Citrus Sinensis ID: 028887

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200--
Protein Sequence
MAAIAISAAHPILVTRVNHKLSSPNSIDFTNRAFLPVSISLKPLRAVLSSSAVSTEELAAGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVLYSLTSY
Secondary Structure (PSIPRED)
cHHHHHHHHcccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHccccccccccEEEEcccHHHHHHHHHHHHHHHcccccccccccccEEEEEEccccHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHcccEEEEEccccccccccccHHHccccccHHHHcccHHHHHHHHHHHcccEEcccccccccHHHHHccccHHHHHHHHHcccccccccHHHHHHHHHccccEEEEccccHHHHHHHHHHHHHHcccccccccEEEEcccHHHHHHHHHHHHHHcHHcccccccccccEEEEEEccccHHHHHHHHHcccccccc
Coil and Loop (DISEMBL)
MAAIAISAAHPILVTRvnhklsspnsidftnraflpvsislKPLRAVLsssavsteelaagtgnnslTLRELCQGHVPEHVLRRMEEtgyvlptdiqrealpvlfssrdcilhaqtgsgkTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAakpldtdlEHKLCTVMALLDGGMLRRHKSWLKVLYSLTSY
Flexible Loop (DISEMBL)
maaiaisaahpilVTRVNHKLSSPNSIDFTNRAFLPVSISLKPLRAVLSSSAVSTEELaagtgnnsltlRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVptrelgmqVTKVARVLAAkpldtdlehKLCTVMALldggmlrrhKSWLKVLYSLTSY
Low Complexity Region (SEG)
MAAIAISAAHPILVTRVNHKLSSPNSIDFTNRAFLPVSISLKPLRAVLSSSAVSTEELAAGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVLYSLTSY
Disordered region (IsUnstruct)
****AISAAHPILVTRVNHKLSSPNSIDFTNRAFLPVSISLKPLRAVLS**********AGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVLYSL***
Disordered Region (DISOPRED)
*********************************************************************RELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVLYSL***
Disordered Region (DISEMBL)
MAAIAISAAHPILVTRVNHKLSSPNSIDFTNRAFLPVSISLKPLRAVLSSSAVSTEELAAGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVLYSLTSY
Disordered Region (DISPRO)
*AAIAISAAHPILVTRVNHKLSSPNSIDFTNRAFLPVSISLKPLRAVLSSSAVSTEELAAGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVLYSLTSY
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAAIAISAAHPILVTRVNHKLSSPNSIDFTNRAFLPVSISLKPLRAVLSSSAVSTEELAAGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVLYSLTSY
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	202	2.2.26 [Sep-21-2011]
Q3E9C3	472	DEAD-box ATP-dependent RN	yes	no	0.618	0.264	0.804	3e-56
Q0JFN7	438	DEAD-box ATP-dependent RN	no	no	0.584	0.269	0.692	8e-47
Q6H874	573	DEAD-box ATP-dependent RN	no	no	0.727	0.256	0.319	6e-14
Q8W4E1	551	DEAD-box ATP-dependent RN	no	no	0.396	0.145	0.387	9e-14
Q10PV9	573	DEAD-box ATP-dependent RN	no	no	0.727	0.256	0.319	2e-13
Q54E49	423	Probable ATP-dependent RN	yes	no	0.509	0.243	0.339	3e-13
Q8RXK6	505	DEAD-box ATP-dependent RN	no	no	0.623	0.249	0.295	6e-13
Q62780	1032	Probable ATP-dependent RN	yes	no	0.435	0.085	0.408	2e-12
Q5R6D8	1032	Probable ATP-dependent RN	yes	no	0.435	0.085	0.408	2e-12
Q569Z5	1032	Probable ATP-dependent RN	yes	no	0.435	0.085	0.408	2e-12

>sp|Q3E9C3|RH58_ARATH DEAD-box ATP-dependent RNA helicase 58, chloroplastic OS=Arabidopsis thaliana GN=RH58 PE=2 SV=1

 Score =  218 bits (554), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 103/128 (80%), Positives = 115/128 (89%), Gaps = 3/128 (2%)

Query: 67  LTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLL 126
           LTLR++CQG VPEH+L RMEE G+V PTDIQREALP LF+ RDCILHAQTGSGKTLTYLL
Sbjct: 73  LTLRQICQGFVPEHILHRMEEIGFVFPTDIQREALPTLFTGRDCILHAQTGSGKTLTYLL 132

Query: 127 LIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGML 186
           LIFSL+N QRS+VQAVIVVPTRELGMQVTKVAR+LAAK   ++++ K CTVMALLDGG L
Sbjct: 133 LIFSLINPQRSSVQAVIVVPTRELGMQVTKVARMLAAK---SEIDVKGCTVMALLDGGTL 189

Query: 187 RRHKSWLK 194
           RRHKSWLK
Sbjct: 190 RRHKSWLK 197

Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q0JFN7|RH58_ORYSJ DEAD-box ATP-dependent RNA helicase 58, chloroplastic OS=Oryza sativa subsp. japonica GN=Os01g0970600 PE=2 SV=2

 Score =  186 bits (472), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 88/127 (69%), Positives = 104/127 (81%), Gaps = 9/127 (7%)

Query: 68  TLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLL 127
           TLRE+C G VPEHVL+R EE GYV+PT++Q ++LPVL S +DCILHAQTGSGKTL YLL 
Sbjct: 39  TLREVCAGRVPEHVLQRAEEVGYVVPTEVQEQSLPVLLSGQDCILHAQTGSGKTLAYLLS 98

Query: 128 IFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLR 187
           +FS ++  RS+VQA++VVPTRELGMQVTKVAR+LAAK          CTVMALLDGGMLR
Sbjct: 99  VFSAIDFGRSSVQALVVVPTRELGMQVTKVARILAAKA---------CTVMALLDGGMLR 149

Query: 188 RHKSWLK 194
           R KSW+K
Sbjct: 150 RQKSWVK 156

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q6H874|RH47A_ORYSJ DEAD-box ATP-dependent RNA helicase 47A OS=Oryza sativa subsp. japonica GN=Os02g0636300 PE=2 SV=1

 Score = 77.4 bits (189), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 54/169 (31%), Positives = 86/169 (50%), Gaps = 22/169 (13%)

Query: 38  SISLKPLRAVLSSSAVSTEELAAGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQ 97
           S + KP+++ L  SAV  + L      +  + +   +  +P  ++ R+ + G   PT++Q
Sbjct: 101 SFNAKPVKSALPKSAVLKKTLK--IDESLFSAKSFEELGLPPLLIDRLNKEGLTAPTEVQ 158

Query: 98  REALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNA-----------QRSAVQAVIVVP 146
             A+P++    D ++ + TGSGKTL YLL I S +             +RS V+AVIV P
Sbjct: 159 SAAIPIISQKHDAVIQSYTGSGKTLAYLLPILSEIGPLKRPTEQDSSDKRSGVEAVIVAP 218

Query: 147 TRELGMQVTK-VARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK 194
           +RELGMQ+ + V ++L   P D  L      V  L+ G    R +  LK
Sbjct: 219 SRELGMQIVREVEKILG--PNDKRL------VQQLVGGANRSRQEEALK 259

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q8W4E1|RH47_ARATH DEAD-box ATP-dependent RNA helicase 47, mitochondrial OS=Arabidopsis thaliana GN=RH47 PE=1 SV=2

 Score = 76.6 bits (187), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 36/93 (38%), Positives = 56/93 (60%), Gaps = 13/93 (13%)

Query: 77  VPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLV---- 132
           +P+ +L  +E  G+ +PTD+Q  A+P +    D ++ + TGSGKTL YLL I S +    
Sbjct: 117 LPDSLLDSLEREGFSVPTDVQSAAVPAIIKGHDAVIQSYTGSGKTLAYLLPILSEIGPLA 176

Query: 133 ---------NAQRSAVQAVIVVPTRELGMQVTK 156
                    N +R+ +QA+IV P+RELGMQ+ +
Sbjct: 177 EKSRSSHSENDKRTEIQAMIVAPSRELGMQIVR 209

Essential protein required during embryogenesis. Required for mitochondrial metabolism. Necessary for normal plasmodesmata (PD) development and aperture regulation.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q10PV9|RH47B_ORYSJ DEAD-box ATP-dependent RNA helicase 47B OS=Oryza sativa subsp. japonica GN=Os03g0219700 PE=2 SV=1

 Score = 75.9 bits (185), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 54/169 (31%), Positives = 85/169 (50%), Gaps = 22/169 (13%)

Query: 38  SISLKPLRAVLSSSAVSTEELAAGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQ 97
           S + KP ++ L  SAV  + L      +  + +   +  +P  ++ R+ + G   PT++Q
Sbjct: 101 SFNSKPAKSTLPKSAVVKKTLK--IDESLFSAKSFEELGLPPLLIDRLNKEGLSTPTEVQ 158

Query: 98  REALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNA-----------QRSAVQAVIVVP 146
             A+P++    D ++ + TGSGKTL YLL I S +             +RS V+AVIV P
Sbjct: 159 SAAIPIISQKHDAVIQSYTGSGKTLAYLLPILSEIGPLKRPTEQDGSDKRSGVEAVIVAP 218

Query: 147 TRELGMQVTK-VARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK 194
           +RELGMQ+ + V ++L   P D  L      V  L+ G    R +  LK
Sbjct: 219 SRELGMQIVREVEKILG--PNDKRL------VQQLVGGANRSRQEEALK 259

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q54E49|DDX6_DICDI Probable ATP-dependent RNA helicase ddx6 OS=Dictyostelium discoideum GN=ddx6 PE=3 SV=1

 Score = 74.7 bits (182), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 37/109 (33%), Positives = 63/109 (57%), Gaps = 6/109 (5%)

Query: 54  STEELAAGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILH 113
            TE++ A  GN+   L      H+   +LR + E GYV P+ IQ +A+P+  + RD +  
Sbjct: 39  QTEDVTATEGNDFDDL------HLKRDLLRGIFEKGYVKPSPIQEKAIPIALAGRDIMAR 92

Query: 114 AQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA 162
           A+ G+GKT ++L+      +  +  +Q +I+VPTREL +Q ++V + L 
Sbjct: 93  AKNGTGKTASFLIPALEKTDPTKDVIQVLILVPTRELALQTSQVCKELG 141

ATP-dependent RNA helicase which may be involved in mRNA turnover.

Dictyostelium discoideum (taxid: 44689)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q8RXK6|RH8_ARATH DEAD-box ATP-dependent RNA helicase 8 OS=Arabidopsis thaliana GN=RH8 PE=2 SV=1

 Score = 73.9 bits (180), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 44/149 (29%), Positives = 73/149 (48%), Gaps = 23/149 (15%)

Query: 17  VNHKLSSPNSIDFTNRAFLPVSISLKPLRAVLSSSAVSTEELAAGTGN---NSLTLRELC 73
           V  ++  PNS D+  R  LP              +   TE++ A  GN   +    REL 
Sbjct: 95  VQSEVIDPNSEDWKARLKLPAP-----------DTRYRTEDVTATKGNEFEDYFLKRELL 143

Query: 74  QGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVN 133
            G         + E G+  P+ IQ E++P+  + RD +  A+ G+GKT  + + +   ++
Sbjct: 144 MG---------IYEKGFERPSPIQEESIPIALTGRDILARAKNGTGKTAAFCIPVLEKID 194

Query: 134 AQRSAVQAVIVVPTRELGMQVTKVARVLA 162
              + +QAVI+VPTREL +Q ++V + L 
Sbjct: 195 QDNNVIQAVIIVPTRELALQTSQVCKELG 223

ATP-dependent RNA helicase involved in mRNA turnover, and more specifically in mRNA decapping.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q62780|DDX46_RAT Probable ATP-dependent RNA helicase DDX46 OS=Rattus norvegicus GN=Ddx46 PE=1 SV=1

 Score = 72.4 bits (176), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 38/93 (40%), Positives = 57/93 (61%), Gaps = 5/93 (5%)

Query: 69  LRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLI 128
           ++   Q  +   +L  +++ GY  PT IQ +A+P + S RD I  A+TGSGKT+ +LL +
Sbjct: 371 IKSWVQCGISMKILNSLKKHGYEKPTPIQTQAIPAIMSGRDLIGIAKTGSGKTIAFLLPM 430

Query: 129 FSLVNAQRSAVQ-----AVIVVPTRELGMQVTK 156
           F  +  QRS  +     AVI+ PTREL +Q+TK
Sbjct: 431 FRHIMDQRSLEEGEGPIAVIMTPTRELALQITK 463

Plays an essential role in splicing, either prior to, or during A complex formation.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5R6D8|DDX46_PONAB Probable ATP-dependent RNA helicase DDX46 OS=Pongo abelii GN=DDX46 PE=2 SV=1

 Score = 72.4 bits (176), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 38/93 (40%), Positives = 57/93 (61%), Gaps = 5/93 (5%)

Query: 69  LRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLI 128
           ++   Q  +   +L  +++ GY  PT IQ +A+P + S RD I  A+TGSGKT+ +LL +
Sbjct: 371 IKSWVQCGISMKILNSLKKHGYEKPTPIQTQAIPAIMSGRDLIGIAKTGSGKTIAFLLPM 430

Query: 129 FSLVNAQRSAVQ-----AVIVVPTRELGMQVTK 156
           F  +  QRS  +     AVI+ PTREL +Q+TK
Sbjct: 431 FRHIMDQRSLEEGEGPIAVIMTPTRELALQITK 463

Plays an essential role in splicing, either prior to, or during A complex formation.

Pongo abelii (taxid: 9601)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q569Z5|DDX46_MOUSE Probable ATP-dependent RNA helicase DDX46 OS=Mus musculus GN=Ddx46 PE=1 SV=2

 Score = 72.4 bits (176), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 38/93 (40%), Positives = 57/93 (61%), Gaps = 5/93 (5%)

Query: 69  LRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLI 128
           ++   Q  +   +L  +++ GY  PT IQ +A+P + S RD I  A+TGSGKT+ +LL +
Sbjct: 371 IKSWVQCGISMKILNSLKKHGYEKPTPIQTQAIPAIMSGRDLIGIAKTGSGKTIAFLLPM 430

Query: 129 FSLVNAQRSAVQ-----AVIVVPTRELGMQVTK 156
           F  +  QRS  +     AVI+ PTREL +Q+TK
Sbjct: 431 FRHIMDQRSLEEGEGPIAVIMTPTRELALQITK 463

Plays an essential role in splicing, either prior to, or during A complex formation.

Mus musculus (taxid: 10090)

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	202
225432566	482	PREDICTED: DEAD-box ATP-dependent RNA he	0.881	0.369	0.631	4e-59
297737002	486	unnamed protein product [Vitis vinifera]	0.881	0.366	0.607	3e-56
255552301	476	dead box ATP-dependent RNA helicase, put	0.782	0.331	0.656	6e-55
297807977	473	hypothetical protein ARALYDRAFT_488806 [	0.722	0.308	0.721	1e-54
42573431	472	DEAD-box ATP-dependent RNA helicase 58 [	0.618	0.264	0.804	1e-54
356520045	472	PREDICTED: DEAD-box ATP-dependent RNA he	0.712	0.305	0.68	3e-54
11385586	466	putative chloroplast RNA helicase VDL is	0.935	0.405	0.581	8e-54
449433337	473	PREDICTED: DEAD-box ATP-dependent RNA he	0.821	0.350	0.654	2e-52
11596133	365	putative chloroplast RNA helicase VDL' i	0.935	0.517	0.566	1e-51
11596137	289	putative chloroplast RNA helicase VDL' i	0.935	0.653	0.566	2e-51

>gi|225432566|ref|XP_002277780.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 58, chloroplastic-like [Vitis vinifera]

 Score =  233 bits (594), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 115/182 (63%), Positives = 146/182 (80%), Gaps = 4/182 (2%)

Query: 13  LVTRVNHKLSSPNSIDFTNRAFLPVSISLKPLRAVLSSSAVSTEELAAGTGNNSLTLREL 72
           L   +N    + +++ FT R     + + KP +A L+SS+++    A+  G  +LTLRE+
Sbjct: 26  LAPSLNSNRRTDSTVHFTRRV-SNSNCNAKPAQATLNSSSITE---ASDIGERTLTLREI 81

Query: 73  CQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLV 132
           CQG VPEHVLRR+EE G+++PTD+Q++ALPVL S RDCILHAQTGSGKTLTYLLLIFS+V
Sbjct: 82  CQGCVPEHVLRRIEEVGFIVPTDVQQQALPVLLSGRDCILHAQTGSGKTLTYLLLIFSVV 141

Query: 133 NAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSW 192
           N + SAVQA+IVVPTRELG+QVTKVAR+LAAKP++ +LE K CTVMALLDGGML+RHKSW
Sbjct: 142 NTKISAVQALIVVPTRELGIQVTKVARMLAAKPMEPELEQKSCTVMALLDGGMLKRHKSW 201

Query: 193 LK 194
           LK
Sbjct: 202 LK 203

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297737002|emb|CBI26203.3| unnamed protein product [Vitis vinifera]

 Score =  223 bits (569), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 113/186 (60%), Positives = 145/186 (77%), Gaps = 8/186 (4%)

Query: 13  LVTRVNHKLSSPNSIDFTNRAFLPVSISLKPLRAVLSSSAVSTEELAAGTGNNSLTLREL 72
           L   +N    + +++ FT R     + + KP +A L+SS+++    A+  G  +LTLRE+
Sbjct: 26  LAPSLNSNRRTDSTVHFTRRV-SNSNCNAKPAQATLNSSSITE---ASDIGERTLTLREI 81

Query: 73  CQGHVPEHVLR----RMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLI 128
           CQG VPEHV+     R+EE G+++PTD+Q++ALPVL S RDCILHAQTGSGKTLTYLLLI
Sbjct: 82  CQGCVPEHVIALICFRIEEVGFIVPTDVQQQALPVLLSGRDCILHAQTGSGKTLTYLLLI 141

Query: 129 FSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRR 188
           FS+VN + SAVQA+IVVPTRELG+QVTKVAR+LAAKP++ +LE K CTVMALLDGGML+R
Sbjct: 142 FSVVNTKISAVQALIVVPTRELGIQVTKVARMLAAKPMEPELEQKSCTVMALLDGGMLKR 201

Query: 189 HKSWLK 194
           HKSWLK
Sbjct: 202 HKSWLK 207

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255552301|ref|XP_002517195.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis] gi|223543830|gb|EEF45358.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis]

 Score =  219 bits (558), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 113/172 (65%), Positives = 131/172 (76%), Gaps = 14/172 (8%)

Query: 29  FTNRAFLPVSISLKPLRAVLSSSAVSTEELAAGT------GNNSLTLRELCQGHVPEHVL 82
           F NR  L  ++S   L+AVL+SS     +            N+ LTLRELCQ +VPE VL
Sbjct: 38  FKNRGLLS-TLSFSHLQAVLNSSTSLITKEEEEEEQFDPKSNHFLTLRELCQNYVPEPVL 96

Query: 83  RRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAV 142
            RMEE GYV+PTD+QR+ALPVLFS +DCILH QTGSGKTL YLLLI+S++NAQRSAVQA+
Sbjct: 97  HRMEEIGYVMPTDVQRQALPVLFSGQDCILHGQTGSGKTLAYLLLIYSVINAQRSAVQAL 156

Query: 143 IVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK 194
           I+VPTRELGMQVTKVAR+LAAKP+D        TVMALLDGGMLRRHKSWLK
Sbjct: 157 IIVPTRELGMQVTKVARMLAAKPMDV-------TVMALLDGGMLRRHKSWLK 201

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297807977|ref|XP_002871872.1| hypothetical protein ARALYDRAFT_488806 [Arabidopsis lyrata subsp. lyrata] gi|297317709|gb|EFH48131.1| hypothetical protein ARALYDRAFT_488806 [Arabidopsis lyrata subsp. lyrata]

 Score =  218 bits (555), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 109/151 (72%), Positives = 126/151 (83%), Gaps = 5/151 (3%)

Query: 44  LRAVLSSSAVSTEELAAGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPV 103
           L+AV  +S  S  E  + T   +LTLR++CQG VPEH+L RMEE G++ PTDIQREALP 
Sbjct: 53  LQAVAETS--SEIESNSATDTAALTLRKICQGFVPEHILHRMEEIGFISPTDIQREALPT 110

Query: 104 LFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA 163
           LF+ RDCILHAQTGSGKTLTYLLLIFSL+N QRS+VQAVIVVPTRELGMQVTKVAR+LAA
Sbjct: 111 LFTGRDCILHAQTGSGKTLTYLLLIFSLINPQRSSVQAVIVVPTRELGMQVTKVARMLAA 170

Query: 164 KPLDTDLEHKLCTVMALLDGGMLRRHKSWLK 194
           K   ++++ K CTVMALLDGG LRRHKSWLK
Sbjct: 171 K---SEIDVKGCTVMALLDGGTLRRHKSWLK 198

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42573431|ref|NP_974812.1| DEAD-box ATP-dependent RNA helicase 58 [Arabidopsis thaliana] gi|108861900|sp|Q3E9C3.1|RH58_ARATH RecName: Full=DEAD-box ATP-dependent RNA helicase 58, chloroplastic; Flags: Precursor gi|332005287|gb|AED92670.1| DEAD-box ATP-dependent RNA helicase 58 [Arabidopsis thaliana]

 Score =  218 bits (554), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 103/128 (80%), Positives = 115/128 (89%), Gaps = 3/128 (2%)

Query: 67  LTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLL 126
           LTLR++CQG VPEH+L RMEE G+V PTDIQREALP LF+ RDCILHAQTGSGKTLTYLL
Sbjct: 73  LTLRQICQGFVPEHILHRMEEIGFVFPTDIQREALPTLFTGRDCILHAQTGSGKTLTYLL 132

Query: 127 LIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGML 186
           LIFSL+N QRS+VQAVIVVPTRELGMQVTKVAR+LAAK   ++++ K CTVMALLDGG L
Sbjct: 133 LIFSLINPQRSSVQAVIVVPTRELGMQVTKVARMLAAK---SEIDVKGCTVMALLDGGTL 189

Query: 187 RRHKSWLK 194
           RRHKSWLK
Sbjct: 190 RRHKSWLK 197

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356520045|ref|XP_003528676.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 58, chloroplastic-like [Glycine max]

 Score =  216 bits (551), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 102/150 (68%), Positives = 123/150 (82%), Gaps = 6/150 (4%)

Query: 45  RAVLSSSAVSTEELAAGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVL 104
           +A+L++S ++  E+   T      LRELCQ HVPEH+L+RMEE GYV+PTDIQREALP L
Sbjct: 54  QAILNTSPIAPSEVTTPT------LRELCQSHVPEHILQRMEEIGYVMPTDIQREALPYL 107

Query: 105 FSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK 164
           FS  DCILHAQTGSGKTLTYLLLI S++NA +S+VQA+++VPTRELGMQVTKVAR LAAK
Sbjct: 108 FSGLDCILHAQTGSGKTLTYLLLIHSIINAAKSSVQALVLVPTRELGMQVTKVARTLAAK 167

Query: 165 PLDTDLEHKLCTVMALLDGGMLRRHKSWLK 194
           P   D E K C++MALLDGG L+RHK+WLK
Sbjct: 168 PTGVDGEQKSCSIMALLDGGTLKRHKTWLK 197

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|11385586|gb|AAG34873.1|AF261020_1 putative chloroplast RNA helicase VDL isoform 1 [Nicotiana tabacum] gi|11385590|gb|AAG34876.1|AF261021_1 putative chloroplast RNA helicase VDL isoform 1 [Nicotiana tabacum]

 Score =  215 bits (548), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 114/196 (58%), Positives = 141/196 (71%), Gaps = 7/196 (3%)

Query: 1   MAAIAISAAHPILVTRVNHKLSSPNSIDFTNRA--FLPVSISLKPLRAVLSSSAVSTEEL 58
           MA  + +  H +L T   ++ S     ++T R   FL      KPL A  S+S V  E  
Sbjct: 1   MACFSATQLHTLLWTSSLNRTSHHFKPNYTYRTPKFL---FRQKPLIASFSTSDV--EAR 55

Query: 59  AAGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGS 118
                +++ TLRELC GHVPEHV+RR+EE GYV+PT++Q +ALP L+S RDC+LHAQTGS
Sbjct: 56  TETKDSSTATLRELCHGHVPEHVIRRVEEVGYVIPTEVQLQALPFLYSGRDCVLHAQTGS 115

Query: 119 GKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVM 178
           GKTL YLL I S++++QRSAVQA+IVVPTRELGMQVTKVAR+LAAKP + +   K CTVM
Sbjct: 116 GKTLAYLLQILSVIDSQRSAVQALIVVPTRELGMQVTKVARMLAAKPSELESGPKSCTVM 175

Query: 179 ALLDGGMLRRHKSWLK 194
           ALLDGGML RHKSWLK
Sbjct: 176 ALLDGGMLNRHKSWLK 191

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449433337|ref|XP_004134454.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 58, chloroplastic-like [Cucumis sativus] gi|449531697|ref|XP_004172822.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 58, chloroplastic-like [Cucumis sativus]

 Score =  211 bits (536), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 112/171 (65%), Positives = 136/171 (79%), Gaps = 5/171 (2%)

Query: 24  PNSIDFTNRAFLPVSISLKPLRAVLSSSAVSTEELAAGTGNNSLTLRELCQGHVPEHVLR 83
           PN I+ TN      S S +PL+A+LSSS++      A +   + TLRE+C GHVPEH+LR
Sbjct: 33  PNFIN-TNGPIYSTSKS-RPLQALLSSSSLKN---VAESNFEASTLREICNGHVPEHILR 87

Query: 84  RMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVI 143
           R EE G+V PTD+QR+ALPVLFS RDC+LHAQTGSGKTLTYLLLIFS++NA++SAVQA+I
Sbjct: 88  RTEEIGFVAPTDVQRQALPVLFSGRDCVLHAQTGSGKTLTYLLLIFSVINAKKSAVQALI 147

Query: 144 VVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK 194
           VVPTRELGMQVTKVAR+LAAKP  ++       VMALLDGG+LRRHK+WLK
Sbjct: 148 VVPTRELGMQVTKVARMLAAKPAASEDGLNSYVVMALLDGGLLRRHKTWLK 198

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|11596133|gb|AAG38493.1|AF261032_1 putative chloroplast RNA helicase VDL' isoform 1 [Nicotiana tabacum]

 Score =  208 bits (529), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 111/196 (56%), Positives = 137/196 (69%), Gaps = 7/196 (3%)

Query: 1   MAAIAISAAHPILVTRVNHKLSSPNSIDFTNRA--FLPVSISLKPLRAVLSSSAVSTEEL 58
           MA  + +  H +L T   ++ S     ++T R   FL      KPL A  S+S +  E  
Sbjct: 1   MACFSATQLHTLLWTSSLNRTSHHFKPNYTYRTPKFL---FRQKPLIASFSTSDI--EAR 55

Query: 59  AAGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGS 118
                +++ T RELC GHVPEHV+RR+EE GYV+PT++Q  ALP L+S RDC+LHAQTGS
Sbjct: 56  TETKDSSTATPRELCHGHVPEHVIRRVEEVGYVIPTEVQLLALPFLYSGRDCVLHAQTGS 115

Query: 119 GKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVM 178
           GKTL YLL + S++++QRSAVQA+IVVPTRELGMQVTKVAR LAAKP +     K CTVM
Sbjct: 116 GKTLAYLLQMLSVIDSQRSAVQALIVVPTRELGMQVTKVARTLAAKPSELKSGPKSCTVM 175

Query: 179 ALLDGGMLRRHKSWLK 194
           ALLDGGML RHKSWLK
Sbjct: 176 ALLDGGMLNRHKSWLK 191

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|11596137|gb|AAG38497.1|AF261032_5 putative chloroplast RNA helicase VDL' isoform 5 [Nicotiana tabacum]

 Score =  207 bits (527), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 111/196 (56%), Positives = 137/196 (69%), Gaps = 7/196 (3%)

Query: 1   MAAIAISAAHPILVTRVNHKLSSPNSIDFTNRA--FLPVSISLKPLRAVLSSSAVSTEEL 58
           MA  + +  H +L T   ++ S     ++T R   FL      KPL A  S+S +  E  
Sbjct: 1   MACFSATQLHTLLWTSSLNRTSHHFKPNYTYRTPKFL---FRQKPLIASFSTSDI--EAR 55

Query: 59  AAGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGS 118
                +++ T RELC GHVPEHV+RR+EE GYV+PT++Q  ALP L+S RDC+LHAQTGS
Sbjct: 56  TETKDSSTATPRELCHGHVPEHVIRRVEEVGYVIPTEVQLLALPFLYSGRDCVLHAQTGS 115

Query: 119 GKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVM 178
           GKTL YLL + S++++QRSAVQA+IVVPTRELGMQVTKVAR LAAKP +     K CTVM
Sbjct: 116 GKTLAYLLQMLSVIDSQRSAVQALIVVPTRELGMQVTKVARTLAAKPSELKSGPKSCTVM 175

Query: 179 ALLDGGMLRRHKSWLK 194
           ALLDGGML RHKSWLK
Sbjct: 176 ALLDGGMLNRHKSWLK 191

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	202
TAIR|locus:2182202	472	AT5G19210 [Arabidopsis thalian	0.722	0.309	0.717	1.3e-50
DICTYBASE|DDB_G0291804	423	ddx6 "DEAD/DEAH box helicase"	0.5	0.238	0.345	1.9e-12
TAIR|locus:2010306	551	EMB1586 "embryo defective 1586	0.420	0.154	0.383	5.3e-12
UNIPROTKB|Q81QF0	450	BAS2301 "ATP-dependent RNA hel	0.405	0.182	0.430	6e-12
TIGR_CMR|BA_2475	450	BA_2475 "ATP-dependent RNA hel	0.405	0.182	0.430	6e-12
UNIPROTKB|Q83DM8	420	rhlE "ATP-dependent RNA helica	0.455	0.219	0.415	6.7e-12
TIGR_CMR|CBU_0670	420	CBU_0670 "ATP-dependent RNA he	0.455	0.219	0.415	6.7e-12
UNIPROTKB|D6RJA6	471	DDX46 "Probable ATP-dependent	0.376	0.161	0.456	1.1e-11
TAIR|locus:2075034	541	AT3G09720 [Arabidopsis thalian	0.450	0.168	0.375	1.4e-11
ZFIN|ZDB-GENE-030131-6611	483	wu:fk48d07 "wu:fk48d07" [Danio	0.549	0.229	0.299	2.4e-11

TAIR|locus:2182202 AT5G19210 [Arabidopsis thaliana (taxid:3702)]

 Score = 526 (190.2 bits), Expect = 1.3e-50, P = 1.3e-50
 Identities = 109/152 (71%), Positives = 126/152 (82%)

Query:    44 LRAVL-SSSAVSTEELAAGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALP 102
             L+AV  +SS + +  +   T    LTLR++CQG VPEH+L RMEE G+V PTDIQREALP
Sbjct:    51 LQAVAETSSEIESNSVTETTV--PLTLRQICQGFVPEHILHRMEEIGFVFPTDIQREALP 108

Query:   103 VLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA 162
              LF+ RDCILHAQTGSGKTLTYLLLIFSL+N QRS+VQAVIVVPTRELGMQVTKVAR+LA
Sbjct:   109 TLFTGRDCILHAQTGSGKTLTYLLLIFSLINPQRSSVQAVIVVPTRELGMQVTKVARMLA 168

Query:   163 AKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK 194
             AK   ++++ K CTVMALLDGG LRRHKSWLK
Sbjct:   169 AK---SEIDVKGCTVMALLDGGTLRRHKSWLK 197

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0009507 "chloroplast" evidence=ISM

DICTYBASE|DDB_G0291804 ddx6 "DEAD/DEAH box helicase" [Dictyostelium discoideum (taxid:44689)]

 Score = 173 (66.0 bits), Expect = 1.9e-12, P = 1.9e-12
 Identities = 37/107 (34%), Positives = 63/107 (58%)

Query:    55 TEELAAGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHA 114
             TE++ A  GN+   L      H+   +LR + E GYV P+ IQ +A+P+  + RD +  A
Sbjct:    40 TEDVTATEGNDFDDL------HLKRDLLRGIFEKGYVKPSPIQEKAIPIALAGRDIMARA 93

Query:   115 QTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL 161
             + G+GKT ++L+      +  +  +Q +I+VPTREL +Q ++V + L
Sbjct:    94 KNGTGKTASFLIPALEKTDPTKDVIQVLILVPTRELALQTSQVCKEL 140

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

GO:0005524 "ATP binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

TAIR|locus:2010306 EMB1586 "embryo defective 1586" [Arabidopsis thaliana (taxid:3702)]

 Score = 171 (65.3 bits), Expect = 5.3e-12, P = 5.3e-12
 Identities = 38/99 (38%), Positives = 60/99 (60%)

Query:    77 VPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLV---- 132
             +P+ +L  +E  G+ +PTD+Q  A+P +    D ++ + TGSGKTL YLL I S +    
Sbjct:   117 LPDSLLDSLEREGFSVPTDVQSAAVPAIIKGHDAVIQSYTGSGKTLAYLLPILSEIGPLA 176

Query:   133 ---------NAQRSAVQAVIVVPTRELGMQVTK-VARVL 161
                      N +R+ +QA+IV P+RELGMQ+ + V ++L
Sbjct:   177 EKSRSSHSENDKRTEIQAMIVAPSRELGMQIVREVEKLL 215

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0009507 "chloroplast" evidence=ISM

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

GO:0009663 "plasmodesma organization" evidence=IMP

GO:0003724 "RNA helicase activity" evidence=ISS

GO:0005739 "mitochondrion" evidence=IDA

GO:0010497 "plasmodesmata-mediated intercellular transport" evidence=IMP

UNIPROTKB|Q81QF0 BAS2301 "ATP-dependent RNA helicase, DEAD/DEAH box family" [Bacillus anthracis (taxid:1392)]

 Score = 169 (64.5 bits), Expect = 6.0e-12, P = 6.0e-12
 Identities = 37/86 (43%), Positives = 56/86 (65%)

Query:    80 HVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAV 139
             H LR   E G    T IQ +A+PV+ S +D I  A+TG+GKTL ++L I   ++ + S V
Sbjct:    18 HTLR---ENGITEATPIQEKAIPVILSGKDIIGQAKTGTGKTLAFVLPILEKIDPESSDV 74

Query:   140 QAVIVVPTRELGMQVT-KVARVLAAK 164
             QA+IV PTREL +Q+T ++ ++L  +
Sbjct:    75 QALIVAPTRELALQITTEIKKMLVQR 100

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|BA_2475 BA_2475 "ATP-dependent RNA helicase, DEAD/DEAH box family" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 169 (64.5 bits), Expect = 6.0e-12, P = 6.0e-12
 Identities = 37/86 (43%), Positives = 56/86 (65%)

Query:    80 HVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAV 139
             H LR   E G    T IQ +A+PV+ S +D I  A+TG+GKTL ++L I   ++ + S V
Sbjct:    18 HTLR---ENGITEATPIQEKAIPVILSGKDIIGQAKTGTGKTLAFVLPILEKIDPESSDV 74

Query:   140 QAVIVVPTRELGMQVT-KVARVLAAK 164
             QA+IV PTREL +Q+T ++ ++L  +
Sbjct:    75 QALIVAPTRELALQITTEIKKMLVQR 100

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

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q83DM8 rhlE "ATP-dependent RNA helicase" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 168 (64.2 bits), Expect = 6.7e-12, P = 6.7e-12
 Identities = 42/101 (41%), Positives = 60/101 (59%)

Query:    81 VLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLL-----LIFSLVNAQ 135
             +LR + E GYV PT +QR+A+PV+  +RD ++ AQTG+GKT  + L     L  S    Q
Sbjct:    21 LLRAIREQGYVEPTPVQRQAIPVILQARDVMVTAQTGTGKTAGFTLPLLQRLFVSRPPLQ 80

