQEAEYNVE  288 (564)
T ss_pred             eecccEEEECCCCCchhHHH--HHHHHHhC---CC--eEEecccchhhcccccccHHHHHHHHHHHccCCHH
Confidence            44568999999999999843  33444443   12  22211111    11345777788888877665544

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=88.81  E-value=1.5  Score=36.21  Aligned_cols=39  Identities=15%  Similarity=-0.011  Sum_probs=24.7

Q ss_pred             ccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      +..|.-+++.+++|+|||..-+--+.+.+.     .+..++|++
T Consensus        33 ip~gs~~lI~G~pGtGKT~l~~qf~~~~a~-----~Ge~vlyis   71 (259)
T TIGR03878        33 IPAYSVINITGVSDTGKSLMVEQFAVTQAS-----RGNPVLFVT   71 (259)
T ss_pred             eECCcEEEEEcCCCCCHHHHHHHHHHHHHh-----CCCcEEEEE
Confidence            445788999999999999853332333332     233556664

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

>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=88.79  E-value=0.31  Score=38.55  Aligned_cols=20  Identities=30%  Similarity=0.331  Sum_probs=15.2

Q ss_pred             CCcEEEEccCCCchhhHhHH
Q psy12984        105 GRDLVGSAKTGSGKTLAFLV  124 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf~l  124 (178)
                      ...|++++|.|||||.-|..
T Consensus         3 ~~~vlL~Gps~SGKTaLf~~   22 (181)
T PF09439_consen    3 RPTVLLVGPSGSGKTALFSQ   22 (181)
T ss_dssp             --EEEEE-STTSSHHHHHHH
T ss_pred             CceEEEEcCCCCCHHHHHHH
Confidence            46799999999999998864

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.

>PRK08181 transposase; Validated

Probab=88.48  E-value=1.2  Score=37.24  Aligned_cols=47  Identities=13%  Similarity=0.066  Sum_probs=27.7

Q ss_pred             CCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHH
Q psy12984        104 EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYL  156 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~  156 (178)
                      .+.++++.+|+|+|||.... .+...+..    .+.. ++.++..+|..++..
T Consensus       105 ~~~nlll~Gp~GtGKTHLa~-Aia~~a~~----~g~~-v~f~~~~~L~~~l~~  151 (269)
T PRK08181        105 KGANLLLFGPPGGGKSHLAA-AIGLALIE----NGWR-VLFTRTTDLVQKLQV  151 (269)
T ss_pred             cCceEEEEecCCCcHHHHHH-HHHHHHHH----cCCc-eeeeeHHHHHHHHHH
Confidence            57899999999999995433 22222222    1223 334455666666543

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=88.36  E-value=0.52  Score=39.20  Aligned_cols=44  Identities=23%  Similarity=0.327  Sum_probs=26.4

Q ss_pred             HHHCCCCCCcHHHHHhhcccc--CCCcEEEEccCCCchhhHhHHHHHHHH
Q psy12984         83 IADMGFTKMTEIQARTIPPLL--EGRDLVGSAKTGSGKTLAFLVPAVELI  130 (178)
Q Consensus        83 l~~~g~~~pt~iQ~~aip~~l--~g~dvi~~a~TGsGKTlaf~lp~l~~l  130 (178)
                      |.++||   ++-|...|-.++  .+.-++++++||||||... ..++..+
T Consensus        59 l~~lg~---~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l-~all~~i  104 (264)
T cd01129          59 LEKLGL---KPENLEIFRKLLEKPHGIILVTGPTGSGKTTTL-YSALSEL  104 (264)
T ss_pred             HHHcCC---CHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHH-HHHHhhh
Confidence            445565   234444444333  2345899999999999864 3344544

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.

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=88.31  E-value=1.3  Score=36.36  Aligned_cols=55  Identities=16%  Similarity=-0.003  Sum_probs=35.4

Q ss_pred             ccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      +-.|+.+++.+++|||||..-.--+.+.+ +   . +.. ++.+-+.+...++...+..+.
T Consensus        20 ~p~g~~~lI~G~pGsGKT~f~~qfl~~~~-~---~-ge~-vlyvs~~e~~~~l~~~~~~~g   74 (260)
T COG0467          20 LPRGSVVLITGPPGTGKTIFALQFLYEGA-R---E-GEP-VLYVSTEESPEELLENARSFG   74 (260)
T ss_pred             CcCCcEEEEEcCCCCcHHHHHHHHHHHHH-h---c-CCc-EEEEEecCCHHHHHHHHHHcC
Confidence            34578999999999999985332233322 2   1 223 445667787887777776543

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

Probab=88.31  E-value=1  Score=38.99  Aligned_cols=59  Identities=15%  Similarity=0.144  Sum_probs=39.6

Q ss_pred             CcHHHHHhhccc------cCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHH
Q psy12984         91 MTEIQARTIPPL------LEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGV  154 (178)
Q Consensus        91 pt~iQ~~aip~~------l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi  154 (178)
                      +++=|+.++..+      ..|..+++.++-|+|||..+  =.|....+   .....+++.+||-.=|.-+
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~--~~i~~~~~---~~~~~~~~~a~tg~AA~~i   66 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLI--KAIIDYLR---SRGKKVLVTAPTGIAAFNI   66 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHH--HHHHHHhc---cccceEEEecchHHHHHhc
Confidence            345566666555      67899999999999999753  33333333   2344677789997766666

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

>PRK09183 transposase/IS protein; Provisional

Probab=88.22  E-value=1.9  Score=35.70  Aligned_cols=22  Identities=23%  Similarity=0.302  Sum_probs=18.0

Q ss_pred             ccCCCcEEEEccCCCchhhHhH
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAFL  123 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf~  123 (178)
                      +..|.++++.+|+|+|||....
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~  120 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAI  120 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHH
Confidence            4568899999999999996543

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=88.21  E-value=1.6  Score=38.34  Aligned_cols=21  Identities=29%  Similarity=0.222  Sum_probs=17.7

Q ss_pred             CCCcEEEEccCCCchhhHhHH
Q psy12984        104 EGRDLVGSAKTGSGKTLAFLV  124 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~l  124 (178)
                      .|..+++.+|||+|||....-
T Consensus       136 ~g~ii~lvGptGvGKTTtiak  156 (374)
T PRK14722        136 RGGVFALMGPTGVGKTTTTAK  156 (374)
T ss_pred             CCcEEEEECCCCCCHHHHHHH
Confidence            477899999999999987653

>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown

Probab=88.19  E-value=0.98  Score=36.03  Aligned_cols=26  Identities=27%  Similarity=0.287  Sum_probs=20.1

Q ss_pred             CCcEEEEccCCCchhhHhHHHHHHHHH
Q psy12984        105 GRDLVGSAKTGSGKTLAFLVPAVELIY  131 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf~lp~l~~l~  131 (178)
                      ++++.|.|.||||||..-. -+++.+.
T Consensus        23 ~~H~~I~G~TGsGKS~~~~-~ll~~l~   48 (229)
T PF01935_consen   23 NRHIAIFGTTGSGKSNTVK-VLLEELL   48 (229)
T ss_pred             cceEEEECCCCCCHHHHHH-HHHHHHH
Confidence            6899999999999998654 4445554

It contains several conserved aspartates and histidines that could be metal ligands.

>PRK04328 hypothetical protein; Provisional

Probab=88.12  E-value=1.4  Score=36.09  Aligned_cols=52  Identities=13%  Similarity=-0.023  Sum_probs=30.8

Q ss_pred             CCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984        104 EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      .|.-+++.+++|+|||.-.+--+.+.+.+     +..++|++ +-+-..++.+.+..+
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~~~~~-----ge~~lyis-~ee~~~~i~~~~~~~   73 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWNGLQM-----GEPGVYVA-LEEHPVQVRRNMRQF   73 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhc-----CCcEEEEE-eeCCHHHHHHHHHHc
Confidence            47789999999999987433223333322     33555554 444455555555544

>KOG0729|consensus

Probab=88.11  E-value=1.1  Score=38.25  Aligned_cols=41  Identities=17%  Similarity=0.048  Sum_probs=26.2

Q ss_pred             CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHH
Q psy12984        106 RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVY  155 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~  155 (178)
                      +.|++-+|+|+||||+.-.-+         ....-+.|-+---||.+...
T Consensus       212 kgvllygppgtgktl~arava---------nrtdacfirvigselvqkyv  252 (435)
T KOG0729|consen  212 KGVLLYGPPGTGKTLCARAVA---------NRTDACFIRVIGSELVQKYV  252 (435)
T ss_pred             CceEEeCCCCCchhHHHHHHh---------cccCceEEeehhHHHHHHHh
Confidence            679999999999999864221         11223334455567776544

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=88.10  E-value=0.62  Score=40.57  Aligned_cols=26  Identities=19%  Similarity=0.262  Sum_probs=19.5

Q ss_pred             CCCcEEEEccCCCchhhHhHHHHHHHH
Q psy12984        104 EGRDLVGSAKTGSGKTLAFLVPAVELI  130 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~lp~l~~l  130 (178)
                      .+.-+++++|||||||... ..++..+
T Consensus       133 ~~glilI~GpTGSGKTTtL-~aLl~~i  158 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLL-AAIIREL  158 (358)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHH
Confidence            4678999999999999864 3355544

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.

>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD

Probab=87.90  E-value=0.72  Score=42.60  Aligned_cols=42  Identities=21%  Similarity=0.177  Sum_probs=26.6

Q ss_pred             cCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHH
Q psy12984        103 LEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRP  149 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~  149 (178)
                      ...+++++.++||||||.+ +-.++..+...    +.+++|+=|.-+
T Consensus       174 ~e~~h~li~G~tGsGKs~~-i~~ll~~~~~~----g~~~ii~D~~g~  215 (566)
T TIGR02759       174 SETQHILIHGTTGSGKSVA-IRKLLRWIRQR----GDRAIIYDKGCT  215 (566)
T ss_pred             ccccceEEEcCCCCCHHHH-HHHHHHHHHhc----CCeEEEEECCCC
Confidence            4457999999999999963 34455555431    234555555444

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).

>PHA02533 17 large terminase protein; Provisional

Probab=87.69  E-value=2.8  Score=38.52  Aligned_cols=73  Identities=10%  Similarity=0.012  Sum_probs=53.8

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      .|.|.|...+..+..++-.++..+-..|||.+.+.-++.....   .+...+++++|++.-|..+++.++.+...+
T Consensus        59 ~L~p~Q~~i~~~~~~~R~~ii~~aRq~GKStl~a~~al~~a~~---~~~~~v~i~A~~~~QA~~vF~~ik~~ie~~  131 (534)
T PHA02533         59 QMRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCF---NKDKNVGILAHKASMAAEVLDRTKQAIELL  131 (534)
T ss_pred             CCcHHHHHHHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHh---CCCCEEEEEeCCHHHHHHHHHHHHHHHHhC
Confidence            4678999888766556655666777899999877655554443   234477888999999999998888776543

>PHA00729 NTP-binding motif containing protein

Probab=87.59  E-value=2.1  Score=35.08  Aligned_cols=50  Identities=24%  Similarity=0.161  Sum_probs=29.0

Q ss_pred             cEEEEccCCCchhh-HhHHHHHHHHH-hc--------cCCCCCceEEEeecHHHHHHHHHHHH
Q psy12984        107 DLVGSAKTGSGKTL-AFLVPAVELIY-NL--------KFMPRNGKSWQGKLRPLTNGVYLVAC  159 (178)
Q Consensus       107 dvi~~a~TGsGKTl-af~lp~l~~l~-~~--------~~~~~~~~~~l~Ptr~La~qi~~~~~  159 (178)
                      ++++.+++|+|||. |..+  ...+. ..        ..... ...+.+...+|...+...+.
T Consensus        19 nIlItG~pGvGKT~LA~aL--a~~l~~~l~~l~~~~~~~d~~-~~~~fid~~~Ll~~L~~a~~   78 (226)
T PHA00729         19 SAVIFGKQGSGKTTYALKV--ARDVFWKLNNLSTKDDAWQYV-QNSYFFELPDALEKIQDAID   78 (226)
T ss_pred             EEEEECCCCCCHHHHHHHH--HHHHHhhcccccchhhHHhcC-CcEEEEEHHHHHHHHHHHHh
Confidence            79999999999995 3333  22221 00        00112 23456777778877765543

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=87.51  E-value=1.7  Score=34.59  Aligned_cols=21  Identities=29%  Similarity=0.366  Sum_probs=17.1

Q ss_pred             cCCCcEEEEccCCCchhhHhH
Q psy12984        103 LEGRDLVGSAKTGSGKTLAFL  123 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTlaf~  123 (178)
                      ..|..+++.+++|+|||....
T Consensus        18 ~~G~~~~i~G~~G~GKT~l~~   38 (229)
T TIGR03881        18 PRGFFVAVTGEPGTGKTIFCL   38 (229)
T ss_pred             cCCeEEEEECCCCCChHHHHH
Confidence            357889999999999987543

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.

>PRK06835 DNA replication protein DnaC; Validated

Probab=87.50  E-value=2  Score=37.00  Aligned_cols=47  Identities=15%  Similarity=0.081  Sum_probs=29.1

Q ss_pred             CCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHH
Q psy12984        104 EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYL  156 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~  156 (178)
                      .+.++++.++||+|||... ..+...+..    .+.. ++..+..+|..++..
T Consensus       182 ~~~~Lll~G~~GtGKThLa-~aIa~~l~~----~g~~-V~y~t~~~l~~~l~~  228 (329)
T PRK06835        182 NNENLLFYGNTGTGKTFLS-NCIAKELLD----RGKS-VIYRTADELIEILRE  228 (329)
T ss_pred             cCCcEEEECCCCCcHHHHH-HHHHHHHHH----CCCe-EEEEEHHHHHHHHHH
Confidence            3589999999999999732 234444443    1223 444555666665543

>PRK07952 DNA replication protein DnaC; Validated

Probab=87.15  E-value=2.4  Score=34.99  Aligned_cols=46  Identities=11%  Similarity=0.045  Sum_probs=28.6

Q ss_pred             CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHH
Q psy12984        106 RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLV  157 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~  157 (178)
                      ..+++.+++|+|||.... .+...+..    .+.. +++++..+|...+...
T Consensus       100 ~~~~l~G~~GtGKThLa~-aia~~l~~----~g~~-v~~it~~~l~~~l~~~  145 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAA-AICNELLL----RGKS-VLIITVADIMSAMKDT  145 (244)
T ss_pred             ceEEEECCCCCCHHHHHH-HHHHHHHh----cCCe-EEEEEHHHHHHHHHHH
Confidence            478999999999997543 34444433    1223 4455667776655543

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=86.96  E-value=3.7  Score=40.97  Aligned_cols=75  Identities=19%  Similarity=0.092  Sum_probs=49.4

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHhhccccC-CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHH
Q psy12984         75 VCENTLKAIADMGFTKMTEIQARTIPPLLE-GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNG  153 (178)
Q Consensus        75 l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~-g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~q  153 (178)
                      +++..+.+....++ .+++-|..|+..+.. ++-+++++..|+|||...- .++..+..    .+..++.++||--=|..
T Consensus       367 v~~~~l~a~~~~~~-~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~l~-~~~~~~e~----~G~~V~g~ApTgkAA~~  440 (1102)
T PRK13826        367 VREAVLAATFARHA-RLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMMK-AAREAWEA----AGYRVVGGALAGKAAEG  440 (1102)
T ss_pred             CCHHHHHHHHhcCC-CCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHHH-HHHHHHHH----cCCeEEEEcCcHHHHHH
Confidence            44555555444455 789999999987754 5668899999999997543 23333322    34466778999655554


Q ss_pred             HH
Q psy12984        154 VY  155 (178)
Q Consensus       154 i~  155 (178)
                      +.
T Consensus       441 L~  442 (1102)
T PRK13826        441 LE  442 (1102)
T ss_pred             HH
Confidence            43

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=86.95  E-value=1.8  Score=44.64  Aligned_cols=61  Identities=26%  Similarity=0.235  Sum_probs=43.0

Q ss_pred             CCcHHHHHhhccccCC--CcEEEEccCCCchhhHh--HHHHHHHHHhccCCCCCceEEEeecHHHHHH
Q psy12984         90 KMTEIQARTIPPLLEG--RDLVGSAKTGSGKTLAF--LVPAVELIYNLKFMPRNGKSWQGKLRPLTNG  153 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g--~dvi~~a~TGsGKTlaf--~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~q  153 (178)
                      .+++-|..|+..++.+  +-+++++..|+|||...  ++-++..+..   ..+..++.++||--=|..
T Consensus       835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e---~~g~~V~glAPTgkAa~~  899 (1623)
T PRK14712        835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPE---SERPRVVGLGPTHRAVGE  899 (1623)
T ss_pred             ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHhh---ccCceEEEEechHHHHHH
Confidence            6899999999998855  77999999999999873  3344443322   233456678999544433

>PRK12377 putative replication protein; Provisional

Probab=86.94  E-value=2.3  Score=35.12  Aligned_cols=47  Identities=13%  Similarity=0.032  Sum_probs=29.4

Q ss_pred             CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHH
Q psy12984        105 GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLV  157 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~  157 (178)
                      ..++++.+++|+|||.... .+.+.+..    .+.. ++.++..+|..++...
T Consensus       101 ~~~l~l~G~~GtGKThLa~-AIa~~l~~----~g~~-v~~i~~~~l~~~l~~~  147 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAA-AIGNRLLA----KGRS-VIVVTVPDVMSRLHES  147 (248)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHH----cCCC-eEEEEHHHHHHHHHHH
Confidence            3689999999999996432 33344432    1223 4455667777777654

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=86.87  E-value=0.42  Score=40.54  Aligned_cols=21  Identities=33%  Similarity=0.488  Sum_probs=18.0

Q ss_pred             ccCCCcEEEEccCCCchhhHh
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      +..|.+++++++||||||...
T Consensus       141 v~~~~~ili~G~tGsGKTTll  161 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTTFL  161 (308)
T ss_pred             hhCCCEEEEECCCCCCHHHHH
Confidence            457899999999999999853

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.

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=86.73  E-value=1.2  Score=35.60  Aligned_cols=49  Identities=10%  Similarity=0.118  Sum_probs=28.7

Q ss_pred             CCCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhH
Q psy12984         61 EILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus        61 ~~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTla  121 (178)
                      +.....+|+++...-+..++..+...-.            ....+..+++.+++|+|||..
T Consensus        10 ~~~~~~~~d~f~~~~~~~~~~~l~~~~~------------~~~~~~~~~l~G~~G~GKT~L   58 (227)
T PRK08903         10 GPPPPPTFDNFVAGENAELVARLRELAA------------GPVADRFFYLWGEAGSGRSHL   58 (227)
T ss_pred             CCCChhhhcccccCCcHHHHHHHHHHHh------------ccCCCCeEEEECCCCCCHHHH
Confidence            3444456777643334455554444100            122456899999999999954

>PRK06526 transposase; Provisional

Probab=86.57  E-value=0.97  Score=37.43  Aligned_cols=21  Identities=24%  Similarity=0.241  Sum_probs=17.4

Q ss_pred             cCCCcEEEEccCCCchhhHhH
Q psy12984        103 LEGRDLVGSAKTGSGKTLAFL  123 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTlaf~  123 (178)
                      ..+.++++.+|+|+|||....
T Consensus        96 ~~~~nlll~Gp~GtGKThLa~  116 (254)
T PRK06526         96 TGKENVVFLGPPGTGKTHLAI  116 (254)
T ss_pred             hcCceEEEEeCCCCchHHHHH
Confidence            357899999999999996543

>PF05729 NACHT: NACHT domain

Probab=86.45  E-value=2  Score=31.64  Aligned_cols=24  Identities=25%  Similarity=0.254  Sum_probs=17.1

Q ss_pred             EEEEccCCCchhhHhHHHHHHHHHh
Q psy12984        108 LVGSAKTGSGKTLAFLVPAVELIYN  132 (178)
Q Consensus       108 vi~~a~TGsGKTlaf~lp~l~~l~~  132 (178)
                      +++.++.|+|||.... -++..+..
T Consensus         3 l~I~G~~G~GKStll~-~~~~~~~~   26 (166)
T PF05729_consen    3 LWISGEPGSGKSTLLR-KLAQQLAE   26 (166)
T ss_pred             EEEECCCCCChHHHHH-HHHHHHHh
Confidence            7899999999998543 44444444

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=86.41  E-value=1.2  Score=38.43  Aligned_cols=26  Identities=23%  Similarity=0.382  Sum_probs=19.1

Q ss_pred             CCCcEEEEccCCCchhhHhHHHHHHHH
Q psy12984        104 EGRDLVGSAKTGSGKTLAFLVPAVELI  130 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~lp~l~~l  130 (178)
                      .+..+++++|||||||... ..++..+
T Consensus       121 ~~g~ili~G~tGSGKTT~l-~al~~~i  146 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTL-ASMIDYI  146 (343)
T ss_pred             cCcEEEEECCCCCCHHHHH-HHHHHhh
Confidence            3567999999999999864 2345544

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.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=86.40  E-value=3  Score=34.92  Aligned_cols=20  Identities=30%  Similarity=0.373  Sum_probs=16.2

Q ss_pred             CCCcEEEEccCCCchhhHhH
Q psy12984        104 EGRDLVGSAKTGSGKTLAFL  123 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~  123 (178)
                      .++.+++++|||+|||....
T Consensus       193 ~~~vi~~vGptGvGKTTt~~  212 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLA  212 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHH
Confidence            35678899999999997643

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=86.24  E-value=2.8  Score=32.13  Aligned_cols=65  Identities=20%  Similarity=0.098  Sum_probs=32.5

Q ss_pred             hhcccc-CCCcEEEEccCCCchhhHhHHHHHHHHHhccC-----CCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984         98 TIPPLL-EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKF-----MPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus        98 aip~~l-~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~-----~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      .++-++ .|.=+++.|++|+|||..-+--+...+.....     ....+++|+..-- =..++.+.+..+..
T Consensus        24 li~g~~~~g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~-~~~~~~~rl~~~~~   94 (193)
T PF13481_consen   24 LIDGLLPRGELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLED-SESQIARRLRALLQ   94 (193)
T ss_dssp             EETTEE-TTSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHHHHT
T ss_pred             eECCcccCCeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccC-CHHHHHHHHHHHhc
Confidence            334444 57778999999999998644333333322111     1234556653221 14455555555443

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=86.00  E-value=0.66  Score=30.30  Aligned_cols=25  Identities=28%  Similarity=0.228  Sum_probs=18.3

Q ss_pred             hhccccCCCcEEEEccCCCchhhHh
Q psy12984         98 TIPPLLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus        98 aip~~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      .++.-..|..+++.+++|||||..+
T Consensus        16 ~~~~~~~g~~tli~G~nGsGKSTll   40 (62)
T PF13555_consen   16 TIDFDPRGDVTLITGPNGSGKSTLL   40 (62)
T ss_pred             EEeecCCCcEEEEECCCCCCHHHHH
Confidence            3443344667999999999999753

>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=85.97  E-value=1.5  Score=37.08  Aligned_cols=55  Identities=24%  Similarity=0.234  Sum_probs=37.1

Q ss_pred             ccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEE-------eecHHHHHHHHHHHHHHh
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQ-------GKLRPLTNGVYLVACNVF  162 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l-------~Ptr~La~qi~~~~~~l~  162 (178)
                      +..|.-+++.+|+|||||..  +-+|+++..    +..+.+.+       .|..+|-+.+..+++..+
T Consensus        24 I~~gef~vliGpSGsGKTTt--LkMINrLie----pt~G~I~i~g~~i~~~d~~~LRr~IGYviQqig   85 (309)
T COG1125          24 IEEGEFLVLIGPSGSGKTTT--LKMINRLIE----PTSGEILIDGEDISDLDPVELRRKIGYVIQQIG   85 (309)
T ss_pred             ecCCeEEEEECCCCCcHHHH--HHHHhcccC----CCCceEEECCeecccCCHHHHHHhhhhhhhhcc
Confidence            34677788899999999985  456666654    33333433       456778888877777644

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=85.86  E-value=2.4  Score=34.36  Aligned_cols=21  Identities=14%  Similarity=0.257  Sum_probs=17.4

Q ss_pred             ccCCCcEEEEccCCCchhhHh
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      +..|.-+++.+++|+|||...
T Consensus        21 i~~g~~~~i~G~~G~GKTtl~   41 (230)
T PRK08533         21 IPAGSLILIEGDESTGKSILS   41 (230)
T ss_pred             CCCCcEEEEECCCCCCHHHHH
Confidence            345788999999999999863

>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=85.83  E-value=0.53  Score=33.40  Aligned_cols=14  Identities=36%  Similarity=0.506  Sum_probs=12.4

Q ss_pred             EEEEccCCCchhhH
Q psy12984        108 LVGSAKTGSGKTLA  121 (178)
Q Consensus       108 vi~~a~TGsGKTla  121 (178)
                      +++.+++|||||..
T Consensus         2 I~I~G~~gsGKST~   15 (121)
T PF13207_consen    2 IIISGPPGSGKSTL   15 (121)
T ss_dssp             EEEEESTTSSHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            67899999999975

...

>PRK08084 DNA replication initiation factor; Provisional

Probab=85.74  E-value=1.5  Score=35.50  Aligned_cols=47  Identities=11%  Similarity=0.129  Sum_probs=28.1

Q ss_pred             CCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhH
Q psy12984         62 ILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus        62 ~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTla  121 (178)
                      .....+|+++-..-+...+.++...           +  ....+..+++.+|+|+|||-.
T Consensus        15 ~~~~~~fd~f~~~~n~~a~~~l~~~-----------~--~~~~~~~l~l~Gp~G~GKThL   61 (235)
T PRK08084         15 LPDDETFASFYPGDNDSLLAALQNA-----------L--RQEHSGYIYLWSREGAGRSHL   61 (235)
T ss_pred             CCCcCCccccccCccHHHHHHHHHH-----------H--hCCCCCeEEEECCCCCCHHHH
Confidence            4445568777533344444444332           1  112346789999999999954

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=85.40  E-value=0.5  Score=34.44  Aligned_cols=14  Identities=29%  Similarity=0.458  Sum_probs=12.4

Q ss_pred             EEEEccCCCchhhH
Q psy12984        108 LVGSAKTGSGKTLA  121 (178)
Q Consensus       108 vi~~a~TGsGKTla  121 (178)
                      +++++++|||||..
T Consensus         2 ii~~G~pgsGKSt~   15 (143)
T PF13671_consen    2 IILCGPPGSGKSTL   15 (143)
T ss_dssp             EEEEESTTSSHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            68899999999975

...

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=85.26  E-value=2  Score=34.80  Aligned_cols=34  Identities=18%  Similarity=0.168  Sum_probs=22.0

Q ss_pred             CCcHHHHHhhcccc----CCC-cEEEEccCCCchhhHhH
Q psy12984         90 KMTEIQARTIPPLL----EGR-DLVGSAKTGSGKTLAFL  123 (178)
Q Consensus        90 ~pt~iQ~~aip~~l----~g~-dvi~~a~TGsGKTlaf~  123 (178)
                      .+++.+..++..+.    .+. .+++.+++|+|||....
T Consensus        23 ~~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~   61 (269)
T TIGR03015        23 YPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIR   61 (269)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHH
Confidence            45555555554332    233 58899999999997643

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=85.04  E-value=0.76  Score=38.55  Aligned_cols=19  Identities=21%  Similarity=0.230  Sum_probs=16.2

Q ss_pred             CCCcEEEEccCCCchhhHh
Q psy12984        104 EGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf  122 (178)
                      .+.++++.+++|||||...
T Consensus        57 ~~~~vll~G~pGTGKT~lA   75 (284)
T TIGR02880        57 PTLHMSFTGNPGTGKTTVA   75 (284)
T ss_pred             CCceEEEEcCCCCCHHHHH
Confidence            4668999999999999754

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.

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=84.80  E-value=0.97  Score=44.61  Aligned_cols=79  Identities=20%  Similarity=0.065  Sum_probs=51.5

Q ss_pred             HHHHHhhcccc--------CCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984         93 EIQARTIPPLL--------EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus        93 ~iQ~~aip~~l--------~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      ..|-.|+..+.        .|--++--|.||+|||++=. -|+..|..  ...+.+..+..-+|.|..|..+.++.-++-
T Consensus       411 ~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aNA-RImyaLsd--~~~g~RfsiALGLRTLTLQTGda~r~rL~L  487 (1110)
T TIGR02562       411 RWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLANA-RAMYALRD--DKQGARFAIALGLRSLTLQTGHALKTRLNL  487 (1110)
T ss_pred             chHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHHH-HHHHHhCC--CCCCceEEEEccccceeccchHHHHHhcCC
Confidence            36666665543        24456778999999999843 12222221  134447777788999999999999987765


Q ss_pred             cCCCCcceEE
Q psy12984        165 TQPPTVIKVQ  174 (178)
Q Consensus       165 ~~~~~~~~v~  174 (178)
                      -.-.+.+.|+
T Consensus       488 ~~ddLAVlIG  497 (1110)
T TIGR02562       488 SDDDLAVLIG  497 (1110)
T ss_pred             CccceEEEEC
Confidence            5555444443

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

>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=84.58  E-value=0.66  Score=32.85  Aligned_cols=14  Identities=43%  Similarity=0.351  Sum_probs=12.4

Q ss_pred             EEEEccCCCchhhH
Q psy12984        108 LVGSAKTGSGKTLA  121 (178)
Q Consensus       108 vi~~a~TGsGKTla  121 (178)
                      |++.+.+|||||..
T Consensus         1 I~i~G~~GsGKtTi   14 (129)
T PF13238_consen    1 IGISGIPGSGKTTI   14 (129)
T ss_dssp             EEEEESTTSSHHHH
T ss_pred             CEEECCCCCCHHHH
Confidence            67899999999975

...

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=84.54  E-value=0.7  Score=32.85  Aligned_cols=15  Identities=27%  Similarity=0.348  Sum_probs=12.8

Q ss_pred             EEEEccCCCchhhHh
Q psy12984        108 LVGSAKTGSGKTLAF  122 (178)
Q Consensus       108 vi~~a~TGsGKTlaf  122 (178)
                      +++.+|+|+|||...
T Consensus         1 ill~G~~G~GKT~l~   15 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLA   15 (132)
T ss_dssp             EEEESSTTSSHHHHH
T ss_pred             CEEECcCCCCeeHHH
Confidence            578999999999853

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 ....

>KOG0924|consensus

Probab=84.19  E-value=3.2  Score=39.52  Aligned_cols=62  Identities=18%  Similarity=0.145  Sum_probs=34.4

Q ss_pred             cHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHH
Q psy12984         92 TEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLV  157 (178)
Q Consensus        92 t~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~  157 (178)
                      +..+..-+..+....-|++.+.||||||.-..    +.|+........-..+--|-|.-|.-+...
T Consensus       358 f~~R~~ll~~ir~n~vvvivgETGSGKTTQl~----QyL~edGY~~~GmIGcTQPRRvAAiSVAkr  419 (1042)
T KOG0924|consen  358 FACRDQLLSVIRENQVVVIVGETGSGKTTQLA----QYLYEDGYADNGMIGCTQPRRVAAISVAKR  419 (1042)
T ss_pred             HHHHHHHHHHHhhCcEEEEEecCCCCchhhhH----HHHHhcccccCCeeeecCchHHHHHHHHHH
Confidence            34444555556667788999999999997532    223332222211112223667766655443

>KOG1942|consensus

Probab=84.12  E-value=1.4  Score=38.12  Aligned_cols=27  Identities=22%  Similarity=0.394  Sum_probs=20.7

Q ss_pred             cCCCcEEEEccCCCchhhHhHHHHHHHH
Q psy12984        103 LEGRDLVGSAKTGSGKTLAFLVPAVELI  130 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTlaf~lp~l~~l  130 (178)
                      +.||-+++++|.|+|||... +.+-+-|
T Consensus        62 maGravLlaGppgtGKTAlA-laisqEL   88 (456)
T KOG1942|consen   62 MAGRAVLLAGPPGTGKTALA-LAISQEL   88 (456)
T ss_pred             ccCcEEEEecCCCCchhHHH-HHHHHHh
Confidence            57999999999999999754 3444433

>KOG1131|consensus

Probab=84.00  E-value=5.5  Score=36.87  Aligned_cols=74  Identities=11%  Similarity=0.064  Sum_probs=41.2

Q ss_pred             CCCCcHHHHHhhccc----cCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         88 FTKMTEIQARTIPPL----LEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        88 ~~~pt~iQ~~aip~~----l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      |..-+|-|..-+..+    -.+-+.++-.|+|+|||.+.+--++..-...+. .....+|-+.|-.-.......++++.
T Consensus        14 Y~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~-~~~KliYCSRTvpEieK~l~El~~l~   91 (755)
T KOG1131|consen   14 YDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPD-EHRKLIYCSRTVPEIEKALEELKRLM   91 (755)
T ss_pred             CcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCc-ccceEEEecCcchHHHHHHHHHHHHH
Confidence            455567776555433    245678889999999999977666654444322 22244444444333333333444443

>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=83.89  E-value=0.69  Score=33.82  Aligned_cols=15  Identities=27%  Similarity=0.344  Sum_probs=13.4

Q ss_pred             cEEEEccCCCchhhH
Q psy12984        107 DLVGSAKTGSGKTLA  121 (178)
Q Consensus       107 dvi~~a~TGsGKTla  121 (178)
                      +|++.+++|+|||..
T Consensus         1 ~vlL~G~~G~GKt~l   15 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTL   15 (139)
T ss_dssp             EEEEEESSSSSHHHH
T ss_pred             CEEEECCCCCCHHHH
Confidence            588999999999975

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.

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=83.63  E-value=2.9  Score=44.10  Aligned_cols=61  Identities=15%  Similarity=0.104  Sum_probs=42.6

Q ss_pred             CCcHHHHHhhccccCC--CcEEEEccCCCchhhHhH---HHHHHHHHhccCCCCCceEEEeecHHHHHHH
Q psy12984         90 KMTEIQARTIPPLLEG--RDLVGSAKTGSGKTLAFL---VPAVELIYNLKFMPRNGKSWQGKLRPLTNGV  154 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g--~dvi~~a~TGsGKTlaf~---lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi  154 (178)
                      .+++.|..|+..++.+  +-+++++..|+|||....   -++.+...    ..+..++.++||-.=|..+
T Consensus      1019 ~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~----~~g~~v~glApT~~Aa~~L 1084 (1960)
T TIGR02760      1019 RLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFE----SEQLQVIGLAPTHEAVGEL 1084 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHH----hcCCeEEEEeChHHHHHHH
Confidence            6899999999988765  567889999999997652   23333222    2344666789996655544

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>TIGR03689 pup_AAA proteasome ATPase

Probab=83.50  E-value=1.2  Score=40.68  Aligned_cols=54  Identities=13%  Similarity=0.198  Sum_probs=31.1

Q ss_pred             CccchHhhcccCCHHHHHHHHH--CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhH
Q psy12984         64 SSTQFEALKGKVCENTLKAIAD--MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus        64 ~~~~f~~l~~~l~~~ll~~l~~--~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTla  121 (178)
                      +..+|++++ ++++.+.+....  .-+.+|--+...-++.   .+.+++.+|+|+|||+.
T Consensus       177 p~v~~~dIg-Gl~~~i~~i~~~v~lp~~~~~l~~~~gl~~---p~GILLyGPPGTGKT~L  232 (512)
T TIGR03689       177 PDVTYADIG-GLDSQIEQIRDAVELPFLHPELYREYDLKP---PKGVLLYGPPGCGKTLI  232 (512)
T ss_pred             CCCCHHHcC-ChHHHHHHHHHHHHHHhhCHHHHHhccCCC---CcceEEECCCCCcHHHH
Confidence            345688876 355443322111  2333444444433332   46799999999999974

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=83.41  E-value=3.3  Score=32.96  Aligned_cols=18  Identities=39%  Similarity=0.475  Sum_probs=15.3

Q ss_pred             CCCcEEEEccCCCchhhH
Q psy12984        104 EGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTla  121 (178)
                      .|.-+++.+++|+|||..
T Consensus        15 ~g~~~li~G~~G~GKt~~   32 (224)
T TIGR03880        15 EGHVIVVIGEYGTGKTTF   32 (224)
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            467889999999999874

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.

>PLN03025 replication factor C subunit; Provisional

Probab=83.26  E-value=1.8  Score=36.59  Aligned_cols=45  Identities=18%  Similarity=0.240  Sum_probs=27.4

Q ss_pred             CCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhH
Q psy12984         62 ILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus        62 ~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTla  121 (178)
                      .+...+|+++-  -++.++..|...       ++.      -...++++.+|+|+|||..
T Consensus         6 kyrP~~l~~~~--g~~~~~~~L~~~-------~~~------~~~~~lll~Gp~G~GKTtl   50 (319)
T PLN03025          6 KYRPTKLDDIV--GNEDAVSRLQVI-------ARD------GNMPNLILSGPPGTGKTTS   50 (319)
T ss_pred             hcCCCCHHHhc--CcHHHHHHHHHH-------Hhc------CCCceEEEECCCCCCHHHH
Confidence            34456777774  455555555431       110      1124689999999999954

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=83.17  E-value=5.3  Score=39.42  Aligned_cols=16  Identities=38%  Similarity=0.411  Sum_probs=13.5

Q ss_pred             EEEEccCCCchhhHhH
Q psy12984        108 LVGSAKTGSGKTLAFL  123 (178)
Q Consensus       108 vi~~a~TGsGKTlaf~  123 (178)
                      ++|.++||+|||++--
T Consensus       784 LYIyG~PGTGKTATVK  799 (1164)
T PTZ00112        784 LYISGMPGTGKTATVY  799 (1164)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            4599999999999843

>TIGR03744 traC_PFL_4706 conjugative transfer ATPase, PFL_4706 family

Probab=83.12  E-value=3  Score=40.59  Aligned_cols=41  Identities=15%  Similarity=0.059  Sum_probs=27.0

Q ss_pred             CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHH
Q psy12984        105 GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRP  149 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~  149 (178)
                      ..|++|.++||||||.....=+.+.+..    .+.+++|+=|-++
T Consensus       475 n~n~~I~G~TGSGKS~l~~~li~q~~~~----~~~~v~IiD~g~s  515 (893)
T TIGR03744       475 NAHLLILGPTGAGKSATLTNLLMQVMAV----HRPRLFIVEAGNS  515 (893)
T ss_pred             cccEEEECCCCCCHHHHHHHHHHHHHHh----cCCEEEEEcCCCC
Confidence            3588999999999998755444443322    2346666766655

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.