Query:   136 RSA---VQAVIVVPTRELGMQVTKVARVLAAK-PLDTDLEH 172
             RSA   ++A+I+ PTREL +QV +  R      PL   + H
Sbjct:    81 RSAKPVIRALILTPTRELAVQVFECVRAYGKYLPLKATVVH 121

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|CBU_0670 CBU_0670 "ATP-dependent RNA helicase RhlE, putative" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 168 (64.2 bits), Expect = 6.7e-12, P = 6.7e-12
 Identities = 42/101 (41%), Positives = 60/101 (59%)

Query:    81 VLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLL-----LIFSLVNAQ 135
             +LR + E GYV PT +QR+A+PV+  +RD ++ AQTG+GKT  + L     L  S    Q
Sbjct:    21 LLRAIREQGYVEPTPVQRQAIPVILQARDVMVTAQTGTGKTAGFTLPLLQRLFVSRPPLQ 80

Query:   136 RSA---VQAVIVVPTRELGMQVTKVARVLAAK-PLDTDLEH 172
             RSA   ++A+I+ PTREL +QV +  R      PL   + H
Sbjct:    81 RSAKPVIRALILTPTRELAVQVFECVRAYGKYLPLKATVVH 121

GO:0008150 "biological_process" evidence=ND

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

UNIPROTKB|D6RJA6 DDX46 "Probable ATP-dependent RNA helicase DDX46" [Homo sapiens (taxid:9606)]

 Score = 167 (63.8 bits), Expect = 1.1e-11, P = 1.1e-11
 Identities = 37/81 (45%), Positives = 53/81 (65%)

Query:    81 VLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQ 140
             +L  +++ GY  PT IQ +A+P + S RD I  A+TGSGKT+ +LL +F  +  QRS  +
Sbjct:   335 ILNSLKKHGYEKPTPIQTQAIPAIMSGRDLIGIAKTGSGKTIAFLLPMFRHIMDQRSLEE 394

Query:   141 -----AVIVVPTRELGMQVTK 156
                  AVI+ PTREL +Q+TK
Sbjct:   395 GEGPIAVIMTPTRELALQITK 415

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

TAIR|locus:2075034 AT3G09720 [Arabidopsis thaliana (taxid:3702)]

 Score = 167 (63.8 bits), Expect = 1.4e-11, P = 1.4e-11
 Identities = 36/96 (37%), Positives = 55/96 (57%)

Query:    67 LTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLL 126
             L+ R  C+G++    LR + E G+  PT IQR+A+P+L S R+C   A TGSGKT  ++ 
Sbjct:   142 LSSRYGCEGYI----LRNLAELGFKEPTPIQRQAIPILLSGRECFACAPTGSGKTFAFIC 197

Query:   127 -LIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL 161
              ++  L       ++AVI+ P REL  Q  +  + L
Sbjct:   198 PMLIKLKRPSTDGIRAVILSPARELAAQTAREGKKL 233

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA

ZFIN|ZDB-GENE-030131-6611 wu:fk48d07 "wu:fk48d07" [Danio rerio (taxid:7955)]

 Score = 164 (62.8 bits), Expect = 2.4e-11, P = 2.4e-11
 Identities = 35/117 (29%), Positives = 67/117 (57%)

Query:    42 KPLRAVLSSSAVSTEELAAGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREAL 101
             K L+     + V T ++ A  GN      + C   +   +L  + E G+  P+ IQ E++
Sbjct:    66 KCLQLPPKDTRVRTTDVTATKGNE---FEDYC---LKRELLMGIFEMGWEKPSPIQEESI 119

Query:   102 PVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVA 158
             P+  S RD +  A+ G+GK+  YL+ +   ++ ++  +QA+++VPTREL +QV++++
Sbjct:   120 PIALSGRDILARAKNGTGKSGAYLIPLLERIDLKKDYIQAIVLVPTRELALQVSQIS 176

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0016787 "hydrolase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q3E9C3	RH58_ARATH	3, ., 6, ., 4, ., 1, 3	0.8046	0.6188	0.2648	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00019925001 SubName- Full=Chromosome chr5 scaffold_2, whole genome shotgun sequence; (486 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	202
cd00268	203	cd00268, DEADc, DEAD-box helicases	1e-23
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	1e-21
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	1e-18
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	1e-15
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	4e-15
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	6e-15
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	2e-13
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	2e-13
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	3e-12
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	5e-12
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	5e-12
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	5e-12
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	8e-12
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	6e-09
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	9e-07
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	6e-06
COG1205	851	COG1205, COG1205, Distinct helicase family with a	1e-05
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	3e-05
pfam04851	100	pfam04851, ResIII, Type III restriction enzyme, re	3e-04
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	3e-04
COG1199	654	COG1199, DinG, Rad3-related DNA helicases [Transcr	8e-04

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

 Score = 92.9 bits (232), Expect = 1e-23
 Identities = 37/89 (41%), Positives = 51/89 (57%), Gaps = 2/89 (2%)

Query: 76  HVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ 135
            +   +LR +   G+  PT IQ  A+P L S RD I  AQTGSGKT  +L+ I   ++  
Sbjct: 5   GLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPS 64

Query: 136 RS--AVQAVIVVPTRELGMQVTKVARVLA 162
                 QA+I+ PTREL +Q+ +VAR L 
Sbjct: 65  PKKDGPQALILAPTRELALQIAEVARKLG 93

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 = 91.4 bits (227), Expect = 1e-21
 Identities = 31/88 (35%), Positives = 51/88 (57%), Gaps = 2/88 (2%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ-- 135
              +L+ +++ G+  PT IQ  A+P++ + RD +  AQTG+GKT  +LL +   +     
Sbjct: 37  SPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVE 96

Query: 136 RSAVQAVIVVPTRELGMQVTKVARVLAA 163
           R  V A+I+ PTREL +Q+ +  R L  
Sbjct: 97  RKYVSALILAPTRELAVQIAEELRKLGK 124

Length = 513

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

 Score = 78.8 bits (195), Expect = 1e-18
 Identities = 27/72 (37%), Positives = 43/72 (59%)

Query: 94  TDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQ 153
           T IQ +A+P + S +D ++ A TGSGKTL +LL I   +  ++   QA+++ PTREL  Q
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQ 60

Query: 154 VTKVARVLAAKP 165
           + +  + L    
Sbjct: 61  IYEELKKLFKIL 72

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

 Score = 74.1 bits (182), Expect = 1e-15
 Identities = 31/80 (38%), Positives = 47/80 (58%), Gaps = 6/80 (7%)

Query: 81  VLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ----- 135
           +LR + E GY  PT IQ++A+P +   RD +  AQTG+GKT  + L +   +  +     
Sbjct: 12  ILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAK 71

Query: 136 -RSAVQAVIVVPTRELGMQV 154
            R  V+A+I+ PTREL  Q+
Sbjct: 72  GRRPVRALILTPTRELAAQI 91

Length = 456

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

 Score = 72.5 bits (179), Expect = 4e-15
 Identities = 35/85 (41%), Positives = 51/85 (60%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS 137
           P  +L  + E GY   T IQ ++LP + + +D I  A+TGSGKT  + L +   ++ +R 
Sbjct: 12  PPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRF 71

Query: 138 AVQAVIVVPTRELGMQVTKVARVLA 162
            VQA+++ PTREL  QV K  R LA
Sbjct: 72  RVQALVLCPTRELADQVAKEIRRLA 96

Length = 460

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

 Score = 69.8 bits (171), Expect = 6e-15
 Identities = 29/78 (37%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 86  EETGYVLPTDIQREALPVLFSS-RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIV 144
           E+ G+      Q+EA+  L S  RD IL A TGSGKTL  LL     +  +    + +++
Sbjct: 2   EKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEAL-KRGKGGRVLVL 60

Query: 145 VPTRELGMQVTKVARVLA 162
           VPTREL  Q  +  + L 
Sbjct: 61  VPTRELAEQWAEELKKLG 78

Length = 201

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

 Score = 67.9 bits (166), Expect = 2e-13
 Identities = 32/91 (35%), Positives = 49/91 (53%), Gaps = 5/91 (5%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS 137
           P+++L+ ++  G+  PT IQ +  P+  S RD I  A+TGSGKTL +LL     +NAQ  
Sbjct: 138 PDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPL 197

Query: 138 AVQA-----VIVVPTRELGMQVTKVARVLAA 163
                    +++ PTREL  Q+ +      A
Sbjct: 198 LRYGDGPIVLVLAPTRELAEQIREQCNKFGA 228

Length = 545

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

 Score = 67.5 bits (165), Expect = 2e-13
 Identities = 35/92 (38%), Positives = 52/92 (56%), Gaps = 7/92 (7%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFS---LVNA 134
           P  +L  +E  GY  PT IQ +A+P   S R  ++ A TGSGKT ++L+ I S    + +
Sbjct: 129 PPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRS 188

Query: 135 QRSAVQ----AVIVVPTRELGMQVTKVARVLA 162
              + Q    A+++ PTREL +QV   A+VL 
Sbjct: 189 GHPSEQRNPLAMVLTPTRELCVQVEDQAKVLG 220

Length = 518

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

 Score = 64.1 bits (156), Expect = 3e-12
 Identities = 30/84 (35%), Positives = 48/84 (57%)

Query: 79  EHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSA 138
           E +LR +   G+  P+ IQ+  +  +    D I  AQ+G+GKT T+++    L++   +A
Sbjct: 37  EDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNA 96

Query: 139 VQAVIVVPTRELGMQVTKVARVLA 162
            QA+I+ PTREL  Q+ KV   L 
Sbjct: 97  CQALILAPTRELAQQIQKVVLALG 120

Length = 401

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

 Score = 63.4 bits (155), Expect = 5e-12
 Identities = 39/96 (40%), Positives = 51/96 (53%), Gaps = 7/96 (7%)

Query: 79  EHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLL--LIFSLVNAQR 136
           E +L  +++ GY  PT IQ EA+P     RD +  A TG+GKT  +LL  L   L   +R
Sbjct: 10  ESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRR 69

Query: 137 SAVQAVIVV--PTRELGMQVTKVARVLAAKPLDTDL 170
            +    I++  PTREL MQV   AR LA     T L
Sbjct: 70  KSGPPRILILTPTRELAMQVADQARELAK---HTHL 102

Length = 434

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

 Score = 63.5 bits (155), Expect = 5e-12
 Identities = 33/90 (36%), Positives = 46/90 (51%), Gaps = 7/90 (7%)

Query: 81  VLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIF-----SLVNAQ 135
           V+  +E+ G+   T IQ  ALP+  + RD    AQTG+GKT+ +L   F           
Sbjct: 19  VVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPED 78

Query: 136 RSAVQ--AVIVVPTRELGMQVTKVARVLAA 163
           R   Q  A+I+ PTREL +Q+   A  LA 
Sbjct: 79  RKVNQPRALIMAPTRELAVQIHADAEPLAQ 108

Length = 423

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

 Score = 63.7 bits (155), Expect = 5e-12
 Identities = 29/74 (39%), Positives = 45/74 (60%)

Query: 81  VLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQ 140
           +L  + + GY  P+ IQ E +P L + RD +  AQTGSGKT  + L +   ++ +  A Q
Sbjct: 17  ILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQ 76

Query: 141 AVIVVPTRELGMQV 154
            +++ PTREL +QV
Sbjct: 77  ILVLAPTRELAVQV 90

Length = 629

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

 Score = 60.0 bits (146), Expect = 8e-12
 Identities = 24/60 (40%), Positives = 36/60 (60%), Gaps = 1/60 (1%)

Query: 108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLD 167
           RD +L A TGSGKTL  LL I  L+++ +   Q +++ PTREL  QV +  + L  + + 
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDSLK-GGQVLVLAPTRELANQVAERLKELFGEGIK 59

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

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

 Score = 54.6 bits (131), Expect = 6e-09
 Identities = 29/81 (35%), Positives = 43/81 (53%), Gaps = 7/81 (8%)

Query: 85  MEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIF-------SLVNAQRS 137
           +E  G+   T IQ   LPV     D    AQTG+GKTL +L+ +        +L + +  
Sbjct: 24  LESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPE 83

Query: 138 AVQAVIVVPTRELGMQVTKVA 158
             +A+I+ PTREL +Q+ K A
Sbjct: 84  DPRALILAPTRELAIQIHKDA 104

Length = 572

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

 Score = 48.0 bits (114), Expect = 9e-07
 Identities = 35/108 (32%), Positives = 51/108 (47%), Gaps = 16/108 (14%)

Query: 85  MEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFS-LVNAQ------RS 137
           + + G+   T IQ + L    +  D I  AQTG+GKT  +L+ I + L+           
Sbjct: 102 IHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMG 161

Query: 138 AVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGM 185
             +A+I+ PTREL +Q+ K A  L      T L      VM  + GGM
Sbjct: 162 EPRALIIAPTRELVVQIAKDAAALTKY---TGLN-----VMTFV-GGM 200

Length = 475

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

 Score = 45.7 bits (109), Expect = 6e-06
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 5/74 (6%)

Query: 82  LRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLV-----NAQR 136
           +R   +  +   T  QR A+P + S  + ++ A TGSGKT    L + + +         
Sbjct: 12  VREWFKRKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLE 71

Query: 137 SAVQAVIVVPTREL 150
             + A+ + P + L
Sbjct: 72  DGIYALYISPLKAL 85

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 = 44.7 bits (106), Expect = 1e-05
 Identities = 32/117 (27%), Positives = 53/117 (45%), Gaps = 21/117 (17%)

Query: 97  QREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGM-QVT 155
           Q +AL ++   R+ ++   TGSGKT ++LL I   +    SA +A+++ PT  L   Q  
Sbjct: 75  QVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSA-RALLLYPTNALANDQAE 133

Query: 156 KVARVLAAKPL---------DTDLE----------HKLCTVMALLDGGMLRRHKSWL 193
           ++  +++  P          DT  E            L T   +L   +LR H +WL
Sbjct: 134 RLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWL 190

Length = 851

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

 Score = 43.5 bits (103), Expect = 3e-05
 Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 3/59 (5%)

Query: 97  QREAL-PVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQV 154
           Q+EA+   L S  + ++ A TGSGKTL  LL I S +       + V +VP + L  + 
Sbjct: 36  QQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLL--EGGGKVVYIVPLKALAEEK 92

Length = 766

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

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 3/61 (4%)

Query: 93  PTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGM 152
               Q EA+  L   +  ++   TGSGKTLT   LI  L   ++     + VVP ++L  
Sbjct: 4   LRPYQEEAIERLLEKKRGLIVMATGSGKTLTAAALIARLAKGKKK---VLFVVPRKDLLE 60

Query: 153 Q 153
           Q
Sbjct: 61  Q 61

Length = 100

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

 Score = 40.1 bits (94), Expect = 3e-04
 Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 10/65 (15%)

Query: 93  PTDIQREALPVLFSSRDC----ILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTR 148
               Q EAL  L  +R      ++   TG+GKT+     I  L          +++VPT+
Sbjct: 37  LRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELKR------STLVLVPTK 90

Query: 149 ELGMQ 153
           EL  Q
Sbjct: 91  ELLDQ 95

Length = 442

>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

 Score = 39.4 bits (92), Expect = 8e-04
 Identities = 20/80 (25%), Positives = 30/80 (37%), Gaps = 6/80 (7%)

Query: 79  EHVLRRMEETGYVLPTDIQREAL----PVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNA 134
                         P   QRE        L      ++ A TG+GKTL Y  L+ +L  A
Sbjct: 2   SDDGYLAVAFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAY--LLPALAYA 59

Query: 135 QRSAVQAVIVVPTRELGMQV 154
           +    + +I   T+ L  Q+
Sbjct: 60  REEGKKVIISTRTKALQEQL 79

Length = 654

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	202
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	99.91
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	99.9
PTZ00110	545	helicase; Provisional	99.89
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.89
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.88
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.88
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	99.88
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	99.87
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.87
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.87
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.86
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.86
KOG0346	569	consensus RNA helicase [RNA processing and modific	99.86
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	99.85
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.84
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	99.84
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.84
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	99.84
KOG0334	997	consensus RNA helicase [RNA processing and modific	99.83
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	99.83
PTZ00424	401	helicase 45; Provisional	99.82
KOG0347	731	consensus RNA helicase [RNA processing and modific	99.82
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	99.81
KOG0343	758	consensus RNA Helicase [RNA processing and modific	99.81
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.79
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	99.79
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	99.79
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	99.78
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.77
KOG0327	397	consensus Translation initiation factor 4F, helica	99.76
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	99.75
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	99.73
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	99.73
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	99.72
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	99.71
PRK02362	737	ski2-like helicase; Provisional	99.69
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.65
KOG4284	980	consensus DEAD box protein [Transcription]	99.65
PRK00254	720	ski2-like helicase; Provisional	99.64
COG1205	851	Distinct helicase family with a unique C-terminal	99.64
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.61
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.6
PRK13767	876	ATP-dependent helicase; Provisional	99.59
PRK01172	674	ski2-like helicase; Provisional	99.59
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	99.59
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.58
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.57
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.57
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.56
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.53
PRK14701	1638	reverse gyrase; Provisional	99.51
PRK10689	1147	transcription-repair coupling factor; Provisional	99.5
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.48
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.46
PRK09401	1176	reverse gyrase; Reviewed	99.45
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.43
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.41
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.41
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.38
PHA02558	501	uvsW UvsW helicase; Provisional	99.35
PRK05580	679	primosome assembly protein PriA; Validated	99.33
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.31
COG1204	766	Superfamily II helicase [General function predicti	99.18
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.13
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.13
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.13
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.09
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	99.04
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.03
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.01
PHA02653	675	RNA helicase NPH-II; Provisional	99.0
COG1202	830	Superfamily II helicase, archaea-specific [General	98.97
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	98.97
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	98.96
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	98.95
TIGR00595	505	priA primosomal protein N'. All proteins in this f	98.94
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	98.91
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	98.9
PRK13766	773	Hef nuclease; Provisional	98.89
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	98.86
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	98.8
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	98.75
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	98.74
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	98.74
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.71
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	98.71
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	98.71
KOG0354	746	consensus DEAD-box like helicase [General function	98.66
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	98.63
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	98.61
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	98.59
PRK12904	830	preprotein translocase subunit SecA; Reviewed	98.58
PRK09694	878	helicase Cas3; Provisional	98.57
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	98.52
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.5
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	98.45
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	98.44
KOG0353	695	consensus ATP-dependent DNA helicase [General func	98.44
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	98.39
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	98.39
PRK13107	908	preprotein translocase subunit SecA; Reviewed	98.36
PRK14873	665	primosome assembly protein PriA; Provisional	98.31
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.25
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	98.24
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.22
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	98.19
PF13245	76	AAA_19: Part of AAA domain	98.17
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.11
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.07
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	98.05
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	98.03
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	98.0
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.99
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	97.91
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	97.83
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	97.82
PRK12326	764	preprotein translocase subunit SecA; Reviewed	97.8
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	97.79
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	97.67
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	97.61
TIGR00376	637	DNA helicase, putative. The gene product may repre	97.59
KOG1803	649	consensus DNA helicase [Replication, recombination	97.51
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.41
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.26
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	97.13
CHL00122	870	secA preprotein translocase subunit SecA; Validate	97.07
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	96.93
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	96.91
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	96.87
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	96.84
KOG1802	935	consensus RNA helicase nonsense mRNA reducing fact	96.81
PRK04914	956	ATP-dependent helicase HepA; Validated	96.69
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	96.68
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	96.68
PRK15483	986	type III restriction-modification system StyLTI en	96.66
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	96.65
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	96.63
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	96.59
PRK11054	684	helD DNA helicase IV; Provisional	96.58
COG4096	875	HsdR Type I site-specific restriction-modification	96.51
PRK10536	262	hypothetical protein; Provisional	96.51
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	96.45
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	96.31
COG4889	1518	Predicted helicase [General function prediction on	96.26
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.21
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	96.21
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	96.07
PRK05298	652	excinuclease ABC subunit B; Provisional	96.02
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	95.98
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	95.96
PRK05973	237	replicative DNA helicase; Provisional	95.9
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	95.75
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	95.73
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	95.7
PRK13833	323	conjugal transfer protein TrbB; Provisional	95.7
PRK08181	269	transposase; Validated	95.64
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	95.63
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	95.52
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	95.45
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	95.43
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.42
COG3973	747	Superfamily I DNA and RNA helicases [General funct	95.4
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	95.34
PRK13889	988	conjugal transfer relaxase TraA; Provisional	95.33
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	95.32
PRK06526	254	transposase; Provisional	95.3
PRK10875	615	recD exonuclease V subunit alpha; Provisional	95.26
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	95.15
COG1484	254	DnaC DNA replication protein [DNA replication, rec	95.11
PRK13851	344	type IV secretion system protein VirB11; Provision	94.92
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	94.79
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	94.77
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	94.66
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	94.57
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	94.5
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	94.38
PRK06921	266	hypothetical protein; Provisional	94.26
TIGR02237	209	recomb_radB DNA repair and recombination protein R	94.19
PRK04328	249	hypothetical protein; Provisional	94.14
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	94.11
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	94.07
PRK06835	329	DNA replication protein DnaC; Validated	94.03
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	93.99
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	93.87
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	93.79
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	93.74
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	93.68
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	93.58
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	93.56
PRK12377	248	putative replication protein; Provisional	93.55
KOG1123	776	consensus RNA polymerase II transcription initiati	93.54
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	93.53
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	93.5
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	93.48
PRK08533	230	flagellar accessory protein FlaH; Reviewed	93.39
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	93.36
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	93.31
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	93.27
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	93.25
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	93.19
PRK13826	1102	Dtr system oriT relaxase; Provisional	93.02
PF12846	304	AAA_10: AAA-like domain	92.88
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	92.86
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	92.85
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	92.85
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	92.81
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	92.79
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	92.78
PRK10436	462	hypothetical protein; Provisional	92.77
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	92.76
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	92.73
KOG1131	755	consensus RNA polymerase II transcription initiati	92.7
PRK07952	244	DNA replication protein DnaC; Validated	92.68
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	92.68
smart00382	148	AAA ATPases associated with a variety of cellular	92.68
KOG1002	791	consensus Nucleotide excision repair protein RAD16	92.55
PRK08727	233	hypothetical protein; Validated	92.38
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	92.36
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	92.31
COG0210	655	UvrD Superfamily I DNA and RNA helicases [DNA repl	92.28
KOG2340	698	consensus Uncharacterized conserved protein [Funct	92.28
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	92.26
PRK06067	234	flagellar accessory protein FlaH; Validated	92.26
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	92.26
PRK08116	268	hypothetical protein; Validated	92.23
TIGR02533	486	type_II_gspE general secretory pathway protein E.	92.21
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	92.21
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	92.16
PRK09183	259	transposase/IS protein; Provisional	92.14
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	92.06
PRK13764	602	ATPase; Provisional	91.96
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	91.93
cd00983	325	recA RecA is a bacterial enzyme which has roles in	91.89
cd01394	218	radB RadB. The archaeal protein radB shares simila	91.77
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	91.77
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	91.75
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	91.67
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	91.65
PRK04296	190	thymidine kinase; Provisional	91.63
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	91.58
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	91.48
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	91.35
COG3972	660	Superfamily I DNA and RNA helicases [General funct	91.33
KOG0387	923	consensus Transcription-coupled repair protein CSB	91.32
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	91.31
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	91.2
PRK09354	349	recA recombinase A; Provisional	91.13
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	91.13
TIGR03754	643	conj_TOL_TraD conjugative coupling factor TraD, TO	91.11
KOG1805	1100	consensus DNA replication helicase [Replication, r	91.0
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	90.87
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	90.76
KOG4439	901	consensus RNA polymerase II transcription terminat	90.69
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	90.59
COG3587	985	Restriction endonuclease [Defense mechanisms]	90.58
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	90.51
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	90.32
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	90.15
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	90.09
PRK09302	509	circadian clock protein KaiC; Reviewed	89.82
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	89.66
PRK13897	606	type IV secretion system component VirD4; Provisio	89.63
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	89.62
PRK05642	234	DNA replication initiation factor; Validated	89.57
PRK13700	732	conjugal transfer protein TraD; Provisional	89.51
PF13555	62	AAA_29: P-loop containing region of AAA domain	89.44
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	89.34
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	89.33
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	89.33
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	89.3
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	89.29
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	89.28
PRK11823	446	DNA repair protein RadA; Provisional	89.11
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	89.0
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	88.86
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	88.81
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	88.75
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	88.7
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	88.64
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	88.63
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	88.51
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	88.49
PF00004	132	AAA: ATPase family associated with various cellula	88.47
COG0610	962	Type I site-specific restriction-modification syst	88.38
PRK09302	509	circadian clock protein KaiC; Reviewed	88.27
PRK13850	670	type IV secretion system protein VirD4; Provisiona	88.24
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	88.19
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	87.92
PRK08084	235	DNA replication initiation factor; Provisional	87.85
PRK14087	450	dnaA chromosomal replication initiation protein; P	87.79
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	87.74
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	87.74
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	87.65
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	87.44
PRK06893	229	DNA replication initiation factor; Validated	87.36
PRK08903	227	DnaA regulatory inactivator Hda; Validated	87.31
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	87.28
TIGR02773	1158	addB_Gpos ATP-dependent nuclease subunit B. DNA re	87.25
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	87.21
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	87.14
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	86.92
PRK00149	450	dnaA chromosomal replication initiation protein; R	86.7
CHL00181	287	cbbX CbbX; Provisional	86.68
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	86.64
PRK08939	306	primosomal protein DnaI; Reviewed	86.61
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	86.53
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	86.48
PRK13880	636	conjugal transfer coupling protein TraG; Provision	86.46
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	86.37
PF05729	166	NACHT: NACHT domain	86.29
KOG1807	1025	consensus Helicases [Replication, recombination an	86.08
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	86.07
PRK13822	641	conjugal transfer coupling protein TraG; Provision	86.04
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	85.96
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	85.95
cd01363	186	Motor_domain Myosin and Kinesin motor domain. Thes	85.82
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	85.74
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	85.73
PHA02533	534	17 large terminase protein; Provisional	85.61
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	85.52
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	85.52
PRK04301	317	radA DNA repair and recombination protein RadA; Va	85.52
PTZ00035	337	Rad51 protein; Provisional	85.31
PRK13876	663	conjugal transfer coupling protein TraG; Provision	85.28
TIGR02759	566	TraD_Ftype type IV conjugative transfer system cou	85.2
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	85.19
PF09439	181	SRPRB: Signal recognition particle receptor beta s	85.01
PRK14974	336	cell division protein FtsY; Provisional	84.87
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	84.7
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	84.42
TIGR00064	272	ftsY signal recognition particle-docking protein F	84.41
cd03115	173	SRP The signal recognition particle (SRP) mediates	84.39
KOG1533	290	consensus Predicted GTPase [General function predi	84.36
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	84.27
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	84.14
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	84.12
PHA02244	383	ATPase-like protein	84.12
PRK14729	300	miaA tRNA delta(2)-isopentenylpyrophosphate transf	84.01
PRK13531	498	regulatory ATPase RavA; Provisional	83.98
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	83.91
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	83.75
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	83.5
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	83.47
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	83.46
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	83.41
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	83.29
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	83.03
PRK00131	175	aroK shikimate kinase; Reviewed	82.93
PRK05707	328	DNA polymerase III subunit delta'; Validated	82.72
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	82.7
PRK12402	337	replication factor C small subunit 2; Reviewed	82.69
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	82.59
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	82.5
PRK08506	472	replicative DNA helicase; Provisional	82.16
COG0606	490	Predicted ATPase with chaperone activity [Posttran	82.15
PRK10867	433	signal recognition particle protein; Provisional	82.09
TIGR02746	797	TraC-F-type type-IV secretion system protein TraC.	82.08
PRK14088	440	dnaA chromosomal replication initiation protein; P	82.01
COG0714	329	MoxR-like ATPases [General function prediction onl	81.99
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	81.88
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	81.53
PRK10416	318	signal recognition particle-docking protein FtsY;	81.52
PLN02165	334	adenylate isopentenyltransferase	81.15
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	81.02
PRK04220	301	2-phosphoglycerate kinase; Provisional	80.95
cd01367	322	KISc_KIF2_like Kinesin motor domain, KIF2-like gro	80.84
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	80.79
PRK09519	790	recA DNA recombination protein RecA; Reviewed	80.79
cd01370	338	KISc_KIP3_like Kinesin motor domain, KIP3-like sub	80.72
cd01368	345	KISc_KIF23_like Kinesin motor domain, KIF23-like s	80.71
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	80.71
PTZ00301	210	uridine kinase; Provisional	80.62
PRK00300	205	gmk guanylate kinase; Provisional	80.37
cd01373	337	KISc_KLP2_like Kinesin motor domain, KLP2-like sub	80.23
KOG2373	514	consensus Predicted mitochondrial DNA helicase twi	80.2
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	80.14
PF00225	335	Kinesin: Kinesin motor domain; InterPro: IPR001752	80.12
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	80.06
cd01376	319	KISc_KID_like Kinesin motor domain, KIF22/Kid-like	80.05

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

Probab=99.91  E-value=5.4e-24  Score=180.66  Aligned_cols=124  Identities=29%  Similarity=0.349  Sum_probs=114.9

Q ss_pred             cchHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEec
Q 028887           66 SLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVV  145 (202)
Q Consensus        66 ~~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~  145 (202)
                      ...+.+|.++|+.+++++++.+.||..||++|+++||.++.|+|+|.-|.||||||.+|++|+++.+......+.+|||+
T Consensus        57 ~e~~~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVLt  136 (476)
T KOG0330|consen   57 DESFKSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVLT  136 (476)
T ss_pred             hhhhcchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCCCceEEEec
Confidence            35677888889999999999999999999999999999999999999999999999999999999998888889999999


Q ss_pred             CCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHHHhc
Q 028887          146 PTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVLY  197 (202)
Q Consensus       146 Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~l~  197 (202)
                      ||||||.||.++|..++...        ++++..+.||.++..|...+.+-.
T Consensus       137 PtRELA~QI~e~fe~Lg~~i--------glr~~~lvGG~~m~~q~~~L~kkP  180 (476)
T KOG0330|consen  137 PTRELAQQIAEQFEALGSGI--------GLRVAVLVGGMDMMLQANQLSKKP  180 (476)
T ss_pred             CcHHHHHHHHHHHHHhcccc--------CeEEEEEecCchHHHHHHHhhcCC
Confidence            99999999999999999887        799999999999999877765433

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

Probab=99.90  E-value=2.5e-23  Score=184.43  Aligned_cols=117  Identities=29%  Similarity=0.400  Sum_probs=109.0

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHh------cCCccEEEEe
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNA------QRSAVQAVIV  144 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~------~~~~~~~Lil  144 (202)
                      .|.+.++.+++...++..||+.|||+|.+.||.++.|+|++..|.||||||++|++|++.++..      ..++|++|||
T Consensus        92 ~f~~~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL  171 (519)
T KOG0331|consen   92 AFQELGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVL  171 (519)
T ss_pred             hhhcccccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEE
Confidence            7777799999999999999999999999999999999999999999999999999999999986      2357899999


Q ss_pred             cCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHHH
Q 028887          145 VPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKV  195 (202)
Q Consensus       145 ~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~  195 (202)
                      +||||||.|+.+.+++++...        .++++|+|||.....|.+.++.
T Consensus       172 ~PTRELA~QV~~~~~~~~~~~--------~~~~~cvyGG~~~~~Q~~~l~~  214 (519)
T KOG0331|consen  172 APTRELAVQVQAEAREFGKSL--------RLRSTCVYGGAPKGPQLRDLER  214 (519)
T ss_pred             cCcHHHHHHHHHHHHHHcCCC--------CccEEEEeCCCCccHHHHHHhc
Confidence            999999999999999999886        5789999999999999888765

>PTZ00110 helicase; Provisional

Probab=99.89  E-value=5e-22  Score=180.55  Aligned_cols=159  Identities=25%  Similarity=0.328  Sum_probs=122.7

Q ss_pred             CCCccccccccCCCCCCchHHHHHhccCCCCHHHHHcccCCCcchHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHh
Q 028887           24 PNSIDFTNRAFLPVSISLKPLRAVLSSSAVSTEELAAGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPV  103 (202)
Q Consensus        24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~  103 (202)
                      +....|....+.....+...+..+.....+...    .....+.++.+|.+.++++.+++.|.++||.+||++|.++||.
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~----~g~~~p~p~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~  163 (545)
T PTZ00110         88 PFEKNFYKEHPEVSALSSKEVDEIRKEKEITII----AGENVPKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPI  163 (545)
T ss_pred             chhhhcccCChhhhcCCHHHHHHHHHhcCcEEe----cCCCCCcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHH
Confidence            334444444444445555555555444433321    1122345667788889999999999999999999999999999


Q ss_pred             HHcCCcEEEeccCCCchHHHHHHHHHHHHHhc-----CCccEEEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEE
Q 028887          104 LFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ-----RSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVM  178 (202)
Q Consensus       104 i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~-----~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~  178 (202)
                      ++.|+|++++|+||||||++|++|++..+...     ..++++|||+||||||.|+.+.+++++...        .+++.
T Consensus       164 ~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp~~LIL~PTreLa~Qi~~~~~~~~~~~--------~i~~~  235 (545)
T PTZ00110        164 ALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASS--------KIRNT  235 (545)
T ss_pred             HhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCcEEEEECChHHHHHHHHHHHHHHhccc--------CccEE
Confidence            99999999999999999999999999887543     236789999999999999999999998765        57888


Q ss_pred             EEEeCCccHHHHHHHH
Q 028887          179 ALLDGGMLRRHKSWLK  194 (202)
Q Consensus       179 ~~~~g~~~~~~~~~l~  194 (202)
                      .+++|.....|...++
T Consensus       236 ~~~gg~~~~~q~~~l~  251 (545)
T PTZ00110        236 VAYGGVPKRGQIYALR  251 (545)
T ss_pred             EEeCCCCHHHHHHHHH
Confidence            8999988877766554

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

Probab=99.89  E-value=2.8e-22  Score=180.89  Aligned_cols=119  Identities=31%  Similarity=0.464  Sum_probs=105.9

Q ss_pred             HHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHh--cCCccEEEEecCC
Q 028887           70 RELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNA--QRSAVQAVIVVPT  147 (202)
Q Consensus        70 ~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~--~~~~~~~Lil~Pt  147 (202)
                      ..|.+.++.+.+++++.++||..|||+|.++||.++.|+|++++|+||||||.+|++|+++.+..  ......+|||+||
T Consensus        29 ~~F~~l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aLil~PT  108 (513)
T COG0513          29 PEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPT  108 (513)
T ss_pred             CCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccccCCCceEEECCC
Confidence            55667799999999999999999999999999999999999999999999999999999999874  2222229999999


Q ss_pred             HHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHHH
Q 028887          148 RELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKV  195 (202)
Q Consensus       148 r~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~  195 (202)
                      ||||.|+++.++.++.+..       .+++..++||.+...|.+.++.
T Consensus       109 RELA~Qi~~~~~~~~~~~~-------~~~~~~i~GG~~~~~q~~~l~~  149 (513)
T COG0513         109 RELAVQIAEELRKLGKNLG-------GLRVAVVYGGVSIRKQIEALKR  149 (513)
T ss_pred             HHHHHHHHHHHHHHHhhcC-------CccEEEEECCCCHHHHHHHHhc
Confidence            9999999999999998752       3678999999999999877765

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.88  E-value=4.2e-22  Score=175.87  Aligned_cols=116  Identities=28%  Similarity=0.376  Sum_probs=101.4

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC-------CccEEEE
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR-------SAVQAVI  143 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~-------~~~~~Li  143 (202)
                      .|.+.|+++.+++++.++||..||++|.++||.++.|+|++++||||||||++|++|+++.+....       .++++||
T Consensus         9 ~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~li   88 (423)
T PRK04837          9 KFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALI   88 (423)
T ss_pred             CHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEEE
Confidence            456669999999999999999999999999999999999999999999999999999999886422       3578999


Q ss_pred             ecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          144 VVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       144 l~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      |+||+|||.|+++++..++...        ++.+..++||.....+.+.++
T Consensus        89 l~PtreLa~Qi~~~~~~l~~~~--------~~~v~~~~gg~~~~~~~~~l~  131 (423)
T PRK04837         89 MAPTRELAVQIHADAEPLAQAT--------GLKLGLAYGGDGYDKQLKVLE  131 (423)
T ss_pred             ECCcHHHHHHHHHHHHHHhccC--------CceEEEEECCCCHHHHHHHhc
Confidence            9999999999999999998876        577777888877777665543

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

Probab=99.88  E-value=1.2e-21  Score=177.12  Aligned_cols=121  Identities=29%  Similarity=0.456  Sum_probs=107.3

Q ss_pred             cchHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHh-------cCCc
Q 028887           66 SLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNA-------QRSA  138 (202)
Q Consensus        66 ~~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~-------~~~~  138 (202)
                      ..++.+|.+.++++.+++.+.+.||..|||+|.++||.++.|+|+++.++||||||++|++|++..+..       ...+
T Consensus       117 p~pi~~f~~~~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~  196 (518)
T PLN00206        117 PPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRN  196 (518)
T ss_pred             CchhcCHHhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCC
Confidence            367888888899999999999999999999999999999999999999999999999999999988753       1246


Q ss_pred             cEEEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          139 VQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       139 ~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      +++|||+||||||.|+.+.++.++...        .+.+..++||.....|..+++
T Consensus       197 ~~aLIL~PTreLa~Qi~~~~~~l~~~~--------~~~~~~~~gG~~~~~q~~~l~  244 (518)
T PLN00206        197 PLAMVLTPTRELCVQVEDQAKVLGKGL--------PFKTALVVGGDAMPQQLYRIQ  244 (518)
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHHhCCC--------CceEEEEECCcchHHHHHHhc
Confidence            799999999999999999999998765        477888999988888766553

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

Probab=99.88  E-value=2.1e-22  Score=169.37  Aligned_cols=119  Identities=26%  Similarity=0.403  Sum_probs=108.9

Q ss_pred             hHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCC
Q 028887           68 TLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPT  147 (202)
Q Consensus        68 ~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Pt  147 (202)
                      +-..|..+|+.+++.+.+..+|+..|||+|..|||.|+.|+|++.+|.||||||.+|.+|+++++..+..+..++|++||
T Consensus         5 t~~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTPT   84 (442)
T KOG0340|consen    5 TAKPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTPT   84 (442)
T ss_pred             ccCchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCCCcceEEEecch
Confidence            34556667999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          148 RELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       148 r~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      ||||.|+.+.|..++...        ++++..++||.++-.|...|.
T Consensus        85 rELA~QiaEQF~alGk~l--------~lK~~vivGG~d~i~qa~~L~  123 (442)
T KOG0340|consen   85 RELALQIAEQFIALGKLL--------NLKVSVIVGGTDMIMQAAILS  123 (442)
T ss_pred             HHHHHHHHHHHHHhcccc--------cceEEEEEccHHHhhhhhhcc
Confidence            999999999999999876        688888999988777765553

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

Probab=99.87  E-value=3.9e-22  Score=174.23  Aligned_cols=119  Identities=30%  Similarity=0.390  Sum_probs=108.8

Q ss_pred             HHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC---CccEEEEec
Q 028887           69 LRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR---SAVQAVIVV  145 (202)
Q Consensus        69 ~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~---~~~~~Lil~  145 (202)
                      ..+|.+++|...+++++..+||..|||+|..+||..+-|+|++.||.||||||.+|++|+++++....   ...++|||+
T Consensus       180 ~~sF~~mNLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~  259 (691)
T KOG0338|consen  180 NESFQSMNLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKKVAATRVLVLV  259 (691)
T ss_pred             hhhHHhcccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCcccCcceeEEEEe
Confidence            55788889999999999999999999999999999999999999999999999999999999986433   346899999


Q ss_pred             CCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHHH
Q 028887          146 PTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKV  195 (202)
Q Consensus       146 Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~  195 (202)
                      |||||+.|++.+.++++...        .+.+..++||-+.+.|...|+.
T Consensus       260 PTRELaiQv~sV~~qlaqFt--------~I~~~L~vGGL~lk~QE~~LRs  301 (691)
T KOG0338|consen  260 PTRELAIQVHSVTKQLAQFT--------DITVGLAVGGLDLKAQEAVLRS  301 (691)
T ss_pred             ccHHHHHHHHHHHHHHHhhc--------cceeeeeecCccHHHHHHHHhh
Confidence            99999999999999999987        6899999999999999887764

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.87  E-value=2.3e-21  Score=172.88  Aligned_cols=117  Identities=33%  Similarity=0.439  Sum_probs=103.7

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHh
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTREL  150 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~L  150 (202)
                      .|.+.++++.+++++.++||..|||+|.++||.+++|+|++++||||||||++|++|+++.+......+++|||+||+||
T Consensus         5 ~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~PtreL   84 (460)
T PRK11776          5 AFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTREL   84 (460)
T ss_pred             ChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCHHH
Confidence            46667999999999999999999999999999999999999999999999999999999999876667799999999999


Q ss_pred             HHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          151 GMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       151 a~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      +.|+.+.++.++....       ++.+..++||.+...|.+.++
T Consensus        85 a~Q~~~~~~~~~~~~~-------~~~v~~~~Gg~~~~~~~~~l~  121 (460)
T PRK11776         85 ADQVAKEIRRLARFIP-------NIKVLTLCGGVPMGPQIDSLE  121 (460)
T ss_pred             HHHHHHHHHHHHhhCC-------CcEEEEEECCCChHHHHHHhc
Confidence            9999999999986532       367777888888877766554

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.87  E-value=3.1e-21  Score=176.20  Aligned_cols=116  Identities=28%  Similarity=0.378  Sum_probs=102.9

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC-------CccEEEE
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR-------SAVQAVI  143 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~-------~~~~~Li  143 (202)
                      +|.+.+|++.++++|.++||..||++|.++||.++.|+|+++++|||||||++|++|+++.+....       ..+++||
T Consensus        10 ~f~~l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raLI   89 (572)
T PRK04537         10 TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALI   89 (572)
T ss_pred             ChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEEE
Confidence            356669999999999999999999999999999999999999999999999999999999885421       2479999


Q ss_pred             ecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          144 VVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       144 l~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      |+||+||+.|+++.++.++...        ++++..++||.....|.++++
T Consensus        90 l~PTreLa~Qi~~~~~~l~~~~--------~i~v~~l~Gg~~~~~q~~~l~  132 (572)
T PRK04537         90 LAPTRELAIQIHKDAVKFGADL--------GLRFALVYGGVDYDKQRELLQ  132 (572)
T ss_pred             EeCcHHHHHHHHHHHHHHhccC--------CceEEEEECCCCHHHHHHHHh
Confidence            9999999999999999998765        578888888888888777664

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.86  E-value=3.4e-21  Score=171.78  Aligned_cols=115  Identities=29%  Similarity=0.429  Sum_probs=101.4

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC------CccEEEEe
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR------SAVQAVIV  144 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~------~~~~~Lil  144 (202)
                      .|.+.|+++.+++.+.++||..||++|.++||.++.|+|+++++|||||||++|++|+++.+....      ..+++|||
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil   81 (456)
T PRK10590          2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALIL   81 (456)
T ss_pred             CHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEE
Confidence            356679999999999999999999999999999999999999999999999999999999986432      24589999


Q ss_pred             cCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHH
Q 028887          145 VPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWL  193 (202)
Q Consensus       145 ~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l  193 (202)
                      +||+|||.|+.+.++.+....        .+.+..+++|.....|..++
T Consensus        82 ~PtreLa~Qi~~~~~~~~~~~--------~~~~~~~~gg~~~~~~~~~l  122 (456)
T PRK10590         82 TPTRELAAQIGENVRDYSKYL--------NIRSLVVFGGVSINPQMMKL  122 (456)
T ss_pred             eCcHHHHHHHHHHHHHHhccC--------CCEEEEEECCcCHHHHHHHH
Confidence            999999999999999998765        57788888888877765544

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.86  E-value=6.9e-21  Score=175.35  Aligned_cols=116  Identities=29%  Similarity=0.416  Sum_probs=103.2

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHh
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTREL  150 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~L  150 (202)
                      .|.+.+|++.+++++.++||..||++|.++||.++.|+|++++||||||||++|++|+++.+......+++|||+||++|
T Consensus         7 ~f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PTreL   86 (629)
T PRK11634          7 TFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTREL   86 (629)
T ss_pred             CHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCcHHH
Confidence            36666999999999999999999999999999999999999999999999999999999998776667899999999999


Q ss_pred             HHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHH
Q 028887          151 GMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWL  193 (202)
Q Consensus       151 a~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l  193 (202)
                      +.|+.+.++.+.....       ++.++.+++|.....|.+.+
T Consensus        87 a~Qv~~~l~~~~~~~~-------~i~v~~~~gG~~~~~q~~~l  122 (629)
T PRK11634         87 AVQVAEAMTDFSKHMR-------GVNVVALYGGQRYDVQLRAL  122 (629)
T ss_pred             HHHHHHHHHHHHhhcC-------CceEEEEECCcCHHHHHHHh
Confidence            9999999999886542       46788889998877665544

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=99.86  E-value=1e-21  Score=169.12  Aligned_cols=124  Identities=28%  Similarity=0.326  Sum_probs=103.7

Q ss_pred             hHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHh------cCCccEE
Q 028887           68 TLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNA------QRSAVQA  141 (202)
Q Consensus        68 ~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~------~~~~~~~  141 (202)
                      ....|++.|+++.+++++.+.||+.||-+|+.+||.++.|+|++..|.||||||.+|++|+++.+..      +..++.+
T Consensus        17 ~~ktFe~~gLD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa   96 (569)
T KOG0346|consen   17 KEKTFEEFGLDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSA   96 (569)
T ss_pred             hhccHHHhCCCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhccccccccee
Confidence            3366777799999999999999999999999999999999999999999999999999999998753      3357899


Q ss_pred             EEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHHHhc
Q 028887          142 VIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVLY  197 (202)
Q Consensus       142 Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~l~  197 (202)
                      +||+||||||.|++.++.++..+...      .++++-+....+......||-.+.
T Consensus        97 ~iLvPTkEL~qQvy~viekL~~~c~k------~lr~~nl~s~~sdsv~~~~L~d~p  146 (569)
T KOG0346|consen   97 VILVPTKELAQQVYKVIEKLVEYCSK------DLRAINLASSMSDSVNSVALMDLP  146 (569)
T ss_pred             EEEechHHHHHHHHHHHHHHHHHHHH------hhhhhhhhcccchHHHHHHHccCC
Confidence            99999999999999999888766532      366666666655555556665443

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

Probab=99.85  E-value=1e-20  Score=163.88  Aligned_cols=120  Identities=28%  Similarity=0.462  Sum_probs=102.0

Q ss_pred             hHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC-----CccEEE
Q 028887           68 TLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR-----SAVQAV  142 (202)
Q Consensus        68 ~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~-----~~~~~L  142 (202)
                      .|.+|.. .|.+++++++...||+.+||+|..+||.+++++|+++.++||||||+||++|+++.+.+..     ..+.+|
T Consensus         5 ~~~~l~~-~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgal   83 (567)
T KOG0345|consen    5 SFSSLAP-PLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGAL   83 (567)
T ss_pred             chhhcCC-CccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEE
Confidence            3444432 2669999999999999999999999999999999999999999999999999999995432     135799


Q ss_pred             EecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHHH
Q 028887          143 IVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKV  195 (202)
Q Consensus       143 il~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~  195 (202)
                      ||+|||||+.||.+++..|.....       ++...+++||....+..+.++.
T Consensus        84 IIsPTRELa~QI~~V~~~F~~~l~-------~l~~~l~vGG~~v~~Di~~fke  129 (567)
T KOG0345|consen   84 IISPTRELARQIREVAQPFLEHLP-------NLNCELLVGGRSVEEDIKTFKE  129 (567)
T ss_pred             EecCcHHHHHHHHHHHHHHHHhhh-------ccceEEEecCccHHHHHHHHHH
Confidence            999999999999999999988732       5788899999888887666554

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.84  E-value=3.7e-20  Score=165.83  Aligned_cols=116  Identities=27%  Similarity=0.375  Sum_probs=100.9

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC-------CccEEEE
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR-------SAVQAVI  143 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~-------~~~~~Li  143 (202)
                      .|...++++.++++|.+.||..||++|.++|+.+++|+|+++.++||||||++|++|+++.+....       ..+++||
T Consensus        88 ~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~aLi  167 (475)
T PRK01297         88 RFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALI  167 (475)
T ss_pred             CHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceEEE
Confidence            355569999999999999999999999999999999999999999999999999999999886542       1468999


Q ss_pred             ecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          144 VVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       144 l~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      |+||+||+.|+.+.++.+....        ++.+..++||.+...+.+.+.
T Consensus       168 l~PtreLa~Q~~~~~~~l~~~~--------~~~v~~~~gg~~~~~~~~~~~  210 (475)
T PRK01297        168 IAPTRELVVQIAKDAAALTKYT--------GLNVMTFVGGMDFDKQLKQLE  210 (475)
T ss_pred             EeCcHHHHHHHHHHHHHhhccC--------CCEEEEEEccCChHHHHHHHh
Confidence            9999999999999999998765        467777788877777665543

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

Probab=99.84  E-value=1.2e-20  Score=165.67  Aligned_cols=120  Identities=33%  Similarity=0.500  Sum_probs=99.6

Q ss_pred             hHHHHHhCCCCHHHHHHHH-HCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhc------CCccE
Q 028887           68 TLRELCQGHVPEHVLRRME-ETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ------RSAVQ  140 (202)
Q Consensus        68 ~~~~l~~~gl~~~l~~~l~-~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~------~~~~~  140 (202)
                      +-..|...|+++.+...|+ .+++..||.+|+++||.+++|+|++|.++||||||++|++|+++.+...      ..++-
T Consensus       134 ts~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~  213 (708)
T KOG0348|consen  134 TSAAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPY  213 (708)
T ss_pred             ccccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccccccCCce
Confidence            3445667799999999994 5799999999999999999999999999999999999999999998653      35788


Q ss_pred             EEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCC-ccHHHHHHHHH
Q 028887          141 AVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGG-MLRRHKSWLKV  195 (202)
Q Consensus       141 ~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~-~~~~~~~~l~~  195 (202)
                      ||||+||||||.|+++.+.++....        -..|.|++-|+ ....++..|++
T Consensus       214 ALVivPTREL~~Q~y~~~qKLl~~~--------hWIVPg~lmGGEkkKSEKARLRK  261 (708)
T KOG0348|consen  214 ALVIVPTRELALQIYETVQKLLKPF--------HWIVPGVLMGGEKKKSEKARLRK  261 (708)
T ss_pred             EEEEechHHHHHHHHHHHHHHhcCc--------eEEeeceeecccccccHHHHHhc
Confidence            9999999999999999999998865        45666655554 44444555543

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.84  E-value=3.8e-20  Score=163.80  Aligned_cols=116  Identities=31%  Similarity=0.459  Sum_probs=101.1

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhc----CCccEEEEecC
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ----RSAVQAVIVVP  146 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~----~~~~~~Lil~P  146 (202)
                      +|++.++++.+++.+.++||..|+++|.++|+.++.|+|+++++|||+|||++|++|+++.+...    ...+++|||+|
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~P   81 (434)
T PRK11192          2 TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTP   81 (434)
T ss_pred             CHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEECC
Confidence            46777999999999999999999999999999999999999999999999999999999988532    22468999999


Q ss_pred             CHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          147 TRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       147 tr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      |+||+.|+.+++..++...        ++.+..++||.....+..++.
T Consensus        82 t~eLa~Q~~~~~~~l~~~~--------~~~v~~~~gg~~~~~~~~~l~  121 (434)
T PRK11192         82 TRELAMQVADQARELAKHT--------HLDIATITGGVAYMNHAEVFS  121 (434)
T ss_pred             cHHHHHHHHHHHHHHHccC--------CcEEEEEECCCCHHHHHHHhc
Confidence            9999999999999998775        467777777777777665543

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

Probab=99.84  E-value=2.4e-21  Score=159.13  Aligned_cols=123  Identities=28%  Similarity=0.408  Sum_probs=114.2

Q ss_pred             CCcchHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEE
Q 028887           64 NNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVI  143 (202)
Q Consensus        64 ~~~~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Li  143 (202)
                      ........|.++|+.+++++++.+.||++|+.+|+.||+.|+.|+|+++++.+|+|||.+|-+.+++.++-+.+..++||
T Consensus        21 ~~~~v~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~li  100 (400)
T KOG0328|consen   21 EKVKVIPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDISVRETQALI  100 (400)
T ss_pred             cCcccccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccccceeeEEE
Confidence            34456778888999999999999999999999999999999999999999999999999999999999988888889999


Q ss_pred             ecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          144 VVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       144 l~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      |+||||||.|+.+++..++++.        ++.+-+|+||.+..+..+.+.
T Consensus       101 lsPTRELa~Qi~~vi~alg~~m--------nvq~hacigg~n~gedikkld  143 (400)
T KOG0328|consen  101 LSPTRELAVQIQKVILALGDYM--------NVQCHACIGGKNLGEDIKKLD  143 (400)
T ss_pred             ecChHHHHHHHHHHHHHhcccc--------cceEEEEecCCccchhhhhhc
Confidence            9999999999999999999987        789999999999888877765

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=99.83  E-value=1.3e-20  Score=175.42  Aligned_cols=123  Identities=32%  Similarity=0.442  Sum_probs=113.8

Q ss_pred             cchHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhc-----CCccE
Q 028887           66 SLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ-----RSAVQ  140 (202)
Q Consensus        66 ~~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~-----~~~~~  140 (202)
                      ..++..|.+.|+...++..++++||.+|++||.+|||.|+.|+|+|.+|.||||||++|++|++.++...     ..+|.
T Consensus       361 pkpv~sW~q~gl~~~il~tlkkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi  440 (997)
T KOG0334|consen  361 PKPVTSWTQCGLSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPI  440 (997)
T ss_pred             CcccchHhhCCchHHHHHHHHHhcCCCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCChhhCCCce
Confidence            4688899999999999999999999999999999999999999999999999999999999999877533     24899


Q ss_pred             EEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHHHh
Q 028887          141 AVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVL  196 (202)
Q Consensus       141 ~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~l  196 (202)
                      +|||+|||||+.||++.++.|+...        +++++++|||.....|+..++..
T Consensus       441 ~li~aPtrela~QI~r~~~kf~k~l--------~ir~v~vygg~~~~~qiaelkRg  488 (997)
T KOG0334|consen  441 ALILAPTRELAMQIHREVRKFLKLL--------GIRVVCVYGGSGISQQIAELKRG  488 (997)
T ss_pred             EEEEcCCHHHHHHHHHHHHHHHhhc--------CceEEEecCCccHHHHHHHHhcC
Confidence            9999999999999999999999875        79999999999999999998865

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

Probab=99.83  E-value=2.9e-20  Score=161.79  Aligned_cols=125  Identities=27%  Similarity=0.403  Sum_probs=111.3

Q ss_pred             CCcchHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC----Ccc
Q 028887           64 NNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR----SAV  139 (202)
Q Consensus        64 ~~~~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~----~~~  139 (202)
                      .+..+-..|++..|++..+++++++||+.+|++|+.+|++++.|+|+++.|.||||||++|++|.++.+...+    .+.
T Consensus        76 ~s~~~~~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~  155 (543)
T KOG0342|consen   76 DSITTTFRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGT  155 (543)
T ss_pred             cchhhhhHhhccccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCCCCCe
Confidence            3456677788889999999999999999999999999999999999999999999999999999999987643    467


Q ss_pred             EEEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHHH
Q 028887          140 QAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKV  195 (202)
Q Consensus       140 ~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~  195 (202)
                      .++|++||||||.|++.+++++..+..       .+.+..++||.+.....+.+..
T Consensus       156 ~vlIi~PTRELA~Q~~~eak~Ll~~h~-------~~~v~~viGG~~~~~e~~kl~k  204 (543)
T KOG0342|consen  156 GVLIICPTRELAMQIFAEAKELLKYHE-------SITVGIVIGGNNFSVEADKLVK  204 (543)
T ss_pred             eEEEecccHHHHHHHHHHHHHHHhhCC-------CcceEEEeCCccchHHHHHhhc
Confidence            899999999999999999999998864       4788889999988877776654

>PTZ00424 helicase 45; Provisional

Probab=99.82  E-value=2.1e-19  Score=157.06  Aligned_cols=115  Identities=29%  Similarity=0.425  Sum_probs=99.3

Q ss_pred             hHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCC
Q 028887           68 TLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPT  147 (202)
Q Consensus        68 ~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Pt  147 (202)
                      ....|.+.|+++.+.+++.+.||..|+++|.++|+.+++|+|+++++|||||||++|++|+++.+.......++|||+|+
T Consensus        26 ~~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~Pt  105 (401)
T PTZ00424         26 IVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPT  105 (401)
T ss_pred             ccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECCC
Confidence            45677778999999999999999999999999999999999999999999999999999999988765556789999999


Q ss_pred             HHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHH
Q 028887          148 RELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHK  190 (202)
Q Consensus       148 r~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~  190 (202)
                      ++|+.|+.+.++.++...        .+.+..+++|.....+.
T Consensus       106 ~~L~~Q~~~~~~~~~~~~--------~~~~~~~~g~~~~~~~~  140 (401)
T PTZ00424        106 RELAQQIQKVVLALGDYL--------KVRCHACVGGTVVRDDI  140 (401)
T ss_pred             HHHHHHHHHHHHHHhhhc--------CceEEEEECCcCHHHHH
Confidence            999999999999998654        34555566666555443

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=99.82  E-value=2.6e-20  Score=163.99  Aligned_cols=125  Identities=28%  Similarity=0.410  Sum_probs=111.9

Q ss_pred             CCcchHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcC-CcEEEeccCCCchHHHHHHHHHHHHHhc-------
Q 028887           64 NNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSS-RDCILHAQTGSGKTLTYLLLIFSLVNAQ-------  135 (202)
Q Consensus        64 ~~~~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g-~~~l~~a~TGsGKT~~~l~~~l~~l~~~-------  135 (202)
                      .....+.+|...+++..++++|..+||..||++|..+||++..| .|++..|.||||||+||-+||++.+...       
T Consensus       175 ~~~~DvsAW~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~  254 (731)
T KOG0347|consen  175 SSKVDVSAWKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQEL  254 (731)
T ss_pred             ccccChHHHhcCCCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhh
Confidence            35567888988899999999999999999999999999999998 8999999999999999999999955321       


Q ss_pred             ----CCccE--EEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHHHh
Q 028887          136 ----RSAVQ--AVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVL  196 (202)
Q Consensus       136 ----~~~~~--~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~l  196 (202)
                          ..+++  +||++||||||.|+.+.+..++..+        ++++..++||-..++|.+.|+..
T Consensus       255 ~~~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t--------~i~v~si~GGLavqKQqRlL~~~  313 (731)
T KOG0347|consen  255 SNTSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKT--------QIRVASITGGLAVQKQQRLLNQR  313 (731)
T ss_pred             hhHHhccCcceeEEecChHHHHHHHHHHHHHhcccc--------CeEEEEeechhHHHHHHHHHhcC
Confidence                23455  9999999999999999999999987        79999999999999999888763

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

Probab=99.81  E-value=6e-21  Score=159.03  Aligned_cols=113  Identities=30%  Similarity=0.513  Sum_probs=105.3

Q ss_pred             HHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCH
Q 028887           69 LRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTR  148 (202)
Q Consensus        69 ~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr  148 (202)
                      =..|++.++.++++..+.+.||+.|+|+|.++||.++.|+|+++.|..|+|||-+|++|+++.++..+...+++|++|||
T Consensus        84 G~efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPtr  163 (459)
T KOG0326|consen   84 GNEFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPTR  163 (459)
T ss_pred             CccHHHhhhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCccccceeEEEEeecc
Confidence            34566669999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHH
Q 028887          149 ELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRH  189 (202)
Q Consensus       149 ~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~  189 (202)
                      |||.|+.+.++++++..        ++.+....||.++++.
T Consensus       164 elALQtSqvc~~lskh~--------~i~vmvttGGT~lrDD  196 (459)
T KOG0326|consen  164 ELALQTSQVCKELSKHL--------GIKVMVTTGGTSLRDD  196 (459)
T ss_pred             hhhHHHHHHHHHHhccc--------CeEEEEecCCcccccc
Confidence            99999999999999987        6888888888888765

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=99.81  E-value=6.2e-20  Score=161.78  Aligned_cols=122  Identities=25%  Similarity=0.429  Sum_probs=109.6

Q ss_pred             CcchHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC----CccE
Q 028887           65 NSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR----SAVQ  140 (202)
Q Consensus        65 ~~~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~----~~~~  140 (202)
                      ...++..|.+..|....+++|.+.+|..||.+|+.+||..+.|+|++..|.||||||++|++|+++.+.+.+    .+.-
T Consensus        64 ~~~~~~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlG  143 (758)
T KOG0343|consen   64 DSTTIKKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLG  143 (758)
T ss_pred             hhhhhhhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCCCCCCce
Confidence            356778899999999999999999999999999999999999999999999999999999999999998643    5788


Q ss_pred             EEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          141 AVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       141 ~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      ||||+||||||.|+++++++.+.+.        .+..-.++||.+...+.+.+.
T Consensus       144 alIISPTRELA~QtFevL~kvgk~h--------~fSaGLiiGG~~~k~E~eRi~  189 (758)
T KOG0343|consen  144 ALIISPTRELALQTFEVLNKVGKHH--------DFSAGLIIGGKDVKFELERIS  189 (758)
T ss_pred             eEEecchHHHHHHHHHHHHHHhhcc--------ccccceeecCchhHHHHHhhh
Confidence            9999999999999999999999987        577778888888766655544

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

Probab=99.79  E-value=1.1e-18  Score=163.54  Aligned_cols=108  Identities=23%  Similarity=0.366  Sum_probs=93.4

Q ss_pred             CCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHH
Q 028887           76 HVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVT  155 (202)
Q Consensus        76 gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~  155 (202)
                      .+++.+.+.+.+.||..||++|.++|+.++.|+|+++.+|||||||++|++|+++.+..+ ...++|||+|||||+.|+.
T Consensus        20 ~l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~-~~~~aL~l~PtraLa~q~~   98 (742)
T TIGR03817        20 WAHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADD-PRATALYLAPTKALAADQL   98 (742)
T ss_pred             cCCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhC-CCcEEEEEcChHHHHHHHH
Confidence            488999999999999999999999999999999999999999999999999999998753 4569999999999999999


Q ss_pred             HHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          156 KVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       156 ~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      +.+++++..         +++ +.+++|.....++++++
T Consensus        99 ~~l~~l~~~---------~i~-v~~~~Gdt~~~~r~~i~  127 (742)
T TIGR03817        99 RAVRELTLR---------GVR-PATYDGDTPTEERRWAR  127 (742)
T ss_pred             HHHHHhccC---------CeE-EEEEeCCCCHHHHHHHh
Confidence            999999721         234 46677766666666554

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.

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

Probab=99.79  E-value=3.1e-19  Score=156.20  Aligned_cols=122  Identities=30%  Similarity=0.364  Sum_probs=111.9

Q ss_pred             CcchHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhc-----CCcc
Q 028887           65 NSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ-----RSAV  139 (202)
Q Consensus        65 ~~~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~-----~~~~  139 (202)
                      ...++..|+.-|+.+.|..++++..|+.||++|.+++|..+.|+|++..|.||||||-+|+.|++.+++..     +.+|
T Consensus       218 ~~rpvtsfeh~gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL~~g~gP  297 (731)
T KOG0339|consen  218 PPRPVTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKPGEGP  297 (731)
T ss_pred             CCCCcchhhhcCchHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhhcCCCCC
Confidence            44566677777999999999999999999999999999999999999999999999999999999888643     3578


Q ss_pred             EEEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          140 QAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       140 ~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      .++|+|||||||.|++.++++|++..        +++++++|||++..+|.+.|+
T Consensus       298 i~vilvPTrela~Qi~~eaKkf~K~y--------gl~~v~~ygGgsk~eQ~k~Lk  344 (731)
T KOG0339|consen  298 IGVILVPTRELASQIFSEAKKFGKAY--------GLRVVAVYGGGSKWEQSKELK  344 (731)
T ss_pred             eEEEEeccHHHHHHHHHHHHHhhhhc--------cceEEEeecCCcHHHHHHhhh
Confidence            99999999999999999999999877        799999999999999999887

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

Probab=99.79  E-value=1.2e-19  Score=159.02  Aligned_cols=121  Identities=27%  Similarity=0.388  Sum_probs=108.2

Q ss_pred             chHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC----------
Q 028887           67 LTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR----------  136 (202)
Q Consensus        67 ~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~----------  136 (202)
                      ..+..|.+..+.+.+..++...||..|||+|+.+||.+..|+|+++||+||||||.+|++|++..+...+          
T Consensus        71 ~~i~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~  150 (482)
T KOG0335|consen   71 PHIPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGG  150 (482)
T ss_pred             CCcccccccchhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccCCC
Confidence            4566888888999999999999999999999999999999999999999999999999999999987543          


Q ss_pred             CccEEEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHHH
Q 028887          137 SAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKV  195 (202)
Q Consensus       137 ~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~  195 (202)
                      .+|++|||+|||||+.|++++.+++....        .+..+.+|+|.+...|.+.++.
T Consensus       151 ~~P~~lIlapTReL~~Qi~nea~k~~~~s--------~~~~~~~ygg~~~~~q~~~~~~  201 (482)
T KOG0335|consen  151 VYPRALILAPTRELVDQIYNEARKFSYLS--------GMKSVVVYGGTDLGAQLRFIKR  201 (482)
T ss_pred             CCCceEEEeCcHHHhhHHHHHHHhhcccc--------cceeeeeeCCcchhhhhhhhcc
Confidence            36899999999999999999999998876        6888999999888888766554

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

Probab=99.78  E-value=1.1e-18  Score=153.20  Aligned_cols=122  Identities=28%  Similarity=0.391  Sum_probs=110.3

Q ss_pred             CcchHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhc---------
Q 028887           65 NSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ---------  135 (202)
Q Consensus        65 ~~~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~---------  135 (202)
                      -..+++.|++.|++.++++.+.+.||..|+|+|.++||..+..+|+|..+.||||||.+|++|++..+..-         
T Consensus       240 lpnplrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~~~~en~  319 (673)
T KOG0333|consen  240 LPNPLRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMARLENN  319 (673)
T ss_pred             CCccccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccCCccccchhhHHHHHHcCCCcchhhhc
Confidence            34689999999999999999999999999999999999999999999999999999999999999877532         


Q ss_pred             CCccEEEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          136 RSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       136 ~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      -.++.++||.|||+|+.||.+.-.+|+...        +++++.++||.+..+|--.+.
T Consensus       320 ~~gpyaiilaptReLaqqIeeEt~kf~~~l--------g~r~vsvigg~s~EEq~fqls  370 (673)
T KOG0333|consen  320 IEGPYAIILAPTRELAQQIEEETNKFGKPL--------GIRTVSVIGGLSFEEQGFQLS  370 (673)
T ss_pred             ccCceeeeechHHHHHHHHHHHHHHhcccc--------cceEEEEecccchhhhhhhhh
Confidence            247899999999999999999999999887        699999999999998844443

>cd00268 DEADc DEAD-box helicases

Probab=99.77  E-value=1.4e-17  Score=132.65  Aligned_cols=110  Identities=35%  Similarity=0.535  Sum_probs=94.5

Q ss_pred             HhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhc--CCccEEEEecCCHHh
Q 028887           73 CQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ--RSAVQAVIVVPTREL  150 (202)
Q Consensus        73 ~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~--~~~~~~Lil~Ptr~L  150 (202)
                      .+.++++.+.+.+.+.|++.|++.|.++++.+.+|+++++.+|||+|||++|++|+++.+...  ..+++++|++|+++|
T Consensus         2 ~~~~~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~L   81 (203)
T cd00268           2 EELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTREL   81 (203)
T ss_pred             CcCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHHH
Confidence            456899999999999999999999999999999999999999999999999999999998876  456799999999999


Q ss_pred             HHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHH
Q 028887          151 GMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHK  190 (202)
Q Consensus       151 a~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~  190 (202)
                      +.|+.+.++.+....        ++.+..+.++....+..
T Consensus        82 ~~q~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~  113 (203)
T cd00268          82 ALQIAEVARKLGKHT--------NLKVVVIYGGTSIDKQI  113 (203)
T ss_pred             HHHHHHHHHHHhccC--------CceEEEEECCCCHHHHH
Confidence            999999999988653        35555555555544433

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

Probab=99.76  E-value=5.8e-19  Score=149.85  Aligned_cols=122  Identities=30%  Similarity=0.420  Sum_probs=112.2

Q ss_pred             chHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecC
Q 028887           67 LTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP  146 (202)
Q Consensus        67 ~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~P  146 (202)
                      ..+.+|++++|.++|++.+...||++|+.+|++||.++..|.|+++++.+|+|||.+|++++++.++-.....+||+++|
T Consensus        23 evvdsfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~ke~qalilaP  102 (397)
T KOG0327|consen   23 EVVDSFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILAP  102 (397)
T ss_pred             HHhhhhhhcCCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcchHHHHHHHhcc
Confidence            46678999999999999999999999999999999999999999999999999999999999999987777889999999


Q ss_pred             CHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHHHh
Q 028887          147 TRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVL  196 (202)
Q Consensus       147 tr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~l  196 (202)
                      +||||.|+.++...++...        +..+..++||.....+...++..
T Consensus       103 treLa~qi~~v~~~lg~~~--------~~~v~~~igg~~~~~~~~~i~~~  144 (397)
T KOG0327|consen  103 TRELAQQIQKVVRALGDHM--------DVSVHACIGGTNVRREDQALLKD  144 (397)
T ss_pred             hHHHHHHHHHHHHhhhccc--------ceeeeeecCcccchhhhhhhhcc
Confidence            9999999999999999886        67888899999988777666654

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

Probab=99.75  E-value=1.8e-18  Score=148.46  Aligned_cols=115  Identities=30%  Similarity=0.476  Sum_probs=104.6

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC-CccEEEEecCCHH
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR-SAVQAVIVVPTRE  149 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~-~~~~~Lil~Ptr~  149 (202)
                      .|..+||...+++++.+.||..|||+|+..||.++.|+|++..+.||||||.+|++|+++.+.... .+.++++++||||
T Consensus        22 ~fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s~~g~Ralilsptre  101 (529)
T KOG0337|consen   22 GFQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHSQTGLRALILSPTRE  101 (529)
T ss_pred             CccccCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhccccccceeeccCcHH
Confidence            345559999999999999999999999999999999999999999999999999999999987644 4679999999999


Q ss_pred             hHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHH
Q 028887          150 LGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWL  193 (202)
Q Consensus       150 La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l  193 (202)
                      |+.|+.++++.++...        .++..+++||..+.+|-..|
T Consensus       102 La~qtlkvvkdlgrgt--------~lr~s~~~ggD~~eeqf~~l  137 (529)
T KOG0337|consen  102 LALQTLKVVKDLGRGT--------KLRQSLLVGGDSIEEQFILL  137 (529)
T ss_pred             HHHHHHHHHHHhcccc--------chhhhhhcccchHHHHHHHh
Confidence            9999999999999987        57888899999999886555

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

Probab=99.73  E-value=3.5e-18  Score=146.56  Aligned_cols=158  Identities=27%  Similarity=0.378  Sum_probs=117.4