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=83.03  E-value=1.1  Score=36.72  Aligned_cols=29  Identities=21%  Similarity=0.234  Sum_probs=20.7

Q ss_pred             ccCCCcEEEEccCCCchhhHhHHHHHHHHHh
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAFLVPAVELIYN  132 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~  132 (178)
                      +..|.-+.+.+|+|||||.  ++-+|..+.+
T Consensus        28 i~~Ge~vaI~GpSGSGKST--LLniig~ld~   56 (226)
T COG1136          28 IEAGEFVAIVGPSGSGKST--LLNLLGGLDK   56 (226)
T ss_pred             EcCCCEEEEECCCCCCHHH--HHHHHhcccC
Confidence            3568889999999999997  3344444443

>PRK00131 aroK shikimate kinase; Reviewed

Probab=82.95  E-value=0.97  Score=33.91  Aligned_cols=19  Identities=32%  Similarity=0.468  Sum_probs=16.4

Q ss_pred             cCCCcEEEEccCCCchhhH
Q psy12984        103 LEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTla  121 (178)
                      ..+..+++++++|||||..
T Consensus         2 ~~~~~i~l~G~~GsGKstl   20 (175)
T PRK00131          2 LKGPNIVLIGFMGAGKSTI   20 (175)
T ss_pred             CCCCeEEEEcCCCCCHHHH
Confidence            4577899999999999975

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

Probab=82.91  E-value=6.1  Score=38.38  Aligned_cols=28  Identities=25%  Similarity=0.273  Sum_probs=19.9

Q ss_pred             cccCCCcEEEEccCCCchhhHhHHHHHH
Q psy12984        101 PLLEGRDLVGSAKTGSGKTLAFLVPAVE  128 (178)
Q Consensus       101 ~~l~g~dvi~~a~TGsGKTlaf~lp~l~  128 (178)
                      ++.+..-++++++||||||...=.-+++
T Consensus        61 ai~~~~vvii~getGsGKTTqlP~~lle   88 (845)
T COG1643          61 AIEQNQVVIIVGETGSGKTTQLPQFLLE   88 (845)
T ss_pred             HHHhCCEEEEeCCCCCChHHHHHHHHHh
Confidence            3445566899999999999974444443

>PRK05642 DNA replication initiation factor; Validated

Probab=82.89  E-value=17  Score=29.45  Aligned_cols=16  Identities=19%  Similarity=0.144  Sum_probs=13.8

Q ss_pred             CcEEEEccCCCchhhH
Q psy12984        106 RDLVGSAKTGSGKTLA  121 (178)
Q Consensus       106 ~dvi~~a~TGsGKTla  121 (178)
                      ..+++.+++|+|||--
T Consensus        46 ~~l~l~G~~G~GKTHL   61 (234)
T PRK05642         46 SLIYLWGKDGVGRSHL   61 (234)
T ss_pred             CeEEEECCCCCCHHHH
Confidence            5688999999999964

>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=82.81  E-value=3.7  Score=32.58  Aligned_cols=15  Identities=33%  Similarity=0.403  Sum_probs=12.8

Q ss_pred             EEEEccCCCchhhHh
Q psy12984        108 LVGSAKTGSGKTLAF  122 (178)
Q Consensus       108 vi~~a~TGsGKTlaf  122 (178)
                      +++.+|||+|||.+-
T Consensus         4 i~lvGptGvGKTTt~   18 (196)
T PF00448_consen    4 IALVGPTGVGKTTTI   18 (196)
T ss_dssp             EEEEESTTSSHHHHH
T ss_pred             EEEECCCCCchHhHH
Confidence            577899999999863

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 ....

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=82.75  E-value=3  Score=37.68  Aligned_cols=54  Identities=19%  Similarity=0.113  Sum_probs=32.1

Q ss_pred             cCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984        103 LEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      ..|+-+++.+++|+|||...+--+.+.+.+    .+..++|++ .-|-..++...+..+
T Consensus        19 p~g~~~Li~G~pGsGKT~la~qfl~~g~~~----~ge~~lyvs-~eE~~~~l~~~~~~~   72 (484)
T TIGR02655        19 PIGRSTLVSGTSGTGKTLFSIQFLYNGIIH----FDEPGVFVT-FEESPQDIIKNARSF   72 (484)
T ss_pred             CCCeEEEEEcCCCCCHHHHHHHHHHHHHHh----CCCCEEEEE-EecCHHHHHHHHHHc
Confidence            357889999999999998654444444432    123556554 234444555554443

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.

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=82.66  E-value=0.87  Score=40.15  Aligned_cols=20  Identities=30%  Similarity=0.512  Sum_probs=15.1

Q ss_pred             cCCCcEEEEccCCCchhhHh
Q psy12984        103 LEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTlaf  122 (178)
                      +.|+-+|+.+|+|||||...
T Consensus        48 ~aGr~iLiaGppGtGKTAlA   67 (398)
T PF06068_consen   48 IAGRAILIAGPPGTGKTALA   67 (398)
T ss_dssp             -TT-EEEEEE-TTSSHHHHH
T ss_pred             ccCcEEEEeCCCCCCchHHH
Confidence            46899999999999999754

The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=82.64  E-value=1.7  Score=39.59  Aligned_cols=43  Identities=16%  Similarity=0.148  Sum_probs=27.8

Q ss_pred             HHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHh
Q psy12984         79 TLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus        79 ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      +...|.+.=+.+-.-| ..++-+++.|.+|++.+++|+|||...
T Consensus        14 l~~~l~~~i~gre~vI-~lll~aalag~hVLL~GpPGTGKT~LA   56 (498)
T PRK13531         14 LSSALEKGLYERSHAI-RLCLLAALSGESVFLLGPPGIAKSLIA   56 (498)
T ss_pred             HHHHHhhhccCcHHHH-HHHHHHHccCCCEEEECCCChhHHHHH
Confidence            3344444223333334 334446788999999999999999864

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=82.53  E-value=1.3  Score=36.70  Aligned_cols=24  Identities=29%  Similarity=0.357  Sum_probs=17.2

Q ss_pred             CcEEEEccCCCchhhHhHHHHHHHH
Q psy12984        106 RDLVGSAKTGSGKTLAFLVPAVELI  130 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~lp~l~~l  130 (178)
                      -.+++.|++|||||. |++-++..+
T Consensus        14 fr~viIG~sGSGKT~-li~~lL~~~   37 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTT-LIKSLLYYL   37 (241)
T ss_pred             ceEEEECCCCCCHHH-HHHHHHHhh
Confidence            368899999999997 344444433

This is thought to be an ATPase involved in viral DNA packaging [].

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=82.52  E-value=3.4  Score=43.10  Aligned_cols=64  Identities=22%  Similarity=0.148  Sum_probs=42.5

Q ss_pred             CCcHHHHHhhccccCC--CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHH
Q psy12984         90 KMTEIQARTIPPLLEG--RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGV  154 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g--~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi  154 (178)
                      .+++-|..|+..++.+  +-+++++..|+|||...- .++..+.......+..++.++||--=|..+
T Consensus       967 ~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l~-~v~~~~~~l~~~~~~~V~glAPTgrAAk~L 1032 (1747)
T PRK13709        967 GLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQFR-AVMSAVNTLPESERPRVVGLGPTHRAVGEM 1032 (1747)
T ss_pred             CCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHHH-HHHHHHHHhhcccCceEEEECCcHHHHHHH
Confidence            6899999999998875  578999999999997632 233322211112334566689996444433

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=82.52  E-value=2.8  Score=32.86  Aligned_cols=25  Identities=32%  Similarity=0.276  Sum_probs=18.8

Q ss_pred             CCCcEEEEccCCCchhhHhHHHHHH
Q psy12984        104 EGRDLVGSAKTGSGKTLAFLVPAVE  128 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~lp~l~  128 (178)
                      .|.=+.+.+++|+|||..-+.-+.+
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~~~~~~   35 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICMILAVN   35 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4677889999999999865444444

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

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=82.17  E-value=1  Score=39.73  Aligned_cols=20  Identities=30%  Similarity=0.484  Sum_probs=17.7

Q ss_pred             cCCCcEEEEccCCCchhhHh
Q psy12984        103 LEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTlaf  122 (178)
                      +.|+-+++.+|+|||||...
T Consensus        63 ~aGrgiLi~GppgTGKTAlA   82 (450)
T COG1224          63 MAGRGILIVGPPGTGKTALA   82 (450)
T ss_pred             ccccEEEEECCCCCcHHHHH
Confidence            57899999999999999754

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=82.03  E-value=0.77  Score=34.74  Aligned_cols=28  Identities=25%  Similarity=0.383  Sum_probs=15.0

Q ss_pred             CCCcEEEEccCCCchhhHhHHHHHHHHHh
Q psy12984        104 EGRDLVGSAKTGSGKTLAFLVPAVELIYN  132 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~lp~l~~l~~  132 (178)
                      .++.+++.+++|+|||..-. -++..+..
T Consensus        23 ~~~~~ll~G~~G~GKT~ll~-~~~~~~~~   50 (185)
T PF13191_consen   23 SPRNLLLTGESGSGKTSLLR-ALLDRLAE   50 (185)
T ss_dssp             ----EEE-B-TTSSHHHHHH-HHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHH-HHHHHHHh
Confidence            35789999999999997522 24444433

>PF03237 Terminase_6: Terminase-like family; InterPro: IPR004921 The terminase is a component of the molecular motor that translocates genomic DNA into empty capsids during DNA packaging []

Probab=82.02  E-value=5.7  Score=32.98  Aligned_cols=45  Identities=13%  Similarity=-0.021  Sum_probs=26.8

Q ss_pred             EEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHH-HHHHHHH
Q psy12984        109 VGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRP-LTNGVYL  156 (178)
Q Consensus       109 i~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~-La~qi~~  156 (178)
                      ++.++.|+|||...++-++.++...   +....+++++|.. |+..+..
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~---~~~~~vi~~~~~~~~~~~~~~   46 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTR---PPGRRVIIASTYRQARDIFGR   46 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSS---SS--EEEEEESSHHHHHHHHH
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhC---CCCcEEEEecCHHHHHHHHHH
Confidence            3567889999999988888887663   3224455557754 4544333

The large subunit heterodimerises with the small terminase protein, which is docked on the capsid portal protein. The latter forms a ring through which genomic DNA is translocated into the capsid. The terminase protein may have or induce an endonuclease activity to cleave DNA after encapsidation. This entry represents a family of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg2 (RCAP_rcc01683) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2O0K_A 3CPE_A 2O0J_A 2O0H_A 3C6H_A 3C6A_A.

>COG4185 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=81.75  E-value=0.78  Score=36.04  Aligned_cols=18  Identities=22%  Similarity=0.357  Sum_probs=14.5

Q ss_pred             EEEEccCCCchhhHhHHH
Q psy12984        108 LVGSAKTGSGKTLAFLVP  125 (178)
Q Consensus       108 vi~~a~TGsGKTlaf~lp  125 (178)
                      .|++++.|||||..|..-
T Consensus         5 ~IvaG~NGsGKstv~~~~   22 (187)
T COG4185           5 DIVAGPNGSGKSTVYAST   22 (187)
T ss_pred             EEEecCCCCCceeeeecc
Confidence            467899999999987643

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=81.71  E-value=2.1  Score=37.80  Aligned_cols=48  Identities=25%  Similarity=0.289  Sum_probs=36.0

Q ss_pred             CCCCCCcHHHHHhhccccCC--CcEEEEccCCCchhhHhHHHHHHHHHhc
Q psy12984         86 MGFTKMTEIQARTIPPLLEG--RDLVGSAKTGSGKTLAFLVPAVELIYNL  133 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g--~dvi~~a~TGsGKTlaf~lp~l~~l~~~  133 (178)
                      .|+..-.--|..|+.++++-  .=|...++.|||||+-.+-..+++....
T Consensus       224 wGi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~  273 (436)
T COG1875         224 WGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLER  273 (436)
T ss_pred             hccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHH
Confidence            47755566888999888865  2355678889999998888887776653

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=81.40  E-value=4.5  Score=32.42  Aligned_cols=51  Identities=6%  Similarity=-0.117  Sum_probs=28.5

Q ss_pred             CCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHH
Q psy12984        104 EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACN  160 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~  160 (178)
                      .|.-+++.+++|+|||.-.+.-+...+.+     +..++|+. +.+-..++...+..
T Consensus        24 ~g~~~~i~G~~GsGKt~l~~~~~~~~~~~-----g~~~~y~~-~e~~~~~~~~~~~~   74 (234)
T PRK06067         24 FPSLILIEGDHGTGKSVLSQQFVYGALKQ-----GKKVYVIT-TENTSKSYLKQMES   74 (234)
T ss_pred             CCcEEEEECCCCCChHHHHHHHHHHHHhC-----CCEEEEEE-cCCCHHHHHHHHHH
Confidence            46788999999999997544333333322     33444443 33333444444444

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=81.32  E-value=2.3  Score=35.63  Aligned_cols=16  Identities=44%  Similarity=0.532  Sum_probs=14.0

Q ss_pred             cEEEEccCCCchhhHh
Q psy12984        107 DLVGSAKTGSGKTLAF  122 (178)
Q Consensus       107 dvi~~a~TGsGKTlaf  122 (178)
                      ++++.+|+|+|||...
T Consensus        38 ~lll~Gp~GtGKT~la   53 (337)
T PRK12402         38 HLLVQGPPGSGKTAAV   53 (337)
T ss_pred             eEEEECCCCCCHHHHH
Confidence            7999999999999653

>KOG0989|consensus

Probab=80.96  E-value=3.3  Score=35.72  Aligned_cols=53  Identities=19%  Similarity=0.137  Sum_probs=33.3

Q ss_pred             CcCCCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHH
Q psy12984         59 ALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPA  126 (178)
Q Consensus        59 ~~~~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~  126 (178)
                      ....|...+|+++-  -.+.+.+.|...       ++.      ..+-+.+..+|.|+|||-+.++-.
T Consensus        26 wteKYrPkt~de~~--gQe~vV~~L~~a-------~~~------~~lp~~LFyGPpGTGKTStalafa   78 (346)
T KOG0989|consen   26 WTEKYRPKTFDELA--GQEHVVQVLKNA-------LLR------RILPHYLFYGPPGTGKTSTALAFA   78 (346)
T ss_pred             hHHHhCCCcHHhhc--chHHHHHHHHHH-------Hhh------cCCceEEeeCCCCCcHhHHHHHHH
Confidence            34556667788874  444555555441       221      234577889999999998765433

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=80.94  E-value=1.2  Score=34.58  Aligned_cols=18  Identities=28%  Similarity=0.342  Sum_probs=15.5

Q ss_pred             CCcEEEEccCCCchhhHh
Q psy12984        105 GRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf  122 (178)
                      |..+++.+|+|+|||...
T Consensus         2 g~~i~l~G~sGsGKsTl~   19 (186)
T PRK10078          2 GKLIWLMGPSGSGKDSLL   19 (186)
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            667899999999999854

>CHL00181 cbbX CbbX; Provisional

Probab=80.74  E-value=1.5  Score=36.88  Aligned_cols=20  Identities=30%  Similarity=0.401  Sum_probs=16.7

Q ss_pred             CCCcEEEEccCCCchhhHhH
Q psy12984        104 EGRDLVGSAKTGSGKTLAFL  123 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~  123 (178)
                      .|.++++.+++|+|||....
T Consensus        58 ~~~~ill~G~pGtGKT~lAr   77 (287)
T CHL00181         58 PGLHMSFTGSPGTGKTTVAL   77 (287)
T ss_pred             CCceEEEECCCCCCHHHHHH
Confidence            46789999999999997643

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=80.64  E-value=3.5  Score=29.92  Aligned_cols=16  Identities=44%  Similarity=0.443  Sum_probs=13.4

Q ss_pred             EEEEccCCCchhhHhH
Q psy12984        108 LVGSAKTGSGKTLAFL  123 (178)
Q Consensus       108 vi~~a~TGsGKTlaf~  123 (178)
                      +++.+++|+|||....
T Consensus         2 ~~i~G~~G~GKT~l~~   17 (165)
T cd01120           2 ILVFGPTGSGKTTLAL   17 (165)
T ss_pred             eeEeCCCCCCHHHHHH
Confidence            6789999999998544

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.

>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional

Probab=80.57  E-value=1.1  Score=38.15  Aligned_cols=16  Identities=19%  Similarity=0.063  Sum_probs=13.4

Q ss_pred             CcEEEEccCCCchhhH
Q psy12984        106 RDLVGSAKTGSGKTLA  121 (178)
Q Consensus       106 ~dvi~~a~TGsGKTla  121 (178)
                      +=+++.+|||||||..
T Consensus         5 ~ii~I~GpTasGKS~L   20 (300)
T PRK14729          5 KIVFIFGPTAVGKSNI   20 (300)
T ss_pred             cEEEEECCCccCHHHH
Confidence            3478999999999974

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=80.55  E-value=1.9  Score=38.64  Aligned_cols=19  Identities=26%  Similarity=0.356  Sum_probs=16.3

Q ss_pred             CCCcEEEEccCCCchhhHh
Q psy12984        104 EGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf  122 (178)
                      .++.+++.+|+|+|||+..
T Consensus       216 ~p~gVLL~GPPGTGKT~LA  234 (438)
T PTZ00361        216 PPKGVILYGPPGTGKTLLA  234 (438)
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4578999999999999864

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=80.35  E-value=1.5  Score=39.64  Aligned_cols=28  Identities=18%  Similarity=0.258  Sum_probs=21.9

Q ss_pred             HHhhccccCCCcEEEEccCCCchhhHhH
Q psy12984         96 ARTIPPLLEGRDLVGSAKTGSGKTLAFL  123 (178)
Q Consensus        96 ~~aip~~l~g~dvi~~a~TGsGKTlaf~  123 (178)
                      ...+..+..++++++.+++|+|||....
T Consensus       185 e~l~~~L~~~~~iil~GppGtGKT~lA~  212 (459)
T PRK11331        185 ETILKRLTIKKNIILQGPPGVGKTFVAR  212 (459)
T ss_pred             HHHHHHHhcCCCEEEECCCCCCHHHHHH
Confidence            3445556679999999999999996543

>PHA02244 ATPase-like protein

Probab=80.33  E-value=1.8  Score=38.17  Aligned_cols=21  Identities=19%  Similarity=0.121  Sum_probs=17.8

Q ss_pred             cccCCCcEEEEccCCCchhhH
Q psy12984        101 PLLEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       101 ~~l~g~dvi~~a~TGsGKTla  121 (178)
                      .+..+.+|++.+|||+|||..
T Consensus       115 ~l~~~~PVLL~GppGtGKTtL  135 (383)
T PHA02244        115 IVNANIPVFLKGGAGSGKNHI  135 (383)
T ss_pred             HHhcCCCEEEECCCCCCHHHH
Confidence            345788999999999999954

>KOG0060|consensus

Probab=80.32  E-value=1.2  Score=41.34  Aligned_cols=21  Identities=29%  Similarity=0.507  Sum_probs=18.5

Q ss_pred             ccCCCcEEEEccCCCchhhHh
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      +-+|.+++|++|+|+|||--|
T Consensus       458 V~~g~~LLItG~sG~GKtSLl  478 (659)
T KOG0060|consen  458 VPSGQNLLITGPSGCGKTSLL  478 (659)
T ss_pred             ecCCCeEEEECCCCCchhHHH
Confidence            567999999999999999754

>PRK14530 adenylate kinase; Provisional

Probab=80.11  E-value=1.2  Score=35.41  Aligned_cols=18  Identities=17%  Similarity=0.209  Sum_probs=15.4

Q ss_pred             CCCcEEEEccCCCchhhH
Q psy12984        104 EGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTla  121 (178)
                      .|..+++.+++|||||..
T Consensus         2 ~~~~I~i~G~pGsGKsT~   19 (215)
T PRK14530          2 SQPRILLLGAPGAGKGTQ   19 (215)
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            467899999999999964

>PLN02165 adenylate isopentenyltransferase

Probab=80.10  E-value=1.2  Score=38.63  Aligned_cols=21  Identities=29%  Similarity=0.275  Sum_probs=16.8

Q ss_pred             cCCCcEEEEccCCCchhhHhH
Q psy12984        103 LEGRDLVGSAKTGSGKTLAFL  123 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTlaf~  123 (178)
                      ..|.-+++.+|||||||....
T Consensus        41 ~~g~iivIiGPTGSGKStLA~   61 (334)
T PLN02165         41 CKDKVVVIMGATGSGKSRLSV   61 (334)
T ss_pred             CCCCEEEEECCCCCcHHHHHH
Confidence            346678999999999997643

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=80.10  E-value=2  Score=38.02  Aligned_cols=18  Identities=28%  Similarity=0.409  Sum_probs=15.9

Q ss_pred             CCCcEEEEccCCCchhhH
Q psy12984        104 EGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTla  121 (178)
                      .++.+++.+|+|+|||+.
T Consensus       178 ~pkgvLL~GppGTGKT~L  195 (398)
T PTZ00454        178 PPRGVLLYGPPGTGKTML  195 (398)
T ss_pred             CCceEEEECCCCCCHHHH
Confidence            467899999999999986

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	178
3ly5_A	262	Ddx18 Dead-Domain Length = 262		6e-27
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		4e-12
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		4e-10
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		3e-09
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		4e-09
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		4e-09
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		4e-09
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		4e-09
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		8e-09
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		6e-08
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		7e-08
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		2e-07
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		2e-07
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		5e-07
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		7e-07
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		1e-06
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		1e-06
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		2e-06
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		2e-06
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		3e-06
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		3e-06
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		3e-06
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		5e-06
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		6e-06
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-05
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-05
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		3e-05
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		3e-05
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		3e-05
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		3e-05
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		3e-05
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		3e-05
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		4e-05
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		8e-05
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		8e-05
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		9e-05
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		1e-04

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score =  116 bits (291), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 60/103 (58%), Positives = 74/103 (71%), Gaps = 6/103 (5%)
Query: 38  DANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQAR 97
           D +EDE +  ++ + L G+         T F +L   V ENTLKAI +MGFT MTEIQ +
Sbjct: 30  DNDEDESEVPSLPLGLTGA------FEDTSFASLCNLVNENTLKAIKEMGFTNMTEIQHK 83
Query: 98  TIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
           +I PLLEGRDL+ +AKTGSGKTLAFL+PAVELI  L+FMPRNG
Sbjct: 84  SIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNG 126

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score = 67.4 bits (163), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 31/66 (46%), Positives = 48/66 (72%)
Query: 75  VCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLK 134
           + + TLK + +  +  +TEIQ +TI   L+G+D++G+AKTGSGKTLAFLVP +E +Y L+
Sbjct: 32  LSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQ 91
Query: 135 FMPRNG 140
           +   +G
Sbjct: 92  WTSTDG 97

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 60.8 bits (146), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 40/53 (75%)
Query: 77  ENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVEL 129
           E   +AI +MGF   TE+Q++TIP +L+G+++V  AKTGSGKT A+ +P +EL
Sbjct: 3   EKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL 55

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 58.2 bits (139), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 36/105 (34%), Positives = 58/105 (55%), Gaps = 10/105 (9%)
Query: 39  ANEDEDQ------TNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMT 92
           + ED+D+      T +  + +P  D + E+   +  E  +G + +   KAI  M F  +T
Sbjct: 39  SREDDDEVHFDKTTFSKLIHVPKEDNSKEVTLDSLLE--EGVLDKEIHKAITRMEFPGLT 96
Query: 93  EIQARTIPPLL--EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKF 135
            +Q +TI P+L  E  D++  AKTG+GKT AFL+P  + + N KF
Sbjct: 97  PVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKF 141

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 57.4 bits (137), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 32/79 (40%), Positives = 47/79 (59%), Gaps = 1/79 (1%)
Query: 47  NAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGR 106
           N  ++ + G+D+   I +  Q +  + K+    L+ I D GF   T IQ + IP +L GR
Sbjct: 9   NKHKIHVQGTDLPDPIATFQQLDQ-EYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGR 67
Query: 107 DLVGSAKTGSGKTLAFLVP 125
           +L+ SA TGSGKTLAF +P
Sbjct: 68  ELLASAPTGSGKTLAFSIP 86

>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion) Bound To Ssrna And Amp-Pnp Length = 512

Iteration: 1
 Score = 57.4 bits (137), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 32/87 (36%), Positives = 50/87 (57%), Gaps = 4/87 (4%)
Query: 51  VQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLL--EGRDL 108
           + +P  D + E+   +  E  +G + +   KAI  M F  +T +Q +TI P+L  E  D+
Sbjct: 6   IHVPKEDNSKEVTLDSLLE--EGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDV 63
Query: 109 VGSAKTGSGKTLAFLVPAVELIYNLKF 135
           +  AKTG+GKT AFL+P  + + N KF
Sbjct: 64  IARAKTGTGKTFAFLIPIFQHLINTKF 90

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 57.4 bits (137), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 29/61 (47%), Positives = 40/61 (65%)
Query: 78  NTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMP 137
           N +  IA   FT+ T IQA+  P  L G D+VG A+TGSGKTL++L+PA+  I +  F+ 
Sbjct: 39  NVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLE 98
Query: 138 R 138
           R
Sbjct: 99  R 99

>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human Dead-Box Rna Helicase Ddx5 (P68) Length = 253

Iteration: 1
 Score = 57.4 bits (137), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 29/61 (47%), Positives = 40/61 (65%)
Query: 78  NTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMP 137
           N +  IA   FT+ T IQA+  P  L G D+VG A+TGSGKTL++L+PA+  I +  F+ 
Sbjct: 53  NVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLE 112
Query: 138 R 138
           R
Sbjct: 113 R 113

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 56.6 bits (135), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 32/87 (36%), Positives = 50/87 (57%), Gaps = 4/87 (4%)
Query: 51  VQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLL--EGRDL 108
           + +P  D + E+   +  E  +G + +   KAI  M F  +T +Q +TI P+L  E  D+
Sbjct: 6   IHVPKEDNSKEVTLDSLLE--EGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDV 63
Query: 109 VGSAKTGSGKTLAFLVPAVELIYNLKF 135
           +  AKTG+GKT AFL+P  + + N KF
Sbjct: 64  IARAKTGTGKTFAFLIPIFQHLINTKF 90

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score = 53.5 bits (127), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 26/49 (53%), Positives = 34/49 (69%)
Query: 80  LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVE 128
           L+A+   G T  T IQA  +P  LEG+DL+G A+TG+GKTLAF +P  E
Sbjct: 13  LEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAE 61

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 53.1 bits (126), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 42/70 (60%), Gaps = 6/70 (8%)
Query: 88  FTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYN------LKFMPRNGK 141
           +T+ T +Q   IP + E RDL+  A+TGSGKT AFL+P +  IY+      L+ M  NG+
Sbjct: 35  YTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGR 94
Query: 142 SWQGKLRPLT 151
             + K  P++
Sbjct: 95  YGRRKQYPIS 104

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/49 (51%), Positives = 34/49 (69%)
Query: 80  LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVE 128
           L+A+   G T  T I+A  +P  LEG+DL+G A+TG+GKTLAF +P  E
Sbjct: 13  LEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAE 61

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 38/57 (66%), Gaps = 1/57 (1%)
Query: 75  VCENTLKAIADMGFTKMTEIQARTIPPLL-EGRDLVGSAKTGSGKTLAFLVPAVELI 130
           + +N L AI + GF K T+IQ + IP  L +  ++V  A+TGSGKT +F +P +EL+
Sbjct: 13  LSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELV 69

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score = 50.4 bits (119), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 26/51 (50%), Positives = 35/51 (68%), Gaps = 4/51 (7%)
Query: 75  VCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVP 125
           +CE    A   +G+TK T+IQ   IP  L+GRD++G A+TGSGKT AF +P
Sbjct: 54  LCE----ACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALP 100

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score = 50.1 bits (118), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 25/51 (49%), Positives = 33/51 (64%)
Query: 80  LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
           ++AI  + F K TEIQ R IP  L G   VG ++TG+GKT A+L+P  E I
Sbjct: 16  IEAIKTLRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLPIXEKI 66

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 32/81 (39%), Positives = 47/81 (58%), Gaps = 5/81 (6%)
Query: 45  QTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLE 104
           + N + V++ GSDV   I   T  + L+  + +N  K+    G+   T IQ  +IP +  
Sbjct: 38  KYNNIPVKVTGSDVPQPIQHFTSAD-LRDIIIDNVNKS----GYKIPTPIQKCSIPVISS 92
Query: 105 GRDLVGSAKTGSGKTLAFLVP 125
           GRDL+  A+TGSGKT AFL+P
Sbjct: 93  GRDLMACAQTGSGKTAAFLLP 113

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 30/98 (30%), Positives = 50/98 (51%), Gaps = 15/98 (15%)
Query: 33  AEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMT 92
           +E  +D  E + QTN  +V     D+ L+               EN L+ +   GF + +
Sbjct: 2   SEGITDIEESQIQTNYDKVVYKFDDMELD---------------ENLLRGVFGYGFEEPS 46
Query: 93  EIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
            IQ R I P++EG D++  A++G+GKT  F + A++ I
Sbjct: 47  AIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRI 84

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 30/98 (30%), Positives = 49/98 (50%), Gaps = 15/98 (15%)
Query: 33  AEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMT 92
           +E  +D  E + QTN  +V     D  L+               EN L+ +   GF + +
Sbjct: 1   SEGITDIEESQIQTNYDKVVYKFDDXELD---------------ENLLRGVFGYGFEEPS 45
Query: 93  EIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
            IQ R I P++EG D++  A++G+GKT  F + A++ I
Sbjct: 46  AIQQRAIXPIIEGHDVLAQAQSGTGKTGTFSIAALQRI 83

>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of Djvlgb, A Pranarian Vasa-Like Rna Helicase Length = 253

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 29/85 (34%), Positives = 46/85 (54%), Gaps = 5/85 (5%)
Query: 44  DQTNAVEVQLPGSDV-ALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPL 102
           D+ +++ V + G D  A  ++ +     L   +  N L A     + + T IQ   IP +
Sbjct: 2   DKYDSIPVSVTGPDYSATNVIENFDELKLDPTIRNNILLA----SYQRPTPIQKNAIPAI 57
Query: 103 LEGRDLVGSAKTGSGKTLAFLVPAV 127
           LE RD++  A+TGSGKT AFL+P +
Sbjct: 58  LEHRDIMACAQTGSGKTAAFLIPII 82

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/49 (44%), Positives = 31/49 (63%)
Query: 80  LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVE 128
           L  I + GF K + IQ   IP  + GRD++  AK G+GKT AF++P +E
Sbjct: 33  LMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLE 81

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/49 (44%), Positives = 33/49 (67%)
Query: 80  LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVE 128
           L  I +MG+ K + IQ  +IP  L GRD++  AK G+GK+ A+L+P +E
Sbjct: 15  LMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLE 63

>pdb|1QDE|A Chain A, Crystal Structure Of The Atpase Domain Of Translation Initiation Factor 4a From Saccharomyces Cerevisiae-The Prototype Of The Dead Box Protein Family Length = 224

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 21/54 (38%), Positives = 35/54 (64%)
Query: 77  ENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
           EN L+ +   GF + + IQ R I P++EG D++  A++G+GKT  F + A++ I
Sbjct: 23  ENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRI 76

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score = 47.0 bits (110), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 22/49 (44%), Positives = 35/49 (71%)
Query: 78  NTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPA 126
           + LK+I  +G  K T IQ++  P +L+G DL+  A+TG+GKTL++L+P 
Sbjct: 30  DLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPG 78

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score = 47.0 bits (110), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 29/98 (29%), Positives = 49/98 (50%), Gaps = 15/98 (15%)
Query: 33  AEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMT 92
           +E  +D  E + QTN  +V     D+ L+               E  L+ +   GF + +
Sbjct: 1   SEGITDIEESQIQTNYQKVVYKFDDMELD---------------EQLLRGVFGYGFEEPS 45
Query: 93  EIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
            IQ R I P++EG D++  A++G+GKT  F + A++ I
Sbjct: 46  AIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRI 83

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 34/54 (62%)
Query: 77  ENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
           E+ L+ I   GF K + IQ R I  +++GRD++  +++G+GKT  F V  ++ +
Sbjct: 10  EDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCL 63

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 34/54 (62%)
Query: 77  ENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
           E+ L+ I   GF K + IQ R I  +++GRD++  +++G+GKT  F V  ++ +
Sbjct: 10  EDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCL 63

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 34/56 (60%)
Query: 75  VCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
           + E+ L+ I   GF K + IQ R I P ++G D++  A++G+GKT  F +  ++ I
Sbjct: 47  LSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQI 102

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 34/56 (60%)
Query: 75  VCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
           + E+ L+ I   GF K + IQ R I P ++G D++  A++G+GKT  F +  ++ I
Sbjct: 21  LSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQI 76

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 34/54 (62%)
Query: 77  ENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
           E+ L+ I   GF K + IQ R I  +++GRD++  +++G+GKT  F +  ++ +
Sbjct: 25  EDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCL 78

>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 413

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 34/54 (62%)
Query: 77  ENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
           E+ L+ I   GF K + IQ R I  +++GRD++  +++G+GKT  F +  ++ +
Sbjct: 47  EDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCL 100

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 34/54 (62%)
Query: 77  ENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
           E+ L+ I   GF K + IQ R I  +++GRD++  +++G+GKT  F +  ++ +
Sbjct: 46  EDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCL 99

>pdb|2XB2|A Chain A, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 411

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 34/54 (62%)
Query: 77  ENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
           E+ L+ I   GF K + IQ R I  +++GRD++  +++G+GKT  F +  ++ +
Sbjct: 47  EDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCL 100

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 19/52 (36%), Positives = 32/52 (61%)
Query: 77  ENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVE 128
           E+ L+ I   GF K + IQ R I P ++G D++  A++G+GKT  F +  ++
Sbjct: 39  ESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQ 90

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score = 43.1 bits (100), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 30/49 (61%)
Query: 80  LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVE 128
           L+AI D GF   +E+Q   IP  + G D++  AK+G GKT  F++  ++
Sbjct: 26  LRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 74

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 43.1 bits (100), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 30/49 (61%)
Query: 80  LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVE 128
           L+AI D GF   +E+Q   IP  + G D++  AK+G GKT  F++  ++
Sbjct: 20  LRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 68

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 43.1 bits (100), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 30/49 (61%)
Query: 80  LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVE 128
           L+AI D GF   +E+Q   IP  + G D++  AK+G GKT  F++  ++
Sbjct: 20  LRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 68

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 30/49 (61%)
Query: 80  LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVE 128
           L+AI D GF   +E+Q   IP  + G D++  AK+G GKT  F++  ++
Sbjct: 19  LRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 67

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	178
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	3e-39
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	7e-36
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	5e-34
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	3e-33
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	5e-24
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	2e-22
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	2e-21
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	4e-21
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	4e-21
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	1e-20
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	1e-20
3bor_A	237	Human initiation factor 4A-II; translation initiat	2e-20
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	2e-20
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	3e-20
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	4e-20
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	4e-20
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	5e-20
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-19
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	1e-19
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	1e-19
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	4e-19
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	1e-18
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	1e-18
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	2e-18
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	4e-18
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	5e-18
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	8e-18
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	1e-17
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	2e-17
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	2e-17
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	6e-12
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-06
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	1e-04

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens} Length = 262

 Score =  133 bits (336), Expect = 3e-39
 Identities = 62/124 (50%), Positives = 78/124 (62%), Gaps = 6/124 (4%)

Query: 17  EKKKLKILQSKEKSKPAEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVC 76
               L       +S    +  D +EDE +  ++ + L G+         T F +L   V 
Sbjct: 9   SGVDLGTENLYFQSMNNVEKPDNDEDESEVPSLPLGLTGAF------EDTSFASLCNLVN 62

Query: 77  ENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFM 136
           ENTLKAI +MGFT MTEIQ ++I PLLEGRDL+ +AKTGSGKTLAFL+PAVELI  L+FM
Sbjct: 63  ENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFM 122

Query: 137 PRNG 140
           PRNG
Sbjct: 123 PRNG 126

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* Length = 563

 Score =  129 bits (327), Expect = 7e-36
 Identities = 36/142 (25%), Positives = 63/142 (44%), Gaps = 4/142 (2%)

Query: 1   MSKDTEKHLMNKITKREKKKLKILQSKEKSKPAEKDSDANEDEDQTNAVEVQLPGSDVAL 60
            ++D      N+      +      +      + +D D    +  T +  + +P  D + 
Sbjct: 7   GNRDQRNFGRNQRNNNSNRYRNSRFNSRPRTRSREDDDEVHFDKTTFSKLIHVPKEDNSK 66

Query: 61  EILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLL--EGRDLVGSAKTGSGK 118
           E+   +  E     + +   KAI  M F  +T +Q +TI P+L  E  D++  AKTG+GK
Sbjct: 67  EVTLDSLLEEGV--LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGK 124

Query: 119 TLAFLVPAVELIYNLKFMPRNG 140
           T AFL+P  + + N KF  +  
Sbjct: 125 TFAFLIPIFQHLINTKFDSQYM 146

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens} Length = 236

 Score =  119 bits (300), Expect = 5e-34
 Identities = 36/104 (34%), Positives = 60/104 (57%), Gaps = 7/104 (6%)

Query: 37  SDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQA 96
           S   E E  +  ++     +   + +   T+F      + + TLK + +  +  +TEIQ 
Sbjct: 1   SMQVERESISRLMQ-----NYEKINVNEITRFSDFP--LSKKTLKGLQEAQYRLVTEIQK 53

Query: 97  RTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
           +TI   L+G+D++G+AKTGSGKTLAFLVP +E +Y L++   +G
Sbjct: 54  QTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDG 97

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C} Length = 579

 Score =  123 bits (309), Expect = 3e-33
 Identities = 31/96 (32%), Positives = 51/96 (53%), Gaps = 4/96 (4%)

Query: 47  NAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLL--E 104
           ++  + +P  D + E+   +  E     + +   KAI  M F  +T +Q +TI P+L  E
Sbjct: 2   SSKLIHVPKEDNSKEVTLDSLLEEGV--LDKEIHKAITRMEFPGLTPVQQKTIKPILSSE 59

Query: 105 GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNG 140
             D++  AKTG+GKT AFL+P  + + N KF  +  
Sbjct: 60  DHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYM 95

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score = 92.6 bits (231), Expect = 5e-24
 Identities = 28/67 (41%), Positives = 39/67 (58%), Gaps = 2/67 (2%)

Query: 64  SSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFL 123
           + TQF           ++AI  + F K TEIQ R IP  L G  +VG ++TG+GKT A+L
Sbjct: 2   AETQFTRFP--FQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYL 59

Query: 124 VPAVELI 130
           +P +E I
Sbjct: 60  LPIMEKI 66

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens} Length = 249

 Score = 89.3 bits (222), Expect = 2e-22
 Identities = 30/114 (26%), Positives = 48/114 (42%), Gaps = 4/114 (3%)

Query: 25  QSKEKSKPAEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIA 84
                S       +      + +    +     V  E   +  F+ L   V +   +A  
Sbjct: 4   HHHHSSGVDLGTENLYFQSMEEHDSPTEASQPIVEEEETKT--FKDLG--VTDVLCEACD 59

Query: 85  DMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPR 138
            +G+TK T+IQ   IP  L+GRD++G A+TGSGKT AF +P +  +        
Sbjct: 60  QLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLF 113

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19 Length = 206

 Score = 85.7 bits (213), Expect = 2e-21
 Identities = 24/65 (36%), Positives = 38/65 (58%), Gaps = 2/65 (3%)

Query: 66  TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVP 125
            +FE     +    L  I +MG+ K + IQ  +IP  L GRD++  AK G+GK+ A+L+P
Sbjct: 3   NEFEDYC--LKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIP 60

Query: 126 AVELI 130
            +E +
Sbjct: 61  LLERL 65

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A Length = 410

 Score = 88.0 bits (219), Expect = 4e-21
 Identities = 21/101 (20%), Positives = 50/101 (49%), Gaps = 9/101 (8%)

Query: 30  SKPAEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFT 89
           +  + +     E++      E     +   +++  +  F+ +   + E+ L+ I   GF 
Sbjct: 8   TSGSARKRLLKEEDMTKVEFE-----TSEEVDVTPT--FDTMG--LREDLLRGIYAYGFE 58

Query: 90  KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
           K + IQ R I  +++GRD++  +++G+GKT  F +  ++ +
Sbjct: 59  KPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCL 99

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens} Length = 414

 Score = 87.6 bits (218), Expect = 4e-21
 Identities = 26/106 (24%), Positives = 46/106 (43%), Gaps = 15/106 (14%)

Query: 25  QSKEKSKPAEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIA 84
               +S+    D    E   ++N  E+                F+ +     E+ L+ I 
Sbjct: 12  SQDSRSRDNGPDGMEPEGVIESNWNEI-------------VDSFDDMNLS--ESLLRGIY 56

Query: 85  DMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
             GF K + IQ R I P ++G D++  A++G+GKT  F +  ++ I
Sbjct: 57  AYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQI 102

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A* Length = 230

 Score = 84.2 bits (209), Expect = 1e-20
 Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 2/67 (2%)

Query: 64  SSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFL 123
               FE+L        L+ +   GF + + +Q + IP    G DL+  AK+G+GKT  F 
Sbjct: 22  EPADFESLLLS--RPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFS 79

Query: 124 VPAVELI 130
             A++ +
Sbjct: 80  TIALDSL 86

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A Length = 400

 Score = 86.1 bits (214), Expect = 1e-20
 Identities = 25/66 (37%), Positives = 35/66 (53%), Gaps = 2/66 (3%)

Query: 65  STQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLV 124
              FE    K     L  I + GF K + IQ   IP  + GRD++  AK G+GKT AF++
Sbjct: 20  GNTFEDFYLK--RELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVI 77

Query: 125 PAVELI 130
           P +E +
Sbjct: 78  PTLEKV 83

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A* Length = 237

 Score = 83.8 bits (208), Expect = 2e-20
 Identities = 23/107 (21%), Positives = 45/107 (42%), Gaps = 15/107 (14%)

Query: 24  LQSKEKSKPAEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAI 83
           +          ++        ++N  E+                F+ +  K  E+ L+ I
Sbjct: 1   MHHHHHHSSGRENLYFQGGVIESNWNEI-------------VDNFDDMNLK--ESLLRGI 45

Query: 84  ADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
              GF K + IQ R I P ++G D++  A++G+GKT  F +  ++ +
Sbjct: 46  YAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQL 92

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A* Length = 394

 Score = 86.0 bits (214), Expect = 2e-20
 Identities = 29/98 (29%), Positives = 51/98 (52%), Gaps = 15/98 (15%)

Query: 33  AEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMT 92
           +E  +D  E + QTN  +V               +F+ ++    EN L+ +   GF + +
Sbjct: 1   SEGITDIEESQIQTNYDKV-------------VYKFDDMELD--ENLLRGVFGYGFEEPS 45

Query: 93  EIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
            IQ R I P++EG D++  A++G+GKT  F + A++ I
Sbjct: 46  AIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRI 83

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A Length = 207

 Score = 82.6 bits (205), Expect = 3e-20
 Identities = 27/63 (42%), Positives = 38/63 (60%), Gaps = 2/63 (3%)

Query: 68  FEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAV 127
           F+     +    L+A+   G T  T IQA  +P  LEG+DL+G A+TG+GKTLAF +P  
Sbjct: 3   FKDFP--LKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIA 60

Query: 128 ELI 130
           E +
Sbjct: 61  ERL 63

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens} Length = 245

 Score = 83.0 bits (206), Expect = 4e-20
 Identities = 35/96 (36%), Positives = 52/96 (54%), Gaps = 8/96 (8%)

Query: 37  SDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKG--KVCENTLKAIADMGFTKMTEI 94
              N   ++ + + VQ  G+D+   I +   F+ L    K+    L+ I D GF   T I
Sbjct: 2   MKINFLRNK-HKIHVQ--GTDLPDPIAT---FQQLDQEYKINSRLLQNILDAGFQMPTPI 55

Query: 95  QARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
           Q + IP +L GR+L+ SA TGSGKTLAF +P +  +
Sbjct: 56  QMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQL 91

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19 Length = 367

 Score = 84.9 bits (211), Expect = 4e-20
 Identities = 27/68 (39%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 64  SSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGR-DLVGSAKTGSGKTLAF 122
               F  L   + +N L AI + GF K T+IQ + IP  L    ++V  A+TGSGKT +F
Sbjct: 4   EYMNFNELN--LSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASF 61

Query: 123 LVPAVELI 130
            +P +EL+
Sbjct: 62  AIPLIELV 69

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii} Length = 337

 Score = 84.1 bits (209), Expect = 5e-20
 Identities = 26/52 (50%), Positives = 39/52 (75%)

Query: 77  ENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVE 128
           E   +AI +MGF   TE+Q++TIP +L+G+++V  AKTGSGKT A+ +P +E
Sbjct: 3   EKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILE 54

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens} Length = 479

 Score = 84.3 bits (209), Expect = 1e-19
 Identities = 24/108 (22%), Positives = 50/108 (46%), Gaps = 4/108 (3%)

Query: 25  QSKEKSKPAEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIA 84
           + KE        +         N  +V++   D    + S   FE L+  +    L+ + 
Sbjct: 51  EEKEDRAAQSLLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSFEELR--LKPQLLQGVY 108

Query: 85  DMGFTKMTEIQARTIPPLLEG--RDLVGSAKTGSGKTLAFLVPAVELI 130
            MGF + ++IQ   +P +L    ++L+  +++G+GKT AF++  +  +
Sbjct: 109 AMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 156

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A Length = 224

 Score = 81.4 bits (202), Expect = 1e-19
 Identities = 22/65 (33%), Positives = 40/65 (61%), Gaps = 2/65 (3%)

Query: 66  TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVP 125
            +F+ ++    EN L+ +   GF + + IQ R I P++EG D++  A++G+GKT  F + 
Sbjct: 14  YKFDDMELD--ENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIA 71

Query: 126 AVELI 130
           A++ I
Sbjct: 72  ALQRI 76

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19 Length = 220

 Score = 81.1 bits (201), Expect = 1e-19
 Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 2/67 (2%)

Query: 64  SSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFL 123
            S+ F      +    L+AI D GF   +E+Q   IP  + G D++  AK+G GKT  F+
Sbjct: 12  HSSGFRDFL--LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFV 69

Query: 124 VPAVELI 130
           +  ++ +
Sbjct: 70  LATLQQL 76

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19 Length = 253

 Score = 80.7 bits (200), Expect = 4e-19
 Identities = 28/97 (28%), Positives = 41/97 (42%), Gaps = 5/97 (5%)

Query: 49  VEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDL 108
           V V  P       I +   F+ LK  +       I    + + T IQ   IP +LE RD+
Sbjct: 9   VSVTGPDYSATNVIEN---FDELK--LDPTIRNNILLASYQRPTPIQKNAIPAILEHRDI 63

Query: 109 VGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG 145
           +  A+TGSGKT AFL+P +  +       +       
Sbjct: 64  MACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAY 100

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A Length = 391

 Score = 81.1 bits (201), Expect = 1e-18
 Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 2/66 (3%)

Query: 65  STQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLV 124
           S+ F     K     L+AI D GF   +E+Q   IP  + G D++  AK+G GKT  F++
Sbjct: 7   SSGFRDFLLK--PELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVL 64

Query: 125 PAVELI 130
             ++ +
Sbjct: 65  ATLQQL 70

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens} Length = 228

 Score = 78.8 bits (195), Expect = 1e-18
 Identities = 22/51 (43%), Positives = 35/51 (68%)

Query: 80  LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
           LK+I  +G  K T IQ++  P +L+G DL+  A+TG+GKTL++L+P    +
Sbjct: 32  LKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHL 82

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens} Length = 300

 Score = 79.4 bits (196), Expect = 2e-18
 Identities = 24/108 (22%), Positives = 50/108 (46%), Gaps = 4/108 (3%)

Query: 25  QSKEKSKPAEKDSDANEDEDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIA 84
           + KE        +         N  +V++   D    + S   FE L+  +    L+ + 
Sbjct: 51  EEKEDRAAQSLLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSFEELR--LKPQLLQGVY 108

Query: 85  DMGFTKMTEIQARTIPPLLEG--RDLVGSAKTGSGKTLAFLVPAVELI 130
            MGF + ++IQ   +P +L    ++L+  +++G+GKT AF++  +  +
Sbjct: 109 AMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 156

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} Length = 242

 Score = 77.6 bits (192), Expect = 4e-18
 Identities = 29/63 (46%), Positives = 40/63 (63%)

Query: 77  ENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFM 136
            N +  IA   FT+ T IQA+  P  L G D+VG A+TGSGKTL++L+PA+  I +  F+
Sbjct: 38  ANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFL 97

Query: 137 PRN 139
            R 
Sbjct: 98  ERG 100

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B Length = 412

 Score = 79.1 bits (196), Expect = 5e-18
 Identities = 27/89 (30%), Positives = 47/89 (52%), Gaps = 6/89 (6%)

Query: 44  DQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLL 103
           D TN VEV     +  L   S   FE L+ K     L+ +  MGF + ++IQ   +P +L
Sbjct: 5   DNTNQVEVLQRDPNSPLY--SVKSFEELRLK--PQLLQGVYAMGFNRPSKIQENALPLML 60

Query: 104 EG--RDLVGSAKTGSGKTLAFLVPAVELI 130
               ++L+  +++G+GKT AF++  +  +
Sbjct: 61  AEPPQNLIAQSQSGTGKTAAFVLAMLSQV 89

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A* Length = 395

 Score = 78.8 bits (195), Expect = 8e-18
 Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 4/69 (5%)

Query: 64  SSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEG--RDLVGSAKTGSGKTLA 121
            +  F+ L   +    LK I  M F K ++IQ R +P LL    R+++  +++G+GKT A
Sbjct: 3   MAKSFDELG--LAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAA 60

Query: 122 FLVPAVELI 130
           F +  +  +
Sbjct: 61  FSLTMLTRV 69

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster} Length = 434

 Score = 78.4 bits (194), Expect = 1e-17
 Identities = 29/89 (32%), Positives = 46/89 (51%), Gaps = 5/89 (5%)

Query: 44  DQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLL 103
            + N + V++ GSDV   I     F +    + +  +  +   G+   T IQ  +IP + 
Sbjct: 37  SKYNNIPVKVTGSDVPQPIQH---FTSAD--LRDIIIDNVNKSGYKIPTPIQKCSIPVIS 91

Query: 104 EGRDLVGSAKTGSGKTLAFLVPAVELIYN 132
            GRDL+  A+TGSGKT AFL+P +  +  
Sbjct: 92  SGRDLMACAQTGSGKTAAFLLPILSKLLE 120

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 77.8 bits (192), Expect = 2e-17
 Identities = 12/54 (22%), Positives = 21/54 (38%)

Query: 77  ENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELI 130
           E+            +T  Q      +++G+     A TG GKT   ++ A+ L 
Sbjct: 8   EDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA 61

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score = 77.6 bits (192), Expect = 2e-17
 Identities = 30/86 (34%), Positives = 46/86 (53%), Gaps = 7/86 (8%)

Query: 47  NAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGR 106
           + VE    G++    I S   F  ++  + E  +  I    +T+ T +Q   IP + E R
Sbjct: 1   SMVEAT--GNNCPPHIES---FSDVE--MGEIIMGNIELTRYTRPTPVQKHAIPIIKEKR 53

Query: 107 DLVGSAKTGSGKTLAFLVPAVELIYN 132
           DL+  A+TGSGKT AFL+P +  IY+
Sbjct: 54  DLMACAQTGSGKTAAFLLPILSQIYS 79

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 44.5 bits (104), Expect = 7e-06
 Identities = 32/214 (14%), Positives = 67/214 (31%), Gaps = 53/214 (24%)

Query: 4   DTEKHLMNKITKREKKKLKILQSKEKSKPAEKDSDANEDEDQTNAV----EV----QLP- 54
           D E     +   + K  L + +          + D  + +D   ++    E+        
Sbjct: 8   DFE---TGEHQYQYKDILSVFEDAFV-----DNFDCKDVQDMPKSILSKEEIDHIIMSKD 59

Query: 55  ---GSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGS 111
              G+      L S Q E ++ K  E  L+   +  F  M+ I+     P +  R  +  
Sbjct: 60  AVSGTLRLFWTLLSKQEEMVQ-KFVEEVLR--INYKFL-MSPIKTEQRQPSMMTRMYIEQ 115

Query: 112 AKTGSGKTLAFL---VPAVELIYNLKF---------------MPRNGKSW--------QG 145
                     F    V  ++    L+                +  +GK+W          
Sbjct: 116 RDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYK 175

Query: 146 KLRPLTNGVYLVACNVFKSTQPPTVIK-VQTLIF 178
               +   ++ +  N+     P TV++ +Q L++
Sbjct: 176 VQCKMDFKIFWL--NLKNCNSPETVLEMLQKLLY 207

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 40.5 bits (95), Expect = 1e-04
 Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 77  ENTLKAIADMGFTKMTEIQARTIPP-LLEGRDLVGSAKTGSGKTLAF 122
            N ++ I   G  K+   Q   +   LLEG  L+ ++ TGSGKTL  
Sbjct: 17  SNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIA 63

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	178
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.93
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.9
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.9
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.89
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.88
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.88
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.87
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.87
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.87
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.87
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.87
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.87
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.87
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.86
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.86
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.86
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.86
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.85
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.85
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.83
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.81
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.81
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.81
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.8
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.8
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.79
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.79
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.78
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.74
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.68
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.68
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.67
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.67
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.66
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.65
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.64
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.63
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.63
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.62
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.62
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.61
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.58
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.58
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.57
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.53
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.53
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.53
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.52
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.5
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.49
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.49
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.49
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.49
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.48
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.44
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.41
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.4
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.39
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.36
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.31
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.31
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.3
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.29
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.27
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.25
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.24
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.22
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.21
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.19
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.18
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.15
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.07
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.02
3h1t_A	590	Type I site-specific restriction-modification syst	98.91
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	98.84
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	98.78
3jux_A	822	Protein translocase subunit SECA; protein transloc	98.71
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.44
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	98.44
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	98.27
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	97.73
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	97.7
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	97.56
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	97.18
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	97.13
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	97.08
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	96.99
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	96.99
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	96.94
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	96.91
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	96.89
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	96.79
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	96.51
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	96.0
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	95.71
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	95.33
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	93.32
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	93.0
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	91.77
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	91.68
3co5_A	143	Putative two-component system transcriptional RES	90.91
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	90.78
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	89.95
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	89.22
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	88.49
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	88.16
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	87.96
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	87.46
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	87.25
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	87.2
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	87.09
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	86.79
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	86.6
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	86.48
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	86.36
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	86.07
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	86.04
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	85.99
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	85.97
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	85.46
3bos_A	242	Putative DNA replication factor; P-loop containing	85.38
2eyu_A	261	Twitching motility protein PILT; pilus retraction	85.28
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	85.24
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	85.09
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	84.85
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	84.43
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	84.41
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	84.22
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	84.2
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	83.55
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	83.29
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	83.08
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	82.88
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	82.74
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	82.63
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	82.1
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	81.9
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	81.9
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	81.61
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	81.52
2chg_A	226	Replication factor C small subunit; DNA-binding pr	81.51
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	81.44
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	81.39
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	81.34
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	81.2
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	80.98
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	80.97
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	80.92
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	80.9
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	80.73
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	80.71
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	80.6
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	80.59
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	80.49
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	80.44
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	80.1
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	80.08

>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=99.93  E-value=3e-26  Score=191.24  Aligned_cols=111  Identities=22%  Similarity=0.274  Sum_probs=99.7

Q ss_pred             cccCCCCCCcCCCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCC--CcEEEEccCCCchhhHhHHHHHH
Q psy12984         51 VQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEG--RDLVGSAKTGSGKTLAFLVPAVE  128 (178)
Q Consensus        51 ~~~~~~~~~~~~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g--~dvi~~a~TGsGKTlaf~lp~l~  128 (178)
                      +...+.+.+.+..+..+|++++  |++.++++|..+||..||++|..+||.++.|  +|++++|+||||||++|++|+++
T Consensus        77 v~v~~~~~~~p~~~~~~f~~l~--l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~  154 (300)
T 3fmo_B           77 VEVLQRDPNSPLYSVKSFEELR--LKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLS  154 (300)
T ss_dssp             EEEECSSTTCCCCCCCCSGGGT--CCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             ceeccCCCCCCcCCcCCHhhcC--CCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHH
Confidence            3445667777888889999998  9999999999999999999999999999988  99999999999999999999999


Q ss_pred             HHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984        129 LIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus       129 ~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      ++...  ...++++||+|||+||.|++.++..+++++
T Consensus       155 ~l~~~--~~~~~~lil~PtreLa~Q~~~~~~~l~~~~  189 (300)
T 3fmo_B          155 QVEPA--NKYPQCLCLSPTYELALQTGKVIEQMGKFY  189 (300)
T ss_dssp             HCCTT--SCSCCEEEECSSHHHHHHHHHHHHHHTTTS
T ss_pred             hhhcc--CCCceEEEEcCcHHHHHHHHHHHHHHHhhC
Confidence            88653  345589999999999999999999988765

>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=99.90  E-value=9.7e-24  Score=183.39  Aligned_cols=121  Identities=27%  Similarity=0.363  Sum_probs=103.5

Q ss_pred             cccccccccccCCCCCCcCCCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHh
Q psy12984         43 EDQTNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus        43 ~~~~~~~~~~~~~~~~~~~~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      .+..+..++...+.+.+.++.   +|++++  |++.++++|.++||..|||+|..|||.++.|+|++++|+||||||++|
T Consensus        36 ~~~~~~~~~~~~~~~~p~~~~---~f~~~~--l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~  110 (434)
T 2db3_A           36 FSKYNNIPVKVTGSDVPQPIQ---HFTSAD--LRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAF  110 (434)
T ss_dssp             GGGGGGSCEEEESSSCCCCCC---CGGGSC--CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHH
T ss_pred             hhhhcCceeEecCCCCCCCcC---ChhhcC--CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHH
Confidence            344455566777777776654   599998  999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhccC---CCCCceEEEeecHHHHHHHHHHHHHHhhhcCCC
Q psy12984        123 LVPAVELIYNLKF---MPRNGKSWQGKLRPLTNGVYLVACNVFKSTQPP  168 (178)
Q Consensus       123 ~lp~l~~l~~~~~---~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~~~  168 (178)
                      ++|+++++.....   .....++|++|||+||.|+++++..++...+..
T Consensus       111 ~lpil~~l~~~~~~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~  159 (434)
T 2db3_A          111 LLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLK  159 (434)
T ss_dssp             HHHHHHHHHHSCCCCCTTCCSEEEECSSHHHHHHHHHHHHHHTTTSSCC
T ss_pred             HHHHHHHHHhcccccccCCccEEEEecCHHHHHHHHHHHHHHhccCCcE
Confidence            9999999976432   235689999999999999999999988765443

>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=99.90  E-value=1.3e-23  Score=168.98  Aligned_cols=118  Identities=31%  Similarity=0.395  Sum_probs=100.4

Q ss_pred             ccccccccCCCCCCcCCCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHH
Q psy12984         46 TNAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVP  125 (178)
Q Consensus        46 ~~~~~~~~~~~~~~~~~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp  125 (178)
                      .....+...+.+.+.++.+   |++++  |++.++++|.++||..|+++|..+||.++.|+|++++||||||||++|++|
T Consensus        12 ~~~~~i~~~~~~~p~~~~~---f~~~~--l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~   86 (242)
T 3fe2_A           12 RRSKEITVRGHNCPKPVLN---FYEAN--FPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLP   86 (242)
T ss_dssp             HHHHTEEEESSCCCCCCSS---TTTTT--CCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHH
T ss_pred             HhcCceEEeCCCCCCccCC---HhhcC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHH
Confidence            3445555566666665544   88887  999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhccC---CCCCceEEEeecHHHHHHHHHHHHHHhhhcCCC
Q psy12984        126 AVELIYNLKF---MPRNGKSWQGKLRPLTNGVYLVACNVFKSTQPP  168 (178)
Q Consensus       126 ~l~~l~~~~~---~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~~~  168 (178)
                      ++.++.....   ..+..++|++|||+||.|+++.+..++...+..
T Consensus        87 ~l~~l~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~  132 (242)
T 3fe2_A           87 AIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLK  132 (242)
T ss_dssp             HHHHHHTSCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHhccccccCCCCEEEEEeCcHHHHHHHHHHHHHHHhhcCce
Confidence            9999875321   345678999999999999999999998876543

>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=99.89  E-value=5.9e-23  Score=164.74  Aligned_cols=115  Identities=30%  Similarity=0.394  Sum_probs=95.8

Q ss_pred             cccccCCCCCCcCCCCccchHhhc--ccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHH
Q psy12984         49 VEVQLPGSDVALEILSSTQFEALK--GKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPA  126 (178)
Q Consensus        49 ~~~~~~~~~~~~~~~~~~~f~~l~--~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~  126 (178)
                      ..+...+.+.+.++.+   |+++.  ..|++.++++|.++||..|+++|..+|+.++.|+|++++||||||||++|++|+
T Consensus        11 ~~i~~~~~~~p~~~~~---f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~   87 (245)
T 3dkp_A           11 HKIHVQGTDLPDPIAT---FQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPI   87 (245)
T ss_dssp             TTEEEESSSCCCCCSS---HHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHH
T ss_pred             CceEecCCCCCCcccC---HHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHH
Confidence            3444556666666665   66551  139999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhcCC
Q psy12984        127 VELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQP  167 (178)
Q Consensus       127 l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~~  167 (178)
                      +.++.... ..+.+++|++|||+||.|+++.+..++...+.
T Consensus        88 l~~l~~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  127 (245)
T 3dkp_A           88 LMQLKQPA-NKGFRALIISPTRELASQIHRELIKISEGTGF  127 (245)
T ss_dssp             HHHHCSCC-SSSCCEEEECSSHHHHHHHHHHHHHHTTTSCC
T ss_pred             HHHHhhcc-cCCceEEEEeCCHHHHHHHHHHHHHHhcccCc
Confidence            99886422 34558999999999999999999998776554

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.88  E-value=9e-23  Score=161.34  Aligned_cols=104  Identities=32%  Similarity=0.416  Sum_probs=91.5

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      .+|++++  |++.++++|.++||..|+++|.++|+.++.|+|++++++||||||++|++|+++.+...  ....+++|++
T Consensus         4 ~~f~~~~--l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~--~~~~~~lil~   79 (219)
T 1q0u_A            4 TQFTRFP--FQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPE--RAEVQAVITA   79 (219)
T ss_dssp             CCGGGSC--CCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTT--SCSCCEEEEC
T ss_pred             CCHhhCC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhC--cCCceEEEEc
Confidence            5699998  99999999999999999999999999999999999999999999999999999987642  2355899999


Q ss_pred             ecHHHHHHHHHHHHHHhhhcCCCCcceE
Q psy12984        146 KLRPLTNGVYLVACNVFKSTQPPTVIKV  173 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~~~~~~~~~~~v  173 (178)
                      |||+|+.|+++.+..+....+...++++
T Consensus        80 Pt~~L~~q~~~~~~~~~~~~~~~~~~~~  107 (219)
T 1q0u_A           80 PTRELATQIYHETLKITKFCPKDRMIVA  107 (219)
T ss_dssp             SSHHHHHHHHHHHHHHHTTSCGGGCCCE
T ss_pred             CcHHHHHHHHHHHHHHhhhcccccceEE
Confidence            9999999999999999887644333433

>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=99.88  E-value=8.1e-23  Score=178.56  Aligned_cols=109  Identities=21%  Similarity=0.263  Sum_probs=96.4

Q ss_pred             cCCCCCCcCCCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCC--CcEEEEccCCCchhhHhHHHHHHHH
Q psy12984         53 LPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEG--RDLVGSAKTGSGKTLAFLVPAVELI  130 (178)
Q Consensus        53 ~~~~~~~~~~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g--~dvi~~a~TGsGKTlaf~lp~l~~l  130 (178)
                      ..+.+++.+..+..+|++++  |++.++++|.++||..|||+|..+||.++.|  +|+|++|+||||||++|++|+++.+
T Consensus        79 ~~~~~~~~~~~~~~~f~~~~--l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l  156 (479)
T 3fmp_B           79 VLQRDPNSPLYSVKSFEELR--LKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV  156 (479)
T ss_dssp             EECSSTTSCCCCCCCSGGGT--CCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTC
T ss_pred             ecCCCCCCCccCcCCHHHcC--CCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHH
Confidence            34556666777788999998  9999999999999999999999999999987  9999999999999999999999877


Q ss_pred             HhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984        131 YNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus       131 ~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      ...  ....+++||+|||+||.|++.++..+.++.
T Consensus       157 ~~~--~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~  189 (479)
T 3fmp_B          157 EPA--NKYPQCLCLSPTYELALQTGKVIEQMGKFY  189 (479)
T ss_dssp             CTT--SCSCCEEEECSSHHHHHHHHHHHHHHHTTS
T ss_pred             hhc--CCCCcEEEEeChHHHHHHHHHHHHHHHhhC
Confidence            543  234489999999999999999999988764

>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=99.87  E-value=7.1e-23  Score=165.20  Aligned_cols=117  Identities=26%  Similarity=0.324  Sum_probs=96.6

Q ss_pred             cccccccCCCCCCcCCCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHH
Q psy12984         47 NAVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPA  126 (178)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~  126 (178)
                      +...+...+.+.+. .....+|++++  |++.++++|..+||..|+++|..+|+.++.|+|++++++||||||++|++|+
T Consensus         5 ~~~~~~~~~~~~~~-~~~~~~f~~l~--l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~   81 (253)
T 1wrb_A            5 DSIPVSVTGPDYSA-TNVIENFDELK--LDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPI   81 (253)
T ss_dssp             CCCCCCEECCSSSC-CSCCCSSGGGS--CCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHH
T ss_pred             hhCceeeeCCCCCC-CCccCCHhhCC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHH
Confidence            33444445555543 12335699998  9999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcc-------CCCCCceEEEeecHHHHHHHHHHHHHHhhhcC
Q psy12984        127 VELIYNLK-------FMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus       127 l~~l~~~~-------~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      ++++....       ...+.+++|++|||+||.|++..+..++...+
T Consensus        82 l~~l~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  128 (253)
T 1wrb_A           82 INHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTP  128 (253)
T ss_dssp             HHHHHTTCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSS
T ss_pred             HHHHHhhccccccccccCCceEEEEECCHHHHHHHHHHHHHHhccCC
Confidence            99987532       12345899999999999999999999876544

>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=99.87  E-value=2.1e-22  Score=164.47  Aligned_cols=107  Identities=50%  Similarity=0.676  Sum_probs=89.3

Q ss_pred             CCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccC--CCCC
Q psy12984         62 ILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKF--MPRN  139 (178)
Q Consensus        62 ~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~--~~~~  139 (178)
                      .....+|++|+..|++.++++|.++||..|+++|..+|+.++.|+|++++|+||||||++|++|+++.+...+.  ..+.
T Consensus        48 ~~~~~~f~~l~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~  127 (262)
T 3ly5_A           48 AFEDTSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGT  127 (262)
T ss_dssp             BSGGGCC-----CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCC
T ss_pred             ccccCChhHhccccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccccccCCc
Confidence            34456788887679999999999999999999999999999999999999999999999999999999876332  2355


Q ss_pred             ceEEEeecHHHHHHHHHHHHHHhhhcCCC
Q psy12984        140 GKSWQGKLRPLTNGVYLVACNVFKSTQPP  168 (178)
Q Consensus       140 ~~~~l~Ptr~La~qi~~~~~~l~~~~~~~  168 (178)
                      +++|++|||+||.|++..+..++...+..
T Consensus       128 ~~lil~Pt~~La~q~~~~~~~~~~~~~~~  156 (262)
T 3ly5_A          128 GVLILSPTRELAMQTFGVLKELMTHHVHT  156 (262)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTCCSC
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHHhhcCce
Confidence            78999999999999999999988765543

>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=99.87  E-value=9.5e-22  Score=156.13  Aligned_cols=95  Identities=28%  Similarity=0.349  Sum_probs=83.8

Q ss_pred             cchHh-hcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhcc----CCCCCc
Q psy12984         66 TQFEA-LKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLK----FMPRNG  140 (178)
Q Consensus        66 ~~f~~-l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~----~~~~~~  140 (178)
                      .+|.+ ++  +++.++++|.++||..|+++|..+|+.++.|+|++++||||||||++|++|++..+....    ...+.+
T Consensus        19 ~~f~~~~~--l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~~~~   96 (228)
T 3iuy_A           19 CRFKDAFQ--QYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPG   96 (228)
T ss_dssp             CSHHHHHT--TCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC---------CCCS
T ss_pred             hhHhhhhc--cCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchhhccCCCc
Confidence            45888 66  999999999999999999999999999999999999999999999999999999886421    134568


Q ss_pred             eEEEeecHHHHHHHHHHHHHHh
Q psy12984        141 KSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus       141 ~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      ++|++|||+||.|+++.+..+.
T Consensus        97 ~lil~Pt~~L~~q~~~~~~~~~  118 (228)
T 3iuy_A           97 MLVLTPTRELALHVEAECSKYS  118 (228)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHC
T ss_pred             EEEEeCCHHHHHHHHHHHHHhc
Confidence            8999999999999999999875

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.87  E-value=5.8e-22  Score=158.11  Aligned_cols=101  Identities=38%  Similarity=0.534  Sum_probs=90.0

Q ss_pred             ccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccC--CCCCceE
Q psy12984         65 STQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKF--MPRNGKS  142 (178)
Q Consensus        65 ~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~--~~~~~~~  142 (178)
                      ..+|++++  |++.++++|.++||..|+++|..+|+.++.|+|++++++||||||++|++|+++.+.....  ..+.+++
T Consensus        24 ~~~f~~~~--l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~l  101 (236)
T 2pl3_A           24 ITRFSDFP--LSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVL  101 (236)
T ss_dssp             CSBGGGSC--CCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEE
T ss_pred             cCCHhhcC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceEE
Confidence            45699998  9999999999999999999999999999999999999999999999999999999875321  2356889


Q ss_pred             EEeecHHHHHHHHHHHHHHhhhcCC
Q psy12984        143 WQGKLRPLTNGVYLVACNVFKSTQP  167 (178)
Q Consensus       143 ~l~Ptr~La~qi~~~~~~l~~~~~~  167 (178)
                      |++|||+||.|++..+..++...+.
T Consensus       102 il~Pt~~L~~q~~~~~~~~~~~~~~  126 (236)
T 2pl3_A          102 IISPTRELAYQTFEVLRKVGKNHDF  126 (236)
T ss_dssp             EECSSHHHHHHHHHHHHHHTTTSSC
T ss_pred             EEeCCHHHHHHHHHHHHHHhCCCCe
Confidence            9999999999999999988765443

>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=99.87  E-value=6.3e-22  Score=160.46  Aligned_cols=100  Identities=31%  Similarity=0.342  Sum_probs=90.7

Q ss_pred             ccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEE
Q psy12984         65 STQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQ  144 (178)
Q Consensus        65 ~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l  144 (178)
                      ..+|++++  |++.++++|..+||..|+++|.++|+.++.|+|++++|+||||||++|++|++..+...  ..+.+++|+
T Consensus        42 ~~~f~~l~--l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~--~~~~~~lil  117 (249)
T 3ber_A           42 TKTFKDLG--VTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLET--PQRLFALVL  117 (249)
T ss_dssp             HCCTGGGT--CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHS--CCSSCEEEE
T ss_pred             cCCHHHcC--CCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcC--CCCceEEEE
Confidence            45699998  99999999999999999999999999999999999999999999999999999988764  234579999


Q ss_pred             eecHHHHHHHHHHHHHHhhhcCCC
Q psy12984        145 GKLRPLTNGVYLVACNVFKSTQPP  168 (178)
Q Consensus       145 ~Ptr~La~qi~~~~~~l~~~~~~~  168 (178)
                      +|||+||.|+++.+..++..++..
T Consensus       118 ~Ptr~L~~q~~~~~~~~~~~~~~~  141 (249)
T 3ber_A          118 TPTRELAFQISEQFEALGSSIGVQ  141 (249)
T ss_dssp             CSSHHHHHHHHHHHHHHHGGGTCC
T ss_pred             eCCHHHHHHHHHHHHHHhccCCee
Confidence            999999999999999998776543

>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=99.87  E-value=4.9e-22  Score=154.90  Aligned_cols=96  Identities=30%  Similarity=0.376  Sum_probs=87.7

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      .+|++++  |+++++++|.++||..|+++|.++|+.++.|+|+++++|||||||++|++|++..+...  ....+++|++
T Consensus         3 ~~f~~~~--l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~--~~~~~~lil~   78 (206)
T 1vec_A            3 NEFEDYC--LKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLK--KDNIQAMVIV   78 (206)
T ss_dssp             SSGGGSC--CCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTT--SCSCCEEEEC
T ss_pred             CChhhcC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhccc--CCCeeEEEEe
Confidence            4699998  99999999999999999999999999999999999999999999999999999987542  3445899999


Q ss_pred             ecHHHHHHHHHHHHHHhhhc
Q psy12984        146 KLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~~~~  165 (178)
                      |||+|+.|++..+..+.+.+
T Consensus        79 Pt~~L~~q~~~~~~~~~~~~   98 (206)
T 1vec_A           79 PTRELALQVSQICIQVSKHM   98 (206)
T ss_dssp             SCHHHHHHHHHHHHHHTTTS
T ss_pred             CcHHHHHHHHHHHHHHHhhc
Confidence            99999999999999988765

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.87  E-value=7.1e-22  Score=168.12  Aligned_cols=109  Identities=28%  Similarity=0.335  Sum_probs=93.4

Q ss_pred             cCCCCCCcCCCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHh
Q psy12984         53 LPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYN  132 (178)
Q Consensus        53 ~~~~~~~~~~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~  132 (178)
                      ..+.+.+.++.   +|++++  |++.++++|..+||..|||+|..+||.++.|+|++++||||||||++|++|+++.+..
T Consensus         5 ~~~~~~p~~~~---~f~~~~--l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~   79 (417)
T 2i4i_A            5 ATGNNCPPHIE---SFSDVE--MGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYS   79 (417)
T ss_dssp             EESTTCCCCCS---SGGGSC--CCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHH
T ss_pred             cCCCcCCcccC---CHhhCC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHh
Confidence            34555555544   499998  9999999999999999999999999999999999999999999999999999998875


Q ss_pred             ccC----------------CCCCceEEEeecHHHHHHHHHHHHHHhhhcC
Q psy12984        133 LKF----------------MPRNGKSWQGKLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus       133 ~~~----------------~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      ...                .....++|++|||+||.|+++.+..++...+
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  129 (417)
T 2i4i_A           80 DGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSR  129 (417)
T ss_dssp             HCCCHHHHHHHHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTSS
T ss_pred             ccccchhhccccccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcCC
Confidence            321                1235789999999999999999999876544

>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=99.86  E-value=8.5e-22  Score=155.41  Aligned_cols=97  Identities=25%  Similarity=0.305  Sum_probs=87.3

Q ss_pred             ccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEE
Q psy12984         65 STQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQ  144 (178)
Q Consensus        65 ~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l  144 (178)
                      ..+|++++  |++.++++|.++||..|+++|.++|+.++.|+|++++++||+|||++|++|++..+...  ....+++|+
T Consensus        13 ~~~f~~~~--l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~--~~~~~~lil   88 (220)
T 1t6n_A           13 SSGFRDFL--LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV--TGQVSVLVM   88 (220)
T ss_dssp             -CCSTTSC--CCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCC--TTCCCEEEE
T ss_pred             CCCHhhcC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhcc--CCCEEEEEE
Confidence            35699998  99999999999999999999999999999999999999999999999999999977542  234588999


Q ss_pred             eecHHHHHHHHHHHHHHhhhc
Q psy12984        145 GKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus       145 ~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      +||++|+.|+++.+..+...+
T Consensus        89 ~Pt~~L~~q~~~~~~~~~~~~  109 (220)
T 1t6n_A           89 CHTRELAFQISKEYERFSKYM  109 (220)
T ss_dssp             CSCHHHHHHHHHHHHHHTTTS
T ss_pred             eCCHHHHHHHHHHHHHHHhhC
Confidence            999999999999999987665

>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=99.86  E-value=8.7e-22  Score=157.11  Aligned_cols=97  Identities=23%  Similarity=0.258  Sum_probs=87.5

Q ss_pred             ccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEE
Q psy12984         65 STQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQ  144 (178)
Q Consensus        65 ~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l  144 (178)
                      ..+|++++  |++.++++|.++||..|+++|.++|+.++.|+|++++++||||||++|++|++..+...  ....+++|+
T Consensus        23 ~~~f~~l~--l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~--~~~~~~lil   98 (230)
T 2oxc_A           23 PADFESLL--LSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLE--NLSTQILIL   98 (230)
T ss_dssp             -CCGGGGT--CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT--SCSCCEEEE
T ss_pred             CCCHhhcC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhc--CCCceEEEE
Confidence            35699998  99999999999999999999999999999999999999999999999999999987543  335589999


Q ss_pred             eecHHHHHHHHHHHHHHhhhc
Q psy12984        145 GKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus       145 ~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      +|||+|+.|+++.+..++...
T Consensus        99 ~Pt~~L~~q~~~~~~~~~~~~  119 (230)
T 2oxc_A           99 APTREIAVQIHSVITAIGIKM  119 (230)
T ss_dssp             CSSHHHHHHHHHHHHHHTTTS
T ss_pred             eCCHHHHHHHHHHHHHHhccc
Confidence            999999999999999887654

>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=99.86  E-value=6.5e-22  Score=158.69  Aligned_cols=98  Identities=23%  Similarity=0.355  Sum_probs=88.5

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      .+|++++  |++.++++|..+||..|+++|..+|+.++.|+|++++++||||||++|++|+++.+...  ....+++|++
T Consensus        30 ~~f~~l~--l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~--~~~~~~lil~  105 (237)
T 3bor_A           30 DNFDDMN--LKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIE--FKETQALVLA  105 (237)
T ss_dssp             CSGGGSC--CCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTT--SCSCCEEEEC
T ss_pred             CChhhcC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhc--CCCceEEEEE
Confidence            5699998  99999999999999999999999999999999999999999999999999999987542  2455899999


Q ss_pred             ecHHHHHHHHHHHHHHhhhcCC
Q psy12984        146 KLRPLTNGVYLVACNVFKSTQP  167 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~~~~~~  167 (178)
                      |||+|+.|+++.+..++...+.
T Consensus       106 Pt~~L~~q~~~~~~~~~~~~~~  127 (237)
T 3bor_A          106 PTRELAQQIQKVILALGDYMGA  127 (237)
T ss_dssp             SSHHHHHHHHHHHHHHTTTTTC
T ss_pred             CcHHHHHHHHHHHHHHhhhcCc
Confidence            9999999999999998765543

>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=99.86  E-value=1.9e-21  Score=153.61  Aligned_cols=98  Identities=26%  Similarity=0.380  Sum_probs=88.6

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      .+|++++  |++.++++|.++||..|+++|..+|+.++.|+|+++++|||||||++|++|+++.+...  ....++++++
T Consensus        14 ~~f~~l~--l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~--~~~~~~lil~   89 (224)
T 1qde_A           14 YKFDDME--LDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS--VKAPQALMLA   89 (224)
T ss_dssp             CCGGGGT--CCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT--CCSCCEEEEC
T ss_pred             CChhhcC--CCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhcc--CCCceEEEEE
Confidence            4699998  99999999999999999999999999999999999999999999999999999988543  3345899999


Q ss_pred             ecHHHHHHHHHHHHHHhhhcCC
Q psy12984        146 KLRPLTNGVYLVACNVFKSTQP  167 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~~~~~~  167 (178)
                      |||+|+.|+++.+..+....+.
T Consensus        90 Pt~~L~~q~~~~~~~~~~~~~~  111 (224)
T 1qde_A           90 PTRELALQIQKVVMALAFHMDI  111 (224)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSCC
T ss_pred             CCHHHHHHHHHHHHHHhcccCc
Confidence            9999999999999998766543

>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=99.85  E-value=5e-21  Score=149.08  Aligned_cols=96  Identities=32%  Similarity=0.395  Sum_probs=86.7

Q ss_pred             chHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhcc-CCCCCceEEEe
Q psy12984         67 QFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLK-FMPRNGKSWQG  145 (178)
Q Consensus        67 ~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~-~~~~~~~~~l~  145 (178)
                      +|++++  |++.++++|.++||..|+++|.++|+.++.|+|+++++|||||||++|++|+++.+.... .....+++|++
T Consensus         2 ~f~~~~--l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~   79 (207)
T 2gxq_A            2 EFKDFP--LKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLT   79 (207)
T ss_dssp             CGGGSC--CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEEC
T ss_pred             ChhhcC--CCHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEE
Confidence            589998  999999999999999999999999999999999999999999999999999999886432 13456899999


Q ss_pred             ecHHHHHHHHHHHHHHhhh
Q psy12984        146 KLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~~~  164 (178)
                      |||+|+.|+++.+..++..
T Consensus        80 P~~~L~~q~~~~~~~~~~~   98 (207)
T 2gxq_A           80 PTRELALQVASELTAVAPH   98 (207)
T ss_dssp             SSHHHHHHHHHHHHHHCTT
T ss_pred             CCHHHHHHHHHHHHHHhhc
Confidence            9999999999999988654