Q ss_pred             ccccccccCCCCCCchHHHHHhccC-CCCHHHHHcc----cCCCcchHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHH
Q 028887           27 IDFTNRAFLPVSISLKPLRAVLSSS-AVSTEELAAG----TGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREAL  101 (202)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~~~----~~~~~~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i  101 (202)
                      ..|..++......+...+......+ .+..+++.++    .+.+..+|.+-  .+-.+++++.+.+.||.+|||+|.++|
T Consensus       174 knfYke~~e~s~ls~~q~~~~r~en~~it~dd~K~gekrpIPnP~ctFddA--Fq~~pevmenIkK~GFqKPtPIqSQaW  251 (629)
T KOG0336|consen  174 KNFYKESNETSNLSKEQLQEWRKENFNITCDDLKEGEKRPIPNPVCTFDDA--FQCYPEVMENIKKTGFQKPTPIQSQAW  251 (629)
T ss_pred             hhhhhcCchhccCCHHHHHHHHHcCCcEEecccccCCcccCCCCcCcHHHH--HhhhHHHHHHHHhccCCCCCcchhccc
Confidence            3444444444444444444444332 2333333221    23333444331  256789999999999999999999999


Q ss_pred             HhHHcCCcEEEeccCCCchHHHHHHHHHHHHHh------cCCccEEEEecCCHHhHHHHHHHHHHhhcCCCCcccccccc
Q 028887          102 PVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNA------QRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLC  175 (202)
Q Consensus       102 ~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~------~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~  175 (202)
                      |.+++|.|++..|.||+|||++||+|-+.++..      ...++.+|++.|||||+.|+.-+.+++..+         +.
T Consensus       252 PI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~ptreLalqie~e~~kysyn---------g~  322 (629)
T KOG0336|consen  252 PILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTRELALQIEGEVKKYSYN---------GL  322 (629)
T ss_pred             ceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhccCCCceEEEeccHHHHHHHHhHHhHhhhc---------Cc
Confidence            999999999999999999999999998766542      345789999999999999999888888765         57


Q ss_pred             eEEEEEeCCccHHHHHHHHH
Q 028887          176 TVMALLDGGMLRRHKSWLKV  195 (202)
Q Consensus       176 ~~~~~~~g~~~~~~~~~l~~  195 (202)
                      +.+|+|||++..+|.+.++.
T Consensus       323 ksvc~ygggnR~eqie~lkr  342 (629)
T KOG0336|consen  323 KSVCVYGGGNRNEQIEDLKR  342 (629)
T ss_pred             ceEEEecCCCchhHHHHHhc
Confidence            78999999999999888764

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

Probab=99.73  E-value=5.8e-18  Score=137.70  Aligned_cols=126  Identities=21%  Similarity=0.377  Sum_probs=114.1

Q ss_pred             CCCcchHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEE
Q 028887           63 GNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAV  142 (202)
Q Consensus        63 ~~~~~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~L  142 (202)
                      +..+.-|++|   -+.|++++++-++||++|+++|.+|||...-|.|++++|.+|-|||.+|+++.+++++.-...+.+|
T Consensus        38 ~ihssgfrdf---llkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv~g~vsvl  114 (387)
T KOG0329|consen   38 SIHSSGFRDF---LLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVL  114 (387)
T ss_pred             EEeccchhhh---hcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCCCCeEEEE
Confidence            3455667777   6889999999999999999999999999999999999999999999999999999999887888999


Q ss_pred             EecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHHHhcC
Q 028887          143 IVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVLYS  198 (202)
Q Consensus       143 il~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~l~~  198 (202)
                      ++|.|||||.|+.+.+.++..+.+       ..++...+||..++++.+.|+...+
T Consensus       115 vmchtrelafqi~~ey~rfskymP-------~vkvaVFfGG~~Ikkdee~lk~~Ph  163 (387)
T KOG0329|consen  115 VMCHTRELAFQISKEYERFSKYMP-------SVKVSVFFGGLFIKKDEELLKNCPH  163 (387)
T ss_pred             EEeccHHHHHHHHHHHHHHHhhCC-------CceEEEEEcceeccccHHHHhCCCe
Confidence            999999999999999999999876       4788999999999998888876543

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

Probab=99.72  E-value=2.5e-18  Score=146.66  Aligned_cols=129  Identities=26%  Similarity=0.394  Sum_probs=109.9

Q ss_pred             CCcchHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHh--------c
Q 028887           64 NNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNA--------Q  135 (202)
Q Consensus        64 ~~~~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~--------~  135 (202)
                      .-+.++++|.++.++..+++.+.+.|+.+|||+|-+.+|.+++|+|.+..|-||||||++|.+|++-....        .
T Consensus       164 ~ipPPIksF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~  243 (610)
T KOG0341|consen  164 DIPPPIKSFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFAR  243 (610)
T ss_pred             CCCCchhhhhhccCCHHHHHHHHhcCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCcccc
Confidence            45578999999999999999999999999999999999999999999999999999999999999765432        2


Q ss_pred             CCccEEEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          136 RSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       136 ~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      ..+|-.||+||+||||.|+++.+..++........+  .++...|+||..+..|.+-.+
T Consensus       244 ~EGP~gLiicPSRELArQt~~iie~~~~~L~e~g~P--~lRs~LciGG~~v~eql~~v~  300 (610)
T KOG0341|consen  244 GEGPYGLIICPSRELARQTHDIIEQYVAALQEAGYP--ELRSLLCIGGVPVREQLDVVR  300 (610)
T ss_pred             CCCCeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCCh--hhhhhhhhcCccHHHHHHHHh
Confidence            357899999999999999999988887643322222  577788999999999876654

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

Probab=99.71  E-value=1.3e-17  Score=141.50  Aligned_cols=105  Identities=24%  Similarity=0.402  Sum_probs=98.2

Q ss_pred             ccCCCcchHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcC--CcEEEeccCCCchHHHHHHHHHHHHHhcCCc
Q 028887           61 GTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSS--RDCILHAQTGSGKTLTYLLLIFSLVNAQRSA  138 (202)
Q Consensus        61 ~~~~~~~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g--~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~  138 (202)
                      ++..+..+.++|++++|.|++++++..++|.+|+.+|..++|.++..  +++|.++.+|+|||.+|.+.|+.+++.....
T Consensus        81 dpnsPlyS~ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~~~~  160 (477)
T KOG0332|consen   81 DPNSPLYSAKSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPDVVV  160 (477)
T ss_pred             CCCCCccccccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCccccC
Confidence            44556678999999999999999999999999999999999999875  7899999999999999999999999988889


Q ss_pred             cEEEEecCCHHhHHHHHHHHHHhhcCC
Q 028887          139 VQAVIVVPTRELGMQVTKVARVLAAKP  165 (202)
Q Consensus       139 ~~~Lil~Ptr~La~Q~~~~~~~l~~~~  165 (202)
                      |+++.|+||||||.|+.+++.++++..
T Consensus       161 PQ~iCLaPtrELA~Q~~eVv~eMGKf~  187 (477)
T KOG0332|consen  161 PQCICLAPTRELAPQTGEVVEEMGKFT  187 (477)
T ss_pred             CCceeeCchHHHHHHHHHHHHHhcCce
Confidence            999999999999999999999999876

>PRK02362 ski2-like helicase; Provisional

Probab=99.69  E-value=1.9e-16  Score=148.74  Aligned_cols=89  Identities=24%  Similarity=0.279  Sum_probs=82.0

Q ss_pred             HHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHh-HHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHh
Q 028887           72 LCQGHVPEHVLRRMEETGYVLPTDIQREALPV-LFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTREL  150 (202)
Q Consensus        72 l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~-i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~L  150 (202)
                      |++.++++.+++.+.+.||.+|+|+|.+|++. +..|+|+++++|||||||++|.+|+++.+..+.   +++|++|+++|
T Consensus         3 ~~~l~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~~~---kal~i~P~raL   79 (737)
T PRK02362          3 IAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIARGG---KALYIVPLRAL   79 (737)
T ss_pred             hhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhcCC---cEEEEeChHHH
Confidence            45669999999999999999999999999998 778999999999999999999999999987555   89999999999


Q ss_pred             HHHHHHHHHHhhc
Q 028887          151 GMQVTKVARVLAA  163 (202)
Q Consensus       151 a~Q~~~~~~~l~~  163 (202)
                      +.|+++.++++..
T Consensus        80 a~q~~~~~~~~~~   92 (737)
T PRK02362         80 ASEKFEEFERFEE   92 (737)
T ss_pred             HHHHHHHHHHhhc
Confidence            9999999998753

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

Probab=99.65  E-value=2.6e-16  Score=137.65  Aligned_cols=105  Identities=30%  Similarity=0.399  Sum_probs=85.8

Q ss_pred             HHHHHHCCCCCCcHHHHHHHHhHH---------cCCcEEEeccCCCchHHHHHHHHHHHHHhc-CCccEEEEecCCHHhH
Q 028887           82 LRRMEETGYVLPTDIQREALPVLF---------SSRDCILHAQTGSGKTLTYLLLIFSLVNAQ-RSAVQAVIVVPTRELG  151 (202)
Q Consensus        82 ~~~l~~~g~~~~t~~Q~~~i~~i~---------~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~-~~~~~~Lil~Ptr~La  151 (202)
                      .+.+..+++....|+|..++|.++         .++|++|.||||||||++|.+||++.+... -+..+|+|++||++|+
T Consensus       149 ~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v~~LRavVivPtr~L~  228 (620)
T KOG0350|consen  149 DQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTRELA  228 (620)
T ss_pred             HHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHHHccCCccceEEEEEeeHHHHH
Confidence            344788999999999999999874         257999999999999999999999998765 3457999999999999


Q ss_pred             HHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          152 MQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       152 ~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      .|+++.|.+++...        ++.|....|-.+...+.+.|.
T Consensus       229 ~QV~~~f~~~~~~t--------gL~V~~~sgq~sl~~E~~qL~  263 (620)
T KOG0350|consen  229 LQVYDTFKRLNSGT--------GLAVCSLSGQNSLEDEARQLA  263 (620)
T ss_pred             HHHHHHHHHhccCC--------ceEEEecccccchHHHHHHHh
Confidence            99999999999987        566544444455555555443

>KOG4284 consensus DEAD box protein [Transcription]

Probab=99.65  E-value=8e-17  Score=144.44  Aligned_cols=120  Identities=30%  Similarity=0.434  Sum_probs=106.6

Q ss_pred             HHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHH
Q 028887           70 RELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRE  149 (202)
Q Consensus        70 ~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~  149 (202)
                      ..|+++-+...++..|++.+|..||++|..|||.++.+.|+|+++.+|+|||++|.+.+++.+......++++|++||||
T Consensus        25 ~~fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~PTRE  104 (980)
T KOG4284|consen   25 PGFEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTPTRE  104 (980)
T ss_pred             CCHHHHHHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcccCcceeEEEecchh
Confidence            34455578899999999999999999999999999999999999999999999999999999988888899999999999


Q ss_pred             hHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHHHh
Q 028887          150 LGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVL  196 (202)
Q Consensus       150 La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~l  196 (202)
                      +|.|+.+.+..++....       ++++-..+||+.....+..|+..
T Consensus       105 iaVQI~~tv~~v~~sf~-------g~~csvfIGGT~~~~d~~rlk~~  144 (980)
T KOG4284|consen  105 IAVQIKETVRKVAPSFT-------GARCSVFIGGTAHKLDLIRLKQT  144 (980)
T ss_pred             hhhHHHHHHHHhccccc-------CcceEEEecCchhhhhhhhhhhc
Confidence            99999999999998653       57888889998887777666653

>PRK00254 ski2-like helicase; Provisional

Probab=99.64  E-value=2.1e-15  Score=141.44  Aligned_cols=89  Identities=24%  Similarity=0.265  Sum_probs=80.4

Q ss_pred             HHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHh-HHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHh
Q 028887           72 LCQGHVPEHVLRRMEETGYVLPTDIQREALPV-LFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTREL  150 (202)
Q Consensus        72 l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~-i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~L  150 (202)
                      |.+.++++.+.+.+.+.||.+|+++|.++++. ++.|+|+++++|||||||++|.+|+++.+...  +.++|||+|+++|
T Consensus         3 ~~~l~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~--~~~~l~l~P~~aL   80 (720)
T PRK00254          3 VDELRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLRE--GGKAVYLVPLKAL   80 (720)
T ss_pred             HHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhc--CCeEEEEeChHHH
Confidence            45668999999999999999999999999986 78999999999999999999999999987642  3489999999999


Q ss_pred             HHHHHHHHHHhh
Q 028887          151 GMQVTKVARVLA  162 (202)
Q Consensus       151 a~Q~~~~~~~l~  162 (202)
                      +.|+++.++.+.
T Consensus        81 a~q~~~~~~~~~   92 (720)
T PRK00254         81 AEEKYREFKDWE   92 (720)
T ss_pred             HHHHHHHHHHHh
Confidence            999999998764

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

Probab=99.64  E-value=3.5e-16  Score=148.05  Aligned_cols=124  Identities=28%  Similarity=0.345  Sum_probs=96.1

Q ss_pred             CHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHH
Q 028887           78 PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKV  157 (202)
Q Consensus        78 ~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~  157 (202)
                      ...+..++.+.|+..++.+|.+|+..+.+|++++|.++||||||++|++||++.+.++... +||+|.||++||+++.++
T Consensus        56 ~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a-~AL~lYPtnALa~DQ~~r  134 (851)
T COG1205          56 DESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSA-RALLLYPTNALANDQAER  134 (851)
T ss_pred             hhHHHHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcCc-cEEEEechhhhHhhHHHH
Confidence            3345677778899999999999999999999999999999999999999999999877655 789999999999999999


Q ss_pred             HHHhhcCCC----------Cccc----------ccccceEEEEEeCCccHHHHHHHHHhcCCCCC
Q 028887          158 ARVLAAKPL----------DTDL----------EHKLCTVMALLDGGMLRRHKSWLKVLYSLTSY  202 (202)
Q Consensus       158 ~~~l~~~~~----------~~~~----------~~~~~~~~~~~~g~~~~~~~~~l~~l~~~~~~  202 (202)
                      ++++....+          |...          +..-+++..|+|-..++.+.+|++.+++|+||
T Consensus       135 l~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~l  199 (851)
T COG1205         135 LRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYL  199 (851)
T ss_pred             HHHHHHhCCCcceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEE
Confidence            999988654          1110          00133444444444455555677777776654

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

Probab=99.61  E-value=3.9e-15  Score=138.84  Aligned_cols=107  Identities=21%  Similarity=0.240  Sum_probs=92.5

Q ss_pred             CCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhc-----CCccEEEEecCCHHh
Q 028887           76 HVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ-----RSAVQAVIVVPTREL  150 (202)
Q Consensus        76 gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~-----~~~~~~Lil~Ptr~L  150 (202)
                      -+++.+.+.+.+. |..||+.|.++||.+..|+++++.||||||||++.++|++..+...     ..++.+||++|.|+|
T Consensus         7 ~l~~~v~~~~~~~-~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkAL   85 (814)
T COG1201           7 ILDPRVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKAL   85 (814)
T ss_pred             hcCHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHH
Confidence            3778888888877 9999999999999999999999999999999999999999998765     346899999999999


Q ss_pred             HHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHH
Q 028887          151 GMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSW  192 (202)
Q Consensus       151 a~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~  192 (202)
                      .+++.++++..+...        ++.+ .+-||...+.+++.
T Consensus        86 n~Di~~rL~~~~~~~--------G~~v-~vRhGDT~~~er~r  118 (814)
T COG1201          86 NNDIRRRLEEPLREL--------GIEV-AVRHGDTPQSEKQK  118 (814)
T ss_pred             HHHHHHHHHHHHHHc--------CCcc-ceecCCCChHHhhh
Confidence            999999999999876        3444 77888766665443

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

Probab=99.60  E-value=1.3e-14  Score=111.79  Aligned_cols=91  Identities=30%  Similarity=0.461  Sum_probs=76.3

Q ss_pred             cHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCCcccccc
Q 028887           94 TDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHK  173 (202)
Q Consensus        94 t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~  173 (202)
                      ||.|.++++.+..|+++++.||||+|||++|+++++..+.++ ...++++++|+++|+.|+.+.++.++...        
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~-~~~~~lii~P~~~l~~q~~~~~~~~~~~~--------   71 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEG-KDARVLIIVPTRALAEQQFERLRKFFSNT--------   71 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTT-SSSEEEEEESSHHHHHHHHHHHHHHTTTT--------
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccC-CCceEEEEeeccccccccccccccccccc--------
Confidence            789999999999999999999999999999999999999876 44589999999999999999999999873        


Q ss_pred             cceEEEEEeCCccH-HHHHHH
Q 028887          174 LCTVMALLDGGMLR-RHKSWL  193 (202)
Q Consensus       174 ~~~~~~~~~g~~~~-~~~~~l  193 (202)
                      ++.+..++++.... .+..++
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~   92 (169)
T PF00270_consen   72 NVRVVLLHGGQSISEDQREVL   92 (169)
T ss_dssp             TSSEEEESTTSCHHHHHHHHH
T ss_pred             ccccccccccccccccccccc
Confidence            35666666666544 444555

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 ....

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.59  E-value=9.6e-15  Score=139.36  Aligned_cols=82  Identities=26%  Similarity=0.351  Sum_probs=70.8

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhc------CCccEEEEecCCHHh
Q 028887           77 VPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ------RSAVQAVIVVPTREL  150 (202)
Q Consensus        77 l~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~------~~~~~~Lil~Ptr~L  150 (202)
                      +++.+.+.+.+ +|..||++|.++|+.+++|+|++++||||||||++|++|+++.+...      ..++++||++|+|+|
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            56666665554 78999999999999999999999999999999999999999987642      235789999999999


Q ss_pred             HHHHHHHHH
Q 028887          151 GMQVTKVAR  159 (202)
Q Consensus       151 a~Q~~~~~~  159 (202)
                      +.|+++.+.
T Consensus        97 a~di~~~L~  105 (876)
T PRK13767         97 NNDIHRNLE  105 (876)
T ss_pred             HHHHHHHHH
Confidence            999988765

>PRK01172 ski2-like helicase; Provisional

Probab=99.59  E-value=1.2e-14  Score=135.34  Aligned_cols=88  Identities=23%  Similarity=0.270  Sum_probs=80.4

Q ss_pred             HHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhH
Q 028887           72 LCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELG  151 (202)
Q Consensus        72 l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La  151 (202)
                      |.+.++++.+++.+.+.||+ ++++|.++++.+..|+++++++|||||||+++.+++++.+..+.   +++|++|+++|+
T Consensus         3 ~~~~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~~~---k~v~i~P~raLa   78 (674)
T PRK01172          3 ISDLGYDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLAGL---KSIYIVPLRSLA   78 (674)
T ss_pred             HhhcCCCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHhCC---cEEEEechHHHH
Confidence            44568999999999999996 99999999999999999999999999999999999999887655   899999999999


Q ss_pred             HHHHHHHHHhhc
Q 028887          152 MQVTKVARVLAA  163 (202)
Q Consensus       152 ~Q~~~~~~~l~~  163 (202)
                      .|+++.++++..
T Consensus        79 ~q~~~~~~~l~~   90 (674)
T PRK01172         79 MEKYEELSRLRS   90 (674)
T ss_pred             HHHHHHHHHHhh
Confidence            999999987653

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

Probab=99.59  E-value=3.1e-15  Score=132.93  Aligned_cols=89  Identities=35%  Similarity=0.568  Sum_probs=81.9

Q ss_pred             CCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhc-----CCccEEEEecCCHH
Q 028887           75 GHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ-----RSAVQAVIVVPTRE  149 (202)
Q Consensus        75 ~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~-----~~~~~~Lil~Ptr~  149 (202)
                      ..++..+++.+...||..|+++|.+++|.++.++|++.|+|||||||++|++|+++++...     ..+.+++|+.|||+
T Consensus       141 ~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~~~gl~a~Il~ptre  220 (593)
T KOG0344|consen  141 YSMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQEKHKVGLRALILSPTRE  220 (593)
T ss_pred             hhhcHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhhcccCccceEEEEecchHH
Confidence            3577889999999999999999999999999999999999999999999999999988643     35689999999999


Q ss_pred             hHHHHHHHHHHhhc
Q 028887          150 LGMQVTKVARVLAA  163 (202)
Q Consensus       150 La~Q~~~~~~~l~~  163 (202)
                      |+.|++.+++++..
T Consensus       221 La~Qi~re~~k~~~  234 (593)
T KOG0344|consen  221 LAAQIYREMRKYSI  234 (593)
T ss_pred             HHHHHHHHHHhcCC
Confidence            99999999999983

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.58  E-value=1.9e-14  Score=133.07  Aligned_cols=103  Identities=23%  Similarity=0.257  Sum_probs=82.9

Q ss_pred             HHHHHHCCCCCCcHHHHHHHHhHHcC------CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHH
Q 028887           82 LRRMEETGYVLPTDIQREALPVLFSS------RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVT  155 (202)
Q Consensus        82 ~~~l~~~g~~~~t~~Q~~~i~~i~~g------~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~  155 (202)
                      .+.+..++| .||+.|+++|+.++.+      .+.+++|+||||||++|++|++..+..+.   +++||+||++||.|++
T Consensus       226 ~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~g~---qvlilaPT~~LA~Q~~  301 (630)
T TIGR00643       226 TKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGY---QVALMAPTEILAEQHY  301 (630)
T ss_pred             HHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHcCC---cEEEECCHHHHHHHHH
Confidence            344567888 6999999999999876      35899999999999999999999987655   8999999999999999


Q ss_pred             HHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHHHh
Q 028887          156 KVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVL  196 (202)
Q Consensus       156 ~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~l  196 (202)
                      +.+++++...        ++++..++||....+....++.+
T Consensus       302 ~~~~~l~~~~--------gi~v~lltg~~~~~~r~~~~~~i  334 (630)
T TIGR00643       302 NSLRNLLAPL--------GIEVALLTGSLKGKRRKELLETI  334 (630)
T ss_pred             HHHHHHhccc--------CcEEEEEecCCCHHHHHHHHHHH
Confidence            9999998765        46666666665555444444433

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.57  E-value=2.9e-14  Score=132.94  Aligned_cols=98  Identities=20%  Similarity=0.215  Sum_probs=79.0

Q ss_pred             HHCCCCCCcHHHHHHHHhHHcC------CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHH
Q 028887           86 EETGYVLPTDIQREALPVLFSS------RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVAR  159 (202)
Q Consensus        86 ~~~g~~~~t~~Q~~~i~~i~~g------~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~  159 (202)
                      ..++| .||+.|.++++.+..+      ++.+++|+||||||++|++|++..+..+.   +++||+||++||.|+++.++
T Consensus       256 ~~l~f-~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~g~---q~lilaPT~~LA~Q~~~~l~  331 (681)
T PRK10917        256 ASLPF-ELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGY---QAALMAPTEILAEQHYENLK  331 (681)
T ss_pred             HhCCC-CCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHcCC---eEEEEeccHHHHHHHHHHHH
Confidence            45677 6999999999999876      47999999999999999999999887655   99999999999999999999


Q ss_pred             HhhcCCCCcccccccceEEEEEeCCccHHHHHHHHH
Q 028887          160 VLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKV  195 (202)
Q Consensus       160 ~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~  195 (202)
                      +++...        ++++..++||....+..+.+..
T Consensus       332 ~l~~~~--------~i~v~ll~G~~~~~~r~~~~~~  359 (681)
T PRK10917        332 KLLEPL--------GIRVALLTGSLKGKERREILEA  359 (681)
T ss_pred             HHHhhc--------CcEEEEEcCCCCHHHHHHHHHH
Confidence            998765        3565555555554444444433

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.57  E-value=4e-14  Score=135.02  Aligned_cols=107  Identities=21%  Similarity=0.143  Sum_probs=84.2

Q ss_pred             CHHHHHHHH-HCCCCCCcHHHHHHHHhHHcC------CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHh
Q 028887           78 PEHVLRRME-ETGYVLPTDIQREALPVLFSS------RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTREL  150 (202)
Q Consensus        78 ~~~l~~~l~-~~g~~~~t~~Q~~~i~~i~~g------~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~L  150 (202)
                      ...+.+.+. ..+| .||++|..||+.++++      +|.+++|+||+|||++|+.|++..+..+.   +++||+||++|
T Consensus       437 ~~~~~~~~~~~~~f-~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~g~---qvlvLvPT~~L  512 (926)
T TIGR00580       437 DLEWQQEFEDSFPF-EETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGK---QVAVLVPTTLL  512 (926)
T ss_pred             CHHHHHHHHHhCCC-CCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHhCC---eEEEEeCcHHH
Confidence            345555554 4688 5999999999999875      79999999999999999999999987765   99999999999


Q ss_pred             HHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHHHh
Q 028887          151 GMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVL  196 (202)
Q Consensus       151 a~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~l  196 (202)
                      |.|+++.+++++...        ++++..+.++....++.+.++.+
T Consensus       513 A~Q~~~~f~~~~~~~--------~i~v~~Lsg~~~~~e~~~~~~~l  550 (926)
T TIGR00580       513 AQQHFETFKERFANF--------PVTIELLSRFRSAKEQNEILKEL  550 (926)
T ss_pred             HHHHHHHHHHHhccC--------CcEEEEEeccccHHHHHHHHHHH
Confidence            999999999988764        34555555555555555555544

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.

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.56  E-value=3.8e-14  Score=133.05  Aligned_cols=108  Identities=21%  Similarity=0.205  Sum_probs=95.3

Q ss_pred             CCCCHHHHHHHH-----HCCCCCC---cHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecC
Q 028887           75 GHVPEHVLRRME-----ETGYVLP---TDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP  146 (202)
Q Consensus        75 ~gl~~~l~~~l~-----~~g~~~~---t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~P  146 (202)
                      .++.+++.+.+.     .+||..|   +|+|.++++.+..+++++++++||+|||++|++|++..+..+.   .++||+|
T Consensus        67 fal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g~---~v~IVTp  143 (970)
T PRK12899         67 YGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTGK---PVHLVTV  143 (970)
T ss_pred             hCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhcC---CeEEEeC
Confidence            378888888776     6799988   9999999999999999999999999999999999998876554   4899999


Q ss_pred             CHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHH
Q 028887          147 TRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWL  193 (202)
Q Consensus       147 tr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l  193 (202)
                      |++||.|+.+++..+....        ++++.+++||.+..+|++.+
T Consensus       144 TrELA~Qdae~m~~L~k~l--------GLsV~~i~GG~~~~eq~~~y  182 (970)
T PRK12899        144 NDYLAQRDCEWVGSVLRWL--------GLTTGVLVSGSPLEKRKEIY  182 (970)
T ss_pred             CHHHHHHHHHHHHHHHhhc--------CCeEEEEeCCCCHHHHHHHc
Confidence            9999999999999999876        58888999998888876553

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.53  E-value=5.7e-14  Score=125.88  Aligned_cols=70  Identities=21%  Similarity=0.313  Sum_probs=62.9

Q ss_pred             HCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887           87 ETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus        87 ~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      .+||..|+|+|.++|+.++.|+|+++.+|||+|||++|++|++.   .+.   .+||++|+++|+.|+.+.++.++
T Consensus         6 ~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~---~~~---~~lVi~P~~~L~~dq~~~l~~~g   75 (470)
T TIGR00614         6 VFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALC---SDG---ITLVISPLISLMEDQVLQLKASG   75 (470)
T ss_pred             hcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHH---cCC---cEEEEecHHHHHHHHHHHHHHcC
Confidence            46999999999999999999999999999999999999999875   233   69999999999999998887653

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

>PRK14701 reverse gyrase; Provisional

Probab=99.51  E-value=1.9e-13  Score=136.20  Aligned_cols=106  Identities=17%  Similarity=0.157  Sum_probs=79.5

Q ss_pred             HHHHHHH-CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHH
Q 028887           81 VLRRMEE-TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVAR  159 (202)
Q Consensus        81 l~~~l~~-~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~  159 (202)
                      +.+.+++ .|| .|+++|+.+++.++.|+|+++.||||+|||++++++.+.....   +.++|||+||++|+.|+.+.++
T Consensus        68 ~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~~~---g~~aLVl~PTreLa~Qi~~~l~  143 (1638)
T PRK14701         68 FEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLALK---GKKCYIILPTTLLVKQTVEKIE  143 (1638)
T ss_pred             HHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHhc---CCeEEEEECHHHHHHHHHHHHH
Confidence            3444544 799 6999999999999999999999999999999766665544333   3489999999999999999999


Q ss_pred             HhhcCCCCcccccccceEEEEEeCCccHHHHHHHHHh
Q 028887          160 VLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVL  196 (202)
Q Consensus       160 ~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~l  196 (202)
                      .++...+      .++.+..++||.+..++.+.++.+
T Consensus       144 ~l~~~~~------~~v~v~~~~g~~s~~e~~~~~~~l  174 (1638)
T PRK14701        144 SFCEKAN------LDVRLVYYHSNLRKKEKEEFLERI  174 (1638)
T ss_pred             HHHhhcC------CceeEEEEeCCCCHHHHHHHHHHH
Confidence            9987541      124445555555555555544444

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.50  E-value=2.3e-13  Score=132.41  Aligned_cols=103  Identities=20%  Similarity=0.129  Sum_probs=82.8

Q ss_pred             HHHHHHCCCCCCcHHHHHHHHhHHcC------CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHH
Q 028887           82 LRRMEETGYVLPTDIQREALPVLFSS------RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVT  155 (202)
Q Consensus        82 ~~~l~~~g~~~~t~~Q~~~i~~i~~g------~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~  155 (202)
                      .+.....+| .||++|.++|+.++.+      +|++++|+||+|||++|+.+++..+..+.   +++||+||++||.|++
T Consensus       591 ~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~~g~---qvlvLvPT~eLA~Q~~  666 (1147)
T PRK10689        591 QLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHK---QVAVLVPTTLLAQQHY  666 (1147)
T ss_pred             HHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHHcCC---eEEEEeCcHHHHHHHH
Confidence            333466788 6999999999999887      89999999999999999999888776554   9999999999999999


Q ss_pred             HHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHHHh
Q 028887          156 KVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVL  196 (202)
Q Consensus       156 ~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~l  196 (202)
                      +.+++.+...        .+.+..+.++.+..++.+.++.+
T Consensus       667 ~~f~~~~~~~--------~v~i~~l~g~~s~~e~~~il~~l  699 (1147)
T PRK10689        667 DNFRDRFANW--------PVRIEMLSRFRSAKEQTQILAEA  699 (1147)
T ss_pred             HHHHHhhccC--------CceEEEEECCCCHHHHHHHHHHH
Confidence            9999876653        35555566666666666555544

>TIGR01054 rgy reverse gyrase

Probab=99.48  E-value=3.6e-13  Score=131.31  Aligned_cols=82  Identities=23%  Similarity=0.223  Sum_probs=67.0

Q ss_pred             HHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHH
Q 028887           81 VLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARV  160 (202)
Q Consensus        81 l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~  160 (202)
                      +.+.+.+....+|+++|+.+++.++.|+|++++||||+|||. |.+|+...+..  .++++|||+||++|+.|++++++.
T Consensus        67 f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~--~g~~vLIL~PTreLa~Qi~~~l~~  143 (1171)
T TIGR01054        67 FEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAK--KGKRCYIILPTTLLVIQVAEKISS  143 (1171)
T ss_pred             HHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHh--cCCeEEEEeCHHHHHHHHHHHHHH
Confidence            334444433347999999999999999999999999999997 66677666543  246899999999999999999999


Q ss_pred             hhcCC
Q 028887          161 LAAKP  165 (202)
Q Consensus       161 l~~~~  165 (202)
                      ++...
T Consensus       144 l~~~~  148 (1171)
T TIGR01054       144 LAEKA  148 (1171)
T ss_pred             HHHhc
Confidence            98754

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.

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

Probab=99.46  E-value=1.8e-13  Score=128.46  Aligned_cols=105  Identities=18%  Similarity=0.133  Sum_probs=80.4

Q ss_pred             CCCCCCcHHHHHHHHhHHcCC-cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEE-ecCCHHhHHHHHHHHHHhhcCC
Q 028887           88 TGYVLPTDIQREALPVLFSSR-DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVI-VVPTRELGMQVTKVARVLAAKP  165 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~-~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Li-l~Ptr~La~Q~~~~~~~l~~~~  165 (202)
                      .||+ |||+|.++|+.++.|+ ++++++|||||||.+|.++.+. +..+...++.|| ++|||||+.|+++.+++++...
T Consensus        12 ~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~-~~~~~~~~~rLv~~vPtReLa~Qi~~~~~~~~k~l   89 (844)
T TIGR02621        12 HGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLA-VEIGAKVPRRLVYVVNRRTVVDQVTEEAEKIGERL   89 (844)
T ss_pred             hCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhcc-ccccccccceEEEeCchHHHHHHHHHHHHHHHHHh
Confidence            5897 9999999999999998 6888899999999976654442 233444566776 5699999999999999999754


Q ss_pred             CC---------------cccccccceEEEEEeCCccHHHHHHHH
Q 028887          166 LD---------------TDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       166 ~~---------------~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      ..               .......+++..++||.....|.+.++
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~  133 (844)
T TIGR02621        90 PDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDP  133 (844)
T ss_pred             cccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcC
Confidence            21               011222588999999999888866554

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.

>PRK09401 reverse gyrase; Reviewed

Probab=99.45  E-value=6.8e-13  Score=129.36  Aligned_cols=87  Identities=29%  Similarity=0.302  Sum_probs=71.4

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCC
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLD  167 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~  167 (202)
                      .|+ +|+++|..++|.++.|+|++++||||+|||. |.+++...+..  .+.+++||+||++|+.|++++++.++...  
T Consensus        77 ~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~~--~g~~alIL~PTreLa~Qi~~~l~~l~~~~--  150 (1176)
T PRK09401         77 TGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLAK--KGKKSYIIFPTRLLVEQVVEKLEKFGEKV--  150 (1176)
T ss_pred             cCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHHh--cCCeEEEEeccHHHHHHHHHHHHHHhhhc--
Confidence            477 7999999999999999999999999999996 55555555543  35689999999999999999999998865  


Q ss_pred             cccccccceEEEEEeCCcc
Q 028887          168 TDLEHKLCTVMALLDGGML  186 (202)
Q Consensus       168 ~~~~~~~~~~~~~~~g~~~  186 (202)
                            ++.+..+++|+..
T Consensus       151 ------~~~~~~~~g~~~~  163 (1176)
T PRK09401        151 ------GCGVKILYYHSSL  163 (1176)
T ss_pred             ------CceEEEEEccCCc
Confidence                  4555666666553

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.43  E-value=1.4e-12  Score=120.27  Aligned_cols=69  Identities=26%  Similarity=0.365  Sum_probs=62.7

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      +||..++++|.++|+.+++|+|+++.+|||+|||++|++|++..   ++   .+||++|+++|+.|+.+.++.++
T Consensus        21 fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~---~g---~tlVisPl~sL~~dqv~~l~~~g   89 (607)
T PRK11057         21 FGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL---DG---LTLVVSPLISLMKDQVDQLLANG   89 (607)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc---CC---CEEEEecHHHHHHHHHHHHHHcC
Confidence            69999999999999999999999999999999999999998742   23   69999999999999999888753

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

Probab=99.41  E-value=1.1e-12  Score=125.68  Aligned_cols=109  Identities=19%  Similarity=0.141  Sum_probs=81.6

Q ss_pred             HHHhCCCC--HHHHHHHH-HCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCC
Q 028887           71 ELCQGHVP--EHVLRRME-ETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPT  147 (202)
Q Consensus        71 ~l~~~gl~--~~l~~~l~-~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Pt  147 (202)
                      .|...+++  ..+...+. -+||..++++|.++|+.++.|+|+++.+|||+|||++|++|++..   +.   .+|||+|+
T Consensus       436 ~W~~~~fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~---~G---iTLVISPL  509 (1195)
T PLN03137        436 KWSSRNFPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC---PG---ITLVISPL  509 (1195)
T ss_pred             cccccCCCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc---CC---cEEEEeCH
Confidence            34444444  33444443 469999999999999999999999999999999999999999753   23   69999999


Q ss_pred             HHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHHHhc
Q 028887          148 RELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVLY  197 (202)
Q Consensus       148 r~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~l~  197 (202)
                      ++|+.++...+...            ++....+.++....++.+.++.+.
T Consensus       510 iSLmqDQV~~L~~~------------GI~Aa~L~s~~s~~eq~~ilr~l~  547 (1195)
T PLN03137        510 VSLIQDQIMNLLQA------------NIPAASLSAGMEWAEQLEILQELS  547 (1195)
T ss_pred             HHHHHHHHHHHHhC------------CCeEEEEECCCCHHHHHHHHHHHH
Confidence            99998655555432            245566777777777766666543

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.41  E-value=2e-12  Score=118.98  Aligned_cols=70  Identities=23%  Similarity=0.284  Sum_probs=63.0

Q ss_pred             HCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887           87 ETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus        87 ~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      .+||..++++|.++|+.+++|+|+++.+|||+|||++|++|++.   .++   .++|++|+++|+.|+.+.++.++
T Consensus         8 ~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~---~~g---~~lVisPl~sL~~dq~~~l~~~g   77 (591)
T TIGR01389         8 TFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALL---LKG---LTVVISPLISLMKDQVDQLRAAG   77 (591)
T ss_pred             hcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHH---cCC---cEEEEcCCHHHHHHHHHHHHHcC
Confidence            37999999999999999999999999999999999999999874   233   68999999999999999988764

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.