>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=99.85  E-value=4.4e-21  Score=162.47  Aligned_cols=110  Identities=21%  Similarity=0.266  Sum_probs=96.7

Q ss_pred             ccCCCCCCcCCCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCC--CcEEEEccCCCchhhHhHHHHHHH
Q psy12984         52 QLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEG--RDLVGSAKTGSGKTLAFLVPAVEL  129 (178)
Q Consensus        52 ~~~~~~~~~~~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g--~dvi~~a~TGsGKTlaf~lp~l~~  129 (178)
                      .....+.+.++.+..+|++++  |++.++++|.++||..|+++|..+|+.++.|  +|+++++|||||||++|++|+++.
T Consensus        11 ~~~~~~~~~~~~~~~~f~~~~--l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~   88 (412)
T 3fht_A           11 EVLQRDPNSPLYSVKSFEELR--LKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQ   88 (412)
T ss_dssp             HHHTTCTTSTTCCSSCTGGGT--CCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eeecccCCCCccccCCHhhCC--CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHH
Confidence            334556666777888999998  9999999999999999999999999999987  999999999999999999999998


Q ss_pred             HHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984        130 IYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus       130 l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      +...  ....+++|++||++||.|++..+..+...+
T Consensus        89 ~~~~--~~~~~~lil~P~~~L~~q~~~~~~~~~~~~  122 (412)
T 3fht_A           89 VEPA--NKYPQCLCLSPTYELALQTGKVIEQMGKFY  122 (412)
T ss_dssp             CCTT--SCSCCEEEECSSHHHHHHHHHHHHHHTTTS
T ss_pred             hhhc--CCCCCEEEECCCHHHHHHHHHHHHHHHhhc
Confidence            7553  234488999999999999999999987664

>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=99.83  E-value=1.3e-20  Score=160.45  Aligned_cols=99  Identities=21%  Similarity=0.341  Sum_probs=88.7

Q ss_pred             ccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEE
Q psy12984         65 STQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQ  144 (178)
Q Consensus        65 ~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l  144 (178)
                      ..+|++++  |++.++++|..+||..|+|+|..+|+.++.|+|++++++||||||++|++|+++.+...  ....+++|+
T Consensus        36 ~~~f~~~~--l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~--~~~~~~lil  111 (410)
T 2j0s_A           36 TPTFDTMG--LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQ--VRETQALIL  111 (410)
T ss_dssp             CCSGGGGC--CCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTT--SCSCCEEEE
T ss_pred             CCCHhhcC--CCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhc--cCCceEEEE
Confidence            35699998  99999999999999999999999999999999999999999999999999999877432  345689999


Q ss_pred             eecHHHHHHHHHHHHHHhhhcCC
Q psy12984        145 GKLRPLTNGVYLVACNVFKSTQP  167 (178)
Q Consensus       145 ~Ptr~La~qi~~~~~~l~~~~~~  167 (178)
                      +|||+|+.|+++.+..++..++.
T Consensus       112 ~Pt~~L~~q~~~~~~~~~~~~~~  134 (410)
T 2j0s_A          112 APTRELAVQIQKGLLALGDYMNV  134 (410)
T ss_dssp             CSSHHHHHHHHHHHHHHTTTTTC
T ss_pred             cCcHHHHHHHHHHHHHHhccCCe
Confidence            99999999999999998766543

>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=99.81  E-value=7.2e-20  Score=162.62  Aligned_cols=99  Identities=30%  Similarity=0.425  Sum_probs=85.8

Q ss_pred             cchHhhcc--cCCHHHHHHHHHCCCCCCcHHHHHhhcccc--CCCcEEEEccCCCchhhHhHHHHHHHHHhccC--CCCC
Q psy12984         66 TQFEALKG--KVCENTLKAIADMGFTKMTEIQARTIPPLL--EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKF--MPRN  139 (178)
Q Consensus        66 ~~f~~l~~--~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l--~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~--~~~~  139 (178)
                      .+|++|..  .|+++++++|..+||..|+|+|..+|+.++  .|+|++++||||||||++|++|+++++.....  ....
T Consensus        68 ~~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~  147 (563)
T 3i5x_A           68 VTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMV  147 (563)
T ss_dssp             CCHHHHHHTTSSCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSC
T ss_pred             cCHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccccccCCe
Confidence            34666642  399999999999999999999999999999  67999999999999999999999999977542  2245


Q ss_pred             ceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984        140 GKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus       140 ~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      +++||+|||+||.|++..+..++..
T Consensus       148 ~~lil~Ptr~La~Q~~~~~~~~~~~  172 (563)
T 3i5x_A          148 KAVIVAPTRDLALQIEAEVKKIHDM  172 (563)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEcCcHHHHHHHHHHHHHHHhh
Confidence            8899999999999999999998654

>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=99.81  E-value=1e-19  Score=153.24  Aligned_cols=97  Identities=25%  Similarity=0.305  Sum_probs=86.8

Q ss_pred             ccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEE
Q psy12984         65 STQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQ  144 (178)
Q Consensus        65 ~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l  144 (178)
                      ...|++++  |++.++++|.++||..|+|+|.++|+.++.|+|+++++|||+|||++|++|++..+...  ....+++|+
T Consensus         7 ~~~f~~~~--l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~--~~~~~~lil   82 (391)
T 1xti_A            7 SSGFRDFL--LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV--TGQVSVLVM   82 (391)
T ss_dssp             --CGGGGC--CCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCC--TTCCCEEEE
T ss_pred             CCChhhcC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhccc--CCCeeEEEE
Confidence            45799998  99999999999999999999999999999999999999999999999999999877542  334588999


Q ss_pred             eecHHHHHHHHHHHHHHhhhc
Q psy12984        145 GKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus       145 ~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      +||++|+.|++..+..+...+
T Consensus        83 ~P~~~L~~q~~~~~~~~~~~~  103 (391)
T 1xti_A           83 CHTRELAFQISKEYERFSKYM  103 (391)
T ss_dssp             CSCHHHHHHHHHHHHHHTTTC
T ss_pred             CCCHHHHHHHHHHHHHHHhhC
Confidence            999999999999999987665

>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=99.81  E-value=6.9e-20  Score=153.84  Aligned_cols=98  Identities=27%  Similarity=0.350  Sum_probs=88.2

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCC--CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEE
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEG--RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSW  143 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g--~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~  143 (178)
                      .+|++++  |++.++++|.++||..|+|+|..+|+.++.|  +|+++++|||||||++|++|++..+...  .....+++
T Consensus         5 ~~f~~~~--l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~--~~~~~~li   80 (395)
T 3pey_A            5 KSFDELG--LAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPE--DASPQAIC   80 (395)
T ss_dssp             CSSTTSC--CCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTT--CCSCCEEE
T ss_pred             cCHhhCC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccC--CCCccEEE
Confidence            5699998  9999999999999999999999999999988  9999999999999999999999987543  24558899


Q ss_pred             EeecHHHHHHHHHHHHHHhhhcCC
Q psy12984        144 QGKLRPLTNGVYLVACNVFKSTQP  167 (178)
Q Consensus       144 l~Ptr~La~qi~~~~~~l~~~~~~  167 (178)
                      ++||++|+.|++..+..++...+.
T Consensus        81 l~P~~~L~~q~~~~~~~~~~~~~~  104 (395)
T 3pey_A           81 LAPSRELARQTLEVVQEMGKFTKI  104 (395)
T ss_dssp             ECSSHHHHHHHHHHHHHHTTTSCC
T ss_pred             ECCCHHHHHHHHHHHHHHhcccCe
Confidence            999999999999999998765543

>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=99.80  E-value=1.1e-19  Score=153.90  Aligned_cols=98  Identities=29%  Similarity=0.374  Sum_probs=88.4

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      .+|++++  |++.++++|.++||..|+|+|..+|+.++.|+|+++++|||||||++|++|++..+...  ....+++|++
T Consensus        21 ~~f~~~~--l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~--~~~~~~lil~   96 (400)
T 1s2m_A           21 NTFEDFY--LKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPK--LNKIQALIMV   96 (400)
T ss_dssp             CCGGGGC--CCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTT--SCSCCEEEEC
T ss_pred             CChhhcC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhc--cCCccEEEEc
Confidence            5699998  99999999999999999999999999999999999999999999999999999877542  2345889999


Q ss_pred             ecHHHHHHHHHHHHHHhhhcCC
Q psy12984        146 KLRPLTNGVYLVACNVFKSTQP  167 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~~~~~~  167 (178)
                      ||++|+.|+++.+..++...+.
T Consensus        97 P~~~L~~q~~~~~~~~~~~~~~  118 (400)
T 1s2m_A           97 PTRELALQTSQVVRTLGKHCGI  118 (400)
T ss_dssp             SSHHHHHHHHHHHHHHTTTTTC
T ss_pred             CCHHHHHHHHHHHHHHhcccCc
Confidence            9999999999999998876543

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.80  E-value=2e-19  Score=161.18  Aligned_cols=99  Identities=31%  Similarity=0.449  Sum_probs=86.4

Q ss_pred             cchHhhc--ccCCHHHHHHHHHCCCCCCcHHHHHhhcccc--CCCcEEEEccCCCchhhHhHHHHHHHHHhccC--CCCC
Q psy12984         66 TQFEALK--GKVCENTLKAIADMGFTKMTEIQARTIPPLL--EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKF--MPRN  139 (178)
Q Consensus        66 ~~f~~l~--~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l--~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~--~~~~  139 (178)
                      .+|++|.  ..|+++++++|..+||..|+|+|.++|+.++  .|+|++++||||||||++|++|+++.+.....  ....
T Consensus        17 ~~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~   96 (579)
T 3sqw_A           17 VTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMV   96 (579)
T ss_dssp             CCHHHHHHTTSSCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSC
T ss_pred             cCHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccccccCCC
Confidence            3466664  2499999999999999999999999999999  78999999999999999999999999977532  2345


Q ss_pred             ceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984        140 GKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus       140 ~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      +++||+|||+||.|++..+..++..
T Consensus        97 ~~lvl~Ptr~La~Q~~~~~~~~~~~  121 (579)
T 3sqw_A           97 KAVIVAPTRDLALQIEAEVKKIHDM  121 (579)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEcchHHHHHHHHHHHHHHHhh
Confidence            8899999999999999999998754

>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=99.79  E-value=2.6e-19  Score=151.84  Aligned_cols=99  Identities=24%  Similarity=0.367  Sum_probs=89.3

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      .+|++++  +++.++++|.+.||..|+++|..+|+.++.|+|++++++||||||++|++|+++.+...  ....++++++
T Consensus        40 ~~f~~~~--l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~--~~~~~~lil~  115 (414)
T 3eiq_A           40 DSFDDMN--LSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELD--LKATQALVLA  115 (414)
T ss_dssp             CCGGGGC--CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTT--SCSCCEEEEC
T ss_pred             cCHhhCC--CCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhc--CCceeEEEEe
Confidence            5699998  99999999999999999999999999999999999999999999999999999987542  2455789999


Q ss_pred             ecHHHHHHHHHHHHHHhhhcCCC
Q psy12984        146 KLRPLTNGVYLVACNVFKSTQPP  168 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~~~~~~~  168 (178)
                      ||++|+.|+++.+..++...+..
T Consensus       116 P~~~L~~q~~~~~~~~~~~~~~~  138 (414)
T 3eiq_A          116 PTRELAQQIQKVVMALGDYMGAS  138 (414)
T ss_dssp             SSHHHHHHHHHHHHHHGGGSCCC
T ss_pred             ChHHHHHHHHHHHHHHhcccCce
Confidence            99999999999999988766543

>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=99.79  E-value=1.4e-19  Score=152.40  Aligned_cols=98  Identities=26%  Similarity=0.380  Sum_probs=88.3

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      .+|++++  |++.++++|..+||..|+++|.++|+.++.|+|+++++|||+|||++|++|++..+...  .....+++++
T Consensus        21 ~~f~~~~--l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~--~~~~~~lil~   96 (394)
T 1fuu_A           21 YKFDDME--LDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS--VKAPQALMLA   96 (394)
T ss_dssp             CSSGGGC--CCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTT--CCSCCEEEEC
T ss_pred             CChhhcC--CCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhcc--CCCCCEEEEc
Confidence            4599998  99999999999999999999999999999999999999999999999999999987543  3455889999


Q ss_pred             ecHHHHHHHHHHHHHHhhhcCC
Q psy12984        146 KLRPLTNGVYLVACNVFKSTQP  167 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~~~~~~  167 (178)
                      ||++|+.|++..+..+....+.
T Consensus        97 P~~~L~~q~~~~~~~~~~~~~~  118 (394)
T 1fuu_A           97 PTRELALQIQKVVMALAFHMDI  118 (394)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSCC
T ss_pred             CCHHHHHHHHHHHHHHhccCCe
Confidence            9999999999999988766543

>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=99.78  E-value=5e-19  Score=147.20  Aligned_cols=96  Identities=31%  Similarity=0.422  Sum_probs=86.8

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCC-CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEE
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEG-RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQ  144 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g-~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l  144 (178)
                      .+|++++  |++.++++|.++||..|+|+|..+|+.++.| +++++++|||||||++|++|++..+..   .+..+++++
T Consensus         6 ~~f~~~~--l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~---~~~~~~lil   80 (367)
T 1hv8_A            6 MNFNELN--LSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE---NNGIEAIIL   80 (367)
T ss_dssp             CCGGGSS--CCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCS---SSSCCEEEE
T ss_pred             CchhhcC--CCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhcc---cCCCcEEEE
Confidence            4699998  9999999999999999999999999999988 799999999999999999999987754   345688999


Q ss_pred             eecHHHHHHHHHHHHHHhhhcC
Q psy12984        145 GKLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus       145 ~Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      +|+++|+.|+++.+..+....+
T Consensus        81 ~P~~~L~~q~~~~~~~~~~~~~  102 (367)
T 1hv8_A           81 TPTRELAIQVADEIESLKGNKN  102 (367)
T ss_dssp             CSCHHHHHHHHHHHHHHHCSSC
T ss_pred             cCCHHHHHHHHHHHHHHhCCCC
Confidence            9999999999999999876543

>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=99.74  E-value=5.6e-18  Score=139.52  Aligned_cols=86  Identities=36%  Similarity=0.487  Sum_probs=78.3

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHH
Q psy12984         75 VCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGV  154 (178)
Q Consensus        75 l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi  154 (178)
                      |++++.++|.++||..|+|+|..+|+.++.|+++++++|||+|||++|++|+++.        ...+++++|+++|+.|+
T Consensus         1 l~~~i~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~--------~~~~liv~P~~~L~~q~   72 (337)
T 2z0m_A            1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL--------GMKSLVVTPTRELTRQV   72 (337)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH--------TCCEEEECSSHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhh--------cCCEEEEeCCHHHHHHH
Confidence            5789999999999999999999999999999999999999999999999999873        34789999999999999


Q ss_pred             HHHHHHHhhhcCCC
Q psy12984        155 YLVACNVFKSTQPP  168 (178)
Q Consensus       155 ~~~~~~l~~~~~~~  168 (178)
                      +..+..++..++..
T Consensus        73 ~~~~~~~~~~~~~~   86 (337)
T 2z0m_A           73 ASHIRDIGRYMDTK   86 (337)
T ss_dssp             HHHHHHHTTTSCCC
T ss_pred             HHHHHHHhhhcCCc
Confidence            99999987765543

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.68  E-value=7.2e-17  Score=138.08  Aligned_cols=80  Identities=16%  Similarity=0.074  Sum_probs=69.7

Q ss_pred             HHHHHHHH-CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHH
Q psy12984         78 NTLKAIAD-MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYL  156 (178)
Q Consensus        78 ~ll~~l~~-~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~  156 (178)
                      ++.+.+.+ .|| .|||+|..+|+.++.|+|+++++|||||||++|++|++..+     ..+.+++||+|||+||.|++.
T Consensus         9 ~~~~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~-----~~~~~~lil~Pt~~L~~q~~~   82 (414)
T 3oiy_A            9 DFRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA-----RKGKKSALVFPTVTLVKQTLE   82 (414)
T ss_dssp             HHHHHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHH-----TTTCCEEEEESSHHHHHHHHH
T ss_pred             HHHHHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHh-----cCCCEEEEEECCHHHHHHHHH
Confidence            34455655 577 89999999999999999999999999999999999998876     235689999999999999999


Q ss_pred             HHHHHhh
Q psy12984        157 VACNVFK  163 (178)
Q Consensus       157 ~~~~l~~  163 (178)
                      .+..++.
T Consensus        83 ~~~~~~~   89 (414)
T 3oiy_A           83 RLQKLAD   89 (414)
T ss_dssp             HHHHHCC
T ss_pred             HHHHHcc
Confidence            9999765

>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=99.68  E-value=9.2e-17  Score=147.30  Aligned_cols=90  Identities=22%  Similarity=0.257  Sum_probs=82.4

Q ss_pred             chHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhcc-ccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         67 QFEALKGKVCENTLKAIADMGFTKMTEIQARTIPP-LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        67 ~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~-~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      +|++++  |++++.+++...||..|+++|..+|+. ++.|++++++||||||||++|.+|+++.+...    +..++|++
T Consensus         2 ~f~~l~--l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~----~~~~l~i~   75 (720)
T 2zj8_A            2 RVDELR--VDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQ----GGKAVYIV   75 (720)
T ss_dssp             BGGGCC--SCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHH----CSEEEEEC
T ss_pred             cHhhcC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhC----CCEEEEEc
Confidence            589998  999999999999999999999999998 88999999999999999999999999988742    35889999


Q ss_pred             ecHHHHHHHHHHHHHHh
Q psy12984        146 KLRPLTNGVYLVACNVF  162 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~  162 (178)
                      |+|+||.|++..+..+.
T Consensus        76 P~raLa~q~~~~~~~l~   92 (720)
T 2zj8_A           76 PLKALAEEKFQEFQDWE   92 (720)
T ss_dssp             SSGGGHHHHHHHTGGGG
T ss_pred             CcHHHHHHHHHHHHHHH
Confidence            99999999999986543

>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=99.67  E-value=1.3e-17  Score=160.03  Aligned_cols=90  Identities=18%  Similarity=0.197  Sum_probs=77.0

Q ss_pred             chHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEee
Q psy12984         67 QFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGK  146 (178)
Q Consensus        67 ~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~P  146 (178)
                      .|..++  +++.+...+...++..|+++|..||+.++.|+|+|++|+||||||++|.+|++..+..     +.+++|++|
T Consensus       163 ~~~~~~--l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~-----g~rvlvl~P  235 (1108)
T 3l9o_A          163 NYDYTP--IAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN-----KQRVIYTSP  235 (1108)
T ss_dssp             CCCSST--TTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHT-----TCEEEEEES
T ss_pred             CcccCC--CChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhc-----CCeEEEEcC
Confidence            344444  6666666666667778999999999999999999999999999999999999998854     458999999


Q ss_pred             cHHHHHHHHHHHHHHhh
Q psy12984        147 LRPLTNGVYLVACNVFK  163 (178)
Q Consensus       147 tr~La~qi~~~~~~l~~  163 (178)
                      ||+||+|++..+..++.
T Consensus       236 traLa~Q~~~~l~~~~~  252 (1108)
T 3l9o_A          236 IKALSNQKYRELLAEFG  252 (1108)
T ss_dssp             SHHHHHHHHHHHHHHTS
T ss_pred             cHHHHHHHHHHHHHHhC
Confidence            99999999999998775

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.67  E-value=1.9e-16  Score=144.96  Aligned_cols=90  Identities=30%  Similarity=0.389  Sum_probs=82.2

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhcc-ccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEE
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPP-LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQ  144 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~-~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l  144 (178)
                      .+|++++  |++++.+++...||..|+++|..+|+. +..|++++++||||||||++|.+|+++.+...    +..++|+
T Consensus         8 ~~~~~l~--l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~----~~~il~i   81 (715)
T 2va8_A            8 MPIEDLK--LPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKN----GGKAIYV   81 (715)
T ss_dssp             CBGGGSS--SCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHS----CSEEEEE
T ss_pred             CcHHHcC--CCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHC----CCeEEEE
Confidence            4699998  999999999999999999999999999 78999999999999999999999999988642    3588999


Q ss_pred             eecHHHHHHHHHHHHHH
Q psy12984        145 GKLRPLTNGVYLVACNV  161 (178)
Q Consensus       145 ~Ptr~La~qi~~~~~~l  161 (178)
                      +|+|+||.|++..++.+
T Consensus        82 ~P~r~La~q~~~~~~~~   98 (715)
T 2va8_A           82 TPLRALTNEKYLTFKDW   98 (715)
T ss_dssp             CSCHHHHHHHHHHHGGG
T ss_pred             eCcHHHHHHHHHHHHHh
Confidence            99999999999998544

>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=99.66  E-value=1.1e-16  Score=144.75  Aligned_cols=82  Identities=18%  Similarity=0.235  Sum_probs=74.9

Q ss_pred             hhcccCCHHHHHHHHH-CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecH
Q psy12984         70 ALKGKVCENTLKAIAD-MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLR  148 (178)
Q Consensus        70 ~l~~~l~~~ll~~l~~-~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr  148 (178)
                      +++  +++.+.+.|.+ +||..|+|+|..+|+.++.|+|+++.+|||+|||++|++|++..        ...++||+||+
T Consensus        25 ~~~--l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~~--------~g~~lVisP~~   94 (591)
T 2v1x_A           25 DFP--WSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCS--------DGFTLVICPLI   94 (591)
T ss_dssp             CST--THHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHTS--------SSEEEEECSCH
T ss_pred             cCC--CCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHHc--------CCcEEEEeCHH
Confidence            455  89999999998 79999999999999999999999999999999999999999751        34789999999


Q ss_pred             HHHHHHHHHHHHH
Q psy12984        149 PLTNGVYLVACNV  161 (178)
Q Consensus       149 ~La~qi~~~~~~l  161 (178)
                      +|+.|++..+..+
T Consensus        95 ~L~~q~~~~l~~~  107 (591)
T 2v1x_A           95 SLMEDQLMVLKQL  107 (591)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhc
Confidence            9999999999886

>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=99.65  E-value=4.4e-17  Score=149.07  Aligned_cols=90  Identities=19%  Similarity=0.238  Sum_probs=79.1

Q ss_pred             chHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEee
Q psy12984         67 QFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGK  146 (178)
Q Consensus        67 ~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~P  146 (178)
                      +|++|+.+|++.+.+++...||..|+++|.++|+.++.|++++++||||||||++|.+|+++.+..     +.+++|++|
T Consensus         2 ~f~~l~~~l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~-----~~~~l~i~P   76 (702)
T 2p6r_A            2 KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK-----GGKSLYVVP   76 (702)
T ss_dssp             CSHHHHHHHHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT-----TCCEEEEES
T ss_pred             chhhhhhccCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHh-----CCcEEEEeC
Confidence            477886669999999999999999999999999999999999999999999999999999998764     358899999


Q ss_pred             cHHHHHHHHHHHHHH
Q psy12984        147 LRPLTNGVYLVACNV  161 (178)
Q Consensus       147 tr~La~qi~~~~~~l  161 (178)
                      +|+||.|++..++.+
T Consensus        77 ~r~La~q~~~~~~~~   91 (702)
T 2p6r_A           77 LRALAGEKYESFKKW   91 (702)
T ss_dssp             SHHHHHHHHHHHTTT
T ss_pred             cHHHHHHHHHHHHHH
Confidence            999999999998543

>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=99.64  E-value=8.6e-17  Score=143.26  Aligned_cols=85  Identities=24%  Similarity=0.298  Sum_probs=77.6

Q ss_pred             chHhhcccCCHHHHHHHHH-CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         67 QFEALKGKVCENTLKAIAD-MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        67 ~f~~l~~~l~~~ll~~l~~-~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      .|++++  |++.+.+.|.+ +||..|+|+|.++|+.++.|+|+++++|||+|||++|++|++..        ...++||+
T Consensus         3 ~fe~l~--L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~--------~g~~lvi~   72 (523)
T 1oyw_A            3 QAEVLN--LESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL--------NGLTVVVS   72 (523)
T ss_dssp             CCCCSS--HHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS--------SSEEEEEC
T ss_pred             ChhhCC--CCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHh--------CCCEEEEC
Confidence            588887  99999999998 89999999999999999999999999999999999999999742        23679999


Q ss_pred             ecHHHHHHHHHHHHHH
Q psy12984        146 KLRPLTNGVYLVACNV  161 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l  161 (178)
                      |+++|+.|++..+..+
T Consensus        73 P~~aL~~q~~~~l~~~   88 (523)
T 1oyw_A           73 PLISLMKDQVDQLQAN   88 (523)
T ss_dssp             SCHHHHHHHHHHHHHT
T ss_pred             ChHHHHHHHHHHHHHc
Confidence            9999999999998875

>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=99.63  E-value=4.4e-16  Score=144.88  Aligned_cols=76  Identities=20%  Similarity=0.113  Sum_probs=68.5

Q ss_pred             HCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984         85 DMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus        85 ~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      .+|| +||+||..+||.++.|+  |+.++||+|||++|++|++...+.     +.+++||+|||+||.|++.++..+.++
T Consensus        79 ~lG~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL~-----g~~vlVltptreLA~qd~e~~~~l~~~  150 (844)
T 1tf5_A           79 VTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALT-----GKGVHVVTVNEYLASRDAEQMGKIFEF  150 (844)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTT-----SSCEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             HcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHHc-----CCCEEEEeCCHHHHHHHHHHHHHHHhh
Confidence            4899 99999999999999999  899999999999999999854432     458999999999999999999999999


Q ss_pred             cCCC
Q psy12984        165 TQPP  168 (178)
Q Consensus       165 ~~~~  168 (178)
                      ++..
T Consensus       151 lgl~  154 (844)
T 1tf5_A          151 LGLT  154 (844)
T ss_dssp             TTCC
T ss_pred             cCCe
Confidence            8654

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.63  E-value=4e-16  Score=141.53  Aligned_cols=87  Identities=16%  Similarity=0.133  Sum_probs=72.5

Q ss_pred             HHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHH
Q psy12984         80 LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVAC  159 (178)
Q Consensus        80 l~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~  159 (178)
                      ..++..+||..|+++|..+|+.++.|+|+|++++||+|||++|++|+++.+..........+++|+||++|+.|++.++.
T Consensus         3 ~~~l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L~~Q~~~~~~   82 (696)
T 2ykg_A            3 VSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVFS   82 (696)
T ss_dssp             ----CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHHHHHHHHHHH
T ss_pred             CCcccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHHHHHHHHHHH
Confidence            34577889999999999999999999999999999999999999999998876543334688999999999999999999


Q ss_pred             HHhhhcC
Q psy12984        160 NVFKSTQ  166 (178)
Q Consensus       160 ~l~~~~~  166 (178)
                      .++...+
T Consensus        83 ~~~~~~~   89 (696)
T 2ykg_A           83 KYFERHG   89 (696)
T ss_dssp             HHTTTTT
T ss_pred             HHhccCC
Confidence            9886543

>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=99.62  E-value=1e-15  Score=134.30  Aligned_cols=83  Identities=19%  Similarity=0.175  Sum_probs=70.5

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      ++...|+|+|..+|+.++.|+|++++++||||||++|++|+++.+..........++||+||++|+.|++..+..++...
T Consensus         3 ~~~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~   82 (556)
T 4a2p_A            3 METKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQ   82 (556)
T ss_dssp             -----CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGG
T ss_pred             CCCCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhccc
Confidence            34558999999999999999999999999999999999999999987544446789999999999999999999998876


Q ss_pred             CCC
Q psy12984        166 QPP  168 (178)
Q Consensus       166 ~~~  168 (178)
                      +..
T Consensus        83 ~~~   85 (556)
T 4a2p_A           83 GYS   85 (556)
T ss_dssp             TCC
T ss_pred             Cce
Confidence            443

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.61  E-value=1.3e-15  Score=133.22  Aligned_cols=79  Identities=18%  Similarity=0.154  Sum_probs=71.4

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhcCCC
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQPP  168 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~~~  168 (178)
                      .|+|+|..+|+.++.|+|++++++||+|||++|++|+++.+..........++||+||++|+.|++..+..++...+..
T Consensus         4 ~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~   82 (555)
T 3tbk_A            4 KPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFERLGYN   82 (555)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTTTCC
T ss_pred             CCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhccCCcE
Confidence            7999999999999999999999999999999999999999987544446789999999999999999999998776443

>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=99.58  E-value=3.5e-15  Score=142.56  Aligned_cols=82  Identities=15%  Similarity=-0.012  Sum_probs=72.2

Q ss_pred             HHHHHH-HCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHH
Q psy12984         79 TLKAIA-DMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLV  157 (178)
Q Consensus        79 ll~~l~-~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~  157 (178)
                      +.+.+. .+||. | ++|..+||.++.|+|++++|+||||||+ |++|++.++..    .+.++++|+|||+||.|++.+
T Consensus        46 ~~~~~~~~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~----~~~~~lil~PtreLa~Q~~~~  118 (1054)
T 1gku_B           46 FVEFFRKCVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLAL----KGKRCYVIFPTSLLVIQAAET  118 (1054)
T ss_dssp             HHHHHHTTTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHT----TSCCEEEEESCHHHHHHHHHH
T ss_pred             HHHHHHHhcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhh----cCCeEEEEeccHHHHHHHHHH
Confidence            334443 48999 9 9999999999999999999999999999 99999998864    356899999999999999999


Q ss_pred             HHHHhhhcCC
Q psy12984        158 ACNVFKSTQP  167 (178)
Q Consensus       158 ~~~l~~~~~~  167 (178)
                      +..++..++.
T Consensus       119 l~~l~~~~~i  128 (1054)
T 1gku_B          119 IRKYAEKAGV  128 (1054)
T ss_dssp             HHHHHTTTCC
T ss_pred             HHHHHhhcCC
Confidence            9999987765

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}

Probab=99.58  E-value=3.8e-15  Score=138.18  Aligned_cols=84  Identities=18%  Similarity=0.144  Sum_probs=71.5

Q ss_pred             HCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984         85 DMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus        85 ~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      -+|+..|+|+|..+|+.++.|+|+|++++||||||++|++|++..+..........++||+||++|+.|++..+..++..
T Consensus       243 ~~g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~Pt~~L~~Q~~~~~~~~~~~  322 (797)
T 4a2q_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFER  322 (797)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGG
T ss_pred             hcCCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHhccc
Confidence            46899999999999999999999999999999999999999999998754444678999999999999999999999876


Q ss_pred             cCCC
Q psy12984        165 TQPP  168 (178)
Q Consensus       165 ~~~~  168 (178)
                      .+..
T Consensus       323 ~~~~  326 (797)
T 4a2q_A          323 QGYS  326 (797)
T ss_dssp             GTCC
T ss_pred             CCce
Confidence            6433

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.57  E-value=5.3e-15  Score=141.92  Aligned_cols=78  Identities=17%  Similarity=0.064  Sum_probs=67.8

Q ss_pred             HHHHHH-HCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHH
Q psy12984         79 TLKAIA-DMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLV  157 (178)
Q Consensus        79 ll~~l~-~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~  157 (178)
                      +.+.+. ..|| .|||+|..|||.++.|+|++++|+||||||++|++|++..+     ..+.+++||+|||+||.|++..
T Consensus        67 ~~~~~~~~~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~-----~~~~~~Lil~PtreLa~Q~~~~  140 (1104)
T 4ddu_A           67 FRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA-----RKGKKSALVFPTVTLVKQTLER  140 (1104)
T ss_dssp             HHHHHHHHSSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHH-----TTTCCEEEEESSHHHHHHHHHH
T ss_pred             HHHHHHHhcCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHH-----hcCCeEEEEechHHHHHHHHHH
Confidence            334443 3789 69999999999999999999999999999999988888877     2356899999999999999999


Q ss_pred             HHHHh
Q psy12984        158 ACNVF  162 (178)
Q Consensus       158 ~~~l~  162 (178)
                      +..++
T Consensus       141 l~~l~  145 (1104)
T 4ddu_A          141 LQKLA  145 (1104)
T ss_dssp             HHTTS
T ss_pred             HHHhh
Confidence            99865

>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=99.53  E-value=5.5e-15  Score=137.48  Aligned_cols=75  Identities=20%  Similarity=0.106  Sum_probs=67.4

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      +|. +||+||..++|.++.|+  |+.++||||||++|++|++.....     +.++++++|||+||.|++.++..+.+++
T Consensus        71 lg~-~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l~-----g~~vlVltPTreLA~Q~~e~~~~l~~~l  142 (853)
T 2fsf_A           71 FGM-RHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNALT-----GKGVHVVTVNDYLAQRDAENNRPLFEFL  142 (853)
T ss_dssp             HSC-CCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHTT-----SSCCEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred             cCC-CCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHHc-----CCcEEEEcCCHHHHHHHHHHHHHHHHhc
Confidence            576 99999999999999998  899999999999999999875543     4589999999999999999999999988


Q ss_pred             CCC
Q psy12984        166 QPP  168 (178)
Q Consensus       166 ~~~  168 (178)
                      +..
T Consensus       143 gl~  145 (853)
T 2fsf_A          143 GLT  145 (853)
T ss_dssp             TCC
T ss_pred             CCe
Confidence            654

>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=99.53  E-value=9.7e-15  Score=137.98  Aligned_cols=85  Identities=18%  Similarity=0.131  Sum_probs=70.0

Q ss_pred             HHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         83 IADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        83 l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      ..-.|+..|+++|..+|+.++.|+|+|++++||+|||++|++|+++.+..........++||+||++|+.|++..+..++
T Consensus       241 ~~l~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~  320 (936)
T 4a2w_A          241 PPVYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHF  320 (936)
T ss_dssp             -------CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHHHHHHHHHHHHHH
T ss_pred             ccccCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHHh
Confidence            34457889999999999999999999999999999999999999998876543336688999999999999999999998


Q ss_pred             hhcCC
Q psy12984        163 KSTQP  167 (178)
Q Consensus       163 ~~~~~  167 (178)
                      ...+.
T Consensus       321 ~~~~~  325 (936)
T 4a2w_A          321 ERQGY  325 (936)
T ss_dssp             HTTTC
T ss_pred             cccCc
Confidence            76543

>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=99.53  E-value=1.4e-14  Score=143.93  Aligned_cols=95  Identities=17%  Similarity=0.246  Sum_probs=79.5

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHhhccccC-CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHH
Q psy12984         75 VCENTLKAIADMGFTKMTEIQARTIPPLLE-GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNG  153 (178)
Q Consensus        75 l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~-g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~q  153 (178)
                      |.+...+++...+|..++|+|.++|+.++. +.|++++||||||||++|.+|+++.+..   .++.+++|++|||+||+|
T Consensus       911 L~~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~---~~~~kavyi~P~raLa~q  987 (1724)
T 4f92_B          911 LRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQ---SSEGRCVYITPMEALAEQ  987 (1724)
T ss_dssp             SCCHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHH---CTTCCEEEECSCHHHHHH
T ss_pred             ccCHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHh---CCCCEEEEEcChHHHHHH
Confidence            667788889888999999999999999875 5789999999999999999999999976   345589999999999999


Q ss_pred             HHHHHHHHhhhcCCCCcceEEE
Q psy12984        154 VYLVACNVFKSTQPPTVIKVQT  175 (178)
Q Consensus       154 i~~~~~~l~~~~~~~~~~~v~~  175 (178)
                      ++..+...++.   .++++|..
T Consensus       988 ~~~~~~~~f~~---~~g~~V~~ 1006 (1724)
T 4f92_B          988 VYMDWYEKFQD---RLNKKVVL 1006 (1724)
T ss_dssp             HHHHHHHHHTT---TSCCCEEE
T ss_pred             HHHHHHHHhch---hcCCEEEE
Confidence            99998765432   33444443

>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=99.52  E-value=1.8e-14  Score=134.64  Aligned_cols=77  Identities=22%  Similarity=0.132  Sum_probs=68.8

Q ss_pred             HCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984         85 DMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus        85 ~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      .+|+ +||+||..++|.++.|+  |+.++||+|||++|.+|++...+.     +.+++|++||++||.|++.++..+..+
T Consensus       107 ~lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~-----g~~v~VvTpTreLA~Qdae~m~~l~~~  178 (922)
T 1nkt_A          107 VLDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALA-----GNGVHIVTVNDYLAKRDSEWMGRVHRF  178 (922)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTT-----TSCEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             HcCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHh-----CCCeEEEeCCHHHHHHHHHHHHHHHhh
Confidence            3799 99999999999999998  999999999999999999765543     348999999999999999999999999


Q ss_pred             cCCCC
Q psy12984        165 TQPPT  169 (178)
Q Consensus       165 ~~~~~  169 (178)
                      ++..+
T Consensus       179 lGLsv  183 (922)
T 1nkt_A          179 LGLQV  183 (922)
T ss_dssp             TTCCE
T ss_pred             cCCeE
Confidence            86553

>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=99.50  E-value=3.5e-14  Score=110.29  Aligned_cols=79  Identities=19%  Similarity=0.074  Sum_probs=66.7

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhcc-CCCCCceEEEeecHHHHHH-HHHHHHHHhh
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLK-FMPRNGKSWQGKLRPLTNG-VYLVACNVFK  163 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~-~~~~~~~~~l~Ptr~La~q-i~~~~~~l~~  163 (178)
                      .+...|+++|..+++.++.|++++++++||+|||++|+++++..+.... .....++++++|+++|+.| +.+.+..+..
T Consensus        29 ~~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~~~~~~~~~  108 (216)
T 3b6e_A           29 EPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLK  108 (216)
T ss_dssp             SCCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTHHHHHT
T ss_pred             cCCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHHHHHHHHhc
Confidence            4455899999999999999999999999999999999999998876532 1235588999999999999 7777877764


Q ss_pred             h
Q psy12984        164 S  164 (178)
Q Consensus       164 ~  164 (178)
                      .
T Consensus       109 ~  109 (216)
T 3b6e_A          109 K  109 (216)
T ss_dssp             T
T ss_pred             c
Confidence            3

>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=99.49  E-value=4.4e-14  Score=131.44  Aligned_cols=83  Identities=17%  Similarity=0.145  Sum_probs=72.4

Q ss_pred             HHHHHHHCCCCCCcHHHHHhhccccCC------CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHH
Q psy12984         79 TLKAIADMGFTKMTEIQARTIPPLLEG------RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTN  152 (178)
Q Consensus        79 ll~~l~~~g~~~pt~iQ~~aip~~l~g------~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~  152 (178)
                      +.+.+..+|| .||++|..+|+.++.+      +|++++++||||||++|++|++..+..     +.++++++||++||.
T Consensus       358 ~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~-----g~qvlvlaPtr~La~  431 (780)
T 1gm5_A          358 AEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA-----GFQTAFMVPTSILAI  431 (780)
T ss_dssp             HHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH-----TSCEEEECSCHHHHH
T ss_pred             HHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHc-----CCeEEEEeCcHHHHH
Confidence            4444577999 9999999999998865      699999999999999999999998864     458999999999999


Q ss_pred             HHHHHHHHHhhhcCC
Q psy12984        153 GVYLVACNVFKSTQP  167 (178)
Q Consensus       153 qi~~~~~~l~~~~~~  167 (178)
                      |++..+..++..++.
T Consensus       432 Q~~~~l~~~~~~~gi  446 (780)
T 1gm5_A          432 QHYRRTVESFSKFNI  446 (780)
T ss_dssp             HHHHHHHHHHTCSSC
T ss_pred             HHHHHHHHHhhhcCc
Confidence            999999999865543

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.49  E-value=4.3e-14  Score=132.18  Aligned_cols=77  Identities=19%  Similarity=0.144  Sum_probs=68.6

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      +|| +||+||..++|+++.|+  |++++||||||++|++|++.....     +.++++++||++||.|++.++..+..++
T Consensus        76 lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~-----G~qv~VvTPTreLA~Qdae~m~~l~~~l  147 (997)
T 2ipc_A           76 LGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNALT-----GKGVHVVTVNDYLARRDAEWMGPVYRGL  147 (997)
T ss_dssp             TCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTT-----CSCCEEEESSHHHHHHHHHHHHHHHHTT
T ss_pred             hCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHh-----CCCEEEEeCCHHHHHHHHHHHHHHHHhc
Confidence            899 99999999999999998  899999999999999999754443     3478999999999999999999999988


Q ss_pred             CCCCc
Q psy12984        166 QPPTV  170 (178)
Q Consensus       166 ~~~~~  170 (178)
                      +..++
T Consensus       148 GLsv~  152 (997)
T 2ipc_A          148 GLSVG  152 (997)
T ss_dssp             TCCEE
T ss_pred             CCeEE
Confidence            75543

>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=99.49  E-value=1.3e-14  Score=126.83  Aligned_cols=68  Identities=15%  Similarity=0.031  Sum_probs=61.2

Q ss_pred             CCCCCcHHHHHhhccccCCCcE-EEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHH
Q psy12984         87 GFTKMTEIQARTIPPLLEGRDL-VGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVAC  159 (178)
Q Consensus        87 g~~~pt~iQ~~aip~~l~g~dv-i~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~  159 (178)
                      ||..|+|+|+ +||.++.|+|+ +++|+||||||++|++|++..+..    .+.+++|++|||+||.|++..+.
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~----~~~~~lvl~Ptr~La~Q~~~~l~   69 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALL----RRLRTLILAPTRVVAAEMEEALR   69 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHH----TTCCEEEEESSHHHHHHHHHHTT
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHh----cCCcEEEECCCHHHHHHHHHHhc
Confidence            7889999985 79999999888 999999999999999999988765    34689999999999999999875

>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=99.49  E-value=3.1e-15  Score=135.98  Aligned_cols=80  Identities=14%  Similarity=-0.026  Sum_probs=66.3

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHH
Q psy12984         75 VCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGV  154 (178)
Q Consensus        75 l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi  154 (178)
                      +++.++++|... +..|+|+|+.++|.++.|+|++++|+||||||++|++|+++.+..    .+.+++|++|||+||.|+
T Consensus       157 ~~~~~~~~l~~~-~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~----~~~~vLvl~PtreLa~Qi  231 (618)
T 2whx_A          157 KSGDYVSAITQA-ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALK----RRLRTLILAPTRVVAAEM  231 (618)
T ss_dssp             -----CEECBCC-CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHH----TTCCEEEEESSHHHHHHH
T ss_pred             chHHHHHHHhhc-cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHh----CCCeEEEEcChHHHHHHH
Confidence            666666555443 588999999999999999999999999999999999999998865    346899999999999999


Q ss_pred             HHHHH
Q psy12984        155 YLVAC  159 (178)
Q Consensus       155 ~~~~~  159 (178)
                      +..+.
T Consensus       232 ~~~l~  236 (618)
T 2whx_A          232 EEALR  236 (618)
T ss_dssp             HHHTT
T ss_pred             HHHhc
Confidence            98875

>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=99.48  E-value=4.8e-14  Score=140.08  Aligned_cols=81  Identities=20%  Similarity=0.166  Sum_probs=70.6

Q ss_pred             CCCCCcHHHHHhhcccc-CCCcEEEEccCCCchhhHhHHHHHHHHHhccC------CCCCceEEEeecHHHHHHHHHHHH
Q psy12984         87 GFTKMTEIQARTIPPLL-EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKF------MPRNGKSWQGKLRPLTNGVYLVAC  159 (178)
Q Consensus        87 g~~~pt~iQ~~aip~~l-~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~------~~~~~~~~l~Ptr~La~qi~~~~~  159 (178)
                      ||++++++|.+++|.++ .+.|++++||||||||++|.+|+++.+.+...      ..+.+++|++|+||||+|+++.++
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            89999999999999876 57899999999999999999999999976422      234578999999999999999999


Q ss_pred             HHhhhcCC
Q psy12984        160 NVFKSTQP  167 (178)
Q Consensus       160 ~l~~~~~~  167 (178)
                      ..++.++.
T Consensus       156 ~~~~~~gi  163 (1724)
T 4f92_B          156 KRLATYGI  163 (1724)
T ss_dssp             HHHTTTTC
T ss_pred             HHHhhCCC
Confidence            88876554

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.44  E-value=1.4e-14  Score=132.92  Aligned_cols=76  Identities=14%  Similarity=0.123  Sum_probs=64.7

Q ss_pred             HHHHCCCC-----CCcHHHH-----Hhhcccc------CCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         82 AIADMGFT-----KMTEIQA-----RTIPPLL------EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        82 ~l~~~g~~-----~pt~iQ~-----~aip~~l------~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      +|..+||.     .||++|+     .+||.++      .|+|++++|+||||||++|++|++..+..    .+.+++|++
T Consensus       202 ~l~~~Gf~~~~~~~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~----~~~~~lila  277 (673)
T 2wv9_A          202 GLYGNGVILGNGAYVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQ----KRLRTAVLA  277 (673)
T ss_dssp             EEEEEEEECSSSCEEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHH----TTCCEEEEE
T ss_pred             EeeeccccccCCCccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHh----CCCcEEEEc
Confidence            46667888     9999999     9999998      89999999999999999999999998765    346899999


Q ss_pred             ecHHHHHHHHHHHHHH
Q psy12984        146 KLRPLTNGVYLVACNV  161 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l  161 (178)
                      |||+||.|++..+..+
T Consensus       278 PTr~La~Q~~~~l~~~  293 (673)
T 2wv9_A          278 PTRVVAAEMAEALRGL  293 (673)
T ss_dssp             SSHHHHHHHHHHTTTS
T ss_pred             cHHHHHHHHHHHHhcC
Confidence            9999999999987644

>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=99.41  E-value=1.6e-13  Score=124.39  Aligned_cols=75  Identities=19%  Similarity=0.111  Sum_probs=66.6

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccC-CCCCceEEEeecHHHHHHH-HHHHHHHhhh
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKF-MPRNGKSWQGKLRPLTNGV-YLVACNVFKS  164 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~-~~~~~~~~l~Ptr~La~qi-~~~~~~l~~~  164 (178)
                      .|+++|..+|+.++.|+|+|++++||+|||++|++|+++.+..... .....++||+|+++|+.|+ +..+..++..
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            7999999999999999999999999999999999999998876422 2235789999999999999 9999998764

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.40  E-value=3.2e-13  Score=128.63  Aligned_cols=75  Identities=21%  Similarity=0.275  Sum_probs=67.1

Q ss_pred             HHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         83 IADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        83 l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      ....+|. |+++|..||+.++.|++++++||||||||++|.+|++..+..     +.+++|++|||+|++|++..|..++
T Consensus        80 ~~~~~f~-L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~~-----g~rvL~l~PtkaLa~Q~~~~l~~~~  153 (1010)
T 2xgj_A           80 ARTYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN-----KQRVIYTSPIKALSNQKYRELLAEF  153 (1010)
T ss_dssp             SCCCSSC-CCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHT-----TCEEEEEESSHHHHHHHHHHHHHHH
T ss_pred             HHhCCCC-CCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhcc-----CCeEEEECChHHHHHHHHHHHHHHh
Confidence            3446784 999999999999999999999999999999999999988743     3589999999999999999999877


Q ss_pred             h
Q psy12984        163 K  163 (178)
Q Consensus       163 ~  163 (178)
                      .
T Consensus       154 ~  154 (1010)
T 2xgj_A          154 G  154 (1010)
T ss_dssp             S
T ss_pred             C
Confidence            5

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=99.39  E-value=1e-12  Score=104.99  Aligned_cols=87  Identities=8%  Similarity=-0.030  Sum_probs=68.9

Q ss_pred             CHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHH
Q psy12984         76 CENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVY  155 (178)
Q Consensus        76 ~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~  155 (178)
                      ++.+.+.+...+...++++|..+++.+..|++++++|+||||||.+|.+++++.+.........++++++|+|+||.|++
T Consensus        47 ~~~~~~~~~~~~~~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~  126 (235)
T 3llm_A           47 DHDLQAILQERELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVA  126 (235)
T ss_dssp             CHHHHHHHHHHHTSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHH
T ss_pred             CHHHHHHHHHHhcCChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHH
Confidence            34444444443444679999999999999999999999999999999999999877644334557888999999999998


Q ss_pred             HHHHHHh
Q psy12984        156 LVACNVF  162 (178)
Q Consensus       156 ~~~~~l~  162 (178)
                      +.+....
T Consensus       127 ~~~~~~~  133 (235)
T 3llm_A          127 ERVAFER  133 (235)
T ss_dssp             HHHHHTT
T ss_pred             HHHHHHh
Confidence            8776543

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.36  E-value=8.3e-13  Score=125.66  Aligned_cols=73  Identities=18%  Similarity=0.222  Sum_probs=64.3

Q ss_pred             HCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984         85 DMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus        85 ~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      .++| .|+++|..+|+.++.|+|++++++||||||++|++|+...+..     +.+++|++|||+|+.|++..+..++.
T Consensus        35 ~~~f-~l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~~-----g~~vlvl~PtraLa~Q~~~~l~~~~~  107 (997)
T 4a4z_A           35 SWPF-ELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRN-----MTKTIYTSPIKALSNQKFRDFKETFD  107 (997)
T ss_dssp             CCSS-CCCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHHT-----TCEEEEEESCGGGHHHHHHHHHTTC-
T ss_pred             hCCC-CCCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHhc-----CCeEEEEeCCHHHHHHHHHHHHHHcC
Confidence            3577 5899999999999999999999999999999999999886643     45789999999999999999988653

>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=99.31  E-value=4.1e-12  Score=122.39  Aligned_cols=86  Identities=19%  Similarity=0.097  Sum_probs=70.9

Q ss_pred             CCHHHHHHH-HHCCCCCCcHHHHHhhccccC----CC--cEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeec
Q psy12984         75 VCENTLKAI-ADMGFTKMTEIQARTIPPLLE----GR--DLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKL  147 (178)
Q Consensus        75 l~~~ll~~l-~~~g~~~pt~iQ~~aip~~l~----g~--dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Pt  147 (178)
                      ++..+.+.+ ...|| .|||+|..||+.++.    |+  |++++++||+|||++|+++++..+..     +.++++++||
T Consensus       588 ~~~~~~~~~~~~f~~-~~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~-----g~~vlvlvPt  661 (1151)
T 2eyq_A          588 HDREQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN-----HKQVAVLVPT  661 (1151)
T ss_dssp             CCHHHHHHHHHTCCS-CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT-----TCEEEEECSS
T ss_pred             CCHHHHHHHHHhCCC-CCCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHh-----CCeEEEEech
Confidence            445555555 34788 479999999999876    65  99999999999999999999886643     4489999999


Q ss_pred             HHHHHHHHHHHHHHhhhcC
Q psy12984        148 RPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus       148 r~La~qi~~~~~~l~~~~~  166 (178)
                      ++||.|++..+...+..++
T Consensus       662 ~~La~Q~~~~~~~~~~~~~  680 (1151)
T 2eyq_A          662 TLLAQQHYDNFRDRFANWP  680 (1151)
T ss_dssp             HHHHHHHHHHHHHHSTTTT
T ss_pred             HHHHHHHHHHHHHHhhcCC
Confidence            9999999999998776544

>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=99.31  E-value=2.2e-12  Score=105.43  Aligned_cols=70  Identities=14%  Similarity=-0.074  Sum_probs=61.9

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      .|+++|..+++.++.+.+.+++++||+|||+++++++...+..    ....+++++||++|+.|+++.+..++.
T Consensus       113 ~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~----~~~~~lil~Pt~~L~~q~~~~l~~~~~  182 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN----YEGKILIIVPTTALTTQMADDFVDYRL  182 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHH----CSSEEEEECSSHHHHHHHHHHHHHHTS
T ss_pred             CccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHc----CCCeEEEEECCHHHHHHHHHHHHHhcc
Confidence            7999999999999988889999999999999999988887654    223789999999999999999998754

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.30  E-value=2.3e-12  Score=112.97  Aligned_cols=72  Identities=14%  Similarity=-0.089  Sum_probs=63.9

Q ss_pred             CCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984         88 FTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus        88 ~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      ...|+++|..|++.++.++|++++++||+|||++|++|+...+..    ...++++|+||++|+.|++..+..+..
T Consensus       111 ~~~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~----~~~~vlvl~P~~~L~~Q~~~~~~~~~~  182 (510)
T 2oca_A          111 RIEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN----YEGKILIIVPTTALTTQMADDFVDYRL  182 (510)
T ss_dssp             EECCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHH----CSSEEEEEESSHHHHHHHHHHHHHTTS
T ss_pred             CCCCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhC----CCCeEEEEECcHHHHHHHHHHHHHhhc
Confidence            348999999999999999999999999999999999999887764    234889999999999999999988743

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=99.29  E-value=8.8e-12  Score=108.22  Aligned_cols=64  Identities=17%  Similarity=0.039  Sum_probs=58.3

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      .|+++|..+++.++.+.+++++++||+|||++|++++...        ...++|++|+++|+.|++..|..+
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            6899999999999999999999999999999999998763        347899999999999999998873

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.27  E-value=3.1e-12  Score=114.30  Aligned_cols=70  Identities=20%  Similarity=0.126  Sum_probs=59.9

Q ss_pred             CCCCCcHHHHHhhcc----ccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         87 GFTKMTEIQARTIPP----LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        87 g~~~pt~iQ~~aip~----~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      || .|.|.|...+..    +..|+|+++.||||+|||++|++|++.        ...+++|++||++|+.|+.+.+..+.
T Consensus         1 ~~-~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~--------~~~~v~i~~pt~~l~~q~~~~~~~l~   71 (551)
T 3crv_A            1 MV-KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLE--------VKPKVLFVVRTHNEFYPIYRDLTKIR   71 (551)
T ss_dssp             CC-SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHH--------HCSEEEEEESSGGGHHHHHHHHTTCC
T ss_pred             CC-CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHh--------CCCeEEEEcCCHHHHHHHHHHHHHHh
Confidence            45 789999987764    468999999999999999999999997        24588999999999999999888776


Q ss_pred             hhc
Q psy12984        163 KST  165 (178)
Q Consensus       163 ~~~  165 (178)
                      +..
T Consensus        72 ~~~   74 (551)
T 3crv_A           72 EKR   74 (551)
T ss_dssp             CSS
T ss_pred             hhc
Confidence            554

>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=99.25  E-value=9.5e-12  Score=105.66  Aligned_cols=69  Identities=17%  Similarity=0.017  Sum_probs=62.6

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      .|+|+|..+++.++.+ +++++++||+|||++++++++..+..    ....++|++|+++|+.|++..+..+++
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~~----~~~~~liv~P~~~L~~q~~~~~~~~~~   77 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLTK----YGGKVLMLAPTKPLVLQHAESFRRLFN   77 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHHH----SCSCEEEECSSHHHHHHHHHHHHHHBC
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHhc----CCCeEEEEECCHHHHHHHHHHHHHHhC
Confidence            7999999999999999 99999999999999999999988762    345889999999999999999998763

>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=99.24  E-value=6.4e-12  Score=110.01  Aligned_cols=57  Identities=18%  Similarity=0.038  Sum_probs=50.2

Q ss_pred             hccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHH
Q psy12984         99 IPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVAC  159 (178)
Q Consensus        99 ip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~  159 (178)
                      ...+..|++++++|+||||||++|++|+++.+..    .+.+++|++|||+||.|++..+.
T Consensus        15 ~~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~----~~~~~lvl~Ptr~La~Q~~~~l~   71 (459)
T 2z83_A           15 PNMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQ----QRLRTAVLAPTRVVAAEMAEALR   71 (459)
T ss_dssp             CGGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHH----TTCCEEEEECSHHHHHHHHHHTT
T ss_pred             HHHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHh----CCCcEEEECchHHHHHHHHHHhc
Confidence            4456788999999999999999999999998864    24589999999999999999876

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.22  E-value=1.6e-11  Score=111.63  Aligned_cols=72  Identities=17%  Similarity=0.119  Sum_probs=61.2

Q ss_pred             CCcHHHHHhhc----cccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         90 KMTEIQARTIP----PLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        90 ~pt~iQ~~aip----~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      .|.+.|...+.    .+..|+|+++.||||+|||++|++|++.++...    ..+++|++||++|+.|+.+.+..+....
T Consensus         3 ~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~----~~kvli~t~T~~l~~Qi~~el~~l~~~~   78 (620)
T 4a15_A            3 ENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSER----KLKVLYLVRTNSQEEQVIKELRSLSSTM   78 (620)
T ss_dssp             --CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHHH----TCEEEEEESSHHHHHHHHHHHHHHHHHS
T ss_pred             CCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhhc----CCeEEEECCCHHHHHHHHHHHHHHhhcc
Confidence            67888888775    456899999999999999999999999988642    3478999999999999999999988764

>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=99.21  E-value=1e-11  Score=108.18  Aligned_cols=57  Identities=19%  Similarity=0.088  Sum_probs=50.5

Q ss_pred             cccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984        101 PLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus       101 ~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      .++.|+|++++|+||||||++|++|+++.+..    .+.+++|++|||+||.|++..+..+
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~----~~~~~lil~Ptr~La~Q~~~~l~~~   60 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECAR----RRLRTLVLAPTRVVLSEMKEAFHGL   60 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHH----TTCCEEEEESSHHHHHHHHHHTTTS
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHh----cCCeEEEEcchHHHHHHHHHHHhcC
Confidence            57889999999999999999999999998865    2458999999999999999988743

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=99.19  E-value=5e-11  Score=95.78  Aligned_cols=63  Identities=17%  Similarity=0.039  Sum_probs=56.6

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHH
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACN  160 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~  160 (178)
                      .|+++|..++..++.+.+++++++||+|||++++.++...        ...+++++|+++|+.|++..+..
T Consensus        93 ~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~--------~~~~liv~P~~~L~~q~~~~~~~  155 (237)
T 2fz4_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL--------STPTLIVVPTLALAEQWKERLGI  155 (237)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS--------CSCEEEEESSHHHHHHHHHHHGG
T ss_pred             CcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc--------CCCEEEEeCCHHHHHHHHHHHHh
Confidence            6899999999999999999999999999999998887652        34789999999999999999877

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.18  E-value=2.4e-11  Score=108.49  Aligned_cols=67  Identities=22%  Similarity=0.286  Sum_probs=53.7

Q ss_pred             CCCCCCcHHHHHhhc----cccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984         86 MGFTKMTEIQARTIP----PLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip----~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      .|| .|+|+|..++.    .+..|+++++.||||+|||++|++|++..        ..+++|++||++|+.|++..+..+
T Consensus         4 ~~~-~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~--------~~~~~~~~~t~~l~~q~~~~~~~l   74 (540)
T 2vl7_A            4 LKL-QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQL--------KKKVLIFTRTHSQLDSIYKNAKLL   74 (540)
T ss_dssp             ------CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH--------TCEEEEEESCHHHHHHHHHHHGGG
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC--------CCcEEEEcCCHHHHHHHHHHHHhc
Confidence            478 89999999865    45689999999999999999999999753        347899999999999999887663

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=99.15  E-value=7.5e-11  Score=109.61  Aligned_cols=90  Identities=16%  Similarity=0.125  Sum_probs=71.2

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccC-CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEE
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLE-GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQ  144 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~-g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l  144 (178)
                      .+|.+++  +++.+.+.+...| ..|+++|+.+|+.++. |.+++++|+||||||+  ++|++-.........+..++++
T Consensus        72 ~~f~~~~--l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTt--llp~ll~~~~~~~~~g~~ilvl  146 (773)
T 2xau_A           72 NPFTGRE--FTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTT--QIPQFVLFDEMPHLENTQVACT  146 (773)
T ss_dssp             CTTTCSB--CCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHH--HHHHHHHHHHCGGGGTCEEEEE
T ss_pred             CCccccC--CCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHH--HHHHHHHHhccccCCCceEEec
Confidence            4688888  9999999999988 7999999999998775 5789999999999999  6777632222111124467889


Q ss_pred             eecHHHHHHHHHHHHH
Q psy12984        145 GKLRPLTNGVYLVACN  160 (178)
Q Consensus       145 ~Ptr~La~qi~~~~~~  160 (178)
                      +|+|+||.|++..+..
T Consensus       147 ~P~r~La~q~~~~l~~  162 (773)
T 2xau_A          147 QPRRVAAMSVAQRVAE  162 (773)
T ss_dssp             ESCHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHH
Confidence            9999999999876544

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.07  E-value=1.3e-10  Score=100.85  Aligned_cols=52  Identities=19%  Similarity=0.101  Sum_probs=45.3

Q ss_pred             CCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHH
Q psy12984        104 EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVAC  159 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~  159 (178)
                      .|+|++++++||||||++|++|+++.+..    .+.++++++||++||.|++..+.
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~----~g~~~lvl~Pt~~La~Q~~~~~~   52 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVK----KRLRTVILAPTRVVASEMYEALR   52 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHH----TTCCEEEEESSHHHHHHHHHHTT
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHh----CCCCEEEECcHHHHHHHHHHHhC
Confidence            47899999999999999999999977654    34589999999999999998875

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=99.02  E-value=1.2e-10  Score=106.57  Aligned_cols=64  Identities=13%  Similarity=-0.117  Sum_probs=51.2

Q ss_pred             CcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         91 MTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        91 pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      +++.|...++.+..++|++++|+||||||++|.+|+++        .+.+++|++|||+||.|++..+....
T Consensus       218 ~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~--------~g~~vLVl~PTReLA~Qia~~l~~~~  281 (666)
T 3o8b_A          218 VFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAA--------QGYKVLVLNPSVAATLGFGAYMSKAH  281 (666)
T ss_dssp             SCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHH--------TTCCEEEEESCHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHH--------CCCeEEEEcchHHHHHHHHHHHHHHh
Confidence            34455555555668899999999999999999999876        13488999999999999998766544

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=98.91  E-value=3.9e-10  Score=100.82  Aligned_cols=72  Identities=13%  Similarity=0.054  Sum_probs=46.3

Q ss_pred             CCcHHHHHhhccccC----C-CcEEEEccCCCchhhHhHHHHHHHHHhcc-----CCCCCceEEEeecHHHHHHHH-HHH
Q psy12984         90 KMTEIQARTIPPLLE----G-RDLVGSAKTGSGKTLAFLVPAVELIYNLK-----FMPRNGKSWQGKLRPLTNGVY-LVA  158 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~----g-~dvi~~a~TGsGKTlaf~lp~l~~l~~~~-----~~~~~~~~~l~Ptr~La~qi~-~~~  158 (178)
                      .|+++|..||+.++.    | ++++++++||||||++++ +++..+....     .....++++|+||++|+.|++ +.+
T Consensus       178 ~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~-~~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~~  256 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAF-QISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKTF  256 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH-HHHHHHHHTTCCSSCSSSCCCEEEEEC-----------CC
T ss_pred             CchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHH-HHHHHHHhcccccccccCCCeEEEEeCCHHHHHHHHHHHH
Confidence            799999999998875    4 679999999999999954 5555554432     114568999999999999999 776


Q ss_pred             HHHh
Q psy12984        159 CNVF  162 (178)
Q Consensus       159 ~~l~  162 (178)
                      ..+.
T Consensus       257 ~~~~  260 (590)
T 3h1t_A          257 TPFG  260 (590)
T ss_dssp             TTTC
T ss_pred             Hhcc
Confidence            6543

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=98.84  E-value=4.6e-09  Score=96.40  Aligned_cols=52  Identities=19%  Similarity=0.312  Sum_probs=42.8

Q ss_pred             cccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984        101 PLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus       101 ~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      ..+.|++++++||||||||+    +++..+...     ...+|++|||+||.|+++.+..+
T Consensus       151 r~l~rk~vlv~apTGSGKT~----~al~~l~~~-----~~gl~l~PtR~LA~Qi~~~l~~~  202 (677)
T 3rc3_A          151 RAMQRKIIFHSGPTNSGKTY----HAIQKYFSA-----KSGVYCGPLKLLAHEIFEKSNAA  202 (677)
T ss_dssp             HTSCCEEEEEECCTTSSHHH----HHHHHHHHS-----SSEEEEESSHHHHHHHHHHHHHT
T ss_pred             HhcCCCEEEEEcCCCCCHHH----HHHHHHHhc-----CCeEEEeCHHHHHHHHHHHHHhc
Confidence            45789999999999999998    555655542     24488999999999999998875

>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=98.78  E-value=2.9e-09  Score=101.72  Aligned_cols=72  Identities=19%  Similarity=-0.008  Sum_probs=58.9

Q ss_pred             CCCcHHHHHhhccccC--------------CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHH
Q psy12984         89 TKMTEIQARTIPPLLE--------------GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGV  154 (178)
Q Consensus        89 ~~pt~iQ~~aip~~l~--------------g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi  154 (178)
                      ..|+|+|..|++.++.              +++++++++||||||+++ ++++..+...  ....++++|+|+++|+.|+
T Consensus       270 ~~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~~--~~~~rvLvlvpr~eL~~Q~  346 (1038)
T 2w00_A          270 LVMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATEL--DFIDKVFFVVDRKDLDYQT  346 (1038)
T ss_dssp             EECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTTC--TTCCEEEEEECGGGCCHHH
T ss_pred             ccCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHhc--CCCceEEEEeCcHHHHHHH
Confidence            3599999999998765              478999999999999997 7777655431  2235899999999999999


Q ss_pred             HHHHHHHhh
Q psy12984        155 YLVACNVFK  163 (178)
Q Consensus       155 ~~~~~~l~~  163 (178)
                      ...+..+..
T Consensus       347 ~~~f~~f~~  355 (1038)
T 2w00_A          347 MKEYQRFSP  355 (1038)
T ss_dssp             HHHHHTTST
T ss_pred             HHHHHHhcc
Confidence            999888754

>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=98.71  E-value=6.1e-08  Score=89.57  Aligned_cols=80  Identities=24%  Similarity=0.149  Sum_probs=69.8

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      +|. +|+++|.....++..|+  |+...||+|||+++.+|++-..+.     +.++.+++|++.||.|-..++..+..++
T Consensus        72 lg~-r~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL~-----G~~vhVvT~ndyLA~rdae~m~~l~~~L  143 (822)
T 3jux_A           72 LGM-RPFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNALI-----GKGVHLVTVNDYLARRDALWMGPVYLFL  143 (822)
T ss_dssp             TSC-CCCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTT-----SSCEEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred             hCC-CCcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhc-----CCceEEEeccHHHHHhHHHHHHHHHHHh
Confidence            677 89999999998888888  889999999999999999754443     5578899999999999999999999999


Q ss_pred             CCCCcceE
Q psy12984        166 QPPTVIKV  173 (178)
Q Consensus       166 ~~~~~~~v  173 (178)
                      |..+++.+
T Consensus       144 glsvg~i~  151 (822)
T 3jux_A          144 GLRVGVIN  151 (822)
T ss_dssp             TCCEEEEE
T ss_pred             CCEEEEEc
Confidence            98766543

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=98.44  E-value=2.5e-07  Score=83.74  Aligned_cols=71  Identities=18%  Similarity=0.074  Sum_probs=59.7

Q ss_pred             cHHHHHhhccccCCCcEEEEccCCCchh--hHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         92 TEIQARTIPPLLEGRDLVGSAKTGSGKT--LAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        92 t~iQ~~aip~~l~g~dvi~~a~TGsGKT--laf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      ++.|+.|++.++.++++++++++|||||  ++++++.+..+..   ..+.++++++||+.+|.++...+......+
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~---~~~~~vll~APTg~AA~~L~e~~~~~~~~l  223 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMAD---GERCRIRLAAPTGKAAARLTESLGKALRQL  223 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCS---SCCCCEEEEBSSHHHHHHHHHHHTHHHHHS
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhh---cCCCeEEEEeCChhHHHHHHHHHHHHHhcC
Confidence            7899999999999999999999999999  7788888876532   234577889999999999998887766554

>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=98.44  E-value=3.5e-07  Score=79.67  Aligned_cols=70  Identities=10%  Similarity=-0.058  Sum_probs=54.6

Q ss_pred             CCcHHHHHhhccc----cCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984         90 KMTEIQARTIPPL----LEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus        90 ~pt~iQ~~aip~~----l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      .|+|+|..++..+    ..|+++|++.+||+|||+..+ .++..+...  .....++|||| ..|+.|....+.+++.
T Consensus        37 ~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai-~~i~~~~~~--~~~~~~LIv~P-~~l~~qw~~e~~~~~~  110 (500)
T 1z63_A           37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTI-AVFSDAKKE--NELTPSLVICP-LSVLKNWEEELSKFAP  110 (500)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHH-HHHHHHHHT--TCCSSEEEEEC-STTHHHHHHHHHHHCT
T ss_pred             cchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHH-HHHHHHHhc--CCCCCEEEEcc-HHHHHHHHHHHHHHCC
Confidence            6899999999766    357899999999999999965 444444432  33457899999 5688999999988753

>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=98.27  E-value=1.1e-06  Score=83.45  Aligned_cols=70  Identities=11%  Similarity=-0.006  Sum_probs=56.7

Q ss_pred             CCCcHHHHHhhccccC--CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         89 TKMTEIQARTIPPLLE--GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        89 ~~pt~iQ~~aip~~l~--g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      ..|+|+|..++..++.  +.++|++.+||+|||+.++..+...+..   ....+++||||+ .|+.|.+..+...+
T Consensus       152 ~~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~---g~~~rvLIVvP~-sLl~Qw~~E~~~~f  223 (968)
T 3dmq_A          152 TSLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLS---GAAERVLIIVPE-TLQHQWLVEMLRRF  223 (968)
T ss_dssp             SCCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHT---SSCCCEEEECCT-TTHHHHHHHHHHHS
T ss_pred             CCCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHh---CCCCeEEEEeCH-HHHHHHHHHHHHHh
Confidence            3689999999987765  4689999999999999998777766654   334478999999 99999998886543

>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=97.73  E-value=8.3e-05  Score=67.44  Aligned_cols=74  Identities=14%  Similarity=0.014  Sum_probs=55.6

Q ss_pred             CCcHHHHHhhccc---------cCCCcEEEEccCCCchhhHhHHHHHHHHHhccC--CCCCceEEEeecHHHHHHHHHHH
Q psy12984         90 KMTEIQARTIPPL---------LEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKF--MPRNGKSWQGKLRPLTNGVYLVA  158 (178)
Q Consensus        90 ~pt~iQ~~aip~~---------l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~--~~~~~~~~l~Ptr~La~qi~~~~  158 (178)
                      .+.|+|..++..+         ..+..+|++.++|+|||+..+..+...+.....  .....++|++|+ .|..|....+
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            6889999999865         346789999999999999987666655543221  123357889996 8888999898


Q ss_pred             HHHhhh
Q psy12984        159 CNVFKS  164 (178)
Q Consensus       159 ~~l~~~  164 (178)
                      .+++..
T Consensus       134 ~~~~~~  139 (644)
T 1z3i_X          134 GKWLGG  139 (644)
T ss_dssp             HHHHGG
T ss_pred             HHHcCC
Confidence            888653

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=97.70  E-value=4.7e-05  Score=70.67  Aligned_cols=70  Identities=13%  Similarity=0.004  Sum_probs=53.2

Q ss_pred             CCcHHHHHhhcccc----CCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         90 KMTEIQARTIPPLL----EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        90 ~pt~iQ~~aip~~l----~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      .+.|+|..++..++    .|+++|++.++|.|||+..+..+...+...  .....++|||| ..|..|....|.+++
T Consensus       236 ~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~--~~~~~~LIV~P-~sll~qW~~E~~~~~  309 (800)
T 3mwy_W          236 ELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFAR--RQNGPHIIVVP-LSTMPAWLDTFEKWA  309 (800)
T ss_dssp             CCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHH--SCCSCEEEECC-TTTHHHHHHHHHHHS
T ss_pred             CcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhc--CCCCCEEEEEC-chHHHHHHHHHHHHC
Confidence            56789999997554    789999999999999998765554443332  22346799999 778888888888775

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*

Probab=97.56  E-value=0.00033  Score=62.67  Aligned_cols=73  Identities=12%  Similarity=0.038  Sum_probs=56.7

Q ss_pred             CCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984         89 TKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus        89 ~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      ..+++-|..|+..  .+..++|.|+.|||||...+--+...+.... .+..+.+++++|+..|.++...+..+++.
T Consensus         8 ~~Ln~~Q~~av~~--~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~-~~~~~iL~ltft~~aa~e~~~rl~~~~~~   80 (647)
T 3lfu_A            8 DSLNDKQREAVAA--PRSNLLVLAGAGSGKTRVLVHRIAWLMSVEN-CSPYSIMAVTFTNKAAAEMRHRIGQLMGT   80 (647)
T ss_dssp             TTCCHHHHHHHTC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTSC-CCGGGEEEEESSHHHHHHHHHHHHHHHCS
T ss_pred             hcCCHHHHHHHhC--CCCCEEEEECCCCCHHHHHHHHHHHHHHhCC-CChhhEEEEeccHHHHHHHHHHHHHHhcc
Confidence            3678999999963  3567899999999999987766666554422 23457889999999999999998887653

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*

Probab=97.18  E-value=0.00048  Score=62.86  Aligned_cols=67  Identities=22%  Similarity=0.213  Sum_probs=52.0

Q ss_pred             CCCCCcHHHHHhhcccc----CC-CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984         87 GFTKMTEIQARTIPPLL----EG-RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus        87 g~~~pt~iQ~~aip~~l----~g-~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      +| .|++.|..+|..+.    .| +..++.+.||||||+.+.- ++..+.      + .+++|+|+..||.|++..|..+
T Consensus         6 ~~-~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a~-~~~~~~------~-~~lvv~~~~~~A~ql~~el~~~   76 (664)
T 1c4o_A            6 GP-SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAK-VIEALG------R-PALVLAPNKILAAQLAAEFREL   76 (664)
T ss_dssp             SC-CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHHT------C-CEEEEESSHHHHHHHHHHHHHH
T ss_pred             CC-CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHHH-HHHHhC------C-CEEEEecCHHHHHHHHHHHHHH
Confidence            67 89999999987654    34 3567889999999997753 333331      1 4799999999999999999988


Q ss_pred             h
Q psy12984        162 F  162 (178)
Q Consensus       162 ~  162 (178)
                      +
T Consensus        77 ~   77 (664)
T 1c4o_A           77 F   77 (664)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=97.13  E-value=0.0014  Score=59.34  Aligned_cols=72  Identities=13%  Similarity=-0.003  Sum_probs=56.0

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      .+++-|..++-..  +..++|.|..|||||.+..--+...+.... .+..+.++++.|+..|.++...+..+++.
T Consensus         2 ~L~~~Q~~av~~~--~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~-~~~~~IL~lTfT~~Aa~em~~Rl~~~l~~   73 (673)
T 1uaa_A            2 RLNPGQQQAVEFV--TGPCLVLAGAGSGKTRVITNKIAHLIRGCG-YQARHIAAVTFTNKAAREMKERVGQTLGR   73 (673)
T ss_dssp             CCCHHHHHHHHCC--SSEEEECCCTTSCHHHHHHHHHHHHHHHHC-CCGGGEEEEESSHHHHHHHHHHHHHHSCT
T ss_pred             CCCHHHHHHHhCC--CCCEEEEeCCCCChHHHHHHHHHHHHHhcC-CCHHHeEEEeccHHHHHHHHHHHHHHcCc
Confidence            4688999998643  668999999999999987766666665422 23347889999999999999998877644

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=97.08  E-value=0.0013  Score=59.31  Aligned_cols=67  Identities=10%  Similarity=-0.004  Sum_probs=51.5

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHH
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACN  160 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~  160 (178)
                      .+++-|..|+..++.+.-+++++|+|||||.... -++..+..   ....+.++++||..-+.++...+..
T Consensus       180 ~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~-~~i~~l~~---~~~~~ilv~a~tn~A~~~l~~~l~~  246 (624)
T 2gk6_A          180 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA-TIVYHLAR---QGNGPVLVCAPSNIAVDQLTEKIHQ  246 (624)
T ss_dssp             CCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHH-HHHHHHHT---SSSCCEEEEESSHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHH-HHHHHHHH---cCCCeEEEEeCcHHHHHHHHHHHHh
Confidence            4578899999888877788999999999998644 34444443   2345788999999998888877654

>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=96.99  E-value=0.0033  Score=57.72  Aligned_cols=73  Identities=12%  Similarity=0.015  Sum_probs=56.8

Q ss_pred             CCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984         89 TKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus        89 ~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      ..+++-|..|+-.  .+..++|.|..|||||.+..--+...+.... .+..+.++++.|+..|..+...+..+++.
T Consensus        10 ~~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~-~~p~~IL~vTFTnkAA~Em~~Rl~~~l~~   82 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKH-VAPWNILAITFTNKAAREMRERVQSLLGG   82 (724)
T ss_dssp             TTSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTC-CCGGGEEEEESSHHHHHHHHHHHHHHHGG
T ss_pred             hhCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcC-CCHHHeEEEeccHHHHHHHHHHHHHHhcc
Confidence            3688999999865  3467899999999999987766666665322 23347889999999999999988887654

>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=96.99  E-value=0.0017  Score=63.02  Aligned_cols=71  Identities=17%  Similarity=0.101  Sum_probs=57.4

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhcc-CCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLK-FMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~-~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      .+|+-|..+|-.-  +.+++|.|..|||||.+.+--++..+.... ..+..+.+++++|++.|..+...+...+
T Consensus        10 ~~t~eQ~~~i~~~--~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~Tft~~aa~e~~~ri~~~l   81 (1232)
T 3u4q_A           10 TWTDDQWNAIVST--GQDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAEAL   81 (1232)
T ss_dssp             CCCHHHHHHHHCC--SSCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEECSSHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEEeccHHHHHHHHHHHHHHH
Confidence            6799999999654  889999999999999998878887776532 1234478899999999999988877644

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=96.94  E-value=0.002  Score=58.22  Aligned_cols=65  Identities=9%  Similarity=0.017  Sum_probs=47.6

Q ss_pred             CcHHHHHhhccccCCCc-EEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHH
Q psy12984         91 MTEIQARTIPPLLEGRD-LVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACN  160 (178)
Q Consensus        91 pt~iQ~~aip~~l~g~d-vi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~  160 (178)
                      +.+-|..|+-.++..++ .||++|+|||||.+.+--+.+.+.+     +.+.++.+||..=+..+...+..
T Consensus       190 LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~~I~~l~~~-----~~~ILv~a~TN~AvD~i~erL~~  255 (646)
T 4b3f_X          190 LDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQ-----GLKVLCCAPSNIAVDNLVERLAL  255 (646)
T ss_dssp             CCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHHHHHHHHHT-----TCCEEEEESSHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHHHHHHHHhC-----CCeEEEEcCchHHHHHHHHHHHh
Confidence            45689999988887665 5889999999998755444443332     34789999998877777666543

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=96.91  E-value=0.0019  Score=55.96  Aligned_cols=70  Identities=14%  Similarity=0.153  Sum_probs=49.4

Q ss_pred             HHCCCCCCcHHHHHhhccccCC-----CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHH
Q psy12984         84 ADMGFTKMTEIQARTIPPLLEG-----RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLV  157 (178)
Q Consensus        84 ~~~g~~~pt~iQ~~aip~~l~g-----~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~  157 (178)
                      .-+.|..+++-|..|+..++..     ..+++.|+.|||||... .-++..+...   .....++++||...|..+...
T Consensus        19 ~p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll-~~~~~~l~~~---~~~~il~~a~T~~Aa~~l~~~   93 (459)
T 3upu_A           19 SHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLT-KFIIEALIST---GETGIILAAPTHAAKKILSKL   93 (459)
T ss_dssp             --CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHH-HHHHHHHHHT---TCCCEEEEESSHHHHHHHHHH
T ss_pred             CCCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHH-HHHHHHHHhc---CCceEEEecCcHHHHHHHHhh
Confidence            3457889999999999866432     38999999999999643 3455555442   223677889998887766544

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=96.89  E-value=0.0024  Score=59.54  Aligned_cols=68  Identities=10%  Similarity=0.078  Sum_probs=52.0