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.38  E-value=3e-12  Score=117.72  Aligned_cols=84  Identities=25%  Similarity=0.158  Sum_probs=75.3

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCC
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLD  167 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~  167 (202)
                      .|. .|+++|..+++.++.|+  ++++.||+|||++|.+|++.....+.   +++|++||++||.|.++++..++...  
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--LAEMQTGEGKTLTATLPAGTAALAGL---PVHVITVNDYLAERDAELMRPLYEAL--  171 (656)
T ss_pred             hCC-CCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhcCC---eEEEEcCcHHHHHHHHHHHHHHHhhc--
Confidence            465 69999999999999999  99999999999999999998876655   99999999999999999999999876  


Q ss_pred             cccccccceEEEEEeCCc
Q 028887          168 TDLEHKLCTVMALLDGGM  185 (202)
Q Consensus       168 ~~~~~~~~~~~~~~~g~~  185 (202)
                            ++++.+++||.+
T Consensus       172 ------Glsv~~i~gg~~  183 (656)
T PRK12898        172 ------GLTVGCVVEDQS  183 (656)
T ss_pred             ------CCEEEEEeCCCC
Confidence                  688888888754

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.35  E-value=1.1e-12  Score=118.58  Aligned_cols=152  Identities=16%  Similarity=0.056  Sum_probs=94.2

Q ss_pred             ceecccCCCCceeeeccCCCCCCCCccccccccCCCCCCchHHHHHhccCCCCHHHHHcccCCCcchHHHHHhCC-----
Q 028887            2 AAIAISAAHPILVTRVNHKLSSPNSIDFTNRAFLPVSISLKPLRAVLSSSAVSTEELAAGTGNNSLTLRELCQGH-----   76 (202)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g-----   76 (202)
                      +++.++. ++.+..+.+..++++|+..+..++... +. +..+-++++....-      ..|.......-+.+.|     
T Consensus        12 ~~~~~~~-~~~~~~~l~~~~~f~np~~~~~~~~r~-~~-~~~~i~~~~~~~~~------prG~~~~~~~~~~~~g~~~~~   82 (501)
T PHA02558         12 SHVRIEC-EPSIFYELRDYFSFEVPGYKFNPKFKY-GG-WDGKIRLLDYNGLL------PYGLVGQLKKFAKNRGYSIWV   82 (501)
T ss_pred             eEEEEEe-cchHHHHHHhhcceeCCCceecccccC-CC-CCceEEEeccCCCc------ccchHHHHHHHHHhcCCeEec
Confidence            4556666 888889999999999999999887622 11 11122222211100      0011111111111122     


Q ss_pred             ---------CCH-H----HHHHHHHCC--CCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccE
Q 028887           77 ---------VPE-H----VLRRMEETG--YVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQ  140 (202)
Q Consensus        77 ---------l~~-~----l~~~l~~~g--~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~  140 (202)
                               +.+ .    +.......|  ...|++.|.++++.++.+++.++++|||+|||+++...+...+..  ...+
T Consensus        83 ~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~~~~~~~--~~~~  160 (501)
T PHA02558         83 DPRIEENEDISREDFDEWVSSLEIYSGNKKIEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLSRYYLEN--YEGK  160 (501)
T ss_pred             CcccccCCCCCHHHHHhHhhhcccccCCCcCCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHHHHHHhc--CCCe
Confidence                     111 1    111111111  347999999999999999999999999999999876543222332  2348


Q ss_pred             EEEecCCHHhHHHHHHHHHHhhcC
Q 028887          141 AVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus       141 ~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      +|||+||++|+.|+.+++++++..
T Consensus       161 vLilvpt~eL~~Q~~~~l~~~~~~  184 (501)
T PHA02558        161 VLIIVPTTSLVTQMIDDFVDYRLF  184 (501)
T ss_pred             EEEEECcHHHHHHHHHHHHHhccc
Confidence            999999999999999999988753

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.33  E-value=1.3e-11  Score=115.15  Aligned_cols=92  Identities=27%  Similarity=0.351  Sum_probs=74.3

Q ss_pred             CCcHHHHHHHHhHHcC---CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCCc
Q 028887           92 LPTDIQREALPVLFSS---RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDT  168 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g---~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~  168 (202)
                      .+++.|+++++.+.++   ++++++|+||||||++|+.++.+.+..++   ++|||+||++|+.|+.+++++.++..   
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~g~---~vLvLvPt~~L~~Q~~~~l~~~fg~~---  217 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQGK---QALVLVPEIALTPQMLARFRARFGAP---  217 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHcCC---eEEEEeCcHHHHHHHHHHHHHHhCCC---
Confidence            5899999999999874   78999999999999999999988887765   89999999999999999999876432   


Q ss_pred             ccccccceEEEEEeCCccHH--HHHHHHHhcC
Q 028887          169 DLEHKLCTVMALLDGGMLRR--HKSWLKVLYS  198 (202)
Q Consensus       169 ~~~~~~~~~~~~~~g~~~~~--~~~~l~~l~~  198 (202)
                               +.++||+....  ...|.+...+
T Consensus       218 ---------v~~~~s~~s~~~r~~~~~~~~~g  240 (679)
T PRK05580        218 ---------VAVLHSGLSDGERLDEWRKAKRG  240 (679)
T ss_pred             ---------EEEEECCCCHHHHHHHHHHHHcC
Confidence                     55666654333  3456655544

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

Probab=99.31  E-value=1.1e-11  Score=115.16  Aligned_cols=136  Identities=22%  Similarity=0.286  Sum_probs=108.5

Q ss_pred             hccCCCCHHHHHcccCCCcchHHHHHhCCCCHHHHHHHHH-------CC---CCCCcHHHHHHHHhHHcC----CcEEEe
Q 028887           48 LSSSAVSTEELAAGTGNNSLTLRELCQGHVPEHVLRRMEE-------TG---YVLPTDIQREALPVLFSS----RDCILH  113 (202)
Q Consensus        48 ~~~~~~~~~~l~~~~~~~~~~~~~l~~~gl~~~l~~~l~~-------~g---~~~~t~~Q~~~i~~i~~g----~~~l~~  113 (202)
                      ..........+....+.+...++.|++.|+.+.. .....       ..   ...+++.|+.++..+...    ...++.
T Consensus       145 ~~~~~~~~~~l~~~~~~s~~~~~~l~~~g~~~~~-~~~~~~~~~~~~~~~~~~~~Ln~~Q~~a~~~i~~~~~~~~~~Ll~  223 (730)
T COG1198         145 LQGGEWTRSALAHAAGVSLSVLKGLEKKGLIEII-ELEPPLVVAPPDPSLSEWLALNQEQQAAVEAILSSLGGFAPFLLD  223 (730)
T ss_pred             HcCCccchhhhhhhcchhHHHHHHHHhcCceeee-cccCCCcccccccccccccccCHHHHHHHHHHHHhcccccceeEe
Confidence            3334455666777788888999999999988654 22111       11   236789999999998655    679999


Q ss_pred             ccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHH--HH
Q 028887          114 AQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRH--KS  191 (202)
Q Consensus       114 a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~--~~  191 (202)
                      |.||||||++|+-.+.+.+..|+   ++|+|+|+++|..|+.++|+..++..            ++++|.+-.+.+  ..
T Consensus       224 GvTGSGKTEvYl~~i~~~L~~Gk---qvLvLVPEI~Ltpq~~~rf~~rFg~~------------v~vlHS~Ls~~er~~~  288 (730)
T COG1198         224 GVTGSGKTEVYLEAIAKVLAQGK---QVLVLVPEIALTPQLLARFKARFGAK------------VAVLHSGLSPGERYRV  288 (730)
T ss_pred             CCCCCcHHHHHHHHHHHHHHcCC---EEEEEeccccchHHHHHHHHHHhCCC------------hhhhcccCChHHHHHH
Confidence            99999999999999999999998   99999999999999999999999854            778888655544  78


Q ss_pred             HHHHhcCC
Q 028887          192 WLKVLYSL  199 (202)
Q Consensus       192 ~l~~l~~~  199 (202)
                      |++..++-
T Consensus       289 W~~~~~G~  296 (730)
T COG1198         289 WRRARRGE  296 (730)
T ss_pred             HHHHhcCC
Confidence            99988764

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.18  E-value=1e-10  Score=109.93  Aligned_cols=86  Identities=29%  Similarity=0.341  Sum_probs=72.3

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHh-HHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHH
Q 028887           77 VPEHVLRRMEETGYVLPTDIQREALPV-LFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVT  155 (202)
Q Consensus        77 l~~~l~~~l~~~g~~~~t~~Q~~~i~~-i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~  155 (202)
                      +.+.+.+.++..|+..+.+.|+.++.. +..|+|+++++|||||||+.+++.+++.+.++  +.+++|+||+|+||.+.+
T Consensus        16 ~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~--~~k~vYivPlkALa~Ek~   93 (766)
T COG1204          16 LDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG--GGKVVYIVPLKALAEEKY   93 (766)
T ss_pred             ccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc--CCcEEEEeChHHHHHHHH
Confidence            666777777778887888878777766 45579999999999999999999999999875  237999999999999999


Q ss_pred             HHHHHhhcC
Q 028887          156 KVARVLAAK  164 (202)
Q Consensus       156 ~~~~~l~~~  164 (202)
                      +.|.++...
T Consensus        94 ~~~~~~~~~  102 (766)
T COG1204          94 EEFSRLEEL  102 (766)
T ss_pred             HHhhhHHhc
Confidence            999955544

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.13  E-value=2.8e-10  Score=105.70  Aligned_cols=89  Identities=21%  Similarity=0.150  Sum_probs=74.4

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCC
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLD  167 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~  167 (202)
                      +|. .|+++|..+.+.+..|+  ++.++||+|||++|.+|++-....++   ++.|++||++||.|..+++..+....  
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--IAEMKTGEGKTLTATLPAYLNALTGK---GVHVVTVNDYLAQRDAEWMGQVYRFL--  124 (745)
T ss_pred             hCC-CccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHhCC---CEEEEcCCHHHHHHHHHHHHHHhccC--
Confidence            476 69999999999888886  89999999999999999954444455   79999999999999999999999886  


Q ss_pred             cccccccceEEEEEeCCccHHHH
Q 028887          168 TDLEHKLCTVMALLDGGMLRRHK  190 (202)
Q Consensus       168 ~~~~~~~~~~~~~~~g~~~~~~~  190 (202)
                            ++++.++++|.....++
T Consensus       125 ------GLsv~~i~g~~~~~~r~  141 (745)
T TIGR00963       125 ------GLSVGLILSGMSPEERR  141 (745)
T ss_pred             ------CCeEEEEeCCCCHHHHH
Confidence                  57888787776654433

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.

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.13  E-value=8.8e-10  Score=85.41  Aligned_cols=77  Identities=36%  Similarity=0.486  Sum_probs=68.0

Q ss_pred             CCCCCCcHHHHHHHHhHHcC-CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCC
Q 028887           88 TGYVLPTDIQREALPVLFSS-RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKP  165 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g-~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~  165 (202)
                      .++..+++.|.++++.+..+ +.+++.++||+|||.+++.+++..+.... ..++++++|+++++.|+.+.+..++...
T Consensus         4 ~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~-~~~~l~~~p~~~~~~~~~~~~~~~~~~~   81 (201)
T smart00487        4 FGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK-GKRVLVLVPTRELAEQWAEELKKLGPSL   81 (201)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccC-CCcEEEEeCCHHHHHHHHHHHHHHhccC
Confidence            46678999999999999998 99999999999999999999999887652 2379999999999999999999888653

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.13  E-value=3.4e-10  Score=106.28  Aligned_cols=90  Identities=21%  Similarity=0.108  Sum_probs=76.6

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCC
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLD  167 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~  167 (202)
                      .|. .|+++|..+++.+..|+  ++.+.||+|||++|++|++.....+.   +++|++||++||.|.++++..+....  
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--IAEMQTGEGKTLTATMPLYLNALEGK---GVHLITVNDYLAKRDAEEMGQVYEFL--  146 (790)
T ss_pred             hCC-CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHcCC---CeEEEeCCHHHHHHHHHHHHHHHhhc--
Confidence            476 79999999999988887  99999999999999999986666566   89999999999999999999999886  


Q ss_pred             cccccccceEEEEEeCCccHHHHH
Q 028887          168 TDLEHKLCTVMALLDGGMLRRHKS  191 (202)
Q Consensus       168 ~~~~~~~~~~~~~~~g~~~~~~~~  191 (202)
                            ++++..++||.+..++++
T Consensus       147 ------Gl~v~~i~g~~~~~~~r~  164 (790)
T PRK09200        147 ------GLTVGLNFSDIDDASEKK  164 (790)
T ss_pred             ------CCeEEEEeCCCCcHHHHH
Confidence                  578777777766444443

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

Probab=99.09  E-value=1.1e-09  Score=104.78  Aligned_cols=101  Identities=20%  Similarity=0.156  Sum_probs=76.2

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHHHH----hHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHH
Q 028887           79 EHVLRRMEETGYVLPTDIQREALP----VLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQV  154 (202)
Q Consensus        79 ~~l~~~l~~~g~~~~t~~Q~~~i~----~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~  154 (202)
                      +.+.+.+...||+ +++.|.+.+.    .+.+|+++++.|+||+|||++|++|++.....++   +++|.+||++|..|+
T Consensus       233 ~~~~~~~~~~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~~~~---~vvi~t~t~~Lq~Ql  308 (850)
T TIGR01407       233 SLFSKNIDRLGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAITEK---PVVISTNTKVLQSQL  308 (850)
T ss_pred             HHHHHhhhhcCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhcCCC---eEEEEeCcHHHHHHH
Confidence            3556677778985 7899998666    4557899999999999999999999988765333   899999999999998


Q ss_pred             HH-HHHHhhcCCCCcccccccceEEEEEeCCccHHH
Q 028887          155 TK-VARVLAAKPLDTDLEHKLCTVMALLDGGMLRRH  189 (202)
Q Consensus       155 ~~-~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~  189 (202)
                      .. .+..+....+      ..+++..+.|+.+.--.
T Consensus       309 ~~~~~~~l~~~~~------~~~~~~~~kG~~~ylcl  338 (850)
T TIGR01407       309 LEKDIPLLNEILN------FKINAALIKGKSNYLSL  338 (850)
T ss_pred             HHHHHHHHHHHcC------CCceEEEEEcchhhccH
Confidence            65 4555543321      03677777877766433

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.

>KOG0349 consensus Putative DEAD-box RNA helicase DDX1 [RNA processing and modification]

Probab=99.04  E-value=1.8e-10  Score=100.17  Aligned_cols=62  Identities=34%  Similarity=0.521  Sum_probs=59.0

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHH
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLV  132 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l  132 (202)
                      .|++.|+.+++-.+..++.|.-||.+|.++||.|+.|-|++..|.||||||-+|++|+++.+
T Consensus         3 af~e~gv~pel~~a~~e~dw~lptdvqaeaiplilgggdvlmaaetgsgktgaf~lpilqiv   64 (725)
T KOG0349|consen    3 AFEEFGVLPELGMATDELDWTLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPILQIV   64 (725)
T ss_pred             chHhhCcchHhhhhhhhhccccccccccccccEEecCCcEEEEeccCCCCccceehhhHHHH
Confidence            57778999999999999999999999999999999999999999999999999999999865

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.03  E-value=1.6e-09  Score=94.08  Aligned_cols=63  Identities=24%  Similarity=0.290  Sum_probs=54.9

Q ss_pred             HHHHHHHhHHcCCc--EEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           96 IQREALPVLFSSRD--CILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        96 ~Q~~~i~~i~~g~~--~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      +|.++++.+.++.+  +++++|||||||++|++|++.   .+   .++++++|+++|+.|+++++++++..
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~---~~---~~~~~~~P~~aL~~~~~~~~~~~~~~   65 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLH---GE---NDTIALYPTNALIEDQTEAIKEFVDV   65 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHH---cC---CCEEEEeChHHHHHHHHHHHHHHHHh
Confidence            59999999998875  788999999999999999874   22   26899999999999999999998753

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.

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

Probab=99.01  E-value=1.1e-09  Score=103.22  Aligned_cols=76  Identities=24%  Similarity=0.364  Sum_probs=65.2

Q ss_pred             CCCCCCcHHHHHHHHhHHc-CCcEEEeccCCCchHHHHHHHHHHHHHhc-------CCccEEEEecCCHHhHHHHHHHHH
Q 028887           88 TGYVLPTDIQREALPVLFS-SRDCILHAQTGSGKTLTYLLLIFSLVNAQ-------RSAVQAVIVVPTRELGMQVTKVAR  159 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~-g~~~l~~a~TGsGKT~~~l~~~l~~l~~~-------~~~~~~Lil~Ptr~La~Q~~~~~~  159 (202)
                      .+|+.++.+|..++|.+.+ ..++++|||||+|||.+|++.|++.+..+       ++..+++|++|+++||..+.+.+.
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            4677899999999999876 57899999999999999999999998752       356799999999999999887765


Q ss_pred             Hhhc
Q 028887          160 VLAA  163 (202)
Q Consensus       160 ~l~~  163 (202)
                      +-+.
T Consensus       186 kkl~  189 (1230)
T KOG0952|consen  186 KKLA  189 (1230)
T ss_pred             hhcc
Confidence            5444

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.00  E-value=1.7e-09  Score=100.62  Aligned_cols=87  Identities=17%  Similarity=0.093  Sum_probs=64.9

Q ss_pred             cHHHHHHHHhHHcCCcEEEeccCCCchHHH---------HHHHHHHHHHh---cCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887           94 TDIQREALPVLFSSRDCILHAQTGSGKTLT---------YLLLIFSLVNA---QRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus        94 t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~---------~l~~~l~~l~~---~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      ..+|+++++.+++|++++++|+||||||.+         |++|.+..+..   .....++++++|+||||.|+..++.+.
T Consensus       166 ~~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~~  245 (675)
T PHA02653        166 PDVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLKS  245 (675)
T ss_pred             HHHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHHH
Confidence            359999999999999999999999999997         55555555432   334568999999999999999998876


Q ss_pred             hcCCCCcccccccceEEEEEeCCc
Q 028887          162 AAKPLDTDLEHKLCTVMALLDGGM  185 (202)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~~g~~  185 (202)
                      .+...     ..+..+...+||..
T Consensus       246 vg~~~-----~~g~~v~v~~Gg~~  264 (675)
T PHA02653        246 LGFDE-----IDGSPISLKYGSIP  264 (675)
T ss_pred             hCccc-----cCCceEEEEECCcc
Confidence            65421     11234455566654

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

Probab=98.97  E-value=1.6e-09  Score=97.13  Aligned_cols=90  Identities=21%  Similarity=0.186  Sum_probs=79.5

Q ss_pred             HhCCCCHHHHHHHHHCCCCCCcHHHHHHHHh-HHcCCcEEEeccCCCchHHHHHHHHHHHHHh-cCCccEEEEecCCHHh
Q 028887           73 CQGHVPEHVLRRMEETGYVLPTDIQREALPV-LFSSRDCILHAQTGSGKTLTYLLLIFSLVNA-QRSAVQAVIVVPTREL  150 (202)
Q Consensus        73 ~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~-i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~-~~~~~~~Lil~Ptr~L  150 (202)
                      .+..+++.+.+.++..|++.+.|+|..++.. ++.|.|.++.++|+||||++.-++-+..+.. ++   +.|+|+|..+|
T Consensus       197 deLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~~g~---KmlfLvPLVAL  273 (830)
T COG1202         197 DELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSGGK---KMLFLVPLVAL  273 (830)
T ss_pred             cccCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHhCCC---eEEEEehhHHh
Confidence            4458999999999999999999999999987 7899999999999999999999888887765 55   79999999999


Q ss_pred             HHHHHHHHHHhhcCC
Q 028887          151 GMQVTKVARVLAAKP  165 (202)
Q Consensus       151 a~Q~~~~~~~l~~~~  165 (202)
                      |+|-++.|++--...
T Consensus       274 ANQKy~dF~~rYs~L  288 (830)
T COG1202         274 ANQKYEDFKERYSKL  288 (830)
T ss_pred             hcchHHHHHHHhhcc
Confidence            999999997654443

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=98.97  E-value=2.9e-09  Score=99.52  Aligned_cols=82  Identities=23%  Similarity=0.178  Sum_probs=66.8

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCC
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLD  167 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~  167 (202)
                      .|. .|+++|......+..|  .+++++||+|||++|++|++.....++   .++|++|+++||.|+.+++..+....  
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--NIAEMKTGEGKTLTATMPLYLNALTGK---GAMLVTTNDYLAKRDAEEMGPVYEWL--  138 (762)
T ss_pred             cCC-CccHHHHHHHHHhcCC--ceeEecCCcchHHHHHHHHHHHhhcCC---ceEEeCCCHHHHHHHHHHHHHHHhhc--
Confidence            465 6788887777766666  699999999999999999877666555   79999999999999999999988776  


Q ss_pred             cccccccceEEEEEeC
Q 028887          168 TDLEHKLCTVMALLDG  183 (202)
Q Consensus       168 ~~~~~~~~~~~~~~~g  183 (202)
                            ++++..++++
T Consensus       139 ------GLsv~~~~~~  148 (762)
T TIGR03714       139 ------GLTVSLGVVD  148 (762)
T ss_pred             ------CCcEEEEECC
Confidence                  5666666665

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.

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=98.96  E-value=2.3e-09  Score=92.57  Aligned_cols=55  Identities=29%  Similarity=0.333  Sum_probs=48.3

Q ss_pred             cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887          109 DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      ++++.||||||||++|+.++++.+... ...+++|++|+++|+.|++++++.+++.
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~-~~~~ii~v~P~~~L~~q~~~~l~~~f~~   55 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQ-KADRVIIALPTRATINAMYRRAKELFGS   55 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhC-CCCeEEEEeehHHHHHHHHHHHHHHhCc
Confidence            589999999999999999999887543 3458999999999999999999998653

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.

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

Probab=98.95  E-value=6e-09  Score=99.16  Aligned_cols=93  Identities=20%  Similarity=0.250  Sum_probs=71.2

Q ss_pred             CCCCCcHHHHHHHHh----HHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHH-HHHHHhhc
Q 028887           89 GYVLPTDIQREALPV----LFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVT-KVARVLAA  163 (202)
Q Consensus        89 g~~~~t~~Q~~~i~~----i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~-~~~~~l~~  163 (202)
                      || ++++.|.+-+..    +.++..+++.|+||+|||++|++|++...    .+.+++|++||++|+.|+. +.+..+..
T Consensus       243 ~~-e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~----~~~~vvI~t~T~~Lq~Ql~~~~i~~l~~  317 (820)
T PRK07246        243 GL-EERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS----DQRQIIVSVPTKILQDQIMAEEVKAIQE  317 (820)
T ss_pred             CC-ccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc----CCCcEEEEeCcHHHHHHHHHHHHHHHHH
Confidence            55 578899885444    34678899999999999999999988754    2348999999999999994 66777776


Q ss_pred             CCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          164 KPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       164 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      ..        ++.+..+.||.+.--..++-.
T Consensus       318 ~~--------~~~~~~~kg~~~ylcl~k~~~  340 (820)
T PRK07246        318 VF--------HIDCHSLKGPQNYLKLDAFYD  340 (820)
T ss_pred             hc--------CCcEEEEECCcccccHHHHHH
Confidence            54        456677888877665554433

>TIGR00595 priA primosomal protein N'

Probab=98.94  E-value=3.8e-09  Score=95.65  Aligned_cols=73  Identities=27%  Similarity=0.401  Sum_probs=57.1

Q ss_pred             EEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHH--
Q 028887          111 ILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRR--  188 (202)
Q Consensus       111 l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~--  188 (202)
                      +++|+||||||++|+..+.+.+..++   ++|||+|+++|+.|+++++++.++..            +.++|+.....  
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~g~---~vLvlvP~i~L~~Q~~~~l~~~f~~~------------v~vlhs~~~~~er   65 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLALGK---SVLVLVPEIALTPQMIQRFKYRFGSQ------------VAVLHSGLSDSEK   65 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHcCC---eEEEEeCcHHHHHHHHHHHHHHhCCc------------EEEEECCCCHHHH
Confidence            47899999999999988877777766   89999999999999999999876542            55677755443  


Q ss_pred             HHHHHHHhcC
Q 028887          189 HKSWLKVLYS  198 (202)
Q Consensus       189 ~~~~l~~l~~  198 (202)
                      ...|.+...+
T Consensus        66 ~~~~~~~~~g   75 (505)
T TIGR00595        66 LQAWRKVKNG   75 (505)
T ss_pred             HHHHHHHHcC
Confidence            3556655443

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).

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=98.91  E-value=7e-09  Score=97.99  Aligned_cols=91  Identities=21%  Similarity=0.096  Sum_probs=72.6

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCC
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLD  167 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~  167 (202)
                      .|. .|+++|-..--.+..|  -++.++||+|||++|.+|++.....++   .++|++||++||.|..+++..+....  
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-RHFDVQLIGGMVLHEG--NIAEMRTGEGKTLVATLPAYLNAISGR---GVHIVTVNDYLAKRDSQWMKPIYEFL--  150 (896)
T ss_pred             cCC-CcchHHHhhhhhhccC--ccccccCCCCchHHHHHHHHHHHhcCC---CEEEEcCCHHHHHHHHHHHHHHhccc--
Confidence            354 6889996655555555  478999999999999999998776665   69999999999999999999999876  


Q ss_pred             cccccccceEEEEEeCCccHHHHHH
Q 028887          168 TDLEHKLCTVMALLDGGMLRRHKSW  192 (202)
Q Consensus       168 ~~~~~~~~~~~~~~~g~~~~~~~~~  192 (202)
                            ++++.+++||.+...++..
T Consensus       151 ------GLtv~~i~gg~~~~~r~~~  169 (896)
T PRK13104        151 ------GLTVGVIYPDMSHKEKQEA  169 (896)
T ss_pred             ------CceEEEEeCCCCHHHHHHH
Confidence                  5787777777665555443

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

Probab=98.90  E-value=1.4e-08  Score=93.79  Aligned_cols=84  Identities=20%  Similarity=0.167  Sum_probs=63.7

Q ss_pred             HhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh-cCCCCcccccccceEEEE
Q 028887          102 PVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA-AKPLDTDLEHKLCTVMAL  180 (202)
Q Consensus       102 ~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~-~~~~~~~~~~~~~~~~~~  180 (202)
                      ..+.+++.+++.|+||+|||++|++|++..+... .+.++||++||++|+.|+.+.+..+. ....      ..++++.+
T Consensus        11 ~al~~~~~lliEA~TGtGKTlAYLlpal~~~~~~-~~~rvlIstpT~~Lq~Ql~~~l~~l~~~~l~------~~i~~~~l   83 (636)
T TIGR03117        11 TSLRQKRIGMLEASTGVGKTLAMIMAALTMLKER-PDQKIAIAVPTLALMGQLWSELERLTAEGLA------GPVQAGFF   83 (636)
T ss_pred             HHHhcCCeEEEEcCCCCcHHHHHHHHHHHHHHhc-cCceEEEECCcHHHHHHHHHHHHHHHHhhcC------CCeeEEEE
Confidence            3445678899999999999999999999877632 13489999999999999999988887 3221      13667777


Q ss_pred             EeCCccHHHHHH
Q 028887          181 LDGGMLRRHKSW  192 (202)
Q Consensus       181 ~~g~~~~~~~~~  192 (202)
                      .|+.++--..++
T Consensus        84 kGr~nYlCl~rl   95 (636)
T TIGR03117        84 PGSQEFVSPGAL   95 (636)
T ss_pred             ECCcccccHHHH
Confidence            777776544333

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.

>PRK13766 Hef nuclease; Provisional

Probab=98.89  E-value=1.9e-08  Score=95.39  Aligned_cols=89  Identities=19%  Similarity=0.238  Sum_probs=69.5

Q ss_pred             CCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCCccc
Q 028887           91 VLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDL  170 (202)
Q Consensus        91 ~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~  170 (202)
                      -.+.+.|.+.+..++.+ ++++++|||+|||.++++++...+..  .+.++|||+||++|+.|+.+.++++++..     
T Consensus        14 ~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~~--~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~-----   85 (773)
T PRK13766         14 IEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLHK--KGGKVLILAPTKPLVEQHAEFFRKFLNIP-----   85 (773)
T ss_pred             CCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHHh--CCCeEEEEeCcHHHHHHHHHHHHHHhCCC-----
Confidence            36889999999888877 89999999999999999999887742  33489999999999999999999887542     


Q ss_pred             ccccceEEEEEeCCccHHHHH
Q 028887          171 EHKLCTVMALLDGGMLRRHKS  191 (202)
Q Consensus       171 ~~~~~~~~~~~~g~~~~~~~~  191 (202)
                         ... +.+++|.....++.
T Consensus        86 ---~~~-v~~~~g~~~~~~r~  102 (773)
T PRK13766         86 ---EEK-IVVFTGEVSPEKRA  102 (773)
T ss_pred             ---Cce-EEEEeCCCCHHHHH
Confidence               123 44555655444433

>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=98.86  E-value=8.1e-09  Score=79.91  Aligned_cols=67  Identities=31%  Similarity=0.381  Sum_probs=55.8

Q ss_pred             CCcHHHHHHHHhHHc-------CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFS-------SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~-------g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      ++++.|.+++..+..       .+.+++.++||+|||.+++..+.+...      ++++++|+++|+.|+.+.+..+...
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~------~~l~~~p~~~l~~Q~~~~~~~~~~~   76 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELAR------KVLIVAPNISLLEQWYDEFDDFGSE   76 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHC------EEEEEESSHHHHHHHHHHHHHHSTT
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcccc------ceeEecCHHHHHHHHHHHHHHhhhh
Confidence            478999999998863       588999999999999999876555443      7999999999999999999766654

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 ....