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHH
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNV  161 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l  161 (178)
                      .+++-|..|+..++.+.-++|.||+|||||....- ++.++...   ...+.++++||..-+.++...+...
T Consensus       360 ~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~~-~i~~l~~~---~~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          360 QLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSAT-IVYHLSKI---HKDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             CCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHH-HHHHHHHH---HCCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             cCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHH-HHHHHHhC---CCCeEEEEcCcHHHHHHHHHHHHhh
Confidence            45789999999888777789999999999986443 33333321   2457889999999999888887654

>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=96.79  E-value=0.0032  Score=58.72  Aligned_cols=67  Identities=10%  Similarity=-0.004  Sum_probs=51.3

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHH
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACN  160 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~  160 (178)
                      .+++-|..|+..++.+.-+++.+|+|||||.... -++..+..   ....+.++++||..-|.++...+..
T Consensus       356 ~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti~-~~i~~l~~---~~~~~ilv~a~tn~A~~~l~~~l~~  422 (800)
T 2wjy_A          356 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA-TIVYHLAR---QGNGPVLVCAPSNIAVDQLTEKIHQ  422 (800)
T ss_dssp             CCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHHH-HHHHHHHT---TCSSCEEEEESSHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHHH-HHHHHHHH---cCCCcEEEEcCcHHHHHHHHHHHHH
Confidence            3578899999888887788999999999998643 34444443   2345788899999888888777654

>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=96.51  E-value=0.0072  Score=54.22  Aligned_cols=62  Identities=16%  Similarity=0.070  Sum_probs=48.1

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHH
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYL  156 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~  156 (178)
                      .+++-|..++..++.+..+++.++.|||||... ..++..+..    .+..+++++||...|..+..
T Consensus       189 ~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i-~~l~~~l~~----~g~~Vl~~ApT~~Aa~~L~e  250 (574)
T 3e1s_A          189 GLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTT-KAVADLAES----LGLEVGLCAPTGKAARRLGE  250 (574)
T ss_dssp             TCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHH-HHHHHHHHH----TTCCEEEEESSHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHH-HHHHHHHHh----cCCeEEEecCcHHHHHHhHh
Confidence            578999999999998999999999999999653 233343332    24577888999988887765

>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*

Probab=96.00  E-value=0.02  Score=51.33  Aligned_cols=74  Identities=9%  Similarity=0.024  Sum_probs=59.0

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhcC
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      .++|.|...+..+...+-+++..+-|+|||.+...-++..+..   .++..+++++|++..|..++..+..++..++
T Consensus       163 ~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~---~~~~~i~~va~t~~qA~~~~~~i~~~i~~~p  236 (592)
T 3cpe_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCF---NKDKAVGILAHKGSMSAEVLDRTKQAIELLP  236 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHT---SSSCEEEEEESSHHHHHHHHHHHHHHHTTSC
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHh---CCCCeEEEEECCHHHHHHHHHHHHHHHHhCh
Confidence            4789999888766456778999999999999877656555554   3445778899999999999999998887764

>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=95.71  E-value=0.035  Score=47.54  Aligned_cols=74  Identities=9%  Similarity=0.024  Sum_probs=58.3

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhcC
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      .++|.|...+..+...+-+++..+-+.|||...+.-++..+..   .++..+++++|++.-|..++..+..++..+.
T Consensus       163 ~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~---~~g~~v~~vA~t~~qA~~vf~~i~~mi~~~P  236 (385)
T 2o0j_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCF---NKDKAVGILAHKGSMSAEVLDRTKQAIELLP  236 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHS---SSSCEEEEEESSHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHh---CCCCeEEEEeCCHHHHHHHHHHHHHHHHhCh
Confidence            6899999888665445668889999999999877766655543   3445678899999999999998988887654

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B*

Probab=95.33  E-value=0.016  Score=52.75  Aligned_cols=65  Identities=20%  Similarity=0.241  Sum_probs=48.5

Q ss_pred             CCcHHHHHhhcccc----CCC-cEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         90 KMTEIQARTIPPLL----EGR-DLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        90 ~pt~iQ~~aip~~l----~g~-dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      .|+.-|..+|..+.    .|. ..++.+-||||||+...- ++..+      ++ ..++|+|+..+|.|++..|..++
T Consensus        12 ~p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~a~-~~~~~------~~-~~lvv~~~~~~A~~l~~el~~~~   81 (661)
T 2d7d_A           12 QPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSN-LIKEV------NK-PTLVIAHNKTLAGQLYSEFKEFF   81 (661)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHH------CC-CEEEECSSHHHHHHHHHHHHHHC
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHHHH-HHHHh------CC-CEEEEECCHHHHHHHHHHHHHHc
Confidence            68888888877543    343 467789999999987642 33322      12 47899999999999999999885

>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=93.32  E-value=0.21  Score=36.86  Aligned_cols=19  Identities=37%  Similarity=0.422  Sum_probs=16.6

Q ss_pred             CCCcEEEEccCCCchhhHh
Q psy12984        104 EGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf  122 (178)
                      .|+.+++.+|+|+|||...
T Consensus        37 ~g~~~~l~G~~G~GKTtL~   55 (180)
T 3ec2_A           37 EGKGLTFVGSPGVGKTHLA   55 (180)
T ss_dssp             GCCEEEECCSSSSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4889999999999999754

>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=93.00  E-value=0.12  Score=43.85  Aligned_cols=49  Identities=16%  Similarity=0.103  Sum_probs=34.2

Q ss_pred             hccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHH
Q psy12984         99 IPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTN  152 (178)
Q Consensus        99 ip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~  152 (178)
                      +|.-....++++.++||||||..+ -+++..+..    .+..++++=|..++..
T Consensus        47 ~~~~~~~~h~~i~G~tGsGKs~~~-~~li~~~~~----~g~~viv~Dpkge~~~   95 (437)
T 1e9r_A           47 MPRDAEPRHLLVNGATGTGKSVLL-RELAYTGLL----RGDRMVIVDPNGDMLS   95 (437)
T ss_dssp             CCGGGGGGCEEEEECTTSSHHHHH-HHHHHHHHH----TTCEEEEEEETTHHHH
T ss_pred             cccccCcceEEEECCCCCCHHHHH-HHHHHHHHH----CCCcEEEEeCCCchhH
Confidence            344345689999999999999974 455555543    2346677788888864

>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=91.77  E-value=0.077  Score=45.74  Aligned_cols=54  Identities=13%  Similarity=0.121  Sum_probs=29.6

Q ss_pred             CccchHhhcccCCHHHHHHHHHCCCCCCcHHHHH-hh-ccccCCCcEEEEccCCCchhhHh
Q psy12984         64 SSTQFEALKGKVCENTLKAIADMGFTKMTEIQAR-TI-PPLLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus        64 ~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~-ai-p~~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      ...+|+++.  -...+.+.|.+.-.   .|+..- .+ ......+.+++.+|+|+|||...
T Consensus       129 ~~~~~~di~--G~~~~k~~l~~~v~---~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA  184 (444)
T 2zan_A          129 PNVKWSDVA--GLEGAKEALKEAVI---LPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLA  184 (444)
T ss_dssp             CCCCGGGSC--SCHHHHHHHHHHHT---HHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHH
T ss_pred             CCCCHHHhc--CHHHHHHHHHHHHH---HHhhCHHHhhccCCCCceEEEECCCCCCHHHHH
Confidence            345688886  34455555544210   011100 00 01123478999999999999753

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=91.68  E-value=0.3  Score=42.58  Aligned_cols=45  Identities=18%  Similarity=0.102  Sum_probs=33.0

Q ss_pred             CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHH
Q psy12984        106 RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACN  160 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~  160 (178)
                      +=.++.++.|+|||..+.    +.+ .   .  ...++++||++++.++.+.+..
T Consensus       162 ~v~~I~G~aGsGKTt~I~----~~~-~---~--~~~lVlTpT~~aa~~l~~kl~~  206 (446)
T 3vkw_A          162 KVVLVDGVPGCGKTKEIL----SRV-N---F--EEDLILVPGRQAAEMIRRRANA  206 (446)
T ss_dssp             EEEEEEECTTSCHHHHHH----HHC-C---T--TTCEEEESCHHHHHHHHHHHTT
T ss_pred             cEEEEEcCCCCCHHHHHH----HHh-c---c--CCeEEEeCCHHHHHHHHHHhhh
Confidence            446789999999998653    111 1   1  3568999999999988877643

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=90.91  E-value=0.12  Score=37.09  Aligned_cols=20  Identities=10%  Similarity=-0.014  Sum_probs=16.8

Q ss_pred             ccCCCcEEEEccCCCchhhH
Q psy12984        102 LLEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTla  121 (178)
                      +..+.++++.+++|+|||..
T Consensus        24 ~~~~~~vll~G~~GtGKt~l   43 (143)
T 3co5_A           24 AKRTSPVFLTGEAGSPFETV   43 (143)
T ss_dssp             HTCSSCEEEEEETTCCHHHH
T ss_pred             hCCCCcEEEECCCCccHHHH
Confidence            34568999999999999965

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=90.78  E-value=0.16  Score=36.58  Aligned_cols=21  Identities=10%  Similarity=-0.010  Sum_probs=17.7

Q ss_pred             ccCCCcEEEEccCCCchhhHh
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      ...+.+|++.+++|+|||...
T Consensus        21 a~~~~~vll~G~~GtGKt~lA   41 (145)
T 3n70_A           21 SETDIAVWLYGAPGTGRMTGA   41 (145)
T ss_dssp             TTCCSCEEEESSTTSSHHHHH
T ss_pred             hCCCCCEEEECCCCCCHHHHH
Confidence            346789999999999999764

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=89.95  E-value=0.15  Score=42.87  Aligned_cols=19  Identities=32%  Similarity=0.396  Sum_probs=16.2

Q ss_pred             CCCcEEEEccCCCchhhHh
Q psy12984        104 EGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf  122 (178)
                      .++.+++.+++|+|||...
T Consensus       147 ~~~~vLL~GppGtGKT~la  165 (389)
T 3vfd_A          147 PARGLLLFGPPGNGKTMLA  165 (389)
T ss_dssp             CCSEEEEESSTTSCHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            3579999999999999753

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=89.22  E-value=0.21  Score=39.46  Aligned_cols=19  Identities=26%  Similarity=0.342  Sum_probs=16.3

Q ss_pred             cCCCcEEEEccCCCchhhH
Q psy12984        103 LEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTla  121 (178)
                      ..++.+++.+|+|+|||..
T Consensus        49 ~~~~~~ll~G~~GtGKT~l   67 (285)
T 3h4m_A           49 EPPKGILLYGPPGTGKTLL   67 (285)
T ss_dssp             CCCSEEEEESSSSSSHHHH
T ss_pred             CCCCeEEEECCCCCcHHHH
Confidence            4567899999999999975

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=88.49  E-value=0.74  Score=37.62  Aligned_cols=19  Identities=32%  Similarity=0.517  Sum_probs=16.2

Q ss_pred             CCCcEEEEccCCCchhhHh
Q psy12984        104 EGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf  122 (178)
                      .++.+++.+|+|+|||...
T Consensus        69 ~~~~vLl~GppGtGKT~la   87 (368)
T 3uk6_A           69 AGRAVLIAGQPGTGKTAIA   87 (368)
T ss_dssp             TTCEEEEEESTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            3578999999999999753

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=88.16  E-value=0.59  Score=36.42  Aligned_cols=18  Identities=28%  Similarity=0.394  Sum_probs=15.0

Q ss_pred             CCcEEEEccCCCchhhHh
Q psy12984        105 GRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf  122 (178)
                      .+.+++.+++|+|||...
T Consensus        45 ~~~vll~G~~GtGKT~la   62 (257)
T 1lv7_A           45 PKGVLMVGPPGTGKTLLA   62 (257)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CCeEEEECcCCCCHHHHH
Confidence            357999999999999753

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=87.96  E-value=0.37  Score=42.54  Aligned_cols=21  Identities=24%  Similarity=0.235  Sum_probs=17.8

Q ss_pred             ccCCCcEEEEccCCCchhhHh
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      +..|..++++++||||||...
T Consensus       257 v~~g~~i~I~GptGSGKTTlL  277 (511)
T 2oap_1          257 IEHKFSAIVVGETASGKTTTL  277 (511)
T ss_dssp             HHTTCCEEEEESTTSSHHHHH
T ss_pred             HhCCCEEEEECCCCCCHHHHH
Confidence            457889999999999999753

>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=87.46  E-value=0.79  Score=36.94  Aligned_cols=19  Identities=26%  Similarity=0.347  Sum_probs=16.4

Q ss_pred             cCCCcEEEEccCCCchhhH
Q psy12984        103 LEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTla  121 (178)
                      ..++.+++.+|+|+|||..
T Consensus        47 ~~~~~vLL~Gp~GtGKT~l   65 (301)
T 3cf0_A           47 TPSKGVLFYGPPGCGKTLL   65 (301)
T ss_dssp             CCCSEEEEECSSSSSHHHH
T ss_pred             CCCceEEEECCCCcCHHHH
Confidence            3467899999999999975

>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=87.25  E-value=0.19  Score=41.91  Aligned_cols=18  Identities=17%  Similarity=0.242  Sum_probs=15.5

Q ss_pred             CCcEEEEccCCCchhhHh
Q psy12984        105 GRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf  122 (178)
                      .+.+++.+|+|+|||...
T Consensus        84 ~~~iLL~GppGtGKT~la  101 (355)
T 2qp9_X           84 TSGILLYGPPGTGKSYLA  101 (355)
T ss_dssp             CCCEEEECSTTSCHHHHH
T ss_pred             CceEEEECCCCCcHHHHH
Confidence            468999999999999753

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=87.20  E-value=0.38  Score=41.70  Aligned_cols=53  Identities=11%  Similarity=0.256  Sum_probs=33.0

Q ss_pred             CccchHhhcccCCHHHHHHHHHC---CCCCCcHHHHHhhccccCCCcEEEEccCCCchhhH
Q psy12984         64 SSTQFEALKGKVCENTLKAIADM---GFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus        64 ~~~~f~~l~~~l~~~ll~~l~~~---g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTla  121 (178)
                      +..+|++.+  --+...+.|.+.   =+.+|--++..-++   -.+.+|..+|+|+|||+.
T Consensus       176 p~~t~~dig--Gl~~~k~~l~e~v~~pl~~pe~f~~~g~~---~prGvLLyGPPGTGKTll  231 (434)
T 4b4t_M          176 PTETYSDVG--GLDKQIEELVEAIVLPMKRADKFKDMGIR---APKGALMYGPPGTGKTLL  231 (434)
T ss_dssp             CSCCGGGSC--SCHHHHHHHHHHTHHHHHCSHHHHHHCCC---CCCEEEEESCTTSSHHHH
T ss_pred             CCCChHhcC--cHHHHHHHHHHHHHHHHhCHHHHHhCCCC---CCCeeEEECcCCCCHHHH
Confidence            346799987  445555555442   12234444444332   247899999999999975

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=87.09  E-value=0.3  Score=35.23  Aligned_cols=17  Identities=29%  Similarity=0.276  Sum_probs=15.1

Q ss_pred             CCcEEEEccCCCchhhH
Q psy12984        105 GRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       105 g~dvi~~a~TGsGKTla  121 (178)
                      +..+++.+++|+|||..
T Consensus        43 ~~~~ll~G~~G~GKT~l   59 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAI   59 (195)
T ss_dssp             SCEEEEECCTTSCHHHH
T ss_pred             CCceEEECCCCCCHHHH
Confidence            47899999999999975

>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=86.79  E-value=0.38  Score=35.37  Aligned_cols=22  Identities=18%  Similarity=0.169  Sum_probs=18.0

Q ss_pred             cccCCCcEEEEccCCCchhhHh
Q psy12984        101 PLLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       101 ~~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      .+..++.+++.+++|||||...
T Consensus         7 ~~~~~~~i~i~G~~GsGKst~~   28 (180)
T 3iij_A            7 EFMLLPNILLTGTPGVGKTTLG   28 (180)
T ss_dssp             TTCCCCCEEEECSTTSSHHHHH
T ss_pred             ccccCCeEEEEeCCCCCHHHHH
Confidence            3456788999999999999753

>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=86.60  E-value=0.77  Score=35.47  Aligned_cols=18  Identities=28%  Similarity=0.283  Sum_probs=15.4

Q ss_pred             CCCcEEEEccCCCchhhH
Q psy12984        104 EGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTla  121 (178)
                      ..+.+++.+++|+|||..
T Consensus        38 ~~~~vll~G~~GtGKT~l   55 (262)
T 2qz4_A           38 VPKGALLLGPPGCGKTLL   55 (262)
T ss_dssp             CCCEEEEESCTTSSHHHH
T ss_pred             CCceEEEECCCCCCHHHH
Confidence            356899999999999975

>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=86.48  E-value=0.3  Score=39.82  Aligned_cols=49  Identities=16%  Similarity=0.272  Sum_probs=29.3

Q ss_pred             ccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccc-----cCCCcEEEEccCCCchhhH
Q psy12984         65 STQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPL-----LEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus        65 ~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~-----l~g~dvi~~a~TGsGKTla  121 (178)
                      ..+|+++.  -.....+.|.+.=.   .|.   ..|.+     ...+.+++.+|+|+|||..
T Consensus        14 ~~~~~di~--G~~~~~~~l~~~i~---~~~---~~~~~~~~~~~~~~~vLl~GppGtGKT~l   67 (322)
T 3eie_A           14 NVKWEDVA--GLEGAKEALKEAVI---LPV---KFPHLFKGNRKPTSGILLYGPPGTGKSYL   67 (322)
T ss_dssp             CCCGGGSC--SCHHHHHHHHHHTH---HHH---HCGGGCCTTCCCCCEEEEECSSSSCHHHH
T ss_pred             CCCHHHhc--ChHHHHHHHHHHHH---HHH---hCHHHHhcCCCCCCeEEEECCCCCcHHHH
Confidence            35688886  45556666655211   111   11221     2246799999999999975

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=86.36  E-value=1.2  Score=34.00  Aligned_cols=22  Identities=27%  Similarity=0.273  Sum_probs=17.9

Q ss_pred             ccCCCcEEEEccCCCchhhHhH
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAFL  123 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf~  123 (178)
                      +..|.-+++.+++|+|||...+
T Consensus        20 l~~G~~~~i~G~~GsGKTtl~~   41 (247)
T 2dr3_A           20 IPERNVVLLSGGPGTGKTIFSQ   41 (247)
T ss_dssp             EETTCEEEEEECTTSSHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHH
Confidence            4467889999999999998643

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=86.07  E-value=0.32  Score=35.48  Aligned_cols=19  Identities=21%  Similarity=0.328  Sum_probs=16.6

Q ss_pred             CCCcEEEEccCCCchhhHh
Q psy12984        104 EGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf  122 (178)
                      .|..+++.+++|+|||...
T Consensus        35 ~g~~~~l~G~~G~GKTtL~   53 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLL   53 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            6889999999999998753

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=86.04  E-value=1.1  Score=36.56  Aligned_cols=18  Identities=22%  Similarity=0.263  Sum_probs=15.5

Q ss_pred             CCcEEEEccCCCchhhHh
Q psy12984        105 GRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf  122 (178)
                      .+.+++.+|+|+|||...
T Consensus        45 ~~~iLL~GppGtGKT~la   62 (322)
T 1xwi_A           45 WRGILLFGPPGTGKSYLA   62 (322)
T ss_dssp             CSEEEEESSSSSCHHHHH
T ss_pred             CceEEEECCCCccHHHHH
Confidence            378999999999999753

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=85.99  E-value=0.43  Score=38.04  Aligned_cols=19  Identities=21%  Similarity=0.230  Sum_probs=16.1

Q ss_pred             CCCcEEEEccCCCchhhHh
Q psy12984        104 EGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf  122 (178)
                      .+.++++.+++|+|||...
T Consensus        66 ~~~~vll~G~~GtGKT~la   84 (309)
T 3syl_A           66 PTLHMSFTGNPGTGKTTVA   84 (309)
T ss_dssp             CCCEEEEEECTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            4568999999999999764

>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=85.97  E-value=2.2  Score=41.17  Aligned_cols=59  Identities=17%  Similarity=0.126  Sum_probs=42.3

Q ss_pred             cCCCcEEEEccCCCchhhHhHHHHHHHHHhc-------cCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984        103 LEGRDLVGSAKTGSGKTLAFLVPAVELIYNL-------KFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~-------~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      +.|.. +|.|.-|||||.+..-=++..|...       ......+.++++=|++=|..+...+...+
T Consensus        15 l~g~~-lV~AsAGSGKT~~L~~r~lrLll~~g~~~~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~~L   80 (1180)
T 1w36_B           15 LQGER-LIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSNI   80 (1180)
T ss_dssp             CSSCE-EEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHHH
T ss_pred             CCCCE-EEEECCCCCHHHHHHHHHHHHHhcCCcccccCCCCCHHHEEEEeccHHHHHHHHHHHHHHH
Confidence            45655 8899999999999888888888642       11223477888888877776666655544

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=85.46  E-value=1  Score=34.30  Aligned_cols=18  Identities=39%  Similarity=0.545  Sum_probs=15.4

Q ss_pred             CCCcEEEEccCCCchhhH
Q psy12984        104 EGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTla  121 (178)
                      .|.-+++++++|+|||..
T Consensus        29 ~G~l~~i~G~pG~GKT~l   46 (251)
T 2zts_A           29 EGTTVLLTGGTGTGKTTF   46 (251)
T ss_dssp             TTCEEEEECCTTSSHHHH
T ss_pred             CCeEEEEEeCCCCCHHHH
Confidence            467789999999999964

>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=85.38  E-value=0.41  Score=36.21  Aligned_cols=19  Identities=16%  Similarity=0.034  Sum_probs=16.4

Q ss_pred             CCCcEEEEccCCCchhhHh
Q psy12984        104 EGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf  122 (178)
                      .+..+++.+++|+|||...
T Consensus        51 ~~~~~ll~G~~G~GKT~la   69 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLI   69 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4688999999999999753

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=85.28  E-value=0.58  Score=37.39  Aligned_cols=21  Identities=24%  Similarity=0.227  Sum_probs=17.7

Q ss_pred             ccCCCcEEEEccCCCchhhHh
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      +..|.-+++.+|||||||..+
T Consensus        22 i~~g~~v~i~Gp~GsGKSTll   42 (261)
T 2eyu_A           22 HRKMGLILVTGPTGSGKSTTI   42 (261)
T ss_dssp             GCSSEEEEEECSTTCSHHHHH
T ss_pred             hCCCCEEEEECCCCccHHHHH
Confidence            556788999999999999763

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=85.24  E-value=0.39  Score=35.64  Aligned_cols=20  Identities=20%  Similarity=0.122  Sum_probs=16.6

Q ss_pred             cCCCcEEEEccCCCchhhHh
Q psy12984        103 LEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTlaf  122 (178)
                      +.|+-+++++|+|+|||...
T Consensus         3 ~~g~~i~i~GpsGsGKSTL~   22 (180)
T 1kgd_A            3 HMRKTLVLLGAHGVGRRHIK   22 (180)
T ss_dssp             CCCCEEEEECCTTSSHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            35778899999999999753

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=85.09  E-value=0.33  Score=35.10  Aligned_cols=18  Identities=22%  Similarity=0.239  Sum_probs=15.4

Q ss_pred             CCcEEEEccCCCchhhHh
Q psy12984        105 GRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf  122 (178)
                      +.++++.+++|+|||...
T Consensus        43 ~~~vll~G~~G~GKT~la   60 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIV   60 (187)
T ss_dssp             SCEEEEESCGGGCHHHHH
T ss_pred             CCceEEECCCCCCHHHHH
Confidence            568999999999999753

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=84.85  E-value=0.31  Score=40.52  Aligned_cols=27  Identities=7%  Similarity=-0.028  Sum_probs=19.7

Q ss_pred             CCCcEEEEccCCCchhhHhHHHHHHHHH
Q psy12984        104 EGRDLVGSAKTGSGKTLAFLVPAVELIY  131 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~lp~l~~l~  131 (178)
                      .+.++++.+|+|+|||+..- -++..+.
T Consensus        44 ~~~~lli~GpPGTGKT~~v~-~v~~~L~   70 (318)
T 3te6_A           44 QNKLFYITNADDSTKFQLVN-DVMDELI   70 (318)
T ss_dssp             CCCEEEEECCCSHHHHHHHH-HHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHH-HHHHHHH
Confidence            45789999999999998743 2334443

>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=84.43  E-value=1.2  Score=36.20  Aligned_cols=43  Identities=14%  Similarity=0.030  Sum_probs=30.3

Q ss_pred             HHHHHHHHCCCCCCcHHHHHh-hccccCCC-----cEEEEccCCCchhhHhH
Q psy12984         78 NTLKAIADMGFTKMTEIQART-IPPLLEGR-----DLVGSAKTGSGKTLAFL  123 (178)
Q Consensus        78 ~ll~~l~~~g~~~pt~iQ~~a-ip~~l~g~-----dvi~~a~TGsGKTlaf~  123 (178)
                      .+.+.|.-.||.   +++... +-..+.|+     .+++.+|+|+|||+.+.
T Consensus        74 ~i~~~l~~qg~~---~~~~~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~  122 (267)
T 1u0j_A           74 RIYKILELNGYD---PQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAE  122 (267)
T ss_dssp             HHHHHHHHTTCC---HHHHHHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHcCCC---HHHHHHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHH
Confidence            577778888886   555333 33444443     59999999999998765

>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=84.41  E-value=1.6  Score=37.40  Aligned_cols=19  Identities=32%  Similarity=0.475  Sum_probs=16.3

Q ss_pred             CCCcEEEEccCCCchhhHh
Q psy12984        104 EGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf  122 (178)
                      .++++++.+|+|+|||...
T Consensus        62 ~~~~iLl~GppGtGKT~la   80 (456)
T 2c9o_A           62 AGRAVLLAGPPGTGKTALA   80 (456)
T ss_dssp             TTCEEEEECCTTSSHHHHH
T ss_pred             CCCeEEEECCCcCCHHHHH
Confidence            4578999999999999764

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=84.22  E-value=0.77  Score=40.40  Aligned_cols=42  Identities=14%  Similarity=0.185  Sum_probs=27.3

Q ss_pred             HHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhH
Q psy12984         79 TLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus        79 ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTla  121 (178)
                      +...+.. ++.--..+=..++-.+..|.++++.+++|+|||..
T Consensus        16 l~~~l~~-~ivGq~~~i~~l~~al~~~~~VLL~GpPGtGKT~L   57 (500)
T 3nbx_X           16 LSSSLEK-GLYERSHAIRLCLLAALSGESVFLLGPPGIAKSLI   57 (500)
T ss_dssp             HHHHHHT-TCSSCHHHHHHHHHHHHHTCEEEEECCSSSSHHHH
T ss_pred             HHHHHHh-hhHHHHHHHHHHHHHHhcCCeeEeecCchHHHHHH
Confidence            3344443 34333333344455667889999999999999975

>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=84.20  E-value=0.63  Score=36.44  Aligned_cols=19  Identities=21%  Similarity=0.296  Sum_probs=16.3

Q ss_pred             cCCCcEEEEccCCCchhhH
Q psy12984        103 LEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTla  121 (178)
                      ..+..+++.+++|+|||..
T Consensus        27 ~~~~~vll~G~~GtGKt~l   45 (265)
T 2bjv_A           27 PLDKPVLIIGERGTGKELI   45 (265)
T ss_dssp             TSCSCEEEECCTTSCHHHH
T ss_pred             CCCCCEEEECCCCCcHHHH
Confidence            3467999999999999975

>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=83.55  E-value=1.3  Score=37.02  Aligned_cols=41  Identities=17%  Similarity=0.087  Sum_probs=26.4

Q ss_pred             CCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHH
Q psy12984        104 EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRP  149 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~  149 (178)
                      .+.++++.++||+|||...-. ++..+..    .+..++++-|.++
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~-~~~~~~~----~~~~~~~~D~~~~   74 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKM-LLLREYM----QGSRVIIIDPERE   74 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHH-HHHHHHT----TTCCEEEEESSCC
T ss_pred             ccCceEEEcCCCCCHHHHHHH-HHHHHHH----CCCEEEEEeCCcC
Confidence            577999999999999976433 2222222    2345566666654

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=83.29  E-value=0.36  Score=38.76  Aligned_cols=53  Identities=13%  Similarity=0.177  Sum_probs=24.7

Q ss_pred             ccchHhhcccCCHHHHHHHHHC-C--CCCCcHHHHHhhccccCCCcEEEEccCCCchhhHh
Q psy12984         65 STQFEALKGKVCENTLKAIADM-G--FTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus        65 ~~~f~~l~~~l~~~ll~~l~~~-g--~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      ..+|++++  -.+.+.+.|.+. -  +..|.-++...+   .-.+.+++.+|+|+|||...
T Consensus         6 ~~~~~di~--g~~~~~~~l~~~i~~~~~~~~~l~~~~l---~~~~GvlL~Gp~GtGKTtLa   61 (274)
T 2x8a_A            6 NVTWADIG--ALEDIREELTMAILAPVRNPDQFKALGL---VTPAGVLLAGPPGCGKTLLA   61 (274)
T ss_dssp             ------CC--HHHHHHHHHHHHHTHHHHSHHHHHHTTC---CCCSEEEEESSTTSCHHHHH
T ss_pred             CCCHHHhC--CHHHHHHHHHHHHHHHhhCHHHHHHcCC---CCCCeEEEECCCCCcHHHHH
Confidence            35688876  444555555442 1  112222222211   11234999999999999753

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=83.08  E-value=0.63  Score=33.90  Aligned_cols=17  Identities=18%  Similarity=0.227  Sum_probs=14.7

Q ss_pred             CCcEEEEccCCCchhhH
Q psy12984        105 GRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       105 g~dvi~~a~TGsGKTla  121 (178)
                      ++-+++++++|||||..
T Consensus         3 ~~~i~l~G~~GsGKST~   19 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGI   19 (178)
T ss_dssp             CCEEEEECCTTSSHHHH
T ss_pred             ceEEEEECCCCCCHHHH
Confidence            56689999999999975

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=82.88  E-value=0.59  Score=34.92  Aligned_cols=17  Identities=29%  Similarity=0.358  Sum_probs=15.2

Q ss_pred             CcEEEEccCCCchhhHh
Q psy12984        106 RDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf  122 (178)
                      ..+++.+++|+|||...
T Consensus        55 ~~~~l~G~~GtGKT~la   71 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLL   71 (202)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            78999999999999853

>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=82.74  E-value=0.7  Score=35.92  Aligned_cols=16  Identities=25%  Similarity=0.331  Sum_probs=13.7

Q ss_pred             CcEEEEccCCCchhhH
Q psy12984        106 RDLVGSAKTGSGKTLA  121 (178)
Q Consensus       106 ~dvi~~a~TGsGKTla  121 (178)
                      +.+++.+|+|+|||..
T Consensus        50 ~g~ll~G~~G~GKTtl   65 (254)
T 1ixz_A           50 KGVLLVGPPGVGKTHL   65 (254)
T ss_dssp             SEEEEECCTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            3499999999999965

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=82.63  E-value=2.2  Score=34.38  Aligned_cols=18  Identities=28%  Similarity=0.183  Sum_probs=15.3

Q ss_pred             CCcEEEEccCCCchhhHh
Q psy12984        105 GRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf  122 (178)
                      ..++++.+++|+|||...
T Consensus        55 ~~~vll~G~~GtGKT~la   72 (338)
T 3pfi_A           55 LDHILFSGPAGLGKTTLA   72 (338)
T ss_dssp             CCCEEEECSTTSSHHHHH
T ss_pred             CCeEEEECcCCCCHHHHH
Confidence            357999999999999763

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=82.10  E-value=0.85  Score=39.22  Aligned_cols=54  Identities=15%  Similarity=0.287  Sum_probs=31.7

Q ss_pred             CccchHhhcccCCHHHHHHHHHC---CCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHh
Q psy12984         64 SSTQFEALKGKVCENTLKAIADM---GFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus        64 ~~~~f~~l~~~l~~~ll~~l~~~---g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      +..+|++.+ +|. ...+.|.+.   -+.+|--++..-++   -.+.+|..+|+|+|||+..
T Consensus       143 p~v~~~dIg-Gl~-~~k~~l~e~v~~Pl~~pe~f~~~gi~---~prGvLL~GPPGTGKTllA  199 (405)
T 4b4t_J          143 PDSTYDMVG-GLT-KQIKEIKEVIELPVKHPELFESLGIA---QPKGVILYGPPGTGKTLLA  199 (405)
T ss_dssp             CSCCGGGSC-SCH-HHHHHHHHHTHHHHHCHHHHHHHTCC---CCCCEEEESCSSSSHHHHH
T ss_pred             CCCCHHHhC-CHH-HHHHHHHHHHHHHHhCHHHHHhCCCC---CCCceEEeCCCCCCHHHHH
Confidence            346799887 343 344444442   12233333333322   2478999999999999863

>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=81.90  E-value=0.72  Score=36.47  Aligned_cols=18  Identities=28%  Similarity=0.357  Sum_probs=15.7

Q ss_pred             CCCcEEEEccCCCchhhH
Q psy12984        104 EGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTla  121 (178)
                      .+.++++.+++|+|||..
T Consensus        49 ~~~~vll~G~~GtGKT~l   66 (310)
T 1ofh_A           49 TPKNILMIGPTGVGKTEI   66 (310)
T ss_dssp             CCCCEEEECCTTSSHHHH
T ss_pred             CCceEEEECCCCCCHHHH
Confidence            357899999999999975

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=81.90  E-value=0.63  Score=36.97  Aligned_cols=19  Identities=32%  Similarity=0.382  Sum_probs=16.2

Q ss_pred             CCCcEEEEccCCCchhhHh
Q psy12984        104 EGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf  122 (178)
                      .++.+++.+|+|+|||...
T Consensus        53 ~~~~vll~Gp~GtGKT~la   71 (297)
T 3b9p_A           53 PAKGLLLFGPPGNGKTLLA   71 (297)
T ss_dssp             CCSEEEEESSSSSCHHHHH
T ss_pred             CCCeEEEECcCCCCHHHHH
Confidence            3678999999999999753

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=81.61  E-value=0.73  Score=34.61  Aligned_cols=18  Identities=22%  Similarity=0.178  Sum_probs=16.0

Q ss_pred             CCCcEEEEccCCCchhhH
Q psy12984        104 EGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTla  121 (178)
                      .|+.+++.+++|||||..
T Consensus        24 ~~~~i~l~G~~GsGKsTl   41 (199)
T 3vaa_A           24 AMVRIFLTGYMGAGKTTL   41 (199)
T ss_dssp             CCCEEEEECCTTSCHHHH
T ss_pred             CCCEEEEEcCCCCCHHHH
Confidence            577899999999999975

>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=81.52  E-value=4.4  Score=32.49  Aligned_cols=19  Identities=21%  Similarity=0.163  Sum_probs=16.0

Q ss_pred             CCCcEEEEccCCCchhhHh
Q psy12984        104 EGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf  122 (178)
                      .+..+++.+++|+|||...
T Consensus        36 ~~~~lll~G~~GtGKT~la   54 (324)
T 1l8q_A           36 LYNPIFIYGSVGTGKTHLL   54 (324)
T ss_dssp             SCSSEEEECSSSSSHHHHH
T ss_pred             CCCeEEEECCCCCcHHHHH
Confidence            3578999999999999753

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=81.51  E-value=0.8  Score=33.73  Aligned_cols=16  Identities=38%  Similarity=0.461  Sum_probs=14.0

Q ss_pred             CcEEEEccCCCchhhH
Q psy12984        106 RDLVGSAKTGSGKTLA  121 (178)
Q Consensus       106 ~dvi~~a~TGsGKTla  121 (178)
                      ..+++.+++|+|||..
T Consensus        39 ~~~ll~G~~G~GKT~l   54 (226)
T 2chg_A           39 PHLLFSGPPGTGKTAT   54 (226)
T ss_dssp             CCEEEECSTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4699999999999975

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=81.44  E-value=0.75  Score=34.68  Aligned_cols=20  Identities=25%  Similarity=0.223  Sum_probs=17.0

Q ss_pred             ccCCCcEEEEccCCCchhhH
Q psy12984        102 LLEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTla  121 (178)
                      +..|+-+++++++|||||..
T Consensus         9 ~~~~~~i~l~G~sGsGKsTl   28 (204)
T 2qor_A            9 MARIPPLVVCGPSGVGKGTL   28 (204)
T ss_dssp             CCCCCCEEEECCTTSCHHHH
T ss_pred             cccCCEEEEECCCCCCHHHH
Confidence            45678899999999999874

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=81.39  E-value=3.9  Score=34.88  Aligned_cols=30  Identities=23%  Similarity=0.191  Sum_probs=20.9

Q ss_pred             ccccCCCcEEEEccCCCchhhHhHHHHHHHH
Q psy12984        100 PPLLEGRDLVGSAKTGSGKTLAFLVPAVELI  130 (178)
Q Consensus       100 p~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l  130 (178)
                      .-+..|.=++++|++|+|||. |++-+...+
T Consensus       195 gGl~~G~l~ii~G~pg~GKT~-lal~ia~~~  224 (444)
T 2q6t_A          195 GTLGPGSLNIIAARPAMGKTA-FALTIAQNA  224 (444)
T ss_dssp             CCCCTTCEEEEEECTTSCHHH-HHHHHHHHH
T ss_pred             CCcCCCcEEEEEeCCCCCHHH-HHHHHHHHH
Confidence            345567778999999999996 444444433

>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=81.34  E-value=0.69  Score=36.19  Aligned_cols=20  Identities=25%  Similarity=0.463  Sum_probs=16.2

Q ss_pred             cCCCcEEEEccCCCchh-hHh
Q psy12984        103 LEGRDLVGSAKTGSGKT-LAF  122 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKT-laf  122 (178)
                      ..|+-+++.++||+||| ++.
T Consensus        32 ~~g~~ilI~GpsGsGKStLA~   52 (205)
T 2qmh_A           32 IYGLGVLITGDSGVGKSETAL   52 (205)
T ss_dssp             ETTEEEEEECCCTTTTHHHHH
T ss_pred             ECCEEEEEECCCCCCHHHHHH
Confidence            45778999999999997 443

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=81.20  E-value=0.71  Score=34.32  Aligned_cols=20  Identities=30%  Similarity=0.237  Sum_probs=16.5

Q ss_pred             cCCCcEEEEccCCCchhhHh
Q psy12984        103 LEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTlaf  122 (178)
                      ..|.-+++.+++|||||...
T Consensus         4 ~~g~~i~l~G~~GsGKSTl~   23 (207)
T 2j41_A            4 EKGLLIVLSGPSGVGKGTVR   23 (207)
T ss_dssp             CCCCEEEEECSTTSCHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            45778899999999999753

>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=80.98  E-value=2.1  Score=35.40  Aligned_cols=19  Identities=26%  Similarity=0.291  Sum_probs=16.1

Q ss_pred             CCCcEEEEccCCCchhhHh
Q psy12984        104 EGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf  122 (178)
                      ..+.+++.+++|+|||...
T Consensus       116 ~~~~vLl~GppGtGKT~la  134 (357)
T 3d8b_A          116 PPKGILLFGPPGTGKTLIG  134 (357)
T ss_dssp             CCSEEEEESSTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            3578999999999999753

>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=80.97  E-value=0.76  Score=37.95  Aligned_cols=19  Identities=37%  Similarity=0.396  Sum_probs=16.5

Q ss_pred             CCCcEEEEccCCCchhhHh
Q psy12984        104 EGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf  122 (178)
                      .+.++++.+|+|+|||...
T Consensus        50 ~~~~vll~GppGtGKT~la   68 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLA   68 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4678999999999999853

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=80.92  E-value=0.63  Score=40.36  Aligned_cols=54  Identities=15%  Similarity=0.263  Sum_probs=30.8

Q ss_pred             CccchHhhcccCCHHHHHHHHHC---CCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHh
Q psy12984         64 SSTQFEALKGKVCENTLKAIADM---GFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus        64 ~~~~f~~l~~~l~~~ll~~l~~~---g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      +..+|++.+ +| ++..+.|.+.   -+.+|--++..-+   .-.+.+|..+|+|+|||+..
T Consensus       176 p~v~~~dig-Gl-~~~k~~l~e~v~~pl~~p~~f~~~g~---~~prGvLL~GPPGtGKTllA  232 (437)
T 4b4t_L          176 GEITFDGIG-GL-TEQIRELREVIELPLKNPEIFQRVGI---KPPKGVLLYGPPGTGKTLLA  232 (437)
T ss_dssp             CSSCSGGGC-SC-HHHHHHHHHHHHHHHHCHHHHHHHCC---CCCCEEEEESCTTSSHHHHH
T ss_pred             CCCChhHhC-Ch-HHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCeEEEECCCCCcHHHHH
Confidence            345688887 34 3344444331   1222333333322   22478999999999999863

>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=80.90  E-value=2.3  Score=37.61  Aligned_cols=27  Identities=22%  Similarity=0.383  Sum_probs=20.0

Q ss_pred             CCcEEEEccCCCchhhHhHHHHHHHHH
Q psy12984        105 GRDLVGSAKTGSGKTLAFLVPAVELIY  131 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf~lp~l~~l~  131 (178)
                      +.++++.+.||||||.+.-.-++..+.
T Consensus       167 ~pHlLIaG~TGSGKSt~L~~li~sLl~  193 (512)
T 2ius_A          167 MPHLLVAGTTGSGASVGVNAMILSMLY  193 (512)
T ss_dssp             SCSEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHH
Confidence            579999999999999875444444343

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=80.73  E-value=1.2  Score=47.55  Aligned_cols=48  Identities=10%  Similarity=0.102  Sum_probs=32.9

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHH-Hhhc---cccCCCcEEEEccCCCchhhHhH
Q psy12984         75 VCENTLKAIADMGFTKMTEIQA-RTIP---PLLEGRDLVGSAKTGSGKTLAFL  123 (178)
Q Consensus        75 l~~~ll~~l~~~g~~~pt~iQ~-~aip---~~l~g~dvi~~a~TGsGKTlaf~  123 (178)
                      |...+.+.+.++|+ .|++.+. +++.   .+.-.+.+++.+|||||||.+|-
T Consensus       873 l~~ai~~~~~~~~L-~~~~~~v~KviQLye~~~vRhGvmlVGp~gsGKTt~~~  924 (3245)
T 3vkg_A          873 LRKKIQEIAKQRHL-VTKQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSWE  924 (3245)
T ss_dssp             HHHHHHHHHHHTTC-CCCHHHHHHHHHHHHHHTTCSEEEEECSSSSSHHHHHH
T ss_pred             HHHHHHHHHHHcCC-ccCHHHHHHHHHHHHHHHheeeEEEECCCCCCHHHHHH
Confidence            44567777888998 5666332 2222   22345669999999999999875

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=80.71  E-value=0.92  Score=34.27  Aligned_cols=19  Identities=32%  Similarity=0.431  Sum_probs=15.1

Q ss_pred             CCCcEEEEccCCCchhhHh
Q psy12984        104 EGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf  122 (178)
                      .|+-+.+.+|+|+|||...
T Consensus         3 ~g~~i~lvGpsGaGKSTLl   21 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLL   21 (198)
T ss_dssp             --CCEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4778999999999999754

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=80.60  E-value=0.8  Score=38.27  Aligned_cols=21  Identities=38%  Similarity=0.427  Sum_probs=17.9

Q ss_pred             ccCCCcEEEEccCCCchhhHh
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      +..|..+++.++||||||..+
T Consensus       172 i~~G~~i~ivG~sGsGKSTll  192 (361)
T 2gza_A          172 VQLERVIVVAGETGSGKTTLM  192 (361)
T ss_dssp             HHTTCCEEEEESSSSCHHHHH
T ss_pred             HhcCCEEEEECCCCCCHHHHH
Confidence            457899999999999999753

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=80.59  E-value=1.1  Score=36.47  Aligned_cols=19  Identities=21%  Similarity=0.365  Sum_probs=16.5

Q ss_pred             cCCCcEEEEccCCCchhhH
Q psy12984        103 LEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTla  121 (178)
                      ..+..|++.+++|+|||..
T Consensus        23 ~~~~~vLi~Ge~GtGKt~l   41 (304)
T 1ojl_A           23 PSDATVLIHGDSGTGKELV   41 (304)
T ss_dssp             STTSCEEEESCTTSCHHHH
T ss_pred             CCCCcEEEECCCCchHHHH
Confidence            4567899999999999975

>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=80.49  E-value=0.75  Score=34.95  Aligned_cols=19  Identities=32%  Similarity=0.284  Sum_probs=16.1

Q ss_pred             CCCcEEEEccCCCchhhHh
Q psy12984        104 EGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf  122 (178)
                      .|+=+++.+|+|+|||...
T Consensus         7 ~g~~i~l~GpsGsGKsTl~   25 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVR   25 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHH
Confidence            5777899999999999753

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=80.44  E-value=0.82  Score=33.52  Aligned_cols=17  Identities=24%  Similarity=0.176  Sum_probs=14.9

Q ss_pred             CCcEEEEccCCCchhhH
Q psy12984        105 GRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       105 g~dvi~~a~TGsGKTla  121 (178)
                      ++.+++.+++|||||..
T Consensus         5 ~~~i~l~G~~GsGKst~   21 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSV   21 (185)
T ss_dssp             CCEEEEECSTTSSHHHH
T ss_pred             CCEEEEECCCCCCHHHH
Confidence            56799999999999975

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=80.10  E-value=4.2  Score=33.03  Aligned_cols=23  Identities=17%  Similarity=-0.008  Sum_probs=18.1

Q ss_pred             ccccCCCcEEEEccCCCchhhHh
Q psy12984        100 PPLLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       100 p~~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      .-+..|.=++++|++|+|||...
T Consensus        63 gGl~~G~l~li~G~pG~GKTtl~   85 (315)
T 3bh0_A           63 YGYKRRNFVLIAARPSMGKTAFA   85 (315)
T ss_dssp             SSBCTTCEEEEECCTTSSHHHHH
T ss_pred             CCCCCCcEEEEEeCCCCCHHHHH
Confidence            34556778999999999999643

>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=80.08  E-value=0.72  Score=33.98  Aligned_cols=20  Identities=40%  Similarity=0.419  Sum_probs=16.8

Q ss_pred             ccCCCcEEEEccCCCchhhH
Q psy12984        102 LLEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTla  121 (178)
                      +..|.-+++.+++|||||..
T Consensus         6 i~~g~~i~l~G~~GsGKSTl   25 (191)
T 1zp6_A            6 DLGGNILLLSGHPGSGKSTI   25 (191)
T ss_dssp             CCTTEEEEEEECTTSCHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHH
Confidence            44677899999999999974

---

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	178
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	5e-15
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	2e-14
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	2e-14
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	3e-14
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	4e-14
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	5e-14
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	5e-14
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	1e-13
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	2e-13
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	8e-13
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	3e-10
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	1e-09
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	2e-05

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 222

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.9 bits (165), Expect = 5e-15
 Identities = 20/78 (25%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 61  EILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTL 120
           E+  +  F+ +   + E+ L+ I   GF K + IQ R I  +++GRD++  +++G+GKT 
Sbjct: 12  EVDVTPTFDTMG--LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTA 69

Query: 121 AFLVPAVELIYNLKFMPR 138
            F +  ++ +       +
Sbjct: 70  TFSISVLQCLDIQVRETQ 87

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]} Length = 218

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.4 bits (161), Expect = 2e-14
 Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 4/78 (5%)

Query: 61  EILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTL 120
           EI+ S  F+ +   + E+ L+ I   GF K + IQ R I P ++G D++  A++G+GKT 
Sbjct: 9   EIVDS--FDDMN--LSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTA 64

Query: 121 AFLVPAVELIYNLKFMPR 138
            F +  ++ I       +
Sbjct: 65  TFAISILQQIELDLKATQ 82

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]} Length = 238

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

 Score = 66.8 bits (162), Expect = 2e-14
 Identities = 28/97 (28%), Positives = 41/97 (42%), Gaps = 5/97 (5%)

Query: 49  VEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDL 108
           V V  P       I +   F+ LK  +       I    + + T IQ   IP +LE RD+
Sbjct: 7   VSVTGPDYSATNVIEN---FDELK--LDPTIRNNILLASYQRPTPIQKNAIPAILEHRDI 61

Query: 109 VGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG 145
           +  A+TGSGKT AFL+P +  +       +       
Sbjct: 62  MACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAY 98

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 202

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 65.8 bits (159), Expect = 3e-14
 Identities = 13/70 (18%), Positives = 28/70 (40%)

Query: 67  QFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPA 126
           + E L   +    +  + + G  ++   QA  +  +  G++L+ +  T +GKTL   +  
Sbjct: 2   KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAM 61

Query: 127 VELIYNLKFM 136
           V         
Sbjct: 62  VREAIKGGKS 71

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 212

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 65.2 bits (158), Expect = 4e-14
 Identities = 23/73 (31%), Positives = 43/73 (58%), Gaps = 2/73 (2%)

Query: 66  TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVP 125
            +F+ ++  + EN L+ +   GF + + IQ R I P++EG D++  A++G+GKT  F + 
Sbjct: 10  YKFDDME--LDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIA 67

Query: 126 AVELIYNLKFMPR 138
           A++ I      P+
Sbjct: 68  ALQRIDTSVKAPQ 80

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]} Length = 209

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 65.1 bits (157), Expect = 5e-14
 Identities = 24/57 (42%), Positives = 32/57 (56%), Gaps = 2/57 (3%)

Query: 66  TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAF 122
           TQF           ++AI  + F K TEIQ R IP  L G  +VG ++TG+GKT A+
Sbjct: 1   TQFTRFP--FQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAY 55

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.0 bits (157), Expect = 5e-14
 Identities = 23/60 (38%), Positives = 35/60 (58%), Gaps = 2/60 (3%)

Query: 66  TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVP 125
            +FE     +    L  I +MG+ K + IQ  +IP  L GRD++  AK G+GK+ A+L+P
Sbjct: 3   NEFEDYC--LKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIP 60

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 63.9 bits (154), Expect = 1e-13
 Identities = 23/58 (39%), Positives = 32/58 (55%), Gaps = 2/58 (3%)

Query: 68  FEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVP 125
           FE     +    L  I + GF K + IQ   IP  + GRD++  AK G+GKT AF++P
Sbjct: 3   FEDFY--LKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIP 58

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.4 bits (153), Expect = 2e-13
 Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 2/81 (2%)

Query: 66  TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVP 125
           + F      +    L+AI D GF   +E+Q   IP  + G D++  AK+G GKT  F++ 
Sbjct: 1   SGFRDFL--LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLA 58

Query: 126 AVELIYNLKFMPRNGKSWQGK 146
            ++ +  +            +
Sbjct: 59  TLQQLEPVTGQVSVLVMCHTR 79

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 62.2 bits (150), Expect = 8e-13
 Identities = 12/55 (21%), Positives = 17/55 (30%)

Query: 80  LKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLK 134
                     +   IQ      +L       +A TG GKT   L  ++ L    K
Sbjct: 33  FVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKGK 87

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 54.6 bits (130), Expect = 3e-10
 Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 5/67 (7%)

Query: 66  TQFEA--LKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFL 123
            Q E   L+    +  L+     G+ +    Q   I  +L GRD +    TG GK+L + 
Sbjct: 2   AQAEVLNLESGAKQ-VLQET--FGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQ 58

Query: 124 VPAVELI 130
           +PA+ L 
Sbjct: 59  IPALLLN 65

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 208

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 52.8 bits (126), Expect = 1e-09
 Identities = 26/67 (38%), Positives = 39/67 (58%), Gaps = 6/67 (8%)

Query: 60  LEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGR-DLVGSAKTGSGK 118
           +E ++   F  L   + +N L AI + GF K T+IQ + IP  L    ++V  A+TGSGK
Sbjct: 1   VEYMN---FNELN--LSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGK 55

Query: 119 TLAFLVP 125
           T +F +P
Sbjct: 56  TASFAIP 62

>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 = 41.1 bits (95), Expect = 2e-05
 Identities = 7/31 (22%), Positives = 11/31 (35%)

Query: 102 LLEGRDLVGSAKTGSGKTLAFLVPAVELIYN 132
             + R  +     G+GKT  +L   V     
Sbjct: 6   FRKKRLTIMDLHPGAGKTKRYLPAIVREAIK 36

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	178
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.95
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.94
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.94
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.94
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.93
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.93
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.9
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.9
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.89
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.8
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.76
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.71
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.41
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.27
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	98.92
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	98.92
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	98.9
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.83
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	98.74
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	98.56
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	98.0
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.9
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	97.47
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	96.96
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	96.92
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	96.86
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	96.71
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	96.48
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	96.05
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	94.64
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	94.17
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	93.96
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	92.25
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	92.0
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	91.65
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	91.63
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	91.11
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	90.89
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	90.21
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	89.68
d1ls1a2	207	GTPase domain of the signal sequence recognition p	88.91
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	88.72
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	88.63
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	88.62
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	88.61
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	88.22
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	88.21
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	87.72
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	87.48
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	87.33
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	87.1
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	87.03
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	86.65
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	86.57
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	86.48
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	85.92
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	85.71
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	85.54
d1vmaa2	213	GTPase domain of the signal recognition particle r	84.12
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	83.79
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	83.67
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	83.65
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	83.47
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	83.42
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	83.14
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	82.83
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	82.5
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	82.02
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	81.97
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	81.8
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	81.31
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	81.28
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	81.05
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	80.79

>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=99.95  E-value=1.3e-28  Score=196.52  Aligned_cols=101  Identities=21%  Similarity=0.334  Sum_probs=91.4

Q ss_pred             CCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCce
Q psy12984         62 ILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGK  141 (178)
Q Consensus        62 ~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~  141 (178)
                      +....+|++|+  |+++++++|.++||.+|||||+.|||.++.|+|++++|+||||||+||++|+++++...  ...+++
T Consensus        13 ~~~~~sF~~l~--L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~--~~~~~~   88 (222)
T d2j0sa1          13 VDVTPTFDTMG--LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQ--VRETQA   88 (222)
T ss_dssp             CCCCCSGGGGC--CCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTT--SCSCCE
T ss_pred             CCCCCCHHHCC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhccccccccccc--ccCcee
Confidence            33445799998  99999999999999999999999999999999999999999999999999999988654  345689


Q ss_pred             EEEeecHHHHHHHHHHHHHHhhhcC
Q psy12984        142 SWQGKLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus       142 ~~l~Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      ++++||||||.|++.++..+.++.+
T Consensus        89 lil~PtreLa~Qi~~~~~~l~~~~~  113 (222)
T d2j0sa1          89 LILAPTRELAVQIQKGLLALGDYMN  113 (222)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTTT
T ss_pred             EEecchHHHHHHHHHHHHHHhCccc
Confidence            9999999999999999999887654

>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=99.94  E-value=1.8e-27  Score=187.50  Aligned_cols=97  Identities=24%  Similarity=0.289  Sum_probs=89.4

Q ss_pred             chHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEee
Q psy12984         67 QFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGK  146 (178)
Q Consensus        67 ~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~P  146 (178)
                      .|++|+  |+++++++|.++||.+|||||++|||.++.|+|++++|+||||||+||++|+++++...  ..+.++++++|
T Consensus         2 ~F~dl~--L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~--~~~~~~lil~P   77 (207)
T d1t6na_           2 GFRDFL--LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV--TGQVSVLVMCH   77 (207)
T ss_dssp             CSTTSC--CCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCC--TTCCCEEEECS
T ss_pred             CccccC--cCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeeccc--CCCceEEEEec
Confidence            599998  99999999999999999999999999999999999999999999999999999987654  44568999999


Q ss_pred             cHHHHHHHHHHHHHHhhhcCC
Q psy12984        147 LRPLTNGVYLVACNVFKSTQP  167 (178)
Q Consensus       147 tr~La~qi~~~~~~l~~~~~~  167 (178)
                      ||+||.|+++.+..+..+.+.
T Consensus        78 treL~~qi~~~~~~~~~~~~~   98 (207)
T d1t6na_          78 TRELAFQISKEYERFSKYMPN   98 (207)
T ss_dssp             CHHHHHHHHHHHHHHTTTSTT
T ss_pred             cchhhHHHHHHHHHHHhhCCC
Confidence            999999999999998877653

>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=99.94  E-value=3.6e-27  Score=187.34  Aligned_cols=99  Identities=24%  Similarity=0.367  Sum_probs=91.6

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      .+|++|+  |++.++++|.++||.+||+||+.|||.++.|+|++++|+||||||+||++|+++++...  ...+++++++
T Consensus        12 ~sF~~l~--L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~--~~~~~alil~   87 (218)
T d2g9na1          12 DSFDDMN--LSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELD--LKATQALVLA   87 (218)
T ss_dssp             CCGGGSC--CCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTT--CCSCCEEEEC
T ss_pred             CCHHHCC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheeccc--ccCccEEEEc
Confidence            4699998  99999999999999999999999999999999999999999999999999999998653  4567899999


Q ss_pred             ecHHHHHHHHHHHHHHhhhcCCC
Q psy12984        146 KLRPLTNGVYLVACNVFKSTQPP  168 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~~~~~~~  168 (178)
                      |||+||.|++..+..+....+..
T Consensus        88 Pt~eL~~Q~~~~~~~~~~~~~~~  110 (218)
T d2g9na1          88 PTRELAQQIQKVVMALGDYMGAS  110 (218)
T ss_dssp             SSHHHHHHHHHHHHHHHTTTTCC
T ss_pred             ccchhhhhHHHHHhhhcccccee
Confidence            99999999999999998877654

>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=99.94  E-value=3.7e-27  Score=185.50  Aligned_cols=97  Identities=30%  Similarity=0.369  Sum_probs=89.2

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      ++|++|+  |+++++++|.++||.+|||||++|||.++.|+|++++|+||||||+||++|+++++...  ..+.++++++
T Consensus         3 ~~F~~l~--L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~--~~~~~~lil~   78 (206)
T d1veca_           3 NEFEDYC--LKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLK--KDNIQAMVIV   78 (206)
T ss_dssp             SSGGGSC--CCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTT--SCSCCEEEEC
T ss_pred             CChhccC--cCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhccccc--ccCcceEEEe
Confidence            5799998  99999999999999999999999999999999999999999999999999999987654  4556899999


Q ss_pred             ecHHHHHHHHHHHHHHhhhcC
Q psy12984        146 KLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      |||+||.|++.++..+.+...
T Consensus        79 pt~el~~q~~~~~~~~~~~~~   99 (206)
T d1veca_          79 PTRELALQVSQICIQVSKHMG   99 (206)
T ss_dssp             SCHHHHHHHHHHHHHHTTTSS
T ss_pred             ecchhhHHHHHHHHHHhhccc
Confidence            999999999999998876544

>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=99.93  E-value=3e-27  Score=189.98  Aligned_cols=116  Identities=26%  Similarity=0.320  Sum_probs=97.2

Q ss_pred             ccccccCCCCCCcCCCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHH
Q psy12984         48 AVEVQLPGSDVALEILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAV  127 (178)
Q Consensus        48 ~~~~~~~~~~~~~~~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l  127 (178)
                      ...++..+.+... .....+|++|+  |+++++++|.++||.+|||||+.|||.++.|+|++++|+||||||+||++|+|
T Consensus         4 ~~~~~~~~~~~~~-~~~~~~F~~l~--l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l   80 (238)
T d1wrba1           4 SIPVSVTGPDYSA-TNVIENFDELK--LDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPII   80 (238)
T ss_dssp             CCCCCEECCSSSC-CSCCCSSGGGS--CCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHH
T ss_pred             ccceeeeCCCCCC-CCccCCHHHCC--CCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHH
Confidence            3444444554432 22346799998  99999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcc-------CCCCCceEEEeecHHHHHHHHHHHHHHhhhcC
Q psy12984        128 ELIYNLK-------FMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus       128 ~~l~~~~-------~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      +++....       ...++++++|+|||+||.|++.++..+....+
T Consensus        81 ~~l~~~~~~~~~~~~~~~~~alil~pt~el~~q~~~~~~~~~~~~~  126 (238)
T d1wrba1          81 NHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTP  126 (238)
T ss_dssp             HHHHTTCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSS
T ss_pred             HHHHhcccccccccCCCCceEEEeccchhhhcchheeeeecccCCC
Confidence            9986532       23466899999999999999999998877654

>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=99.93  E-value=5e-26  Score=179.92  Aligned_cols=97  Identities=26%  Similarity=0.393  Sum_probs=88.8

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      .+|++|+  |+++++++|.++||.+|||+|++|||.++.|+|++++|+||||||+||++|+++++...  ..++.+++++
T Consensus        10 ~sF~~l~--l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~--~~~~~~lil~   85 (212)
T d1qdea_          10 YKFDDME--LDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS--VKAPQALMLA   85 (212)
T ss_dssp             CCGGGGT--CCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT--CCSCCEEEEC
T ss_pred             cChhhCC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhcc--CCCcceEEEc
Confidence            4599998  99999999999999999999999999999999999999999999999999999998654  4566899999


Q ss_pred             ecHHHHHHHHHHHHHHhhhcC
Q psy12984        146 KLRPLTNGVYLVACNVFKSTQ  166 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~~~~~  166 (178)
                      |||+||.|++..+..+.....
T Consensus        86 pt~el~~q~~~~~~~~~~~~~  106 (212)
T d1qdea_          86 PTRELALQIQKVVMALAFHMD  106 (212)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSC
T ss_pred             ccHHHhhhhhhhhcccccccc
Confidence            999999999999988765544

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.90  E-value=1.5e-24  Score=170.44  Aligned_cols=99  Identities=30%  Similarity=0.400  Sum_probs=89.6

Q ss_pred             ccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCC-cEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEE
Q psy12984         65 STQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGR-DLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSW  143 (178)
Q Consensus        65 ~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~-dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~  143 (178)
                      ..+|++|+  |+++++++|.++||.+|||+|+++||.++.|+ |++++|+||||||++|++|++++...   ..++++++
T Consensus         3 ~msf~~l~--l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~---~~~~~~li   77 (208)
T d1hv8a1           3 YMNFNELN--LSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE---NNGIEAII   77 (208)
T ss_dssp             CCCGGGSS--CCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCS---SSSCCEEE
T ss_pred             ccCHHHcC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeeccccccccc---ccCcceEE
Confidence            35799998  99999999999999999999999999999885 99999999999999999999987654   56779999


Q ss_pred             EeecHHHHHHHHHHHHHHhhhcCCC
Q psy12984        144 QGKLRPLTNGVYLVACNVFKSTQPP  168 (178)
Q Consensus       144 l~Ptr~La~qi~~~~~~l~~~~~~~  168 (178)
                      ++||++||.|++.++..+....+..
T Consensus        78 l~pt~~l~~q~~~~~~~~~~~~~~~  102 (208)
T d1hv8a1          78 LTPTRELAIQVADEIESLKGNKNLK  102 (208)
T ss_dssp             ECSCHHHHHHHHHHHHHHHCSSCCC
T ss_pred             EeeccccchhhhhhhhhhcccCCeE
Confidence            9999999999999999988766544

>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=99.90  E-value=4.1e-24  Score=166.84  Aligned_cols=107  Identities=32%  Similarity=0.419  Sum_probs=94.1

Q ss_pred             cchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe
Q psy12984         66 TQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG  145 (178)
Q Consensus        66 ~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~  145 (178)
                      ++|++|+  |+++++++|.++||.+|||+|++|||.++.|+|++++||||||||+||++|+++.+...  ......++++
T Consensus         1 t~F~~l~--L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~--~~~~~~~~~~   76 (209)
T d1q0ua_           1 TQFTRFP--FQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPE--RAEVQAVITA   76 (209)
T ss_dssp             CCGGGSC--CCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTT--SCSCCEEEEC
T ss_pred             CccccCC--cCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeeccccccc--cccccccccc
Confidence            4799998  99999999999999999999999999999999999999999999999999999987653  3445778899


Q ss_pred             ecHHHHHHHHHHHHHHhhhcCCCCcceEEEe
Q psy12984        146 KLRPLTNGVYLVACNVFKSTQPPTVIKVQTL  176 (178)
Q Consensus       146 Ptr~La~qi~~~~~~l~~~~~~~~~~~v~~~  176 (178)
                      |+++++.+.+..+..............+..+
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  107 (209)
T d1q0ua_          77 PTRELATQIYHETLKITKFCPKDRMIVARCL  107 (209)
T ss_dssp             SSHHHHHHHHHHHHHHHTTSCGGGCCCEEEE
T ss_pred             cccchhHHHHHHHHhhhcccccccccccccc
Confidence            9999999999999888877766655555443

>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=99.89  E-value=9.4e-24  Score=165.35  Aligned_cols=97  Identities=29%  Similarity=0.376  Sum_probs=88.5

Q ss_pred             chHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEee
Q psy12984         67 QFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGK  146 (178)
Q Consensus        67 ~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~P  146 (178)
                      +|++|+  |++.++++|.++||.+|||+|+.|||.++.|+|++++|+||||||+||++|+++++...  ....++++++|
T Consensus         2 sF~~l~--L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~--~~~~~~~~~~~   77 (206)
T d1s2ma1           2 TFEDFY--LKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPK--LNKIQALIMVP   77 (206)
T ss_dssp             CGGGGC--CCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTT--SCSCCEEEECS
T ss_pred             ChHHcC--CCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccc--cccccceeecc
Confidence            699998  99999999999999999999999999999999999999999999999999999987654  44568899999


Q ss_pred             cHHHHHHHHHHHHHHhhhcCC
Q psy12984        147 LRPLTNGVYLVACNVFKSTQP  167 (178)
Q Consensus       147 tr~La~qi~~~~~~l~~~~~~  167 (178)
                      +++++.|.+.++..+....+.
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~   98 (206)
T d1s2ma1          78 TRELALQTSQVVRTLGKHCGI   98 (206)
T ss_dssp             SHHHHHHHHHHHHHHTTTTTC
T ss_pred             chhhhhhhhhhhhhcccccCe
Confidence            999999999998887766554

>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=99.80  E-value=7.5e-20  Score=145.00  Aligned_cols=94  Identities=14%  Similarity=-0.057  Sum_probs=80.3

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHH
Q psy12984         75 VCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGV  154 (178)
Q Consensus        75 l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi  154 (178)
                      +.+.+ .++.+.+|.+|+++|+.+|+.++.|+|++++||||+|||++|++|++.....     +.+++|++||++|+.|+
T Consensus        29 ~~~~~-~~~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~-----~~rvliv~Pt~~La~Q~  102 (237)
T d1gkub1          29 LLKEF-VEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALK-----GKRCYVIFPTSLLVIQA  102 (237)
T ss_dssp             HHHHH-HHHHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTT-----SCCEEEEESCHHHHHHH
T ss_pred             hHHHH-HHHHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHh-----cCeEEEEeccHHHHHHH
Confidence            33444 5566778999999999999999999999999999999999999999886643     45899999999999999


Q ss_pred             HHHHHHHhhhcCCCCcceEE
Q psy12984        155 YLVACNVFKSTQPPTVIKVQ  174 (178)
Q Consensus       155 ~~~~~~l~~~~~~~~~~~v~  174 (178)
                      ++.+++++..++.+....+.
T Consensus       103 ~~~l~~~~~~~~~~~~~~~~  122 (237)
T d1gkub1         103 AETIRKYAEKAGVGTENLIG  122 (237)
T ss_dssp             HHHHHHHHTTTCCSGGGSEE
T ss_pred             HHHHHHHHHHcCCceEEEEe
Confidence            99999999888877655443

>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=99.76  E-value=1.4e-19  Score=140.13  Aligned_cols=90  Identities=20%  Similarity=0.230  Sum_probs=77.1

Q ss_pred             HhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecH
Q psy12984         69 EALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLR  148 (178)
Q Consensus        69 ~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr  148 (178)
                      +++...+++.+++.|.+.||..|+|+|.+||+.+++|+|+++++|||||||.++.++++..+..     ..++++++|++
T Consensus         4 ~~~~~~~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~-----~~~vl~l~P~~   78 (202)
T d2p6ra3           4 EELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK-----GGKSLYVVPLR   78 (202)
T ss_dssp             HHHHHHHHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT-----TCCEEEEESSH
T ss_pred             HHhhhhhhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhc-----cCcceeecccH
Confidence            4444448889999999999999999999999999999999999999999999999999988764     33789999999


Q ss_pred             HHHHHHHHHHHHHhh
Q psy12984        149 PLTNGVYLVACNVFK  163 (178)
Q Consensus       149 ~La~qi~~~~~~l~~  163 (178)
                      +|+.|++..++++..
T Consensus        79 ~L~~q~~~~~~~~~~   93 (202)
T d2p6ra3          79 ALAGEKYESFKKWEK   93 (202)
T ss_dssp             HHHHHHHHHHTTTTT
T ss_pred             HHHHHHHHHHHHHhh
Confidence            999999999877654

>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=99.71  E-value=2.3e-18  Score=133.30  Aligned_cols=86  Identities=22%  Similarity=0.249  Sum_probs=75.3

Q ss_pred             hHhhcccCCHHHHHHHHHC-CCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEee
Q psy12984         68 FEALKGKVCENTLKAIADM-GFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGK  146 (178)
Q Consensus        68 f~~l~~~l~~~ll~~l~~~-g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~P  146 (178)
                      ++.++  |++.+.+.|++. ||..++|+|.+||++++.|+|+++++|||||||++|.+|++..        ...+++++|
T Consensus         4 ~e~~~--l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~--------~~~~~~v~P   73 (206)
T d1oywa2           4 AEVLN--LESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL--------NGLTVVVSP   73 (206)
T ss_dssp             CCCSS--HHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS--------SSEEEEECS
T ss_pred             hhhCC--CCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhc--------cCceEEecc
Confidence            44555  888888888886 9999999999999999999999999999999999999998752        336789999


Q ss_pred             cHHHHHHHHHHHHHHhh
Q psy12984        147 LRPLTNGVYLVACNVFK  163 (178)
Q Consensus       147 tr~La~qi~~~~~~l~~  163 (178)
                      +++|++|++..+..++.
T Consensus        74 ~~~L~~q~~~~l~~~~~   90 (206)
T d1oywa2          74 LISLMKDQVDQLQANGV   90 (206)
T ss_dssp             CHHHHHHHHHHHHHTTC
T ss_pred             chhhhhhHHHHHHhhcc
Confidence            99999999999887653

>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=99.41  E-value=2e-13  Score=103.95  Aligned_cols=71  Identities=15%  Similarity=-0.009  Sum_probs=60.6

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      .|.++|.+++..+. ++|+|+++|||||||+++++++...+.+    ...++++++|+++|+.|.++.+.+++...
T Consensus         9 ~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~----~~~~il~i~P~~~L~~q~~~~~~~~~~~~   79 (200)
T d1wp9a1           9 QPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTK----YGGKVLMLAPTKPLVLQHAESFRRLFNLP   79 (200)
T ss_dssp             CCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHH----SCSCEEEECSSHHHHHHHHHHHHHHBCSC
T ss_pred             CCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHh----cCCcEEEEcCchHHHHHHHHHHHHhhccc
Confidence            89999999998776 6689999999999999999988877654    23478999999999999999999886543

>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=99.27  E-value=1.1e-12  Score=105.10  Aligned_cols=58  Identities=14%  Similarity=0.015  Sum_probs=49.3

Q ss_pred             cccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984        101 PLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus       101 ~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      .+..|+++|+.||||||||++|++|++......    +.+++|++|||+||.|+++.++.+.
T Consensus         5 ~~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~----~~~~lvi~Ptr~La~q~~~~l~~~~   62 (305)
T d2bmfa2           5 IFRKKRLTIMDLHPGAGKTKRYLPAIVREAIKR----GLRTLILAPTRVVAAEMEEALRGLP   62 (305)
T ss_dssp             SSSTTCEEEECCCTTSSTTTTHHHHHHHHHHHH----TCCEEEEESSHHHHHHHHHHTTTSC
T ss_pred             HhhcCCcEEEEECCCCCHHHHHHHHHHHHHHhc----CCEEEEEccHHHHHHHHHHHHhcCC
Confidence            456899999999999999999998998876542    4578999999999999998876553

>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=98.92  E-value=1.8e-09  Score=85.38  Aligned_cols=86  Identities=20%  Similarity=0.128  Sum_probs=69.2

Q ss_pred             HHHHHHHHH-CCCCCCcHHHHHhhccccC----C--CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHH
Q psy12984         77 ENTLKAIAD-MGFTKMTEIQARTIPPLLE----G--RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRP  149 (178)
Q Consensus        77 ~~ll~~l~~-~g~~~pt~iQ~~aip~~l~----g--~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~  149 (178)
                      .+..+.+.+ ..| .+|+-|..++..+..    +  .+.++++.||||||..|+..+...+.+     +.++++++||..
T Consensus        42 ~~~~~~~~~~lP~-~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~-----g~qv~~l~Pt~~  115 (233)
T d2eyqa3          42 REQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN-----HKQVAVLVPTTL  115 (233)
T ss_dssp             HHHHHHHHHTCCS-CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT-----TCEEEEECSSHH
T ss_pred             HHHHHhhhhcccc-ccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHc-----CCceEEEccHHH
Confidence            344444433 455 799999999987642    2  588999999999999999999888744     559999999999


Q ss_pred             HHHHHHHHHHHHhhhcCCC
Q psy12984        150 LTNGVYLVACNVFKSTQPP  168 (178)
Q Consensus       150 La~qi~~~~~~l~~~~~~~  168 (178)
                      ||.|.+..|+.++..++.+
T Consensus       116 La~Q~~~~~~~~~~~~~~~  134 (233)
T d2eyqa3         116 LAQQHYDNFRDRFANWPVR  134 (233)
T ss_dssp             HHHHHHHHHHHHSTTTTCC
T ss_pred             hHHHHHHHHHHHHhhCCCE
Confidence            9999999999998777654

>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=98.92  E-value=3.1e-09  Score=85.44  Aligned_cols=81  Identities=17%  Similarity=0.151  Sum_probs=69.0

Q ss_pred             HHHCCCCCCcHHHHHhhccccC------CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHH
Q psy12984         83 IADMGFTKMTEIQARTIPPLLE------GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYL  156 (178)
Q Consensus        83 l~~~g~~~pt~iQ~~aip~~l~------g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~  156 (178)
                      +..+.| .+|+-|..|+..+..      ..+.++++-||||||..|+..++..+..     +.++++++||..||.|.+.
T Consensus        77 ~~~LPF-eLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~-----g~q~~~m~Pt~~La~Qh~~  150 (264)
T d1gm5a3          77 IKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA-----GFQTAFMVPTSILAIQHYR  150 (264)
T ss_dssp             HHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH-----TSCEEEECSCHHHHHHHHH
T ss_pred             Hhhccc-cCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhc-----ccceeEEeehHhhhHHHHH
Confidence            455778 899999999988742      3578999999999999999999988865     4589999999999999999


Q ss_pred             HHHHHhhhcCCCC
Q psy12984        157 VACNVFKSTQPPT  169 (178)
Q Consensus       157 ~~~~l~~~~~~~~  169 (178)
                      .+..++..++..+
T Consensus       151 ~~~~~f~~~~~~v  163 (264)
T d1gm5a3         151 RTVESFSKFNIHV  163 (264)
T ss_dssp             HHHHHHTCSSCCE
T ss_pred             HHHHhhhhccccc
Confidence            9999997766543

>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=98.90  E-value=8.2e-10  Score=84.96  Aligned_cols=65  Identities=14%  Similarity=0.009  Sum_probs=53.8

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      .|.++|.+++..++.+...++.++||+|||+..+.. +..+       ...++++||+++|+.|..+.+..+.
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~-~~~~-------~~~~Liv~p~~~L~~q~~~~~~~~~  134 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAA-INEL-------STPTLIVVPTLALAEQWKERLGIFG  134 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHH-HHHS-------CSCEEEEESSHHHHHHHHHHHGGGC
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhH-HHHh-------cCceeEEEcccchHHHHHHHHHhhc
Confidence            588899999999998888899999999999876533 3222       2368999999999999999987764

>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=2.6e-09  Score=75.17  Aligned_cols=55  Identities=20%  Similarity=0.095  Sum_probs=45.4

Q ss_pred             ccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHH
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACN  160 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~  160 (178)
                      +..|++++++++||||||..++..++.....    .+...++++|+++|+.|.++.+..
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~~~~~~~~~~----~~~~vli~~p~~~l~~q~~~~~~~   58 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFLPQILAECAR----RRLRTLVLAPTRVVLSEMKEAFHG   58 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHH----TTCCEEEEESSHHHHHHHHHHTTT
T ss_pred             HHcCCcEEEEcCCCCChhHHHHHHHHHHhhh----cCceeeeeecchhHHHHHHHHhhh
Confidence            5679999999999999999887777776654    245789999999999999987643

>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=98.74  E-value=6e-09  Score=84.04  Aligned_cols=69  Identities=12%  Similarity=-0.080  Sum_probs=56.1

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      .|.+.|..|+..++..+..++.+|||+|||+....- +..+..   ....++++|||+++|+.|.++.|..++
T Consensus       113 ~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i-~~~~~~---~~~~k~Liivp~~~Lv~Q~~~~f~~~~  181 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALL-ARYYLE---NYEGKILIIVPTTALTTQMADDFVDYR  181 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHH-HHHHHH---HCSSEEEEECSSHHHHHHHHHHHHHHT
T ss_pred             ccchHHHHHHHHHHhcCCceeEEEcccCccHHHHHH-HHHhhh---cccceEEEEEcCchhHHHHHHHHHHhh
Confidence            689999999999998888999999999999985543 333333   123478999999999999999998875

>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=98.56  E-value=5.4e-08  Score=69.17  Aligned_cols=51  Identities=16%  Similarity=-0.105  Sum_probs=39.0

Q ss_pred             CCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984        105 GRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      .+..++.+|||||||+.+..-+    .    ..+.++++++|+++|++|.+..+...+.
T Consensus         8 ~~~~ll~apTGsGKT~~~~~~~----~----~~~~~vli~~P~~~l~~q~~~~~~~~~~   58 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPAAY----A----AQGYKVLVLNPSVAATLGFGAYMSKAHG   58 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHHHH----H----TTTCCEEEEESCHHHHHHHHHHHHHHHS
T ss_pred             CCEEEEEeCCCCCHHHHHHHHH----H----HcCCcEEEEcChHHHHHHHHHHHHHHhh
Confidence            4567999999999997543222    2    2345789999999999999999887653

>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=98.00  E-value=7.5e-06  Score=64.21  Aligned_cols=71  Identities=13%  Similarity=-0.020  Sum_probs=52.6

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      +++|-|.+|+..  ....++|.|+.|||||.+.+.-+...+.... .+..+.+++++|+++|..+...+..+..
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~-~~~~~ILvlt~tn~a~~~i~~~~~~~~~   71 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCG-YQARHIAAVTFTNKAAREMKERVGQTLG   71 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHC-CCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHHHHHHHHHhcC-CChhHEEEEeCcHHHHHHHHHHHHHhcC
Confidence            367889999854  2346899999999999986655555444432 2334789999999999999888776654

>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=97.90  E-value=2.9e-05  Score=61.40  Aligned_cols=76  Identities=12%  Similarity=0.003  Sum_probs=57.4

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhcCCC
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKSTQPP  168 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~~~~  168 (178)
                      .+++=|..++...  +..++|.|+.|||||.+.+--+...+.... .+..+++++++|+..|..+...+..........
T Consensus        11 ~L~~eQ~~~v~~~--~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~-~~p~~il~lt~t~~aa~~~~~~~~~~~~~~~~~   86 (318)
T d1pjra1          11 HLNKEQQEAVRTT--EGPLLIMAGAGSGKTRVLTHRIAYLMAEKH-VAPWNILAITFTNKAAREMRERVQSLLGGAAED   86 (318)
T ss_dssp             TSCHHHHHHHHCC--SSCEEEEECTTSCHHHHHHHHHHHHHHTTC-CCGGGEEEEESSHHHHHHHHHHHHHHHGGGGTT
T ss_pred             hCCHHHHHHHhCC--CCCEEEEecCCccHHHHHHHHHHHHHHcCC-CCHHHeEeEeccHHHHHHHHHHHHhhccccccc
Confidence            4778899988643  446999999999999988766666554432 233478999999999999999988776654433