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=98.80  E-value=1.4e-08  Score=100.68  Aligned_cols=49  Identities=29%  Similarity=0.472  Sum_probs=42.8

Q ss_pred             EeccCCCchHHHHHHHHHHHHHhc----------CCccEEEEecCCHHhHHHHHHHHHH
Q 028887          112 LHAQTGSGKTLTYLLLIFSLVNAQ----------RSAVQAVIVVPTRELGMQVTKVARV  160 (202)
Q Consensus       112 ~~a~TGsGKT~~~l~~~l~~l~~~----------~~~~~~Lil~Ptr~La~Q~~~~~~~  160 (202)
                      |++|||||||++|++|+++.+...          ..++++|||+|+|+|+.|+.+.++.
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~~~~~~~~~~~~~~~raLYISPLKALa~Dv~~~L~~   59 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQI   59 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhcccccccccccCCCCEEEEEeChHHHHHHHHHHHHH
Confidence            479999999999999999988643          1357999999999999999999875

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

Probab=98.75  E-value=3e-08  Score=94.85  Aligned_cols=75  Identities=20%  Similarity=0.195  Sum_probs=68.0

Q ss_pred             HHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887           85 MEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus        85 l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      ..+.|| .+.+.|++++-.+..|..++++||||+|||++.-.++...+..+.   +++|.+|.++|.+|.++.+...++
T Consensus       113 ~~~~~F-~LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~~q---rviYTsPIKALsNQKyrdl~~~fg  187 (1041)
T COG4581         113 AREYPF-ELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRDGQ---RVIYTSPIKALSNQKYRDLLAKFG  187 (1041)
T ss_pred             HHhCCC-CcCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHcCC---ceEeccchhhhhhhHHHHHHHHhh
Confidence            345677 589999999999999999999999999999999999988888777   799999999999999999887766

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

Probab=98.74  E-value=8.5e-08  Score=87.78  Aligned_cols=100  Identities=23%  Similarity=0.259  Sum_probs=79.8

Q ss_pred             HHHCCCCCCcHHHHHHHHhHHcC------CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHH
Q 028887           85 MEETGYVLPTDIQREALPVLFSS------RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVA  158 (202)
Q Consensus        85 l~~~g~~~~t~~Q~~~i~~i~~g------~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~  158 (202)
                      +..+.| ++|..|++++..|...      .+=+++|.-|||||++.+++++..+..|.   |+..++||--||.|.++.+
T Consensus       256 ~~~LPF-~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~G~---Q~ALMAPTEILA~QH~~~~  331 (677)
T COG1200         256 LAALPF-KLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEAGY---QAALMAPTEILAEQHYESL  331 (677)
T ss_pred             HHhCCC-CccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHcCC---eeEEeccHHHHHHHHHHHH
Confidence            366777 6999999999999765      35689999999999999999999999888   9999999999999999999


Q ss_pred             HHhhcCCCCcccccccceEEEEEeCCccHHHHHHHHHh
Q 028887          159 RVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVL  196 (202)
Q Consensus       159 ~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~l  196 (202)
                      .++++..        ++.|..+.|.......++.+..+
T Consensus       332 ~~~l~~~--------~i~V~lLtG~~kgk~r~~~l~~l  361 (677)
T COG1200         332 RKWLEPL--------GIRVALLTGSLKGKARKEILEQL  361 (677)
T ss_pred             HHHhhhc--------CCeEEEeecccchhHHHHHHHHH
Confidence            9999876        46654444444433334444433

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

Probab=98.74  E-value=3.7e-08  Score=87.91  Aligned_cols=67  Identities=30%  Similarity=0.320  Sum_probs=57.7

Q ss_pred             CCcHHHHHHHHhHHc----CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFS----SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~----g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .+.+.|++++..+.+    ++..++..|||+|||.+++..+....   .   .+|||||+++|+.|+.+.+......
T Consensus        36 ~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~~---~---~~Lvlv~~~~L~~Qw~~~~~~~~~~  106 (442)
T COG1061          36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELK---R---STLVLVPTKELLDQWAEALKKFLLL  106 (442)
T ss_pred             CCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHhc---C---CEEEEECcHHHHHHHHHHHHHhcCC
Confidence            689999999999988    89999999999999999988774422   1   3999999999999999888777664

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

Probab=98.71  E-value=2.4e-07  Score=87.87  Aligned_cols=99  Identities=25%  Similarity=0.287  Sum_probs=78.3

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCC
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLD  167 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~  167 (202)
                      .|+ .|+..|+.....+..|+.+-+.||||.|||..-++..+-...+++   ++++++||..|+.|+++++.+++.... 
T Consensus        79 ~G~-~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~a~kgk---r~yii~PT~~Lv~Q~~~kl~~~~e~~~-  153 (1187)
T COG1110          79 TGF-RPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLAKKGK---RVYIIVPTTTLVRQVYERLKKFAEDAG-  153 (1187)
T ss_pred             hCC-CchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHHHHhcCC---eEEEEecCHHHHHHHHHHHHHHHhhcC-
Confidence            366 899999999999999999999999999999877666555555555   899999999999999999999997653 


Q ss_pred             cccccccceEEEEEeCCccHHH-HHHHHHhc
Q 028887          168 TDLEHKLCTVMALLDGGMLRRH-KSWLKVLY  197 (202)
Q Consensus       168 ~~~~~~~~~~~~~~~g~~~~~~-~~~l~~l~  197 (202)
                            ...+..+||+....++ .+.++.+.
T Consensus       154 ------~~~~~~~yh~~l~~~ekee~le~i~  178 (1187)
T COG1110         154 ------SLDVLVVYHSALPTKEKEEALERIE  178 (1187)
T ss_pred             ------CcceeeeeccccchHHHHHHHHHHh
Confidence                  2344444999865555 45555544

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=98.71  E-value=7.1e-08  Score=81.54  Aligned_cols=73  Identities=27%  Similarity=0.287  Sum_probs=58.9

Q ss_pred             CCCCCcHHHHHHHH----hHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCC---ccEEEEecCCHHhHHHHHHHHHHh
Q 028887           89 GYVLPTDIQREALP----VLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS---AVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus        89 g~~~~t~~Q~~~i~----~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~---~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      .| .|++.|.+.+.    .+..|.++++.+|||+|||++|+.|++..+...+.   ..++++.++|..+..|....++++
T Consensus         6 Py-~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00489        6 PY-EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CC-CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            44 46999999554    45678999999999999999999999877654332   237999999999999988888776


Q ss_pred             h
Q 028887          162 A  162 (202)
Q Consensus       162 ~  162 (202)
                      .
T Consensus        85 ~   85 (289)
T smart00489       85 M   85 (289)
T ss_pred             c
Confidence            4

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=98.71  E-value=7.1e-08  Score=81.54  Aligned_cols=73  Identities=27%  Similarity=0.287  Sum_probs=58.9

Q ss_pred             CCCCCcHHHHHHHH----hHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCC---ccEEEEecCCHHhHHHHHHHHHHh
Q 028887           89 GYVLPTDIQREALP----VLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS---AVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus        89 g~~~~t~~Q~~~i~----~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~---~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      .| .|++.|.+.+.    .+..|.++++.+|||+|||++|+.|++..+...+.   ..++++.++|..+..|....++++
T Consensus         6 Py-~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00488        6 PY-EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CC-CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            44 46999999554    45678999999999999999999999877654332   237999999999999988888776


Q ss_pred             h
Q 028887          162 A  162 (202)
Q Consensus       162 ~  162 (202)
                      .
T Consensus        85 ~   85 (289)
T smart00488       85 M   85 (289)
T ss_pred             c
Confidence            4

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

Probab=98.66  E-value=8.2e-08  Score=88.95  Aligned_cols=71  Identities=21%  Similarity=0.236  Sum_probs=63.1

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .+...|.+.....+ |+++++++|||+|||.+...-+.++++.-.. .++++++|++-|+.|+..++..++..
T Consensus        62 ~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~-~KiVF~aP~~pLv~QQ~a~~~~~~~~  132 (746)
T KOG0354|consen   62 ELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPK-GKVVFLAPTRPLVNQQIACFSIYLIP  132 (746)
T ss_pred             cccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCCc-ceEEEeeCCchHHHHHHHHHhhccCc
Confidence            57889999998888 9999999999999999999999998875433 48999999999999999888888765

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=98.63  E-value=1.5e-07  Score=89.51  Aligned_cols=62  Identities=21%  Similarity=0.233  Sum_probs=51.1

Q ss_pred             HHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887           98 REALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus        98 ~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      .+.+..+.++++++++|+||||||.+|.+++++....+   .+++|+.|+|++|.|+.+++.+..
T Consensus        11 ~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~~~---~~ilvlqPrR~aA~qia~rva~~l   72 (812)
T PRK11664         11 PELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGIN---GKIIMLEPRRLAARNVAQRLAEQL   72 (812)
T ss_pred             HHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCCcC---CeEEEECChHHHHHHHHHHHHHHh
Confidence            34455667789999999999999999999998764322   389999999999999999986543

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

Probab=98.61  E-value=3.7e-07  Score=80.98  Aligned_cols=93  Identities=20%  Similarity=0.234  Sum_probs=73.5

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCCcccc
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLE  171 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~  171 (202)
                      .+...|.......+.+ ++++..|||-|||.+.++-+...+...+.  ++|+|+||+-|+.|..+.+++..+-+.++   
T Consensus        15 e~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~~~--kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~---   88 (542)
T COG1111          15 EPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWFGG--KVLFLAPTKPLVLQHAEFCRKVTGIPEDE---   88 (542)
T ss_pred             cHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhcCC--eEEEecCCchHHHHHHHHHHHHhCCChhh---
Confidence            4566777666665555 89999999999999999999888865443  79999999999999999999999875432   


Q ss_pred             cccceEEEEEeCCccHHHHHHHHHh
Q 028887          172 HKLCTVMALLDGGMLRRHKSWLKVL  196 (202)
Q Consensus       172 ~~~~~~~~~~~g~~~~~~~~~l~~l  196 (202)
                            ++.++|...++.++.++.-
T Consensus        89 ------i~~ltGev~p~~R~~~w~~  107 (542)
T COG1111          89 ------IAALTGEVRPEEREELWAK  107 (542)
T ss_pred             ------eeeecCCCChHHHHHHHhh
Confidence                  6678887777766665543

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

Probab=98.59  E-value=2.1e-07  Score=84.82  Aligned_cols=69  Identities=25%  Similarity=0.333  Sum_probs=62.7

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      +||..+.+.|.++|..+++|+|+++.-|||.||+++|.+|.+-.   .+   -+||++|..+|..++.+.++..+
T Consensus        13 fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~---~G---~TLVVSPLiSLM~DQV~~l~~~G   81 (590)
T COG0514          13 FGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL---EG---LTLVVSPLISLMKDQVDQLEAAG   81 (590)
T ss_pred             hCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc---CC---CEEEECchHHHHHHHHHHHHHcC
Confidence            58999999999999999999999999999999999999998553   22   58999999999999999998776

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=98.58  E-value=1.9e-07  Score=88.08  Aligned_cols=90  Identities=21%  Similarity=0.155  Sum_probs=72.2

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHH-HHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCC
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIF-SLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPL  166 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l-~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~  166 (202)
                      .|. .|+++|-...-.+..|+  +..+.||+|||+++.+|++ ..+ .++   ++-|++||..||.|..+.+..+.... 
T Consensus        78 lg~-~~~dvQlig~l~L~~G~--Iaem~TGeGKTLva~lpa~l~aL-~G~---~V~IvTpn~yLA~rd~e~~~~l~~~L-  149 (830)
T PRK12904         78 LGM-RHFDVQLIGGMVLHEGK--IAEMKTGEGKTLVATLPAYLNAL-TGK---GVHVVTVNDYLAKRDAEWMGPLYEFL-  149 (830)
T ss_pred             hCC-CCCccHHHhhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHH-cCC---CEEEEecCHHHHHHHHHHHHHHHhhc-
Confidence            465 68999988776666664  8899999999999999996 555 344   57799999999999999999999876 


Q ss_pred             CcccccccceEEEEEeCCccHHHHHH
Q 028887          167 DTDLEHKLCTVMALLDGGMLRRHKSW  192 (202)
Q Consensus       167 ~~~~~~~~~~~~~~~~g~~~~~~~~~  192 (202)
                             ++++.++++|.+...+++.
T Consensus       150 -------Glsv~~i~~~~~~~er~~~  168 (830)
T PRK12904        150 -------GLSVGVILSGMSPEERREA  168 (830)
T ss_pred             -------CCeEEEEcCCCCHHHHHHh
Confidence                   6787777777666665544

>PRK09694 helicase Cas3; Provisional

Probab=98.57  E-value=3.1e-07  Score=87.78  Aligned_cols=71  Identities=24%  Similarity=0.286  Sum_probs=56.9

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      .|+|.|+.+......+.-+++.+|||+|||++.+......+..++ ..+++|..||+++++|++++++++..
T Consensus       286 ~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~~~~~-~~gi~~aLPT~Atan~m~~Rl~~~~~  356 (878)
T PRK09694        286 QPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLIDQGL-ADSIIFALPTQATANAMLSRLEALAS  356 (878)
T ss_pred             CChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHHHhCC-CCeEEEECcHHHHHHHHHHHHHHHHH
Confidence            799999988654445667899999999999999887765554432 34799999999999999999987554

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=98.52  E-value=6.6e-07  Score=85.19  Aligned_cols=62  Identities=15%  Similarity=0.175  Sum_probs=51.9

Q ss_pred             HHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887           98 REALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus        98 ~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      .+.+..+.++.+++++|+||||||.+|.+++++....   +.+++|+.|+|++|.|+.+++.+..
T Consensus         8 ~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~~---~~~ilvlqPrR~aA~qiA~rva~~~   69 (819)
T TIGR01970         8 PALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPGI---GGKIIMLEPRRLAARSAAQRLASQL   69 (819)
T ss_pred             HHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhcc---CCeEEEEeCcHHHHHHHHHHHHHHh
Confidence            3455566778999999999999999999999987643   3489999999999999999986443

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.

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

Probab=98.50  E-value=1.3e-06  Score=84.59  Aligned_cols=87  Identities=22%  Similarity=0.215  Sum_probs=64.9

Q ss_pred             CCCCCcHHHHHHHHhH----HcCCcEEEeccCCCchHHHHHHHHHHHHH-hcCCccEEEEecCCHHhHHHHHHH----HH
Q 028887           89 GYVLPTDIQREALPVL----FSSRDCILHAQTGSGKTLTYLLLIFSLVN-AQRSAVQAVIVVPTRELGMQVTKV----AR  159 (202)
Q Consensus        89 g~~~~t~~Q~~~i~~i----~~g~~~l~~a~TGsGKT~~~l~~~l~~l~-~~~~~~~~Lil~Ptr~La~Q~~~~----~~  159 (202)
                      || ++.+.|.+-+..+    ..++.+++.|+||+|||++|++|.+.... .++   +++|-++|+.|..|+.+.    ++
T Consensus       255 ~~-e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~~~~---~vvIsT~T~~LQ~Ql~~kDiP~L~  330 (928)
T PRK08074        255 KY-EKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKKKEE---PVVISTYTIQLQQQLLEKDIPLLQ  330 (928)
T ss_pred             CC-cCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhccCC---eEEEEcCCHHHHHHHHHhhHHHHH
Confidence            55 5799998866544    46788999999999999999999976554 334   799999999999998763    55


Q ss_pred             HhhcCCCCcccccccceEEEEEeCCccHH
Q 028887          160 VLAAKPLDTDLEHKLCTVMALLDGGMLRR  188 (202)
Q Consensus       160 ~l~~~~~~~~~~~~~~~~~~~~~g~~~~~  188 (202)
                      ++.+.         .++++.+-|.++.--
T Consensus       331 ~~~~~---------~~~~~~lKGr~nYlc  350 (928)
T PRK08074        331 KIFPF---------PVEAALLKGRSHYLC  350 (928)
T ss_pred             HHcCC---------CceEEEEEccccccc
Confidence            55543         255666666665443

>TIGR00603 rad25 DNA repair helicase rad25

Probab=98.45  E-value=1.1e-06  Score=82.27  Aligned_cols=66  Identities=17%  Similarity=0.240  Sum_probs=55.1

Q ss_pred             CCcHHHHHHHHhHHc-C--CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887           92 LPTDIQREALPVLFS-S--RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~-g--~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      .+.+.|.+++..++. |  +..++..|||+|||++.+..+.. +  ++   ++|||||+.+|+.||.+.|.+++.
T Consensus       255 ~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~-l--~k---~tLILvps~~Lv~QW~~ef~~~~~  323 (732)
T TIGR00603       255 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACT-V--KK---SCLVLCTSAVSVEQWKQQFKMWST  323 (732)
T ss_pred             CcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHH-h--CC---CEEEEeCcHHHHHHHHHHHHHhcC
Confidence            578999999998873 4  36899999999999998866533 2  23   699999999999999999999864

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).

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=98.44  E-value=1.7e-06  Score=63.01  Aligned_cols=55  Identities=44%  Similarity=0.596  Sum_probs=46.8

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      +++++.++||+|||..++..+......+ ...++++++|++.++.|+.+.+.....
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~-~~~~~lv~~p~~~l~~~~~~~~~~~~~   55 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSL-KGGQVLVLAPTRELANQVAERLKELFG   55 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhcc-cCCCEEEEcCcHHHHHHHHHHHHHHhh
Confidence            4689999999999999999988877642 234799999999999999998888775

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

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

Probab=98.44  E-value=9.2e-07  Score=76.37  Aligned_cols=106  Identities=17%  Similarity=0.224  Sum_probs=78.7

Q ss_pred             HHHHhCCCC--HHHHHHHH-HCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecC
Q 028887           70 RELCQGHVP--EHVLRRME-ETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP  146 (202)
Q Consensus        70 ~~l~~~gl~--~~l~~~l~-~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~P  146 (202)
                      ..|.+.+++  .+..+.|. ....+++.|.|..+|...+.|.|.++.-|||.||+++|.+|.+-   .++   -+||++|
T Consensus        69 aawdkd~fpws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~---adg---~alvi~p  142 (695)
T KOG0353|consen   69 AAWDKDDFPWSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALC---ADG---FALVICP  142 (695)
T ss_pred             cccccCCCCCchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHh---cCC---ceEeech
Confidence            345555544  33334442 23456889999999999999999999999999999999999854   233   6999999


Q ss_pred             CHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          147 TRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       147 tr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      .++|..++.-+++.++-.             ..++......++.+|..
T Consensus       143 lislmedqil~lkqlgi~-------------as~lnansske~~k~v~  177 (695)
T KOG0353|consen  143 LISLMEDQILQLKQLGID-------------ASMLNANSSKEEAKRVE  177 (695)
T ss_pred             hHHHHHHHHHHHHHhCcc-------------hhhccCcccHHHHHHHH
Confidence            999999988899988754             23444555555555553

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

Probab=98.39  E-value=4e-06  Score=80.91  Aligned_cols=97  Identities=24%  Similarity=0.185  Sum_probs=78.8

Q ss_pred             CCCCCCcHHHHHHHHhHHc----C--CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887           88 TGYVLPTDIQREALPVLFS----S--RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~----g--~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      .+| .-|+.|..||..+..    +  .|=++||--|-|||++.+=+++..+..++   |+.|||||--||.|.++.|++-
T Consensus       591 FPy-eET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~GK---QVAvLVPTTlLA~QHy~tFkeR  666 (1139)
T COG1197         591 FPY-EETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMDGK---QVAVLVPTTLLAQQHYETFKER  666 (1139)
T ss_pred             CCC-cCCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhcCCC---eEEEEcccHHhHHHHHHHHHHH
Confidence            455 459999999999864    3  58899999999999999999999999887   9999999999999999999988


Q ss_pred             hcCCCCcccccccceEEEEEeC-CccHHHHHHHHHhc
Q 028887          162 AAKPLDTDLEHKLCTVMALLDG-GMLRRHKSWLKVLY  197 (202)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~~g-~~~~~~~~~l~~l~  197 (202)
                      +.+.+        ++ +.+... .+..+|++.++.+.
T Consensus       667 F~~fP--------V~-I~~LSRF~s~kE~~~il~~la  694 (1139)
T COG1197         667 FAGFP--------VR-IEVLSRFRSAKEQKEILKGLA  694 (1139)
T ss_pred             hcCCC--------ee-EEEecccCCHHHHHHHHHHHh
Confidence            87752        44 344444 55666677777664

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

Probab=98.39  E-value=1.5e-06  Score=83.93  Aligned_cols=89  Identities=21%  Similarity=0.216  Sum_probs=71.6

Q ss_pred             CCCCCcHHHHHHHHhHHcC-CcEEEeccCCCchHHHHHHHHHHHHHhcCC--------ccEEEEecCCHHhHHHHHHHHH
Q 028887           89 GYVLPTDIQREALPVLFSS-RDCILHAQTGSGKTLTYLLLIFSLVNAQRS--------AVQAVIVVPTRELGMQVTKVAR  159 (202)
Q Consensus        89 g~~~~t~~Q~~~i~~i~~g-~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~--------~~~~Lil~Ptr~La~Q~~~~~~  159 (202)
                      |...++.+|....+..+.+ .++++|||||+|||.+.++.+++.+..+.+        ..++.|++|+++|+..+...|.
T Consensus       306 g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKaLvqE~VgsfS  385 (1674)
T KOG0951|consen  306 GKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKALVQEMVGSFS  385 (1674)
T ss_pred             cchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeHHHHHHHHHHHHH
Confidence            5567899999999998876 579999999999999999999999876432        3589999999999999887765


Q ss_pred             HhhcCCCCcccccccceEEEEEeCCc
Q 028887          160 VLAAKPLDTDLEHKLCTVMALLDGGM  185 (202)
Q Consensus       160 ~l~~~~~~~~~~~~~~~~~~~~~g~~  185 (202)
                      +-....        +++|.-+.|.+.
T Consensus       386 kRla~~--------GI~V~ElTgD~~  403 (1674)
T KOG0951|consen  386 KRLAPL--------GITVLELTGDSQ  403 (1674)
T ss_pred             hhcccc--------CcEEEEeccccc
Confidence            554443        577766666544

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=98.36  E-value=1.4e-06  Score=82.59  Aligned_cols=85  Identities=24%  Similarity=0.054  Sum_probs=68.3

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCC
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLD  167 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~  167 (202)
                      .|. .|+++|-..--.+..|  -+...+||+|||++|.+|++.....++   .+.|++|+.+||.|..+++..+....  
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-RHFDVQLLGGMVLDSN--RIAEMRTGEGKTLTATLPAYLNALTGK---GVHVITVNDYLARRDAENNRPLFEFL--  150 (908)
T ss_pred             hCC-CcCchHHhcchHhcCC--ccccccCCCCchHHHHHHHHHHHhcCC---CEEEEeCCHHHHHHHHHHHHHHHHhc--
Confidence            355 5788986554444444  578999999999999999988776666   69999999999999999999999886  


Q ss_pred             cccccccceEEEEEeCCcc
Q 028887          168 TDLEHKLCTVMALLDGGML  186 (202)
Q Consensus       168 ~~~~~~~~~~~~~~~g~~~  186 (202)
                            ++++-++++|.+.
T Consensus       151 ------Glsv~~i~~~~~~  163 (908)
T PRK13107        151 ------GLTVGINVAGLGQ  163 (908)
T ss_pred             ------CCeEEEecCCCCH
Confidence                  6777777776554

>PRK14873 primosome assembly protein PriA; Provisional

Probab=98.31  E-value=2e-06  Score=80.20  Aligned_cols=73  Identities=23%  Similarity=0.294  Sum_probs=60.9

Q ss_pred             EeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhc-CCCCcccccccceEEEEEeCCccHHH-
Q 028887          112 LHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA-KPLDTDLEHKLCTVMALLDGGMLRRH-  189 (202)
Q Consensus       112 ~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~-~~~~~~~~~~~~~~~~~~~g~~~~~~-  189 (202)
                      ..+.+|||||.+|+-.+.+.+..++   ++|||+|++.|+.|+.++|+..++ ..            +.++|......+ 
T Consensus       165 ~~~~~GSGKTevyl~~i~~~l~~Gk---~vLvLvPEi~lt~q~~~rl~~~f~~~~------------v~~lhS~l~~~~R  229 (665)
T PRK14873        165 WQALPGEDWARRLAAAAAATLRAGR---GALVVVPDQRDVDRLEAALRALLGAGD------------VAVLSAGLGPADR  229 (665)
T ss_pred             hhcCCCCcHHHHHHHHHHHHHHcCC---eEEEEecchhhHHHHHHHHHHHcCCCc------------EEEECCCCCHHHH
Confidence            3444699999999999999999888   999999999999999999998886 32            777888665554 


Q ss_pred             -HHHHHHhcCC
Q 028887          190 -KSWLKVLYSL  199 (202)
Q Consensus       190 -~~~l~~l~~~  199 (202)
                       ..|++...+-
T Consensus       230 ~~~w~~~~~G~  240 (665)
T PRK14873        230 YRRWLAVLRGQ  240 (665)
T ss_pred             HHHHHHHhCCC
Confidence             6888887763

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.25  E-value=4.2e-06  Score=78.85  Aligned_cols=74  Identities=24%  Similarity=0.238  Sum_probs=63.4

Q ss_pred             CCCCCcHHHHHHHHhH----HcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887           89 GYVLPTDIQREALPVL----FSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus        89 g~~~~t~~Q~~~i~~i----~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      .|..++|.|.+.+..+    ..|.+.++.+|||+|||++.+.|.+......+...++++.+.|.....|+.+.++++.
T Consensus         7 Py~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~~~~kIiy~sRThsQl~q~i~Elk~~~   84 (705)
T TIGR00604         7 PYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRKLM   84 (705)
T ss_pred             CCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhccccccEEEEcccchHHHHHHHHHHhhh
Confidence            4666799999988764    4678999999999999999999999987654444689999999999999999999864

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).

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

Probab=98.24  E-value=4.2e-06  Score=82.12  Aligned_cols=70  Identities=21%  Similarity=0.226  Sum_probs=55.3

Q ss_pred             CCcHHHHHHHHhHH----cC-CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887           92 LPTDIQREALPVLF----SS-RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~----~g-~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      .+.+.|.+||..+.    .| +..+++.+||||||.+.+..+ ..+.+.....++|+|+|+++|+.|+.+.|+.+.
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~li-~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~~~~  487 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIALM-YRLLKAKRFRRILFLVDRSALGEQAEDAFKDTK  487 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHHHH-HHHHhcCccCeEEEEecHHHHHHHHHHHHHhcc
Confidence            58999999998764    33 678999999999998855444 444433334589999999999999999998774

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.22  E-value=1.3e-05  Score=75.50  Aligned_cols=65  Identities=31%  Similarity=0.490  Sum_probs=51.9

Q ss_pred             CCCCCcHHHHHHHHhH---HcC------CcEEEeccCCCchHHHHHHHHHHHHH-hcCCccEEEEecCCHHhHHHHHHH
Q 028887           89 GYVLPTDIQREALPVL---FSS------RDCILHAQTGSGKTLTYLLLIFSLVN-AQRSAVQAVIVVPTRELGMQVTKV  157 (202)
Q Consensus        89 g~~~~t~~Q~~~i~~i---~~g------~~~l~~a~TGsGKT~~~l~~~l~~l~-~~~~~~~~Lil~Ptr~La~Q~~~~  157 (202)
                      || ++.+.|.+-+..+   +.+      +.+++.|+||+|||++||+|.+.... .++   +++|-+.|+.|-.|+.+.
T Consensus        23 ~~-e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~~~k---~vVIST~T~~LQeQL~~k   97 (697)
T PRK11747         23 GF-IPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARAEKK---KLVISTATVALQEQLVSK   97 (697)
T ss_pred             CC-CcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHHcCC---eEEEEcCCHHHHHHHHhh
Confidence            66 5799998866554   333      67899999999999999999976544 445   799999999999998643

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

Probab=98.19  E-value=5.9e-06  Score=72.39  Aligned_cols=69  Identities=20%  Similarity=0.272  Sum_probs=57.0

Q ss_pred             CCCCC-CcHHHHHHHHhHHcC-CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887           88 TGYVL-PTDIQREALPVLFSS-RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus        88 ~g~~~-~t~~Q~~~i~~i~~g-~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      .|+.. -++.|+.++..+..+ .||.|+.|||+||+++|.+|.+-   .++   ..||++|.++|..++.+.+..+-
T Consensus        15 FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~---~~g---ITIV~SPLiALIkDQiDHL~~LK   85 (641)
T KOG0352|consen   15 FGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALV---HGG---ITIVISPLIALIKDQIDHLKRLK   85 (641)
T ss_pred             hCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHH---hCC---eEEEehHHHHHHHHHHHHHHhcC
Confidence            46654 389999999987654 79999999999999999999754   233   68999999999999888887664

>PF13245 AAA_19: Part of AAA domain

Probab=98.17  E-value=1.1e-05  Score=54.64  Aligned_cols=52  Identities=23%  Similarity=0.317  Sum_probs=40.8

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHh-cCCccEEEEecCCHHhHHHHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNA-QRSAVQAVIVVPTRELGMQVTKVA  158 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~-~~~~~~~Lil~Ptr~La~Q~~~~~  158 (202)
                      +.-+++.|+.|||||...+-.+...+.. ...+.++++++|++..+..+.+++
T Consensus        10 ~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCCHHHHHHHHHHH
Confidence            3446669999999998887777777753 111348999999999999998888

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

Probab=98.11  E-value=1.3e-05  Score=74.76  Aligned_cols=71  Identities=25%  Similarity=0.319  Sum_probs=58.3

Q ss_pred             CCCCCcHHHHHHHHhH----HcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887           89 GYVLPTDIQREALPVL----FSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus        89 g~~~~t~~Q~~~i~~i----~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      ....+++.|.+.+..+    .+++.+++.||||+|||++|+.|.+......+  .+++|.++|+.|-.|+.++...+
T Consensus        12 ~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~~--~~viist~t~~lq~q~~~~~~~~   86 (654)
T COG1199          12 PGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEG--KKVIISTRTKALQEQLLEEDLPI   86 (654)
T ss_pred             CCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHcC--CcEEEECCCHHHHHHHHHhhcch
Confidence            3347999999988664    34566999999999999999999988765433  37999999999999999887665

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

Probab=98.07  E-value=1.1e-05  Score=64.46  Aligned_cols=69  Identities=22%  Similarity=0.311  Sum_probs=51.1

Q ss_pred             CCcHHHHHHHHhHHcCCc-EEEeccCCCchHHHHHHHHHHHH-----HhcCCccEEEEecCCHHhHHHHHHHHHH
Q 028887           92 LPTDIQREALPVLFSSRD-CILHAQTGSGKTLTYLLLIFSLV-----NAQRSAVQAVIVVPTRELGMQVTKVARV  160 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~-~l~~a~TGsGKT~~~l~~~l~~l-----~~~~~~~~~Lil~Ptr~La~Q~~~~~~~  160 (202)
                      ++++.|..|+..++.... .++.||.|||||.+....+...+     .....+.++|+++|+..-+.++.+.+.+
T Consensus         1 ~ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    1 KLNESQREAIQSALSSNGITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             ---HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            367899999999998888 99999999999966554444432     1234455899999999999999999887

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

Probab=98.05  E-value=1.2e-05  Score=74.65  Aligned_cols=70  Identities=16%  Similarity=0.149  Sum_probs=64.0

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .+.|.|..+|-.+-++..++|.|.|.+|||.+.-.+|...+....   +++|-+|-++|.+|-++.+..-+++
T Consensus       129 ~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~kQ---RVIYTSPIKALSNQKYREl~~EF~D  198 (1041)
T KOG0948|consen  129 TLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLREKQ---RVIYTSPIKALSNQKYRELLEEFKD  198 (1041)
T ss_pred             ccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHhcC---eEEeeChhhhhcchhHHHHHHHhcc
Confidence            468899999999999999999999999999999999999998877   9999999999999999888766554

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

Probab=98.03  E-value=9.3e-06  Score=78.03  Aligned_cols=93  Identities=23%  Similarity=0.180  Sum_probs=69.2

Q ss_pred             HHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCC
Q 028887           86 EETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKP  165 (202)
Q Consensus        86 ~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~  165 (202)
                      ...|...+.+.|.++|...+.|+|+++-.|||.||.++|.+|.+-   .++   -.||++|.++|...+...+....   
T Consensus       258 ~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l---~~g---itvVISPL~SLm~DQv~~L~~~~---  328 (941)
T KOG0351|consen  258 EVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALL---LGG---VTVVISPLISLMQDQVTHLSKKG---  328 (941)
T ss_pred             HHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeeccccc---cCC---ceEEeccHHHHHHHHHHhhhhcC---
Confidence            456888999999999999999999999999999999999998733   223   68999999999987766553222   


Q ss_pred             CCcccccccceEEEEEeCCccHHHHHHHHHh
Q 028887          166 LDTDLEHKLCTVMALLDGGMLRRHKSWLKVL  196 (202)
Q Consensus       166 ~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~l  196 (202)
                               +....+-++.....+...+..+
T Consensus       329 ---------I~a~~L~s~q~~~~~~~i~q~l  350 (941)
T KOG0351|consen  329 ---------IPACFLSSIQTAAERLAILQKL  350 (941)
T ss_pred             ---------cceeeccccccHHHHHHHHHHH
Confidence                     3334444445555554444444

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

Probab=98.00  E-value=2.2e-05  Score=74.41  Aligned_cols=74  Identities=18%  Similarity=0.127  Sum_probs=63.0

Q ss_pred             HCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           87 ETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        87 ~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      ..+| .+...|++||-.+..|..++|.|+|-+|||++.-.++.-....+   .+++|-+|-++|.+|-++.|++-++.
T Consensus       293 ~~pF-elD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq~h~---TR~iYTSPIKALSNQKfRDFk~tF~D  366 (1248)
T KOG0947|consen  293 IYPF-ELDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQKHM---TRTIYTSPIKALSNQKFRDFKETFGD  366 (1248)
T ss_pred             hCCC-CccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHHhhc---cceEecchhhhhccchHHHHHHhccc
Confidence            3466 58999999999999999999999999999999776664444333   38999999999999999999988765

>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=97.99  E-value=2.8e-05  Score=65.12  Aligned_cols=70  Identities=24%  Similarity=0.243  Sum_probs=56.6

Q ss_pred             CcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhc-CCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           93 PTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ-RSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        93 ~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~-~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      +|+.|.+++..  ...+++|.|..|||||.+.+.-+...+..+ ....+.|++++|+..+..+.+++......
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~~aa~e~~~ri~~~l~~   71 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTNAAAQEMRERIRELLEE   71 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCHHHHHHHHHHHHHhcCc
Confidence            57889998877  677899999999999999888888777765 34557999999999999999999887654

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 ....

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

Probab=97.91  E-value=3e-05  Score=72.66  Aligned_cols=70  Identities=27%  Similarity=0.305  Sum_probs=55.6

Q ss_pred             CcHHHHHHHHhHH----c------CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887           93 PTDIQREALPVLF----S------SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus        93 ~t~~Q~~~i~~i~----~------g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      +...|..++..+.    .      .+..++..+||||||+..+..+...+. .....++|+|+|.++|..|+.+.|..++
T Consensus       239 ~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~~-~~~~~~vl~lvdR~~L~~Q~~~~f~~~~  317 (667)
T TIGR00348       239 QRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKALE-LLKNPKVFFVVDRRELDYQLMKEFQSLQ  317 (667)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHHh-hcCCCeEEEEECcHHHHHHHHHHHHhhC
Confidence            6778999997752    2      256899999999999987776655443 3345689999999999999999999887


Q ss_pred             c
Q 028887          163 A  163 (202)
Q Consensus       163 ~  163 (202)
                      .
T Consensus       318 ~  318 (667)
T TIGR00348       318 K  318 (667)
T ss_pred             C
Confidence            4

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

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=97.83  E-value=9.6e-05  Score=69.92  Aligned_cols=88  Identities=26%  Similarity=0.152  Sum_probs=70.9

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCC
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLD  167 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~  167 (202)
                      .|. .|+++|-..--.+..|+  +..-.||+|||++..+|++-....|.   ++-+++|+--||.|-++.+..+....  
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--IAEMKTGEGKTLTATLPVYLNALTGK---GVHVVTVNEYLSSRDATEMGELYRWL--  148 (796)
T ss_pred             hCC-CCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHcCC---CeEEEeccHHHHHhhHHHHHHHHHhc--
Confidence            465 68999988877776776  88999999999999999988888777   89999999999999999999998876  


Q ss_pred             cccccccceEEEEEeCCccHHHH
Q 028887          168 TDLEHKLCTVMALLDGGMLRRHK  190 (202)
Q Consensus       168 ~~~~~~~~~~~~~~~g~~~~~~~  190 (202)
                            ++++. ++.|....+++
T Consensus       149 ------Gl~vg-~i~~~~~~~~r  164 (796)
T PRK12906        149 ------GLTVG-LNLNSMSPDEK  164 (796)
T ss_pred             ------CCeEE-EeCCCCCHHHH
Confidence                  46654 44444444433

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

Probab=97.82  E-value=9.4e-05  Score=63.36  Aligned_cols=70  Identities=20%  Similarity=0.179  Sum_probs=60.8

Q ss_pred             CCcHHHHHHHHhH----HcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVL----FSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i----~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .+|+.|+.+-..+    .+..+.+++|.||+|||+...-.+...+..|.   ++.+.+|-.+.+..++.+++.-+..
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEMif~~i~~al~~G~---~vciASPRvDVclEl~~Rlk~aF~~  170 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEMIFQGIEQALNQGG---RVCIASPRVDVCLELYPRLKQAFSN  170 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhhhHHHHHHHHhcCC---eEEEecCcccchHHHHHHHHHhhcc
Confidence            6899998876654    46689999999999999998888888888777   8999999999999999999988874

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=97.80  E-value=0.00016  Score=67.54  Aligned_cols=88  Identities=18%  Similarity=0.130  Sum_probs=70.9

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCC
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLD  167 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~  167 (202)
                      .|. .|+++|-...-.++.|+  ++.-.||+|||++..+|+......|+   ++-+++|+--||.|-++++..+....  
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--VIEMATGEGKTLAGAIAAAGYALQGR---RVHVITVNDYLARRDAEWMGPLYEAL--  146 (764)
T ss_pred             cCC-CcchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHHcCC---CeEEEcCCHHHHHHHHHHHHHHHHhc--
Confidence            465 68999999998888874  67899999999999999988777777   89999999999999999999998876  


Q ss_pred             cccccccceEEEEEeCCccHHHH
Q 028887          168 TDLEHKLCTVMALLDGGMLRRHK  190 (202)
Q Consensus       168 ~~~~~~~~~~~~~~~g~~~~~~~  190 (202)
                            ++++-.+ .+....+++
T Consensus       147 ------GLsvg~i-~~~~~~~er  162 (764)
T PRK12326        147 ------GLTVGWI-TEESTPEER  162 (764)
T ss_pred             ------CCEEEEE-CCCCCHHHH
Confidence                  4665544 444444443

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=97.79  E-value=8.4e-05  Score=70.41  Aligned_cols=73  Identities=23%  Similarity=0.325  Sum_probs=62.1

Q ss_pred             CcHHHHHHHHhHHcC---C-cEEEeccCCCchHHHHHHHHHHHHHh-cCCccEEEEecCCHHhHHHHHHHHHHhhcCC
Q 028887           93 PTDIQREALPVLFSS---R-DCILHAQTGSGKTLTYLLLIFSLVNA-QRSAVQAVIVVPTRELGMQVTKVARVLAAKP  165 (202)
Q Consensus        93 ~t~~Q~~~i~~i~~g---~-~~l~~a~TGsGKT~~~l~~~l~~l~~-~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~  165 (202)
                      ..+.|..++..+..+   . .+++.||||.|||++.+.+....... .....+.+++.|++.+..+++++++..++..
T Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie~~~~r~~~~~~~~  273 (733)
T COG1203         196 GYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGLF  273 (733)
T ss_pred             hhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhccccccceEEEEccHHHHHHHHHHHHHhhhccc
Confidence            478888888877643   4 78999999999999999999888876 3456689999999999999999999887754

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

Probab=97.67  E-value=5.5e-05  Score=67.99  Aligned_cols=67  Identities=28%  Similarity=0.350  Sum_probs=52.5

Q ss_pred             CCcHHHHHHHHhHHcC-----CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFSS-----RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g-----~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .|+..|-+||..+..|     +.-.+-|.||||||..-.--+ ..+  ++   -+||++|.+.||-|.+..|++|++.
T Consensus        12 ~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~AnVI-~~~--~r---PtLV~AhNKTLAaQLy~Efk~fFP~   83 (663)
T COG0556          12 KPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTMANVI-AKV--QR---PTLVLAHNKTLAAQLYSEFKEFFPE   83 (663)
T ss_pred             CCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHHHHHH-HHh--CC---CeEEEecchhHHHHHHHHHHHhCcC
Confidence            6888999999887544     567889999999996643322 222  22   4899999999999999999999984

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=97.61  E-value=0.00032  Score=66.97  Aligned_cols=88  Identities=20%  Similarity=0.073  Sum_probs=67.6

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCC
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLD  167 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~  167 (202)
                      .|. .|+++|-..--.+..|  -+....||+|||++..+|++-....|+   ++-+++|+--||.|-++++..+....  
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--KIAEMRTGEGKTLVGTLAVYLNALSGK---GVHVVTVNDYLARRDANWMRPLYEFL--  150 (913)
T ss_pred             hCC-CcchhHHHhhhHhccC--ccccccCCCCChHHHHHHHHHHHHcCC---CEEEEeCCHHHHHHHHHHHHHHhccc--
Confidence            464 6899997655444444  567899999999999999987777777   89999999999999999999999876  


Q ss_pred             cccccccceEEEEEeCCccHHHH
Q 028887          168 TDLEHKLCTVMALLDGGMLRRHK  190 (202)
Q Consensus       168 ~~~~~~~~~~~~~~~g~~~~~~~  190 (202)
                            ++++.+ +.+.....++
T Consensus       151 ------Gl~v~~-i~~~~~~~er  166 (913)
T PRK13103        151 ------GLSVGI-VTPFQPPEEK  166 (913)
T ss_pred             ------CCEEEE-ECCCCCHHHH
Confidence                  466554 4444444433

>TIGR00376 DNA helicase, putative

Probab=97.59  E-value=0.00031  Score=65.55  Aligned_cols=66  Identities=24%  Similarity=0.290  Sum_probs=55.6

Q ss_pred             CCcHHHHHHHHhHHcC-CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHH
Q 028887           92 LPTDIQREALPVLFSS-RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARV  160 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g-~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~  160 (202)
                      .+++.|..++..++.. ..++++||+|+|||......+.+.+..+.   ++|+++||..-+.++.+.+..
T Consensus       157 ~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~~~g~---~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       157 NLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLVKRGL---RVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHHHcCC---CEEEEcCcHHHHHHHHHHHHh
Confidence            5799999999998876 67889999999999877666666665555   899999999999999888876

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.

>KOG1803 consensus DNA helicase [Replication, recombination and repair]

Probab=97.51  E-value=0.0003  Score=64.09  Aligned_cols=65  Identities=22%  Similarity=0.355  Sum_probs=56.3

Q ss_pred             CCcHHHHHHHHhHHcCCc-EEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHH
Q 028887           92 LPTDIQREALPVLFSSRD-CILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVAR  159 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~-~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~  159 (202)
                      .+.+-|.+|+....+.++ .+++||+|+|||.....-+.+.+.+++   ++|+..||.+-+.-+.+++-
T Consensus       185 ~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk~~k---~VLVcaPSn~AVdNiverl~  250 (649)
T KOG1803|consen  185 NLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQKK---RVLVCAPSNVAVDNIVERLT  250 (649)
T ss_pred             cccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHHcCC---eEEEEcCchHHHHHHHHHhc
Confidence            467899999988887744 789999999999999988888888887   99999999998888888644

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

Probab=97.41  E-value=0.00086  Score=53.45  Aligned_cols=63  Identities=22%  Similarity=0.326  Sum_probs=45.6

Q ss_pred             CCcHHHHHHHHhHHcCC--cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHH
Q 028887           92 LPTDIQREALPVLFSSR--DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKV  157 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~--~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~  157 (202)
                      ++++.|.+++..++.+.  -++++|+.|+|||.+ +..+...+...  +.++++++||...+..+.+.
T Consensus         1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~-l~~~~~~~~~~--g~~v~~~apT~~Aa~~L~~~   65 (196)
T PF13604_consen    1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTL-LKALAEALEAA--GKRVIGLAPTNKAAKELREK   65 (196)
T ss_dssp             -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHH-HHHHHHHHHHT--T--EEEEESSHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHH-HHHHHHHHHhC--CCeEEEECCcHHHHHHHHHh
Confidence            36899999999987543  578899999999975 34455555442  34899999998888876666

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=97.26  E-value=0.00076  Score=54.30  Aligned_cols=59  Identities=25%  Similarity=0.299  Sum_probs=42.5

Q ss_pred             CCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHh
Q 028887           91 VLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTREL  150 (202)
Q Consensus        91 ~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~L  150 (202)
                      ...|..|..++..++...-+++.|+.|||||+..+...++.+.. +..-+.++.-|..+.
T Consensus         3 ~p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~-g~~~kiii~Rp~v~~   61 (205)
T PF02562_consen    3 KPKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKE-GEYDKIIITRPPVEA   61 (205)
T ss_dssp             ---SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHT-TS-SEEEEEE-S--T
T ss_pred             cCCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHh-CCCcEEEEEecCCCC
Confidence            34688999999999988889999999999999999999998876 334467777787653

; 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=97.13  E-value=0.0033  Score=52.29  Aligned_cols=57  Identities=30%  Similarity=0.300  Sum_probs=38.1

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCc--cEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSA--VQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~--~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .+.+++.-..|+|||...+..+..........  ..+||++|. .+..||.+.+.+++..
T Consensus        25 ~~g~lL~de~GlGKT~~~i~~~~~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~~~~~   83 (299)
T PF00176_consen   25 PRGGLLADEMGLGKTITAIALISYLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEKWFDP   83 (299)
T ss_dssp             T-EEEE---TTSSHHHHHHHHHHHHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHHHSGT
T ss_pred             CCCEEEEECCCCCchhhhhhhhhhhhhccccccccceeEeecc-chhhhhhhhhcccccc
Confidence            35789999999999988766655333322211  249999999 8889999999999854

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.

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=97.07  E-value=0.0023  Score=61.04  Aligned_cols=72  Identities=22%  Similarity=0.088  Sum_probs=56.5

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCC
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKP  165 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~  165 (202)
                      .|. .|+++|-...-.+.  +.-++...||.|||+++.+|+.-....|+   .+-|++++..||.+-.+++..+....
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-RHFDVQLIGGLVLN--DGKIAEMKTGEGKTLVATLPAYLNALTGK---GVHIVTVNDYLAKRDQEWMGQIYRFL  144 (870)
T ss_pred             hCC-CCCchHhhhhHhhc--CCccccccCCCCchHHHHHHHHHHHhcCC---ceEEEeCCHHHHHHHHHHHHHHHHHc
Confidence            476 58999977654443  44788999999999999999854443455   78999999999999888888777765

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

Probab=96.93  E-value=0.018  Score=48.26  Aligned_cols=85  Identities=20%  Similarity=0.113  Sum_probs=60.6

Q ss_pred             HCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCC
Q 028887           87 ETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPL  166 (202)
Q Consensus        87 ~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~  166 (202)
                      ..|+ .|+++|..++=.+..|+  ++.-.||-|||++..+|..-....|+   .+=|++..--||..=.+++..+.... 
T Consensus        73 ~~g~-~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~G~---~V~vvT~NdyLA~RD~~~~~~~y~~L-  145 (266)
T PF07517_consen   73 TLGL-RPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQGK---GVHVVTSNDYLAKRDAEEMRPFYEFL-  145 (266)
T ss_dssp             HTS-----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTTSS----EEEEESSHHHHHHHHHHHHHHHHHT-
T ss_pred             HcCC-cccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHhcC---CcEEEeccHHHhhccHHHHHHHHHHh-
Confidence            3465 69999999997777776  89999999999998887766555555   78889999999998888887777765 


Q ss_pred             CcccccccceEEEEEeCCc
Q 028887          167 DTDLEHKLCTVMALLDGGM  185 (202)
Q Consensus       167 ~~~~~~~~~~~~~~~~g~~  185 (202)
                             ++++-.++.+..
T Consensus       146 -------Glsv~~~~~~~~  157 (266)
T PF07517_consen  146 -------GLSVGIITSDMS  157 (266)
T ss_dssp             -------T--EEEEETTTE
T ss_pred             -------hhccccCccccC
Confidence                   456555554444

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 ....

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=96.91  E-value=0.0028  Score=59.39  Aligned_cols=67  Identities=24%  Similarity=0.336  Sum_probs=52.9

Q ss_pred             CCcHHHHHHHHhHHcC-----CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFSS-----RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g-----~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .|+..|..+|..+.++     +..++.|.||||||....- +++.+  ++   .+|||+|.+.+|.|+++.++.+++.
T Consensus         9 ~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~a~-~~~~~--~~---p~Lvi~~n~~~A~ql~~el~~f~p~   80 (655)
T TIGR00631         9 QPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMAN-VIAQV--NR---PTLVIAHNKTLAAQLYNEFKEFFPE   80 (655)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHHHH-HHHHh--CC---CEEEEECCHHHHHHHHHHHHHhCCC
Confidence            6899999999887543     3567999999999977543 33322  22   5899999999999999999999864

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

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=96.87  E-value=0.004  Score=58.64  Aligned_cols=70  Identities=20%  Similarity=0.164  Sum_probs=56.6

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHh-cCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNA-QRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~-~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      .+++.|.+++..  ....++|.|..|||||.+...-+...+.. +-..-++|+|+.|+.-|..+.+++..+.+
T Consensus         2 ~Ln~~Q~~av~~--~~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v~p~~IL~lTFT~kAA~em~~Rl~~~l~   72 (672)
T PRK10919          2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQTLG   72 (672)
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHHhC
Confidence            378999998865  24568889999999999988877777764 33344799999999999999999988765

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

Probab=96.84  E-value=0.0035  Score=60.18  Aligned_cols=70  Identities=26%  Similarity=0.296  Sum_probs=60.0

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      .|...|.+.+..+-.+...++.|||-+|||.+-...+-..+.....+ -+++.+||++|++|+...++..+
T Consensus       511 ~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfisfY~iEKVLResD~~-VVIyvaPtKaLVnQvsa~VyaRF  580 (1330)
T KOG0949|consen  511 CPDEWQRELLDSVDRNESAVIVAPTSAGKTFISFYAIEKVLRESDSD-VVIYVAPTKALVNQVSANVYARF  580 (1330)
T ss_pred             CCcHHHHHHhhhhhcccceEEEeeccCCceeccHHHHHHHHhhcCCC-EEEEecchHHHhhhhhHHHHHhh
Confidence            58899999999988899999999999999999777887777665544 58999999999999987776665

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

Probab=96.81  E-value=0.0042  Score=57.51  Aligned_cols=75  Identities=15%  Similarity=0.195  Sum_probs=61.1

Q ss_pred             HHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887           85 MEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus        85 l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      +...|..+++.-|..|...+++..-.+++||+|+|||.+-.--+.+.+..  ....+|+.+|..--+.|+.+.+.+-
T Consensus       403 ~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~--~~~~VLvcApSNiAVDqLaeKIh~t  477 (935)
T KOG1802|consen  403 FSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ--HAGPVLVCAPSNIAVDQLAEKIHKT  477 (935)
T ss_pred             hcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHh--cCCceEEEcccchhHHHHHHHHHhc
Confidence            33457778999999999999999999999999999998876666666554  2336999999998888888877654

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=96.69  E-value=0.013  Score=57.13  Aligned_cols=70  Identities=20%  Similarity=0.099  Sum_probs=53.8

Q ss_pred             CCcHHHHHHHHhHHc--CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887           92 LPTDIQREALPVLFS--SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~--g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      .|.|+|....-.++.  ...+++.-..|.|||.-..+-+-+.+..+. .-++||+||. .|..||..++.+.+.
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g~-~~rvLIVvP~-sL~~QW~~El~~kF~  223 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTGR-AERVLILVPE-TLQHQWLVEMLRRFN  223 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcCC-CCcEEEEcCH-HHHHHHHHHHHHHhC
Confidence            589999998877654  346899999999999888666555554443 2379999997 899999998865443

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=96.68  E-value=0.005  Score=61.37  Aligned_cols=61  Identities=21%  Similarity=0.311  Sum_probs=40.1

Q ss_pred             HHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHH-HHhcCCccEEEEe--cC----CHHhHHHHHHHHHH
Q 028887           95 DIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSL-VNAQRSAVQAVIV--VP----TRELGMQVTKVARV  160 (202)
Q Consensus        95 ~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~-l~~~~~~~~~Lil--~P----tr~La~Q~~~~~~~  160 (202)
                      ..-.+.+..+.+++.++++|+||||||.  .+|.+-. ...+.   .+.|+  -|    +++||.|+.+++..
T Consensus        77 ~~r~~Il~ai~~~~VviI~GeTGSGKTT--qlPq~lle~g~g~---~g~I~~TQPRRlAArsLA~RVA~El~~  144 (1294)
T PRK11131         77 QKKQDILEAIRDHQVVIVAGETGSGKTT--QLPKICLELGRGV---KGLIGHTQPRRLAARTVANRIAEELET  144 (1294)
T ss_pred             HHHHHHHHHHHhCCeEEEECCCCCCHHH--HHHHHHHHcCCCC---CCceeeCCCcHHHHHHHHHHHHHHHhh
Confidence            3444555666677788999999999999  4674322 22221   22333  25    67999999988875

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

Probab=96.68  E-value=0.0023  Score=48.61  Aligned_cols=53  Identities=21%  Similarity=0.323  Sum_probs=38.4

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHH-HHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFS-LVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~-~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      .|+-.++.-.+|+|||--.+--++. .+.++.   ++|||.|||.++..+.+.++..
T Consensus         3 kg~~~~~d~hpGaGKTr~vlp~~~~~~i~~~~---rvLvL~PTRvva~em~~aL~~~   56 (148)
T PF07652_consen    3 KGELTVLDLHPGAGKTRRVLPEIVREAIKRRL---RVLVLAPTRVVAEEMYEALKGL   56 (148)
T ss_dssp             TTEEEEEE--TTSSTTTTHHHHHHHHHHHTT-----EEEEESSHHHHHHHHHHTTTS
T ss_pred             CCceeEEecCCCCCCcccccHHHHHHHHHccC---eEEEecccHHHHHHHHHHHhcC
Confidence            3555678889999999977765554 555555   8999999999999988887644

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 ....

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

Probab=96.66  E-value=0.0081  Score=58.23  Aligned_cols=51  Identities=25%  Similarity=0.408  Sum_probs=40.2

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVAR  159 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~  159 (202)
                      .++.+..+||+|||.+|+-.|++.... .+..+.||+||+.+.-..+.+.+.
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            368899999999999999998776544 234579999999888777665543

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=96.65  E-value=0.023  Score=55.78  Aligned_cols=72  Identities=22%  Similarity=0.160  Sum_probs=53.0

Q ss_pred             CCcHHHHHHHHhHH----cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLF----SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~----~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .+.+.|.+.+.-+.    +|.+.|+.-..|.|||+..+..+.............||+||. ++..||.+.++++++.
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQaIalL~~L~~~~~~~gp~LIVvP~-SlL~nW~~Ei~kw~p~  244 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPK-STLGNWMNEIRRFCPV  244 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHHHHHHHHHHHhcCCCCCEEEEeCh-HHHHHHHHHHHHHCCC
Confidence            57899999998764    578899999999999987644433222222222258999996 7778899999999864

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=96.63  E-value=0.0085  Score=56.16  Aligned_cols=70  Identities=23%  Similarity=0.191  Sum_probs=56.6

Q ss_pred             CcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHh-cCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           93 PTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNA-QRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        93 ~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~-~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      +++-|.+++..  ...+++|.|..|||||.+.+.-+...+.. +....+.|+++.|+.-+.++.+++.+..+.
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--VTGPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKTLGK   72 (664)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHhCc
Confidence            68899998754  34679999999999999988888777754 334457899999999999999999877653

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

>TIGR01075 uvrD DNA helicase II

Probab=96.59  E-value=0.0077  Score=57.07  Aligned_cols=72  Identities=24%  Similarity=0.189  Sum_probs=57.9

Q ss_pred             CCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhc-CCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           91 VLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ-RSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        91 ~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~-~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      ..+++.|.+++..  ....++|.|..|||||.+...=+...+... -..-++|+|+.|+.-|..+.+++.++.+.
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v~p~~IL~lTFTnkAA~em~~Rl~~~~~~   75 (715)
T TIGR01075         3 DGLNDKQREAVAA--PPGNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKAAAEMRHRIGALLGT   75 (715)
T ss_pred             cccCHHHHHHHcC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCCCHHHeEeeeccHHHHHHHHHHHHHHhcc
Confidence            3589999998854  245799999999999999877776666543 23447999999999999999999988764

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

>PRK11054 helD DNA helicase IV; Provisional

Probab=96.58  E-value=0.018  Score=54.30  Aligned_cols=71  Identities=17%  Similarity=0.096  Sum_probs=55.6

Q ss_pred             CCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC-CccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887           91 VLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR-SAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus        91 ~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~-~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      ..+++.|++++-.  ...+++|.|..|||||.+.+.-+...+..+. ..-++|+|+.|+..|..+.+++....+
T Consensus       195 ~~L~~~Q~~av~~--~~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~lg  266 (684)
T PRK11054        195 SPLNPSQARAVVN--GEDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRERLG  266 (684)
T ss_pred             CCCCHHHHHHHhC--CCCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHhcC
Confidence            3689999998853  3356899999999999998777666665443 234799999999999999998877654

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

Probab=96.51  E-value=0.0074  Score=57.08  Aligned_cols=72  Identities=18%  Similarity=0.087  Sum_probs=57.2

Q ss_pred             CCcHHHHHHHHhH----HcC-CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVL----FSS-RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i----~~g-~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .+...|..||..+    ..| +.+++...||+|||-..+ .++.++.+.+..-++|+|+=.++|..|.+..|..+.+.
T Consensus       165 ~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTAi-aii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P~  241 (875)
T COG4096         165 GPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTAI-AIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLPF  241 (875)
T ss_pred             cchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeHH-HHHHHHHhcchhheeeEEechHHHHHHHHHHHHHhCCC
Confidence            5788999999764    345 348999999999998874 45556655555558999999999999999999888775

>PRK10536 hypothetical protein; Provisional

Probab=96.51  E-value=0.012  Score=49.05  Aligned_cols=60  Identities=13%  Similarity=0.109  Sum_probs=45.8

Q ss_pred             CCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHH
Q 028887           89 GYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRE  149 (202)
Q Consensus        89 g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~  149 (202)
                      ++...+..|...+..+..+..+++.|++|+|||...+...++.+..+. ..++++.-|+.+
T Consensus        56 ~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~~-~~kIiI~RP~v~  115 (262)
T PRK10536         56 PILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHKD-VDRIIVTRPVLQ  115 (262)
T ss_pred             cccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcCC-eeEEEEeCCCCC
Confidence            445568899999999888888999999999999998888887764433 334555556644

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=96.45  E-value=0.012  Score=55.88  Aligned_cols=71  Identities=24%  Similarity=0.206  Sum_probs=57.1

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHh-cCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNA-QRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~-~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .+++.|.+++...  ...++|.|..|||||.+...=+...+.. +-..-++|+|+-|+.-|..+.+++.++.+.
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--LGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQLLGT   80 (721)
T ss_pred             hcCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHHHHHHHHHHHHHhcc
Confidence            5899999988642  4578999999999999987777666653 323447999999999999999999888764

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=96.31  E-value=0.015  Score=58.46  Aligned_cols=69  Identities=19%  Similarity=0.140  Sum_probs=56.8

Q ss_pred             CcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887           93 PTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus        93 ~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      .|+.|.++|.  ..|.+++|.|..|||||.+.+--++..+..+..--+.|+++=|+.-|..+.+++++...
T Consensus         2 ~t~~Q~~ai~--~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~~~~~il~~tFt~~aa~e~~~ri~~~l~   70 (1232)
T TIGR02785         2 WTDEQWQAIY--TRGQNILVSASAGSGKTAVLVERIIKKILRGVDIDRLLVVTFTNAAAREMKERIEEALQ   70 (1232)
T ss_pred             CCHHHHHHHh--CCCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCHhhEEEEeccHHHHHHHHHHHHHHHH
Confidence            5899999996  36889999999999999999888888776553333699999999999998888876554

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.

>COG4889 Predicted helicase [General function prediction only]

Probab=96.26  E-value=0.017  Score=55.42  Aligned_cols=82  Identities=20%  Similarity=0.163  Sum_probs=55.6

Q ss_pred             CCCCCcHHHHHHHHhHHcC-----CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887           89 GYVLPTDIQREALPVLFSS-----RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus        89 g~~~~t~~Q~~~i~~i~~g-----~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      .-.+|.|+|+.||...+.|     +.-++. .-|+|||...+--+ +.+..    .++|+|+|+++|..|..+....-..
T Consensus       158 ~~kk~R~hQq~Aid~a~~~F~~n~RGkLIM-AcGTGKTfTsLkis-Eala~----~~iL~LvPSIsLLsQTlrew~~~~~  231 (1518)
T COG4889         158 KPKKPRPHQQTAIDAAKEGFSDNDRGKLIM-ACGTGKTFTSLKIS-EALAA----ARILFLVPSISLLSQTLREWTAQKE  231 (1518)
T ss_pred             CCCCCChhHHHHHHHHHhhcccccCCcEEE-ecCCCccchHHHHH-HHHhh----hheEeecchHHHHHHHHHHHhhccC
Confidence            3458999999999998765     223333 46899998876543 33433    3799999999999998776653332


Q ss_pred             CCCCcccccccceEEEEEeCCc
Q 028887          164 KPLDTDLEHKLCTVMALLDGGM  185 (202)
Q Consensus       164 ~~~~~~~~~~~~~~~~~~~g~~  185 (202)
                      -         .++..++|....
T Consensus       232 l---------~~~a~aVcSD~k  244 (1518)
T COG4889         232 L---------DFRASAVCSDDK  244 (1518)
T ss_pred             c---------cceeEEEecCcc
Confidence            2         255566665533

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.21  E-value=0.025  Score=48.56  Aligned_cols=47  Identities=34%  Similarity=0.403  Sum_probs=32.5

Q ss_pred             HHHHHCCCCCCcHHHHHHHHh-HHcCCcEEEeccCCCchHHHHHHHHHHHH
Q 028887           83 RRMEETGYVLPTDIQREALPV-LFSSRDCILHAQTGSGKTLTYLLLIFSLV  132 (202)
Q Consensus        83 ~~l~~~g~~~~t~~Q~~~i~~-i~~g~~~l~~a~TGsGKT~~~l~~~l~~l  132 (202)
                      ..+.+.|+  +++.|...+.. +..++++++.|+|||||| .++-.++..+
T Consensus       125 ~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKT-Tll~aL~~~~  172 (319)
T PRK13894        125 DQYVERGI--MTAAQREAIIAAVRAHRNILVIGGTGSGKT-TLVNAIINEM  172 (319)
T ss_pred             HHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHH-HHHHHHHHhh
Confidence            33444454  56677777764 567789999999999999 5555555543

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=96.21  E-value=0.027  Score=54.18  Aligned_cols=72  Identities=21%  Similarity=0.101  Sum_probs=56.0

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCC
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKP  165 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~  165 (202)
                      .|. .|+++|-..--.+..|  -+....||.|||+++.+|+.-....|+   .+-|+++.--||..=.+++..+....
T Consensus        82 lG~-r~ydVQliGgl~Lh~G--~IAEM~TGEGKTL~atlpaylnAL~Gk---gVhVVTvNdYLA~RDae~m~~vy~~L  153 (939)
T PRK12902         82 LGM-RHFDVQLIGGMVLHEG--QIAEMKTGEGKTLVATLPSYLNALTGK---GVHVVTVNDYLARRDAEWMGQVHRFL  153 (939)
T ss_pred             hCC-CcchhHHHhhhhhcCC--ceeeecCCCChhHHHHHHHHHHhhcCC---CeEEEeCCHHHHHhHHHHHHHHHHHh
Confidence            465 6899997665555444  578999999999999998876655566   78999999999998777777666655

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

Probab=96.07  E-value=0.017  Score=55.46  Aligned_cols=87  Identities=21%  Similarity=0.318  Sum_probs=64.7

Q ss_pred             CCCHHHHH-HHHHCCCCCCcHHHHHHH--HhHHcCCcEEEeccCCCchHHHHHHHHHHHHH-hcCCccEEEEecCCHHhH
Q 028887           76 HVPEHVLR-RMEETGYVLPTDIQREAL--PVLFSSRDCILHAQTGSGKTLTYLLLIFSLVN-AQRSAVQAVIVVPTRELG  151 (202)
Q Consensus        76 gl~~~l~~-~l~~~g~~~~t~~Q~~~i--~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~-~~~~~~~~Lil~Ptr~La  151 (202)
                      ++++.+.. ..+..|...++..|.+|+  +.++.+++++...||+.|||++.-+.++..+- ..+   .++.+.|..+-+
T Consensus       206 ~~~~k~~~~~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~rr---~~llilp~vsiv  282 (1008)
T KOG0950|consen  206 RLPTKVSHLYAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCRRR---NVLLILPYVSIV  282 (1008)
T ss_pred             cCchHHHHHHHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHHhh---ceeEecceeehh
Confidence            34444433 345678889999999999  56889999999999999999999888877653 333   578888887777


Q ss_pred             HHHHHHHHHhhcCC
Q 028887          152 MQVTKVARVLAAKP  165 (202)
Q Consensus       152 ~Q~~~~~~~l~~~~  165 (202)
                      ..-...+..+....
T Consensus       283 ~Ek~~~l~~~~~~~  296 (1008)
T KOG0950|consen  283 QEKISALSPFSIDL  296 (1008)
T ss_pred             HHHHhhhhhhcccc
Confidence            66656565555443

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=96.02  E-value=0.019  Score=53.87  Aligned_cols=67  Identities=24%  Similarity=0.320  Sum_probs=52.9

Q ss_pred             CCcHHHHHHHHhHHcC-----CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFSS-----RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g-----~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .|++.|..++..+.++     +..++.|.+|+||++.... +++..  ++   .+|||+|+.+.|.|+++.++.+.+.
T Consensus        12 ~~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~lia~-l~~~~--~r---~vLIVt~~~~~A~~l~~dL~~~~~~   83 (652)
T PRK05298         12 KPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMAN-VIARL--QR---PTLVLAHNKTLAAQLYSEFKEFFPE   83 (652)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHHHH-HHHHh--CC---CEEEEECCHHHHHHHHHHHHHhcCC
Confidence            6999999999887533     2567999999999988542 33322  23   6999999999999999999999764

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

Probab=95.98  E-value=0.0067  Score=59.66  Aligned_cols=69  Identities=20%  Similarity=0.272  Sum_probs=54.1

Q ss_pred             CCcHHHHHHHHhHHcC-CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHH-HHhhcC
Q 028887           92 LPTDIQREALPVLFSS-RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVA-RVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g-~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~-~~l~~~  164 (202)
                      ..+++|.++++.+.+. .++++.+|+|||||.+.-++++.    .....+++++.|.-+.+..+++.+ +++...
T Consensus      1143 ~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~----~~~~~~~vyi~p~~~i~~~~~~~w~~~f~~~ 1213 (1674)
T KOG0951|consen 1143 DFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR----PDTIGRAVYIAPLEEIADEQYRDWEKKFSKL 1213 (1674)
T ss_pred             ccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC----CccceEEEEecchHHHHHHHHHHHHHhhccc
Confidence            4489999999887764 56999999999999999998877    233457999999999988776554 444443

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=95.96  E-value=0.028  Score=53.37  Aligned_cols=71  Identities=20%  Similarity=0.179  Sum_probs=57.4

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC-CccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR-SAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~-~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .+++.|.+++...  ...++|.|..|||||.+...=+...+..++ ..-++|+++-|+.-|..+.+++.++.+.
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--EGPLLIMAGAGSGKTRVLTHRIAHLIAEKNVAPWNILAITFTNKAAREMKERVEKLLGP   75 (726)
T ss_pred             ccCHHHHHHHhCC--CCCEEEEeCCCCCHHHHHHHHHHHHHHcCCCCHHHeeeeeccHHHHHHHHHHHHHHhcc
Confidence            5899999988642  457899999999999998887777776432 3347899999999999999999888653

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

>PRK05973 replicative DNA helicase; Provisional

Probab=95.90  E-value=0.028  Score=46.27  Aligned_cols=66  Identities=26%  Similarity=0.250  Sum_probs=43.7

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      .+||.. +...-+..|.-+++.|++|+|||...+--+.+....+.   .++|++-+-. ..|+.+++..++
T Consensus        50 ~~~p~~-~l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~Ge---~vlyfSlEes-~~~i~~R~~s~g  115 (237)
T PRK05973         50 ATTPAE-ELFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMKSGR---TGVFFTLEYT-EQDVRDRLRALG  115 (237)
T ss_pred             CCCCHH-HhcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCC---eEEEEEEeCC-HHHHHHHHHHcC
Confidence            455533 23344556678999999999999887766666655544   6777754432 566777776664

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=95.75  E-value=0.028  Score=43.54  Aligned_cols=49  Identities=20%  Similarity=0.265  Sum_probs=35.7

Q ss_pred             EEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          110 CILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      +++.|++|+|||...+--+...+..+.   .+++++. -+-..++.+++..++
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g~---~v~~~s~-e~~~~~~~~~~~~~g   50 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGE---PGLYVTL-EESPEELIENAESLG   50 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCC---cEEEEEC-CCCHHHHHHHHHHcC
Confidence            689999999999877666666565555   6787754 466777777777664

A related protein is found in archaea.

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=95.73  E-value=0.094  Score=49.91  Aligned_cols=67  Identities=19%  Similarity=0.212  Sum_probs=49.0

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHH
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTK  156 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~  156 (202)
                      .++ .+++.|++++..+..++.+++.|+.|+|||.+. -.+++.+...+....+++++||-.-|..+.+
T Consensus       320 ~~~-~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l-~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~e  386 (720)
T TIGR01448       320 LRK-GLSEEQKQALDTAIQHKVVILTGGPGTGKTTIT-RAIIELAEELGGLLPVGLAAPTGRAAKRLGE  386 (720)
T ss_pred             cCC-CCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHH-HHHHHHHHHcCCCceEEEEeCchHHHHHHHH
Confidence            454 689999999999988889999999999999754 3444444432212468888999766665543

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.

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

Probab=95.70  E-value=0.023  Score=44.62  Aligned_cols=46  Identities=15%  Similarity=0.204  Sum_probs=29.6

Q ss_pred             HcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHH
Q 028887          105 FSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQV  154 (202)
Q Consensus       105 ~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~  154 (202)
                      ..+.++++.|++|+|||.....-.-+.+..+.   .++++ ...+|...+
T Consensus        45 ~~~~~l~l~G~~G~GKThLa~ai~~~~~~~g~---~v~f~-~~~~L~~~l   90 (178)
T PF01695_consen   45 ENGENLILYGPPGTGKTHLAVAIANEAIRKGY---SVLFI-TASDLLDEL   90 (178)
T ss_dssp             SC--EEEEEESTTSSHHHHHHHHHHHHHHTT-----EEEE-EHHHHHHHH
T ss_pred             ccCeEEEEEhhHhHHHHHHHHHHHHHhccCCc---ceeEe-ecCceeccc
Confidence            45788999999999999887666555555444   55554 555665544

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.

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=95.70  E-value=0.065  Score=46.14  Aligned_cols=39  Identities=23%  Similarity=0.256  Sum_probs=28.8

Q ss_pred             CcHHHHHHHHh-HHcCCcEEEeccCCCchHHHHHHHHHHHH
Q 028887           93 PTDIQREALPV-LFSSRDCILHAQTGSGKTLTYLLLIFSLV  132 (202)
Q Consensus        93 ~t~~Q~~~i~~-i~~g~~~l~~a~TGsGKT~~~l~~~l~~l  132 (202)
                      +++.|...+.. +..+.+++++|+||||||... -+++..+
T Consensus       129 ~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTll-~aL~~~i  168 (323)
T PRK13833        129 MTEAQASVIRSAIDSRLNIVISGGTGSGKTTLA-NAVIAEI  168 (323)
T ss_pred             CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHH
Confidence            56777777655 456789999999999999653 5555554

>PRK08181 transposase; Validated

Probab=95.64  E-value=0.16  Score=42.60  Aligned_cols=58  Identities=17%  Similarity=0.241  Sum_probs=37.0

Q ss_pred             CcHHHHHHHHh----HHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHH
Q 028887           93 PTDIQREALPV----LFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQV  154 (202)
Q Consensus        93 ~t~~Q~~~i~~----i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~  154 (202)
                      +...|..++..    +-.+.++++.||+|+|||........+.+..+.   .++++ +..+|..++
T Consensus        88 ~~~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHLa~Aia~~a~~~g~---~v~f~-~~~~L~~~l  149 (269)
T PRK08181         88 VSKAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHLAAAIGLALIENGW---RVLFT-RTTDLVQKL  149 (269)
T ss_pred             CCHHHHHHHHHHHHHHhcCceEEEEecCCCcHHHHHHHHHHHHHHcCC---ceeee-eHHHHHHHH
Confidence            34566665532    346789999999999999766544444444433   45443 556676654

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=95.63  E-value=0.11  Score=49.63  Aligned_cols=75  Identities=13%  Similarity=0.123  Sum_probs=50.3

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHhHHcC-CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHH
Q 028887           77 VPEHVLRRMEETGYVLPTDIQREALPVLFSS-RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVT  155 (202)
Q Consensus        77 l~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g-~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~  155 (202)
                      +++..+...-..++ .+++.|..++..++.+ +-+++.|+.|+|||... -.+.+.+..  .+.+++.++||---+..+.
T Consensus       338 ~~~~~~~~~l~~~~-~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll-~~i~~~~~~--~g~~V~~~ApTg~Aa~~L~  413 (744)
T TIGR02768       338 VSPPIVDAAIDQHY-RLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTML-KAAREAWEA--AGYRVIGAALSGKAAEGLQ  413 (744)
T ss_pred             CCHHHHHHHHhccC-CCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHH-HHHHHHHHh--CCCeEEEEeCcHHHHHHHH
Confidence            44443333322344 5899999999998874 66899999999999663 334444433  2347889999966655543

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.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=95.52  E-value=0.03  Score=45.77  Aligned_cols=53  Identities=15%  Similarity=0.239  Sum_probs=39.5

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      .|..+++.|++|+|||...+--+.+.+..+.   .+++++ +-+-..|+.+.+..++
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~~~~ge---~~lyvs-~ee~~~~i~~~~~~~g   72 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNGLQMGE---PGIYVA-LEEHPVQVRRNMAQFG   72 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHcCC---cEEEEE-eeCCHHHHHHHHHHhC
Confidence            3567999999999999877666666665555   788877 4466777777777655

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.

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=95.45  E-value=0.076  Score=49.34  Aligned_cols=65  Identities=18%  Similarity=0.307  Sum_probs=45.7

Q ss_pred             cHHHHHHHHhHHcCCcEEEeccCCCchHHHHH--HHHHHHHHhcCCccEEEEecCCHHhHHHHHHHH
Q 028887           94 TDIQREALPVLFSSRDCILHAQTGSGKTLTYL--LLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVA  158 (202)
Q Consensus        94 t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l--~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~  158 (202)
                      .+.|+.++..++.++.+++.|+.|+|||....  +..+..........++++.+||--=+..+.+.+
T Consensus       147 ~~~Qk~A~~~al~~~~~vitGgpGTGKTt~v~~ll~~l~~~~~~~~~~~I~l~APTGkAA~rL~e~~  213 (586)
T TIGR01447       147 QNWQKVAVALALKSNFSLITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAAPTGKAAARLAESL  213 (586)
T ss_pred             cHHHHHHHHHHhhCCeEEEEcCCCCCHHHHHHHHHHHHHHhccccCCCcEEEECCcHHHHHHHHHHH
Confidence            37899999999999999999999999998643  333332222212247889999966665555444

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.