>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=96.96  E-value=0.0023  Score=52.26  Aligned_cols=72  Identities=14%  Similarity=0.004  Sum_probs=51.1

Q ss_pred             CCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHh
Q psy12984         90 KMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVF  162 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~  162 (178)
                      ..+.-|..|+..++.++-++++++.|||||.... -++..+......++.+.++.+||..=|..+...+....
T Consensus       148 ~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~-~~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~~~~~  219 (359)
T d1w36d1         148 DEINWQKVAAAVALTRRISVISGGPGTGKTTTVA-KLLAALIQMADGERCRIRLAAPTGKAAARLTESLGKAL  219 (359)
T ss_dssp             TSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHH-HHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHTHHH
T ss_pred             ccccHHHHHHHHHHcCCeEEEEcCCCCCceehHH-HHHHHHHHHHhccCCeEEEecCcHHHHHHHHHHHHHHH
Confidence            3466899999999999999999999999998732 33333333323455677888999776766666655443

>d1tf5a3 c.37.1.19 (A:1-226,A:349-395) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=96.92  E-value=0.0026  Score=50.20  Aligned_cols=78  Identities=19%  Similarity=0.121  Sum_probs=65.4

Q ss_pred             CCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhhc
Q psy12984         86 MGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKST  165 (178)
Q Consensus        86 ~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~~  165 (178)
                      .|. +|+++|...--++..|+  |+.-.||-|||++..+|+.-..+.     +.++=+++..--||.-=..++..+..++
T Consensus        77 lG~-RhyDVQLiGgi~L~~G~--iaem~TGEGKTL~a~l~a~l~al~-----g~~vhvvTvNdyLA~RDae~m~~iy~~l  148 (273)
T d1tf5a3          77 TGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALT-----GKGVHVVTVNEYLASRDAEQMGKIFEFL  148 (273)
T ss_dssp             HSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTT-----SSCEEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred             hce-EEehhHHHHHHHHHhhh--heeecCCCcchhHHHHHHHHHHhc-----CCCceEEecCccccchhhhHHhHHHHHc
Confidence            577 89999988887777775  789999999999999998765544     4466778888999999999999999999


Q ss_pred             CCCCcc
Q psy12984        166 QPPTVI  171 (178)
Q Consensus       166 ~~~~~~  171 (178)
                      |..++.
T Consensus       149 Glsvg~  154 (273)
T d1tf5a3         149 GLTVGL  154 (273)
T ss_dssp             TCCEEE
T ss_pred             CCCccc
Confidence            987654

>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=96.86  E-value=0.0013  Score=49.76  Aligned_cols=70  Identities=10%  Similarity=-0.058  Sum_probs=48.7

Q ss_pred             CCcHHHHHhhccc----cCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984         90 KMTEIQARTIPPL----LEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus        90 ~pt~iQ~~aip~~----l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      .+.|+|..++.-+    ..+..+|++-..|.|||+..+ .++..+...  .....++|++| ..|..|..+.+..+..
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i-~~~~~~~~~--~~~~~~LIv~p-~~l~~~W~~e~~~~~~   85 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTI-AVFSDAKKE--NELTPSLVICP-LSVLKNWEEELSKFAP   85 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHH-HHHHHHHHT--TCCSSEEEEEC-STTHHHHHHHHHHHCT
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHH-Hhhhhhhhc--ccccccceecc-hhhhhHHHHHHHhhcc
Confidence            4778999998643    245678999999999999854 444444332  33446788888 6667777777776643

>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=96.71  E-value=0.0036  Score=49.04  Aligned_cols=73  Identities=12%  Similarity=0.022  Sum_probs=49.5

Q ss_pred             CCcHHHHHhhccc---------cCCCcEEEEccCCCchhhHhHHHHHHHHHhccC---CCCCceEEEeecHHHHHHHHHH
Q psy12984         90 KMTEIQARTIPPL---------LEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKF---MPRNGKSWQGKLRPLTNGVYLV  157 (178)
Q Consensus        90 ~pt~iQ~~aip~~---------l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~---~~~~~~~~l~Ptr~La~qi~~~  157 (178)
                      .+.|+|..++.-+         -.+..+|++-..|.|||+.-+ .++..+.....   .....++|+||.. |..|....
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qai-a~l~~l~~~~~~~~~~~~~~LIV~P~s-l~~qW~~E  132 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCI-TLIWTLLKQSPDCKPEIDKVIVVSPSS-LVRNWYNE  132 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHH-HHHHHHHHCCTTSSCSCSCEEEEECHH-HHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHH-HHHHHHHHhcccccCCCCcEEEEccch-hhHHHHHH
Confidence            5789999998633         245678999999999997532 33333333221   1233578999964 78888888


Q ss_pred             HHHHhhh
Q psy12984        158 ACNVFKS  164 (178)
Q Consensus       158 ~~~l~~~  164 (178)
                      +.+++..
T Consensus       133 i~k~~~~  139 (298)
T d1z3ix2         133 VGKWLGG  139 (298)
T ss_dssp             HHHHHGG
T ss_pred             HHhhcCC
Confidence            8887654

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=96.48  E-value=0.0013  Score=54.82  Aligned_cols=66  Identities=18%  Similarity=0.246  Sum_probs=48.6

Q ss_pred             CCcHHHHHhhccccC----C-CcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhh
Q psy12984         90 KMTEIQARTIPPLLE----G-RDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFK  163 (178)
Q Consensus        90 ~pt~iQ~~aip~~l~----g-~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~  163 (178)
                      .|+--|-.||..+..    | ++.++.+-||||||+... -++...       ....+||+|+..+|.|+++.+..++.
T Consensus        11 ~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA-~l~~~~-------~rp~LVVt~n~~~A~qL~~dL~~~l~   81 (413)
T d1t5la1          11 EPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTIS-NVIAQV-------NKPTLVIAHNKTLAGQLYSELKEFFP   81 (413)
T ss_dssp             CCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHHH-HHHHHH-------TCCEEEECSSHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHHH-HHHHHh-------CCCEEEEeCCHHHHHHHHHHHHHHcC
Confidence            566677777765543    4 678899999999997543 333322       12468999999999999999998864

>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=94.64  E-value=0.018  Score=46.59  Aligned_cols=49  Identities=16%  Similarity=0.103  Sum_probs=33.6

Q ss_pred             hccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHH
Q psy12984         99 IPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTN  152 (178)
Q Consensus        99 ip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~  152 (178)
                      ||.=...+|+++.++||||||.++ ..++..+..    .+..++++-|.-++..
T Consensus        44 ~~~~~~~~H~~I~G~tGsGKT~~l-~~li~~~~~----~g~~~iiiD~kge~~~   92 (433)
T d1e9ra_          44 MPRDAEPRHLLVNGATGTGKSVLL-RELAYTGLL----RGDRMVIVDPNGDMLS   92 (433)
T ss_dssp             CCGGGGGGCEEEEECTTSSHHHHH-HHHHHHHHH----TTCEEEEEEETTHHHH
T ss_pred             cCCCcccceEEEEeCCCCcHHHHH-HHHHHHHHh----CCCCEEEEeCChhHHH
Confidence            444455689999999999999764 444554443    2336677888877654

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.17  E-value=0.033  Score=38.64  Aligned_cols=26  Identities=27%  Similarity=0.402  Sum_probs=19.8

Q ss_pred             CcEEEEccCCCchhhHhHHHHHHHHHh
Q psy12984        106 RDLVGSAKTGSGKTLAFLVPAVELIYN  132 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~lp~l~~l~~  132 (178)
                      |+|++.+++|+|||. ++--++..+..
T Consensus         2 k~v~ItG~~GtGKTt-l~~~i~~~l~~   27 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTT-LIHKASEVLKS   27 (189)
T ss_dssp             CCEEEESCCSSCHHH-HHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHH-HHHHHHHHHHH
Confidence            789999999999998 44455555544

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=93.96  E-value=0.0078  Score=48.26  Aligned_cols=41  Identities=27%  Similarity=0.411  Sum_probs=26.1

Q ss_pred             HHHHHCCCCCC---cHHHHHhhc-cccCCCcEEEEccCCCchhhH
Q psy12984         81 KAIADMGFTKM---TEIQARTIP-PLLEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus        81 ~~l~~~g~~~p---t~iQ~~aip-~~l~g~dvi~~a~TGsGKTla  121 (178)
                      ..+...|+-..   .+-+...+- ++..+++++++++||||||..
T Consensus       138 ~~l~~~g~~~~~~~~~~~~~~l~~~v~~~~nili~G~tgSGKTT~  182 (323)
T d1g6oa_         138 SFFEEQGFYNLLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKTTY  182 (323)
T ss_dssp             HHHHHTTTTTTCSSHHHHHHHHHHHHHHTCCEEEEESTTSSHHHH
T ss_pred             HHHHHHhhhcccccHHHHHHHHHHHHHhCCCEEEEeeccccchHH
Confidence            34555564332   233333333 345789999999999999985

>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=92.25  E-value=0.029  Score=46.77  Aligned_cols=19  Identities=26%  Similarity=0.298  Sum_probs=16.5

Q ss_pred             CCCcEEEEccCCCchhhHh
Q psy12984        104 EGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf  122 (178)
                      ..+|+|..+|||+|||+..
T Consensus        48 ~ksNILliGPTGvGKTlLA   66 (443)
T d1g41a_          48 TPKNILMIGPTGVGKTEIA   66 (443)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             ccccEEEECCCCCCHHHHH
Confidence            3579999999999999854

>d1c4oa1 c.37.1.19 (A:2-409) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=92.00  E-value=0.098  Score=42.94  Aligned_cols=66  Identities=20%  Similarity=0.176  Sum_probs=44.8

Q ss_pred             CcHHHHHhhccc----cCCC-cEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEeecHHHHHHHHHHHHHHhhh
Q psy12984         91 MTEIQARTIPPL----LEGR-DLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQGKLRPLTNGVYLVACNVFKS  164 (178)
Q Consensus        91 pt~iQ~~aip~~----l~g~-dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~Ptr~La~qi~~~~~~l~~~  164 (178)
                      |+.-|-.||..+    ..|. .+.+.+-+||+|++... .++..+      ++ -.++|+|+...|.+++..+..++..
T Consensus         9 p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~A-~l~~~~------~r-p~LvVt~~~~~A~~l~~dL~~~l~~   79 (408)
T d1c4oa1           9 PKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMA-KVIEAL------GR-PALVLAPNKILAAQLAAEFRELFPE   79 (408)
T ss_dssp             CCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH-HHHHHH------TC-CEEEEESSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHHHH-HHHHHh------CC-CEEEEeCCHHHHHHHHHHHHHhcCc
Confidence            344565566544    3454 46888999999996432 222222      12 4588999999999999999988653

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=91.65  E-value=0.071  Score=39.25  Aligned_cols=47  Identities=19%  Similarity=0.236  Sum_probs=30.4

Q ss_pred             CCCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHh
Q psy12984         61 EILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus        61 ~~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      +.|..++|+++-  .++.+.+.|...       ++..      .-.++|+.+|+|+|||...
T Consensus        16 ~ky~P~~~~dii--g~~~~~~~l~~~-------i~~~------~~~~lll~Gp~G~GKTtla   62 (231)
T d1iqpa2          16 EKYRPQRLDDIV--GQEHIVKRLKHY-------VKTG------SMPHLLFAGPPGVGKTTAA   62 (231)
T ss_dssp             HHTCCCSTTTCC--SCHHHHHHHHHH-------HHHT------CCCEEEEESCTTSSHHHHH
T ss_pred             HHhCCCCHHHcc--CcHHHHHHHHHH-------HHcC------CCCeEEEECCCCCcHHHHH
Confidence            445556788886  566666665442       1111      1236899999999999663

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.63  E-value=0.017  Score=43.20  Aligned_cols=56  Identities=14%  Similarity=0.026  Sum_probs=31.4

Q ss_pred             CCccchHhhcccCCHHHHHHHHHCCCCCCcHHH-HHhhcc-----ccCCCcEEEEccCCCchhhHh
Q psy12984         63 LSSTQFEALKGKVCENTLKAIADMGFTKMTEIQ-ARTIPP-----LLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus        63 ~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ-~~aip~-----~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      |...+|+++.  .++...+.|...  -.-+... ...++.     ....+.+++.+|+|+|||.+.
T Consensus         8 y~P~~~~dli--g~~~~~~~L~~~--l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a   69 (253)
T d1sxja2           8 YAPTNLQQVC--GNKGSVMKLKNW--LANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAA   69 (253)
T ss_dssp             TCCSSGGGCC--SCHHHHHHHHHH--HHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHH
T ss_pred             cCCCCHHHhc--CCHHHHHHHHHH--HHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHH
Confidence            4456788887  677766665441  0000111 111111     112357999999999999763

>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=91.11  E-value=0.29  Score=39.01  Aligned_cols=54  Identities=17%  Similarity=0.084  Sum_probs=36.1

Q ss_pred             CCCcEEEEccCCCchhhHhHHHHHHHHHhccC-------CCCCceEEEeecHHHHHHHHHHH
Q psy12984        104 EGRDLVGSAKTGSGKTLAFLVPAVELIYNLKF-------MPRNGKSWQGKLRPLTNGVYLVA  158 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~-------~~~~~~~~l~Ptr~La~qi~~~~  158 (178)
                      +|. +||.|.-|||||.+.+-=++..|.....       ......++|+=|+.=|..+...+
T Consensus        16 ~g~-~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI   76 (485)
T d1w36b1          16 QGE-RLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRI   76 (485)
T ss_dssp             SSC-EEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHH
T ss_pred             CCC-eEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHH
Confidence            454 7889999999999887777777654221       12235678888876555555444

>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=90.89  E-value=0.16  Score=37.45  Aligned_cols=47  Identities=15%  Similarity=0.113  Sum_probs=31.4

Q ss_pred             CCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHh
Q psy12984         62 ILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus        62 ~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      .|...+|+++.  .++.+.+.|... +.           .-....++++.+|+|+|||...
T Consensus         4 ky~P~~~~dii--g~~~~~~~L~~~-~~-----------~~~~~~~lll~Gp~G~GKTt~~   50 (252)
T d1sxje2           4 KYRPKSLNALS--HNEELTNFLKSL-SD-----------QPRDLPHLLLYGPNGTGKKTRC   50 (252)
T ss_dssp             TTCCCSGGGCC--SCHHHHHHHHTT-TT-----------CTTCCCCEEEECSTTSSHHHHH
T ss_pred             ccCCCCHHHcc--CcHHHHHHHHHH-HH-----------cCCCCCeEEEECCCCCCHHHHH
Confidence            45556799986  677887777542 10           0011235899999999999864

>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=90.21  E-value=0.1  Score=40.87  Aligned_cols=19  Identities=26%  Similarity=0.298  Sum_probs=16.4

Q ss_pred             CCCcEEEEccCCCchhhHh
Q psy12984        104 EGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf  122 (178)
                      .++.++..+|||+|||+..
T Consensus        48 ~~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          48 TPKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            3578999999999999864

>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=89.68  E-value=0.077  Score=36.72  Aligned_cols=18  Identities=28%  Similarity=0.510  Sum_probs=15.6

Q ss_pred             CCCcEEEEccCCCchhhH
Q psy12984        104 EGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTla  121 (178)
                      .+.+|++.+++|||||..
T Consensus         4 k~~~I~i~G~~GsGKTT~   21 (174)
T d1y63a_           4 KGINILITGTPGTGKTSM   21 (174)
T ss_dssp             SSCEEEEECSTTSSHHHH
T ss_pred             CCCEEEEEeCCCCCHHHH
Confidence            356899999999999975

>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=88.91  E-value=0.4  Score=35.47  Aligned_cols=59  Identities=17%  Similarity=0.044  Sum_probs=31.3

Q ss_pred             hccccCCCcEEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEEe--ecHHHHHHHHHHHHHHh
Q psy12984         99 IPPLLEGRDLVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQG--KLRPLTNGVYLVACNVF  162 (178)
Q Consensus        99 ip~~l~g~dvi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l~--Ptr~La~qi~~~~~~l~  162 (178)
                      +|...+.+=++..+|||+|||..-.==+ .++..   . +.++++++  .-|.=|.++...+.+.+
T Consensus         4 lp~~~~~~vi~lvGp~GvGKTTTiaKLA-~~~~~---~-g~kV~lit~Dt~R~gA~eQL~~~a~~l   64 (207)
T d1ls1a2           4 LPVLKDRNLWFLVGLQGSGKTTTAAKLA-LYYKG---K-GRRPLLVAADTQRPAAREQLRLLGEKV   64 (207)
T ss_dssp             CCCCCSSEEEEEECCTTTTHHHHHHHHH-HHHHH---T-TCCEEEEECCSSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcEEEEECCCCCCHHHHHHHHH-HHHHH---C-CCcEEEEecccccchHHHHHHHHHHhc
Confidence            3444443334568999999987633211 12222   1 12333332  33887877766665544

>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=88.72  E-value=0.098  Score=35.22  Aligned_cols=18  Identities=22%  Similarity=0.266  Sum_probs=15.1

Q ss_pred             CCcEEEEccCCCchhhHh
Q psy12984        105 GRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf  122 (178)
                      -++|++.+++|||||...
T Consensus         2 ~k~I~l~G~~GsGKSTva   19 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIG   19 (169)
T ss_dssp             CCCEEEECCTTSCHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            368999999999999743

>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=88.63  E-value=0.22  Score=36.26  Aligned_cols=44  Identities=11%  Similarity=0.242  Sum_probs=28.1

Q ss_pred             CCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhH
Q psy12984         63 LSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus        63 ~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTla  121 (178)
                      +..++|+++-  .++++.+.|...       +....+      .++|+.+|+|+|||..
T Consensus         8 yrP~~~~div--g~~~~~~~L~~~-------i~~~~~------~~lLl~Gp~G~GKttl   51 (227)
T d1sxjc2           8 YRPETLDEVY--GQNEVITTVRKF-------VDEGKL------PHLLFYGPPGTGKTST   51 (227)
T ss_dssp             TCCSSGGGCC--SCHHHHHHHHHH-------HHTTCC------CCEEEECSSSSSHHHH
T ss_pred             hCCCCHHHcc--CcHHHHHHHHHH-------HHcCCC------CeEEEECCCCCChhHH
Confidence            4456788875  566666666442       111111      2589999999999965

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=88.62  E-value=0.095  Score=38.66  Aligned_cols=18  Identities=22%  Similarity=0.196  Sum_probs=15.4

Q ss_pred             CcEEEEccCCCchhhHhH
Q psy12984        106 RDLVGSAKTGSGKTLAFL  123 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~  123 (178)
                      .++|..+|+|+|||...-
T Consensus        36 ~~~L~~GPpGtGKT~lA~   53 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLAH   53 (238)
T ss_dssp             CCEEEESSTTSSHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHH
Confidence            479999999999998643

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=88.61  E-value=0.081  Score=35.93  Aligned_cols=14  Identities=29%  Similarity=0.351  Sum_probs=12.2

Q ss_pred             EEEEccCCCchhhH
Q psy12984        108 LVGSAKTGSGKTLA  121 (178)
Q Consensus       108 vi~~a~TGsGKTla  121 (178)
                      |++++++|||||..
T Consensus         5 Iii~G~pGsGKTTl   18 (152)
T d1ly1a_           5 ILTIGCPGSGKSTW   18 (152)
T ss_dssp             EEEECCTTSSHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            67899999999874

>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=88.22  E-value=0.1  Score=38.41  Aligned_cols=18  Identities=22%  Similarity=0.283  Sum_probs=15.6

Q ss_pred             CCcEEEEccCCCchhhHh
Q psy12984        105 GRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       105 g~dvi~~a~TGsGKTlaf  122 (178)
                      ..++++.+|+|+|||...
T Consensus        43 ~~~lll~GppGtGKT~l~   60 (276)
T d1fnna2          43 YPRATLLGRPGTGKTVTL   60 (276)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CCceEEECCCCCCHHHHH
Confidence            468999999999999764

>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=88.21  E-value=0.37  Score=36.03  Aligned_cols=21  Identities=19%  Similarity=0.272  Sum_probs=16.9

Q ss_pred             ccCCCcEEEEccCCCchhhHh
Q psy12984        102 LLEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTlaf  122 (178)
                      +..|.=+++.|+||+|||...
T Consensus        32 ~~~G~l~vi~G~~G~GKT~~~   52 (277)
T d1cr2a_          32 ARGGEVIMVTSGSGMGKSTFV   52 (277)
T ss_dssp             BCTTCEEEEECSTTSSHHHHH
T ss_pred             CCCCeEEEEEeCCCCCHHHHH
Confidence            455777899999999999643

>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=87.72  E-value=0.11  Score=35.67  Aligned_cols=22  Identities=23%  Similarity=0.267  Sum_probs=18.1

Q ss_pred             ccccCCCcEEEEccCCCchhhH
Q psy12984        100 PPLLEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       100 p~~l~g~dvi~~a~TGsGKTla  121 (178)
                      |.-..|.-|++++.+|||||..
T Consensus         1 ~~~~~g~~I~l~G~~GsGKTTi   22 (183)
T d1m8pa3           1 PRATQGFTIFLTGYMNSGKDAI   22 (183)
T ss_dssp             CTTTCCEEEEEECSTTSSHHHH
T ss_pred             CCCCCCeEEEEECCCCCCHHHH
Confidence            3456788899999999999965

>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=87.48  E-value=0.12  Score=38.09  Aligned_cols=18  Identities=28%  Similarity=0.178  Sum_probs=15.3

Q ss_pred             CcEEEEccCCCchhhHhH
Q psy12984        106 RDLVGSAKTGSGKTLAFL  123 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf~  123 (178)
                      .++|..+|+|+|||...-
T Consensus        36 ~~~Ll~GPpG~GKTtla~   53 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLAH   53 (239)
T ss_dssp             CCEEEECCTTSCHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            579999999999997643

>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=87.33  E-value=0.11  Score=35.94  Aligned_cols=19  Identities=42%  Similarity=0.511  Sum_probs=16.2

Q ss_pred             cCCCcEEEEccCCCchhhH
Q psy12984        103 LEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTla  121 (178)
                      +.|+=|++.+++|||||..
T Consensus         2 ~~g~iI~l~G~~GsGKSTi   20 (176)
T d1zp6a1           2 LGGNILLLSGHPGSGKSTI   20 (176)
T ss_dssp             CTTEEEEEEECTTSCHHHH
T ss_pred             CCCeEEEEECCCCCCHHHH
Confidence            4577788999999999984

>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=87.10  E-value=0.085  Score=36.37  Aligned_cols=17  Identities=18%  Similarity=0.243  Sum_probs=14.7

Q ss_pred             CCcEEEEccCCCchhhH
Q psy12984        105 GRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       105 g~dvi~~a~TGsGKTla  121 (178)
                      -+.|++.+++|||||..
T Consensus         7 ~K~I~i~G~~GsGKTTl   23 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVL   23 (192)
T ss_dssp             CEEEEEECCTTSHHHHH
T ss_pred             ceEEEEECCCCCCHHHH
Confidence            46799999999999974

>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=87.03  E-value=0.36  Score=35.13  Aligned_cols=44  Identities=16%  Similarity=0.252  Sum_probs=28.1

Q ss_pred             CCCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCC--CcEEEEccCCCchhhHh
Q psy12984         62 ILSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEG--RDLVGSAKTGSGKTLAF  122 (178)
Q Consensus        62 ~~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g--~dvi~~a~TGsGKTlaf  122 (178)
                      -+..+.|+++-  -++.+++.|...               +..+  .++|+.+|+|+|||.+.
T Consensus         8 KyrP~~~~d~i--g~~~~~~~L~~~---------------~~~~~~~~~ll~Gp~G~GKTt~a   53 (224)
T d1sxjb2           8 KYRPQVLSDIV--GNKETIDRLQQI---------------AKDGNMPHMIISGMPGIGKTTSV   53 (224)
T ss_dssp             HTCCSSGGGCC--SCTHHHHHHHHH---------------HHSCCCCCEEEECSTTSSHHHHH
T ss_pred             HhCCCCHHHhc--CCHHHHHHHHHH---------------HHcCCCCeEEEECCCCCCchhhH
Confidence            34556788875  555555555431               1112  25899999999999763

>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=86.65  E-value=0.85  Score=33.74  Aligned_cols=26  Identities=23%  Similarity=0.381  Sum_probs=20.5

Q ss_pred             hhccccCCCcEEEEccCCCchhhHhH
Q psy12984         98 TIPPLLEGRDLVGSAKTGSGKTLAFL  123 (178)
Q Consensus        98 aip~~l~g~dvi~~a~TGsGKTlaf~  123 (178)
                      .|+-++.|.-+++.|++|+|||...+
T Consensus        22 li~G~~pg~~~~i~G~~G~GKS~l~l   47 (274)
T d1nlfa_          22 VLPNMVAGTVGALVSPGGAGKSMLAL   47 (274)
T ss_dssp             EETTEETTSEEEEEESTTSSHHHHHH
T ss_pred             HhCCccCCcEEEEEeCCCCCHHHHHH
Confidence            45666678888999999999996543

>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=86.57  E-value=0.16  Score=34.83  Aligned_cols=16  Identities=25%  Similarity=0.399  Sum_probs=13.8

Q ss_pred             CcEEEEccCCCchhhH
Q psy12984        106 RDLVGSAKTGSGKTLA  121 (178)
Q Consensus       106 ~dvi~~a~TGsGKTla  121 (178)
                      ..+++++++|||||..
T Consensus         5 ~~I~i~G~pGsGKTTi   20 (173)
T d1rkba_           5 PNILLTGTPGVGKTTL   20 (173)
T ss_dssp             CCEEEECSTTSSHHHH
T ss_pred             CEEEEECCCCCCHHHH
Confidence            4689999999999963

>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=86.48  E-value=0.14  Score=34.82  Aligned_cols=14  Identities=21%  Similarity=0.401  Sum_probs=12.7

Q ss_pred             EEEEccCCCchhhH
Q psy12984        108 LVGSAKTGSGKTLA  121 (178)
Q Consensus       108 vi~~a~TGsGKTla  121 (178)
                      +++.+++|||||..
T Consensus         5 I~i~G~~GsGKTTv   18 (176)
T d2bdta1           5 YIITGPAGVGKSTT   18 (176)
T ss_dssp             EEEECSTTSSHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            78899999999985

>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=85.92  E-value=0.21  Score=37.89  Aligned_cols=16  Identities=25%  Similarity=0.331  Sum_probs=14.5

Q ss_pred             CcEEEEccCCCchhhH
Q psy12984        106 RDLVGSAKTGSGKTLA  121 (178)
Q Consensus       106 ~dvi~~a~TGsGKTla  121 (178)
                      +.+|+.+|+|+|||+.
T Consensus        43 ~giLl~GppGtGKT~l   58 (247)
T d1ixza_          43 KGVLLVGPPGVGKTHL   58 (247)
T ss_dssp             SEEEEECCTTSSHHHH
T ss_pred             ceEEEecCCCCChhHH
Confidence            5799999999999975

>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=85.71  E-value=0.38  Score=36.58  Aligned_cols=17  Identities=29%  Similarity=0.462  Sum_probs=15.2

Q ss_pred             CCcEEEEccCCCchhhH
Q psy12984        105 GRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       105 g~dvi~~a~TGsGKTla  121 (178)
                      .+.+++.+|+|+|||+.
T Consensus        45 ~~~iLL~GppGtGKT~l   61 (256)
T d1lv7a_          45 PKGVLMVGPPGTGKTLL   61 (256)
T ss_dssp             CCEEEEECCTTSCHHHH
T ss_pred             CCeEEeeCCCCCCccHH
Confidence            36799999999999986

>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=85.54  E-value=0.16  Score=41.34  Aligned_cols=24  Identities=21%  Similarity=0.423  Sum_probs=18.2

Q ss_pred             EEEEccCCCchhhHhHHHHHHHHHh
Q psy12984        108 LVGSAKTGSGKTLAFLVPAVELIYN  132 (178)
Q Consensus       108 vi~~a~TGsGKTlaf~lp~l~~l~~  132 (178)
                      +|+++|||||||.... .++..+.+
T Consensus       161 iLvtGpTGSGKSTTl~-~~l~~~~~  184 (401)
T d1p9ra_         161 ILVTGPTGSGKSTTLY-AGLQELNS  184 (401)
T ss_dssp             EEEECSTTSCHHHHHH-HHHHHHCC
T ss_pred             EEEEcCCCCCccHHHH-HHhhhhcC
Confidence            8899999999998743 35666643

>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=84.12  E-value=1.2  Score=32.92  Aligned_cols=50  Identities=12%  Similarity=0.057  Sum_probs=27.3

Q ss_pred             EEEEccCCCchhhHhHHHHHHHHHhccCCCCCceEEE-eec-HHHHHHHHHHHHHHh
Q psy12984        108 LVGSAKTGSGKTLAFLVPAVELIYNLKFMPRNGKSWQ-GKL-RPLTNGVYLVACNVF  162 (178)
Q Consensus       108 vi~~a~TGsGKTlaf~lp~l~~l~~~~~~~~~~~~~l-~Pt-r~La~qi~~~~~~l~  162 (178)
                      ++.++|||+|||..-.==+ .++..   ... .+.++ +-| |.=|.++...+.+.+
T Consensus        14 i~lvGptGvGKTTTiAKLA-a~~~~---~~~-kV~lit~Dt~R~gA~eQL~~~a~~l   65 (213)
T d1vmaa2          14 IMVVGVNGTGKTTSCGKLA-KMFVD---EGK-SVVLAAADTFRAAAIEQLKIWGERV   65 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHH-HHHHH---TTC-CEEEEEECTTCHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH-HHHHH---CCC-ceEEEeecccccchhHHHHHHhhhc
Confidence            5668999999998743111 22322   122 33333 443 777776665555443

>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=83.79  E-value=0.22  Score=36.84  Aligned_cols=17  Identities=29%  Similarity=0.315  Sum_probs=14.5

Q ss_pred             CcEEEEccCCCchhhHh
Q psy12984        106 RDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf  122 (178)
                      +.+|+.+|+|+|||...
T Consensus        33 ~~ilL~GpPGtGKT~la   49 (273)
T d1gvnb_          33 TAFLLGGQPGSGKTSLR   49 (273)
T ss_dssp             EEEEEECCTTSCTHHHH
T ss_pred             EEEEEECCCCCCHHHHH
Confidence            46999999999999853

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.67  E-value=0.23  Score=36.11  Aligned_cols=16  Identities=25%  Similarity=0.333  Sum_probs=13.7

Q ss_pred             CcEEEEccCCCchhhH
Q psy12984        106 RDLVGSAKTGSGKTLA  121 (178)
Q Consensus       106 ~dvi~~a~TGsGKTla  121 (178)
                      .++++.+|+|+|||..
T Consensus        34 ~~lll~Gp~G~GKTtl   49 (237)
T d1sxjd2          34 PHMLFYGPPGTGKTST   49 (237)
T ss_dssp             CCEEEECSTTSSHHHH
T ss_pred             CeEEEECCCCCChHHH
Confidence            3589999999999864

>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=83.65  E-value=0.14  Score=37.80  Aligned_cols=15  Identities=27%  Similarity=0.242  Sum_probs=12.4

Q ss_pred             EEEEccCCCchhhHh
Q psy12984        108 LVGSAKTGSGKTLAF  122 (178)
Q Consensus       108 vi~~a~TGsGKTlaf  122 (178)
                      +++.+|+|+|||...
T Consensus        49 l~l~GppGtGKT~l~   63 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLA   63 (287)
T ss_dssp             EECTTCCSSSHHHHH
T ss_pred             EEeECCCCCCHHHHH
Confidence            466799999999873

>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=83.47  E-value=0.26  Score=34.30  Aligned_cols=16  Identities=31%  Similarity=0.382  Sum_probs=14.1

Q ss_pred             CcEEEEccCCCchhhH
Q psy12984        106 RDLVGSAKTGSGKTLA  121 (178)
Q Consensus       106 ~dvi~~a~TGsGKTla  121 (178)
                      +++++.+++|+|||..
T Consensus         1 k~I~liG~~GsGKsTi   16 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTL   16 (161)
T ss_dssp             CCEEEECCTTSCHHHH
T ss_pred             CcEEEECCCCCCHHHH
Confidence            5789999999999965

>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=83.42  E-value=0.19  Score=37.99  Aligned_cols=17  Identities=24%  Similarity=0.126  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCchhhHh
Q psy12984        106 RDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf  122 (178)
                      +.||+.+|+|+|||...
T Consensus        41 ~~vLL~GppGtGKT~la   57 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALA   57 (246)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECcCCCCHHHHH
Confidence            57999999999999863

>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=83.14  E-value=0.86  Score=33.52  Aligned_cols=47  Identities=23%  Similarity=0.208  Sum_probs=29.6

Q ss_pred             CCccchHhhcccCCHHHHHHHHHCCCCCCcHHHHHhhccccCCCcEEEEccCCCchhhHhH
Q psy12984         63 LSSTQFEALKGKVCENTLKAIADMGFTKMTEIQARTIPPLLEGRDLVGSAKTGSGKTLAFL  123 (178)
Q Consensus        63 ~~~~~f~~l~~~l~~~ll~~l~~~g~~~pt~iQ~~aip~~l~g~dvi~~a~TGsGKTlaf~  123 (178)
                      |..++|+++-  .++.+.+.|...       ++..-+     .+.+|+.+|+|+|||....
T Consensus         6 yrP~~~~dli--g~~~~~~~L~~~-------i~~~~~-----~~~~Ll~Gp~G~GKtt~a~   52 (239)
T d1njfa_           6 WRPQTFADVV--GQEHVLTALANG-------LSLGRI-----HHAYLFSGTRGVGKTSIAR   52 (239)
T ss_dssp             TCCSSGGGSC--SCHHHHHHHHHH-------HHTTCC-----CSEEEEECSTTSSHHHHHH
T ss_pred             hCCCCHHHcc--ChHHHHHHHHHH-------HHcCCC-----CeeEEEECCCCCcHHHHHH
Confidence            3446788886  677777766441       110001     1347899999999997643

>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=82.83  E-value=0.26  Score=39.53  Aligned_cols=17  Identities=41%  Similarity=0.489  Sum_probs=14.9

Q ss_pred             CcEEEEccCCCchhhHh
Q psy12984        106 RDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       106 ~dvi~~a~TGsGKTlaf  122 (178)
                      .++|.++|||+|||...
T Consensus        69 ~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             cceeeeCCCCccHHHHH
Confidence            67999999999999754

>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=82.50  E-value=0.95  Score=32.72  Aligned_cols=25  Identities=24%  Similarity=0.282  Sum_probs=18.6

Q ss_pred             CCCcEEEEccCCCchhhHhHHHHHH
Q psy12984        104 EGRDLVGSAKTGSGKTLAFLVPAVE  128 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTlaf~lp~l~  128 (178)
                      .|.-+++.+++|+|||...+--+.+
T Consensus        25 ~gsl~li~G~pGsGKT~l~~qia~~   49 (242)
T d1tf7a2          25 KDSIILATGATGTGKTLLVSRFVEN   49 (242)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHH
Confidence            4678999999999999854433333

>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=82.02  E-value=0.49  Score=32.72  Aligned_cols=20  Identities=20%  Similarity=0.051  Sum_probs=16.6

Q ss_pred             ccCCCcEEEEccCCCchhhH
Q psy12984        102 LLEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTla  121 (178)
                      +..|+=+++.+++|+|||..
T Consensus        20 i~~G~v~~i~G~~GsGKT~l   39 (242)
T d1n0wa_          20 IETGSITEMFGEFRTGKTQI   39 (242)
T ss_dssp             EETTSEEEEECCTTSSHHHH
T ss_pred             CcCCEEEEEEeCCCCCHHHH
Confidence            34577899999999999964

>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=81.97  E-value=0.26  Score=33.71  Aligned_cols=16  Identities=31%  Similarity=0.262  Sum_probs=13.2

Q ss_pred             EEEEccCCCchhhHhH
Q psy12984        108 LVGSAKTGSGKTLAFL  123 (178)
Q Consensus       108 vi~~a~TGsGKTlaf~  123 (178)
                      +++.+++|||||...-
T Consensus         9 ivl~G~~GsGKsT~a~   24 (171)
T d1knqa_           9 YVLMGVSGSGKSAVAS   24 (171)
T ss_dssp             EEEECSTTSCHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6779999999997643

>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=81.80  E-value=0.29  Score=34.88  Aligned_cols=16  Identities=38%  Similarity=0.547  Sum_probs=13.8

Q ss_pred             CcEEEEccCCCchhhH
Q psy12984        106 RDLVGSAKTGSGKTLA  121 (178)
Q Consensus       106 ~dvi~~a~TGsGKTla  121 (178)
                      |-|++++|+|+|||..
T Consensus         2 rpIvl~GpsG~GK~tl   17 (186)
T d1gkya_           2 RPIVISGPSGTGKSTL   17 (186)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4589999999999973

>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=81.31  E-value=0.65  Score=33.63  Aligned_cols=20  Identities=25%  Similarity=-0.032  Sum_probs=16.6

Q ss_pred             cCCCcEEEEccCCCchhhHh
Q psy12984        103 LEGRDLVGSAKTGSGKTLAF  122 (178)
Q Consensus       103 l~g~dvi~~a~TGsGKTlaf  122 (178)
                      -.|+-+++.+++|+|||..-
T Consensus        34 p~G~~~li~G~pGsGKT~~~   53 (254)
T d1pzna2          34 ETQAITEVFGEFGSGKTQLA   53 (254)
T ss_dssp             ESSEEEEEEESTTSSHHHHH
T ss_pred             cCCEEEEEEcCCCCCHHHHH
Confidence            34678999999999999853

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=81.28  E-value=0.29  Score=33.82  Aligned_cols=15  Identities=27%  Similarity=0.459  Sum_probs=13.2

Q ss_pred             cEEEEccCCCchhhH
Q psy12984        107 DLVGSAKTGSGKTLA  121 (178)
Q Consensus       107 dvi~~a~TGsGKTla  121 (178)
                      .|++.+|+|+|||.-
T Consensus         2 ki~I~G~~G~GKSTL   16 (178)
T d1ye8a1           2 KIIITGEPGVGKTTL   16 (178)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEECCCCcHHHHH
Confidence            488999999999984

>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=81.05  E-value=0.32  Score=35.01  Aligned_cols=20  Identities=15%  Similarity=-0.004  Sum_probs=16.6

Q ss_pred             ccCCCcEEEEccCCCchhhH
Q psy12984        102 LLEGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       102 ~l~g~dvi~~a~TGsGKTla  121 (178)
                      +..|+-+++.+++|||||..
T Consensus        31 i~~G~~~li~G~pGsGKT~l   50 (251)
T d1szpa2          31 VETGSITELFGEFRTGKSQL   50 (251)
T ss_dssp             EESSSEEEEEESTTSSHHHH
T ss_pred             CcCCeEEEEEcCCCCCHHHH
Confidence            34568899999999999974

>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=80.79  E-value=0.4  Score=32.57  Aligned_cols=18  Identities=17%  Similarity=0.213  Sum_probs=14.3

Q ss_pred             CCCcEEEEccCCCchhhH
Q psy12984        104 EGRDLVGSAKTGSGKTLA  121 (178)
Q Consensus       104 ~g~dvi~~a~TGsGKTla  121 (178)
                      ..+=|++++++|||||..
T Consensus         2 ~~kiI~l~G~~GsGKsTv   19 (178)
T d1qhxa_           2 TTRMIILNGGSSAGKSGI   19 (178)
T ss_dssp             CCCEEEEECCTTSSHHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            345578899999999954