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=95.43  E-value=0.1  Score=44.36  Aligned_cols=40  Identities=25%  Similarity=0.347  Sum_probs=28.0

Q ss_pred             CcHHHHHHHHh-HHcCCcEEEeccCCCchHHHHHHHHHHHHH
Q 028887           93 PTDIQREALPV-LFSSRDCILHAQTGSGKTLTYLLLIFSLVN  133 (202)
Q Consensus        93 ~t~~Q~~~i~~-i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~  133 (202)
                      +++.|...+.. +..+.+++++|+||||||... -.++..+.
T Consensus       117 ~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll-~al~~~i~  157 (299)
T TIGR02782       117 MTAAQRDVLREAVLARKNILVVGGTGSGKTTLA-NALLAEIA  157 (299)
T ss_pred             CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHhh
Confidence            55666666654 456789999999999999653 44555553

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.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.42  E-value=0.56  Score=39.47  Aligned_cols=65  Identities=26%  Similarity=0.200  Sum_probs=38.2

Q ss_pred             hHHHHHhCCCCHHHHHHHHHC--CCCCCcHHHHHHHHhH---H-----------cCCcEEEeccCCCchHHHHHHHHHHH
Q 028887           68 TLRELCQGHVPEHVLRRMEET--GYVLPTDIQREALPVL---F-----------SSRDCILHAQTGSGKTLTYLLLIFSL  131 (202)
Q Consensus        68 ~~~~l~~~gl~~~l~~~l~~~--g~~~~t~~Q~~~i~~i---~-----------~g~~~l~~a~TGsGKT~~~l~~~l~~  131 (202)
                      -.+.|.+.|+++.+.+.+.+.  +..............+   +           .++.+++.||||+|||.....-....
T Consensus       139 l~~~L~~~gv~~~la~~L~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~vi~~vGptGvGKTTt~~kLa~~~  218 (282)
T TIGR03499       139 LLERLLRAGVSPELARELLEKLPERADAEDAWRWLREALEKMLPVKPEEDEILEQGGVIALVGPTGVGKTTTLAKLAARF  218 (282)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHhccCCccccccCCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            456777888988887776442  2222222222222222   1           23468899999999998766544443


Q ss_pred             H
Q 028887          132 V  132 (202)
Q Consensus       132 l  132 (202)
                      .
T Consensus       219 ~  219 (282)
T TIGR03499       219 V  219 (282)
T ss_pred             H
Confidence            3

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

Probab=95.40  E-value=0.086  Score=48.72  Aligned_cols=86  Identities=21%  Similarity=0.225  Sum_probs=58.2

Q ss_pred             HHHHHHHHHCCCCCC-------cHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCC---ccEEEEecCCH
Q 028887           79 EHVLRRMEETGYVLP-------TDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS---AVQAVIVVPTR  148 (202)
Q Consensus        79 ~~l~~~l~~~g~~~~-------t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~---~~~~Lil~Ptr  148 (202)
                      +.|...|.+.--.++       .+.|.+.|.. -.++-++|+|..|||||.+.+.=+.-.+..-+.   ...+||+.|.+
T Consensus       192 EvL~~~Lek~ss~~mrdIV~TIQkEQneIIR~-ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~  270 (747)
T COG3973         192 EVLQRVLEKNSSAKMRDIVETIQKEQNEIIRF-EKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNR  270 (747)
T ss_pred             HHHHHHHHhccchhHHHHHHHhhHhHHHHHhc-cCCCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEEEcCcH
Confidence            344555655433333       3444444321 245668999999999999988766555543221   22499999999


Q ss_pred             HhHHHHHHHHHHhhcCC
Q 028887          149 ELGMQVTKVARVLAAKP  165 (202)
Q Consensus       149 ~La~Q~~~~~~~l~~~~  165 (202)
                      -....+.+++-+++...
T Consensus       271 vFleYis~VLPeLGe~~  287 (747)
T COG3973         271 VFLEYISRVLPELGEEG  287 (747)
T ss_pred             HHHHHHHHhchhhccCc
Confidence            99999999999998764

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

Probab=95.34  E-value=0.04  Score=44.46  Aligned_cols=53  Identities=15%  Similarity=0.231  Sum_probs=37.5

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHh-cCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNA-QRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~-~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      .|..+++.|++|+|||...+--+.+.+.. +.   .+++++ +.+-..++.+.++.++
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge---~vlyvs-~ee~~~~l~~~~~s~g   71 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKNFGE---KVLYVS-FEEPPEELIENMKSFG   71 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHHT-----EEEEE-SSS-HHHHHHHHHTTT
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCC---cEEEEE-ecCCHHHHHHHHHHcC
Confidence            34679999999999998877777777776 66   677776 3444567777777654

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 ....

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=95.33  E-value=0.14  Score=50.32  Aligned_cols=63  Identities=17%  Similarity=0.163  Sum_probs=47.2

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCc-EEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHH
Q 028887           88 TGYVLPTDIQREALPVLFSSRD-CILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQV  154 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~-~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~  154 (202)
                      .|+ .+++.|.+++..++.+++ +++.|..|+|||.. +-.+.+.+..  .+.+++.++||---+..+
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 689999999999998654 78999999999986 4555555543  234789999996655444

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

Probab=95.32  E-value=0.036  Score=48.04  Aligned_cols=52  Identities=15%  Similarity=0.173  Sum_probs=38.3

Q ss_pred             cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887          109 DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      -++|.|..|||||++.+--+... .....+..++++++...|...+.+.+..-
T Consensus         3 v~~I~G~aGTGKTvla~~l~~~l-~~~~~~~~~~~l~~n~~l~~~l~~~l~~~   54 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALNLAKEL-QNSEEGKKVLYLCGNHPLRNKLREQLAKK   54 (352)
T ss_pred             EEEEEecCCcCHHHHHHHHHHHh-hccccCCceEEEEecchHHHHHHHHHhhh
Confidence            47899999999998877665554 11223337999999999998777776543

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

>PRK06526 transposase; Provisional

Probab=95.30  E-value=0.094  Score=43.57  Aligned_cols=47  Identities=13%  Similarity=0.189  Sum_probs=30.3

Q ss_pred             HHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHH
Q 028887          104 LFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQV  154 (202)
Q Consensus       104 i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~  154 (202)
                      +..+.++++.||+|+|||.....-..+.+..+.   ++++. ...++..++
T Consensus        95 i~~~~nlll~Gp~GtGKThLa~al~~~a~~~g~---~v~f~-t~~~l~~~l  141 (254)
T PRK06526         95 VTGKENVVFLGPPGTGKTHLAIGLGIRACQAGH---RVLFA-TAAQWVARL  141 (254)
T ss_pred             hhcCceEEEEeCCCCchHHHHHHHHHHHHHCCC---chhhh-hHHHHHHHH
Confidence            345679999999999999877655555554443   45443 334454444

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=95.26  E-value=0.12  Score=48.30  Aligned_cols=66  Identities=23%  Similarity=0.320  Sum_probs=47.1

Q ss_pred             cHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHh-cCCccEEEEecCCHHhHHHHHHHHH
Q 028887           94 TDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNA-QRSAVQAVIVVPTRELGMQVTKVAR  159 (202)
Q Consensus        94 t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~-~~~~~~~Lil~Ptr~La~Q~~~~~~  159 (202)
                      .+.|+.|+-..+..+.+++.|++|+|||....--+...+.. +....++++.+||.-=|..+.+.+.
T Consensus       154 ~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~  220 (615)
T PRK10875        154 VDWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLTESLG  220 (615)
T ss_pred             CHHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHH
Confidence            58999999999999999999999999997743322222221 1223578888999777776665543

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

Probab=95.15  E-value=0.049  Score=47.53  Aligned_cols=69  Identities=12%  Similarity=0.234  Sum_probs=48.0

Q ss_pred             CCcHHHHHHHHhH------HcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHH--HHHHHHhhc
Q 028887           92 LPTDIQREALPVL------FSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQV--TKVARVLAA  163 (202)
Q Consensus        92 ~~t~~Q~~~i~~i------~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~--~~~~~~l~~  163 (202)
                      .+++.|+.++..+      ..+..+.+.|+-|+|||.++-. +.+.+..  .+..+++++||--=|..+  ...+..+++
T Consensus         1 ~Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~~-i~~~~~~--~~~~~~~~a~tg~AA~~i~~G~T~hs~f~   77 (364)
T PF05970_consen    1 KLNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLIKA-IIDYLRS--RGKKVLVTAPTGIAAFNIPGGRTIHSFFG   77 (364)
T ss_pred             CCCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHHHH-HHHHhcc--ccceEEEecchHHHHHhccCCcchHHhcC
Confidence            3678899998887      6778899999999999976532 2333322  233788899997666666  344555554

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

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

Probab=95.11  E-value=0.06  Score=44.72  Aligned_cols=67  Identities=18%  Similarity=0.246  Sum_probs=44.8

Q ss_pred             CCCCCcHHHHHHHHhHH-------cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHH
Q 028887           89 GYVLPTDIQREALPVLF-------SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVAR  159 (202)
Q Consensus        89 g~~~~t~~Q~~~i~~i~-------~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~  159 (202)
                      .|......+..++..+.       .+.++++.|++|+|||.....-..+.+ ..+   ..++.+++.+|+.++...+.
T Consensus        80 d~~~~~~~~~~~l~~~~~~~~~~~~~~nl~l~G~~G~GKThLa~Ai~~~l~-~~g---~sv~f~~~~el~~~Lk~~~~  153 (254)
T COG1484          80 DFEFQPGIDKKALEDLASLVEFFERGENLVLLGPPGVGKTHLAIAIGNELL-KAG---ISVLFITAPDLLSKLKAAFD  153 (254)
T ss_pred             cccCCcchhHHHHHHHHHHHHHhccCCcEEEECCCCCcHHHHHHHHHHHHH-HcC---CeEEEEEHHHHHHHHHHHHh
Confidence            44445556666665442       567999999999999987655555545 322   24455688888888766544

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=94.92  E-value=0.043  Score=47.64  Aligned_cols=30  Identities=27%  Similarity=0.313  Sum_probs=22.5

Q ss_pred             hHHcCCcEEEeccCCCchHHHHHHHHHHHHH
Q 028887          103 VLFSSRDCILHAQTGSGKTLTYLLLIFSLVN  133 (202)
Q Consensus       103 ~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~  133 (202)
                      .+..+.++++.|+||||||.. +-.++..+.
T Consensus       158 ~v~~~~nilI~G~tGSGKTTl-l~aLl~~i~  187 (344)
T PRK13851        158 CVVGRLTMLLCGPTGSGKTTM-SKTLISAIP  187 (344)
T ss_pred             HHHcCCeEEEECCCCccHHHH-HHHHHcccC
Confidence            356789999999999999954 455555553

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

Probab=94.79  E-value=0.036  Score=47.15  Aligned_cols=26  Identities=31%  Similarity=0.556  Sum_probs=20.1

Q ss_pred             EEEeccCCCchHHHHHHHHHHHHHhcC
Q 028887          110 CILHAQTGSGKTLTYLLLIFSLVNAQR  136 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~l~~~l~~l~~~~  136 (202)
                      ++|.|||||||+.. +.++++.+.+..
T Consensus       128 ILVTGpTGSGKSTT-lAamId~iN~~~  153 (353)
T COG2805         128 ILVTGPTGSGKSTT-LAAMIDYINKHK  153 (353)
T ss_pred             EEEeCCCCCcHHHH-HHHHHHHHhccC
Confidence            88999999999965 466777776543

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.77  E-value=0.46  Score=41.75  Aligned_cols=68  Identities=22%  Similarity=0.156  Sum_probs=41.3

Q ss_pred             cchHHHHHhCCCCHHHHHHHHH-CC----CCCCcHHH---HHHHH----hH-------HcCCcEEEeccCCCchHHHHHH
Q 028887           66 SLTLRELCQGHVPEHVLRRMEE-TG----YVLPTDIQ---REALP----VL-------FSSRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus        66 ~~~~~~l~~~gl~~~l~~~l~~-~g----~~~~t~~Q---~~~i~----~i-------~~g~~~l~~a~TGsGKT~~~l~  126 (202)
                      ..-.+.|.+.|+.+.+.+.+-+ ..    ...+...+   ...+.    .+       ..|..+++.||||+|||.....
T Consensus        77 ~~l~~~L~~~g~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~g~ii~lvGptGvGKTTtiak  156 (374)
T PRK14722         77 GALTKYLFAAGFSAQLVRMIVDNLPEGEGYDTLDAAADWAQSVLAANLPVLDSEDALMERGGVFALMGPTGVGKTTTTAK  156 (374)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHhhhhhcccCCHHHHHHHHHHHHHhcchhhcCCCccccCCcEEEEECCCCCCHHHHHHH
Confidence            3455888899999988888743 21    11221211   11111    11       2356799999999999998776


Q ss_pred             HHHHHHH
Q 028887          127 LIFSLVN  133 (202)
Q Consensus       127 ~~l~~l~  133 (202)
                      -....+.
T Consensus       157 LA~~~~~  163 (374)
T PRK14722        157 LAARCVM  163 (374)
T ss_pred             HHHHHHH
Confidence            6555443

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.66  E-value=0.64  Score=41.52  Aligned_cols=62  Identities=21%  Similarity=0.204  Sum_probs=35.7

Q ss_pred             hHHHHHhCCCCHHHHHHHHHC--CCCCCcH--HHHHHHHhH------------HcCCcEEEeccCCCchHHHHHHHHH
Q 028887           68 TLRELCQGHVPEHVLRRMEET--GYVLPTD--IQREALPVL------------FSSRDCILHAQTGSGKTLTYLLLIF  129 (202)
Q Consensus        68 ~~~~l~~~gl~~~l~~~l~~~--g~~~~t~--~Q~~~i~~i------------~~g~~~l~~a~TGsGKT~~~l~~~l  129 (202)
                      -...|.+.|+.+.+.+.+.+.  +......  ........+            ..|+.+++.||||+|||.....-..
T Consensus       166 ~~~~L~~~gv~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~~~i~~vGptGvGKTTt~~kLA~  243 (424)
T PRK05703        166 LYKRLKRSGLSPEIAEKLLKLLLEHMPPRERTAWRYLLELLANMIPVRVEDILKQGGVVALVGPTGVGKTTTLAKLAA  243 (424)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhCccccccccCCcEEEEECCCCCCHHHHHHHHHH
Confidence            356777888888777776432  0001111  222222222            1245788999999999987654433

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=94.57  E-value=0.081  Score=46.20  Aligned_cols=64  Identities=27%  Similarity=0.280  Sum_probs=50.3

Q ss_pred             CCCCCCcHHHHHHHHhHHcC--CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhH
Q 028887           88 TGYVLPTDIQREALPVLFSS--RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELG  151 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g--~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La  151 (202)
                      .|+..-+..|..|+..++..  .-|.+.|+.|||||+..+.+.+++....+...+.++--|+..+.
T Consensus       224 wGi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG  289 (436)
T COG1875         224 WGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVG  289 (436)
T ss_pred             hccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCcc
Confidence            36666677889999888765  34788899999999999998888877666666788877876654

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

Probab=94.50  E-value=0.073  Score=45.99  Aligned_cols=77  Identities=18%  Similarity=0.223  Sum_probs=48.3

Q ss_pred             CcchHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCC-cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEE
Q 028887           65 NSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSR-DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVI  143 (202)
Q Consensus        65 ~~~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~-~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Li  143 (202)
                      +..+++.|.+.-+.-.   .+-  .|..+++.|...+-.+..++ +++++|.||||||.. +-++...+....   +++.
T Consensus       135 p~lsIRKf~k~~ltl~---dli--~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTl-LNal~~~i~~~e---RvIt  205 (355)
T COG4962         135 PTLSIRKFPKIKLTLL---DLI--IFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTL-LNALSGFIDSDE---RVIT  205 (355)
T ss_pred             CcccccccccccccHH---HHH--HcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHH-HHHHHhcCCCcc---cEEE
Confidence            4456777766555422   222  35679999999998877665 999999999999964 233333333333   4555


Q ss_pred             ecCCHHh
Q 028887          144 VVPTREL  150 (202)
Q Consensus       144 l~Ptr~L  150 (202)
                      +==|.||
T Consensus       206 iEDtaEL  212 (355)
T COG4962         206 IEDTAEL  212 (355)
T ss_pred             Eeehhhh
Confidence            4444444

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=94.38  E-value=0.2  Score=50.36  Aligned_cols=73  Identities=19%  Similarity=0.111  Sum_probs=41.1

Q ss_pred             CCCCCCcHHHH---HHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887           88 TGYVLPTDIQR---EALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus        88 ~g~~~~t~~Q~---~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      ..|...-|+.+   +.+..+.++..++++|+||||||..  +|.+-.-........+++.-|-|--|..+.+++.+..
T Consensus        60 ~~~~~~LPi~~~~~~Il~~l~~~~vvii~g~TGSGKTTq--lPq~lle~~~~~~~~I~~tQPRRlAA~svA~RvA~el  135 (1283)
T TIGR01967        60 IRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQ--LPKICLELGRGSHGLIGHTQPRRLAARTVAQRIAEEL  135 (1283)
T ss_pred             ccCCCCCCHHHHHHHHHHHHHhCceEEEeCCCCCCcHHH--HHHHHHHcCCCCCceEecCCccHHHHHHHHHHHHHHh
Confidence            34554444443   4455566677889999999999994  4543322111112234444476666666665554433

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.

>PRK06921 hypothetical protein; Provisional

Probab=94.26  E-value=0.77  Score=38.34  Aligned_cols=47  Identities=21%  Similarity=0.122  Sum_probs=28.8

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVT  155 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~  155 (202)
                      .+..+++.|++|+|||.... ++...+... .+..++++ +..++..++.
T Consensus       116 ~~~~l~l~G~~G~GKThLa~-aia~~l~~~-~g~~v~y~-~~~~l~~~l~  162 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLT-AAANELMRK-KGVPVLYF-PFVEGFGDLK  162 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHH-HHHHHHhhh-cCceEEEE-EHHHHHHHHH
Confidence            35779999999999996553 444444332 12356665 4456555543

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=94.19  E-value=0.21  Score=39.55  Aligned_cols=38  Identities=18%  Similarity=0.239  Sum_probs=28.9

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCC
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPT  147 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Pt  147 (202)
                      |.-+.+.|++|+|||...+..+.+....+.   +++++.-+
T Consensus        12 g~i~~i~G~~GsGKT~l~~~~~~~~~~~g~---~v~yi~~e   49 (209)
T TIGR02237        12 GTITQIYGPPGSGKTNICMILAVNAARQGK---KVVYIDTE   49 (209)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhCCC---eEEEEECC
Confidence            466899999999999888766666555444   67887765

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

>PRK04328 hypothetical protein; Provisional

Probab=94.14  E-value=0.13  Score=42.53  Aligned_cols=53  Identities=19%  Similarity=0.274  Sum_probs=37.9

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      .|..+++.|++|+|||...+--+.+.+..+.   .+++++ +-+-..++.+.++.++
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~~~~~ge---~~lyis-~ee~~~~i~~~~~~~g   74 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWNGLQMGE---PGVYVA-LEEHPVQVRRNMRQFG   74 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhcCC---cEEEEE-eeCCHHHHHHHHHHcC
Confidence            3567899999999999876666666666655   677776 4455566777766664

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=94.11  E-value=0.07  Score=46.09  Aligned_cols=29  Identities=21%  Similarity=0.267  Sum_probs=22.3

Q ss_pred             HHcCCcEEEeccCCCchHHHHHHHHHHHHH
Q 028887          104 LFSSRDCILHAQTGSGKTLTYLLLIFSLVN  133 (202)
Q Consensus       104 i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~  133 (202)
                      +..+.+++++|+||||||.. +-+++..+.
T Consensus       157 v~~~~nili~G~tgSGKTTl-l~aL~~~ip  185 (332)
T PRK13900        157 VISKKNIIISGGTSTGKTTF-TNAALREIP  185 (332)
T ss_pred             HHcCCcEEEECCCCCCHHHH-HHHHHhhCC
Confidence            45789999999999999955 455556554

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

Probab=94.07  E-value=0.1  Score=41.00  Aligned_cols=33  Identities=24%  Similarity=0.281  Sum_probs=26.3

Q ss_pred             CCcHHHHHHHHh-HHcCCcEEEeccCCCchHHHH
Q 028887           92 LPTDIQREALPV-LFSSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus        92 ~~t~~Q~~~i~~-i~~g~~~l~~a~TGsGKT~~~  124 (202)
                      ..++.|...+.. +..|..+++.|+||||||...
T Consensus         9 ~~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll   42 (186)
T cd01130           9 TFSPLQAAYLWLAVEARKNILISGGTGSGKTTLL   42 (186)
T ss_pred             CCCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH
Confidence            367777777765 456889999999999999764

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.

>PRK06835 DNA replication protein DnaC; Validated

Probab=94.03  E-value=0.42  Score=41.29  Aligned_cols=46  Identities=17%  Similarity=0.247  Sum_probs=28.7

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVT  155 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~  155 (202)
                      .+.++++.|++|+|||.......-+.+..+.   .++++ +..+|..++.
T Consensus       182 ~~~~Lll~G~~GtGKThLa~aIa~~l~~~g~---~V~y~-t~~~l~~~l~  227 (329)
T PRK06835        182 NNENLLFYGNTGTGKTFLSNCIAKELLDRGK---SVIYR-TADELIEILR  227 (329)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHHHCCC---eEEEE-EHHHHHHHHH
Confidence            3578999999999999754433333333333   56554 4566655543

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=93.99  E-value=0.17  Score=45.76  Aligned_cols=40  Identities=33%  Similarity=0.385  Sum_probs=28.4

Q ss_pred             cHHHHHHHHhHHcCCc--EEEeccCCCchHHHHHHHHHHHHHh
Q 028887           94 TDIQREALPVLFSSRD--CILHAQTGSGKTLTYLLLIFSLVNA  134 (202)
Q Consensus        94 t~~Q~~~i~~i~~g~~--~l~~a~TGsGKT~~~l~~~l~~l~~  134 (202)
                      ++.|...+..+++...  +++.||||||||.. +..++..+..
T Consensus       243 ~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTT-LY~~L~~ln~  284 (500)
T COG2804         243 SPFQLARLLRLLNRPQGLILVTGPTGSGKTTT-LYAALSELNT  284 (500)
T ss_pred             CHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHH-HHHHHHHhcC
Confidence            6777777766665543  78999999999965 4555565544

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=93.87  E-value=0.16  Score=40.93  Aligned_cols=53  Identities=15%  Similarity=0.203  Sum_probs=34.5

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      .|..+++.|++|+|||...+.-+.+.+.++.   .++++.- -+...++.++.+.++
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~~~~~~g~---~~~~is~-e~~~~~i~~~~~~~g   71 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAYKGLRDGD---PVIYVTT-EESRESIIRQAAQFG   71 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHHHhcCC---eEEEEEc-cCCHHHHHHHHHHhC
Confidence            3577999999999999876654555555444   6677654 334456655555443

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.

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=93.79  E-value=0.25  Score=43.38  Aligned_cols=26  Identities=23%  Similarity=0.295  Sum_probs=19.2

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVN  133 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~  133 (202)
                      +..++++|+||||||... ..+++.+.
T Consensus       149 ~GlilI~G~TGSGKTT~l-~al~~~i~  174 (372)
T TIGR02525       149 AGLGLICGETGSGKSTLA-ASIYQHCG  174 (372)
T ss_pred             CCEEEEECCCCCCHHHHH-HHHHHHHH
Confidence            346899999999999654 55666554

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).

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=93.74  E-value=0.37  Score=46.57  Aligned_cols=71  Identities=17%  Similarity=0.145  Sum_probs=50.9

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .|. .|+++|-..--.+..|+  +..-.||-|||++..+|+.-....|+   .+-|++..--||..=.+++..+...
T Consensus        75 lG~-r~ydVQliGglvLh~G~--IAEMkTGEGKTLvAtLpayLnAL~Gk---gVhVVTvNdYLA~RDae~mg~vy~f  145 (925)
T PRK12903         75 LGK-RPYDVQIIGGIILDLGS--VAEMKTGEGKTITSIAPVYLNALTGK---GVIVSTVNEYLAERDAEEMGKVFNF  145 (925)
T ss_pred             hCC-CcCchHHHHHHHHhcCC--eeeecCCCCccHHHHHHHHHHHhcCC---ceEEEecchhhhhhhHHHHHHHHHH
Confidence            465 68999988776666663  68999999999999998865444455   5777777778887545555444443

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=93.68  E-value=0.12  Score=48.29  Aligned_cols=42  Identities=26%  Similarity=0.431  Sum_probs=35.8

Q ss_pred             CCcHHHHHHHHhH----HcCCcEEEeccCCCchHHHHHHHHHHHHH
Q 028887           92 LPTDIQREALPVL----FSSRDCILHAQTGSGKTLTYLLLIFSLVN  133 (202)
Q Consensus        92 ~~t~~Q~~~i~~i----~~g~~~l~~a~TGsGKT~~~l~~~l~~l~  133 (202)
                      +|+.+|.+.+..+    -.|+-.|+.+|||+|||+..+-+.+..+.
T Consensus        15 ~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL~   60 (821)
T KOG1133|consen   15 TPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWLR   60 (821)
T ss_pred             CchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHHH
Confidence            6899999988764    46898899999999999998888877664

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=93.58  E-value=0.085  Score=43.73  Aligned_cols=31  Identities=19%  Similarity=0.300  Sum_probs=23.5

Q ss_pred             HHcCCcEEEeccCCCchHHHHHHHHHHHHHhc
Q 028887          104 LFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ  135 (202)
Q Consensus       104 i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~  135 (202)
                      +..+.++++.|+||||||... ..++..+...
T Consensus       124 v~~~~~ili~G~tGSGKTT~l-~all~~i~~~  154 (270)
T PF00437_consen  124 VRGRGNILISGPTGSGKTTLL-NALLEEIPPE  154 (270)
T ss_dssp             HHTTEEEEEEESTTSSHHHHH-HHHHHHCHTT
T ss_pred             cccceEEEEECCCccccchHH-HHHhhhcccc
Confidence            356789999999999999665 5556666544

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 ....

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=93.56  E-value=0.19  Score=41.74  Aligned_cols=39  Identities=10%  Similarity=0.097  Sum_probs=28.9

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCC
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPT  147 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Pt  147 (202)
                      .|.-+++.|++|+|||...+--+.+.+..+.   +++|++-+
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~~~a~~Ge---~vlyis~E   73 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAVTQASRGN---PVLFVTVE   73 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhCCC---cEEEEEec
Confidence            3567999999999999877665555555444   68888754

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

>PRK12377 putative replication protein; Provisional

Probab=93.55  E-value=0.31  Score=40.40  Aligned_cols=45  Identities=11%  Similarity=0.207  Sum_probs=27.7

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTK  156 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~  156 (202)
                      ..+++.|++|+|||...... ...+...+  ..+++ ++..+|..++..
T Consensus       102 ~~l~l~G~~GtGKThLa~AI-a~~l~~~g--~~v~~-i~~~~l~~~l~~  146 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAAAI-GNRLLAKG--RSVIV-VTVPDVMSRLHE  146 (248)
T ss_pred             CeEEEECCCCCCHHHHHHHH-HHHHHHcC--CCeEE-EEHHHHHHHHHH
Confidence            57999999999999655433 33433322  13443 455677766543

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

Probab=93.54  E-value=0.077  Score=48.10  Aligned_cols=70  Identities=17%  Similarity=0.209  Sum_probs=55.5

Q ss_pred             CCcHHHHHHHHhHHcC---CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCC
Q 028887           92 LPTDIQREALPVLFSS---RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLD  167 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g---~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~  167 (202)
                      .+.|.|+.++..++.+   +..++.-|-|+|||++-+-++.. +  .+   ++|+||..---+.||...|+.++...+|
T Consensus       302 ~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~t-i--kK---~clvLcts~VSVeQWkqQfk~wsti~d~  374 (776)
T KOG1123|consen  302 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAACT-I--KK---SCLVLCTSAVSVEQWKQQFKQWSTIQDD  374 (776)
T ss_pred             ccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeeee-e--cc---cEEEEecCccCHHHHHHHHHhhcccCcc
Confidence            4678999999998853   57888899999999987655421 1  23   7999999988999999999988875444

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=93.53  E-value=1.9  Score=37.52  Aligned_cols=54  Identities=11%  Similarity=-0.029  Sum_probs=31.6

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHH---hcCCccEEEEecCCHHh-HHHHHHHHHHh
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVN---AQRSAVQAVIVVPTREL-GMQVTKVARVL  161 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~---~~~~~~~~Lil~Ptr~L-a~Q~~~~~~~l  161 (202)
                      .-+.+.|++|+|||...+-..+....   .+....+++|+..+-.. ..++.+....+
T Consensus       127 ~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~ia~~~  184 (344)
T PLN03187        127 CITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVPIAERF  184 (344)
T ss_pred             eEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHHHHHHc
Confidence            34679999999999876544443322   22223478998875432 33333434443

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=93.50  E-value=0.61  Score=44.54  Aligned_cols=94  Identities=21%  Similarity=0.288  Sum_probs=62.7

Q ss_pred             CCcHHHHHHHHhHH---cCC-------cEEEeccCCCchHHHHHHHHHHHHHhcCCc-----cEEEEecCCHHhHHHHHH
Q 028887           92 LPTDIQREALPVLF---SSR-------DCILHAQTGSGKTLTYLLLIFSLVNAQRSA-----VQAVIVVPTRELGMQVTK  156 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~---~g~-------~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~-----~~~Lil~Ptr~La~Q~~~  156 (202)
                      .+.|+|++.+.-+.   .|.       .+|+.-..|+|||+-.+.-+-..+.. ...     .++||++|. .|..-|.+
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~IsflwtlLrq-~P~~~~~~~k~lVV~P~-sLv~nWkk  315 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCISFIWTLLRQ-FPQAKPLINKPLVVAPS-SLVNNWKK  315 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHHHHHHHHHHHh-CcCccccccccEEEccH-HHHHHHHH
Confidence            57899999998763   232       35666678999998754444333333 222     478999995 78999999


Q ss_pred             HHHHhhcCCCCcccccccceEEEEEeCCcc--HHHHHHHHH
Q 028887          157 VARVLAAKPLDTDLEHKLCTVMALLDGGML--RRHKSWLKV  195 (202)
Q Consensus       157 ~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~--~~~~~~l~~  195 (202)
                      +|.++....        .+....++++...  .++..|+..
T Consensus       316 EF~KWl~~~--------~i~~l~~~~~~~~~w~~~~sil~~  348 (776)
T KOG0390|consen  316 EFGKWLGNH--------RINPLDFYSTKKSSWIKLKSILFL  348 (776)
T ss_pred             HHHHhcccc--------ccceeeeecccchhhhhhHHHHHh
Confidence            999988742        2555666666653  344455533

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=93.48  E-value=1.2  Score=39.62  Aligned_cols=65  Identities=22%  Similarity=0.277  Sum_probs=36.7

Q ss_pred             hHHHHHhCCCCHHHHHHHHH-C--CCC-----CCcHHHHHHHHhH---H--------cCCcEEEeccCCCchHHHHHHHH
Q 028887           68 TLRELCQGHVPEHVLRRMEE-T--GYV-----LPTDIQREALPVL---F--------SSRDCILHAQTGSGKTLTYLLLI  128 (202)
Q Consensus        68 ~~~~l~~~gl~~~l~~~l~~-~--g~~-----~~t~~Q~~~i~~i---~--------~g~~~l~~a~TGsGKT~~~l~~~  128 (202)
                      -.+.|.+.++.+.+.+.+-+ .  .+.     .+..+....+..+   +        .++.+.+.|+||+|||.....-.
T Consensus       183 i~~~L~~~dV~~~~~~~ll~~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~vI~LVGptGvGKTTTiaKLA  262 (436)
T PRK11889        183 VIRMLEQNDVEQYFIHAYAEKLKVKFENATMITEEEVIEYILEDMRSHFNTENVFEKEVQTIALIGPTGVGKTTTLAKMA  262 (436)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHhhhcccccCCHHHHHHHHHHHHHHHhccccccccCCcEEEEECCCCCcHHHHHHHHH
Confidence            35667788888877766522 1  111     1112222222221   1        12468899999999998866554


Q ss_pred             HHHH
Q 028887          129 FSLV  132 (202)
Q Consensus       129 l~~l  132 (202)
                      ....
T Consensus       263 ~~L~  266 (436)
T PRK11889        263 WQFH  266 (436)
T ss_pred             HHHH
Confidence            4433

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=93.39  E-value=0.25  Score=40.34  Aligned_cols=54  Identities=11%  Similarity=0.114  Sum_probs=34.9

Q ss_pred             HcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          105 FSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       105 ~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      ..|..+++.|++|+|||...+-.+...+..+.   ++++++.+ +-..+..+.+.+++
T Consensus        22 ~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~g~---~~~yi~~e-~~~~~~~~~~~~~g   75 (230)
T PRK08533         22 PAGSLILIEGDESTGKSILSQRLAYGFLQNGY---SVSYVSTQ-LTTTEFIKQMMSLG   75 (230)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHhCCC---cEEEEeCC-CCHHHHHHHHHHhC
Confidence            34678999999999999886555555444444   67887743 33345555554443

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.36  E-value=2.1  Score=39.51  Aligned_cols=64  Identities=19%  Similarity=0.011  Sum_probs=39.1

Q ss_pred             chHHHHHhCCCCHHHHHHHHH-CCC-CCCcHHHHHHHHh------------HHcCCcEEEeccCCCchHHHHHHHHHH
Q 028887           67 LTLRELCQGHVPEHVLRRMEE-TGY-VLPTDIQREALPV------------LFSSRDCILHAQTGSGKTLTYLLLIFS  130 (202)
Q Consensus        67 ~~~~~l~~~gl~~~l~~~l~~-~g~-~~~t~~Q~~~i~~------------i~~g~~~l~~a~TGsGKT~~~l~~~l~  130 (202)
                      .-++.|.+.|+.+.+.+.|-+ +.- .............            +..|..+.+.|++|+|||.........
T Consensus       296 ~l~~~L~~~Gvs~~la~~L~~~l~~~~~~~~~~~~l~~~L~~~l~v~~~~~l~~G~vIaLVGPtGvGKTTtaakLAa~  373 (559)
T PRK12727        296 QALELMDDYGFDAGLTRDVAMQIPADTELHRGRGLMLGLLSKRLPVAPVDPLERGGVIALVGPTGAGKTTTIAKLAQR  373 (559)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHhhhcccchhhHHHHHHHHHHHhcCcCccccccCCCEEEEECCCCCCHHHHHHHHHHH
Confidence            456888899999988888743 211 1111111111111            234677889999999999887554443

>KOG1132 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=93.31  E-value=0.34  Score=46.48  Aligned_cols=73  Identities=19%  Similarity=0.215  Sum_probs=51.6

Q ss_pred             CCcHHHHHHHHhHHc----CCcEEEeccCCCchHHHHHHHHHHHHHhc------------C-------------------
Q 028887           92 LPTDIQREALPVLFS----SRDCILHAQTGSGKTLTYLLLIFSLVNAQ------------R-------------------  136 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~----g~~~l~~a~TGsGKT~~~l~~~l~~l~~~------------~-------------------  136 (202)
                      .|++.|..-+..++.    ..+.++..|||+|||++.+-..+.-....            +                   
T Consensus        21 qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~k~~~~~~~~s~~~~~~~p~~~s~~~g~~s~e~  100 (945)
T KOG1132|consen   21 QPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQHLKSRKPKGKISERKAGFIPTQPSDSGGEKSEEA  100 (945)
T ss_pred             CcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHhhccccccchhhhhccccCCCCccCCCCchhhh
Confidence            689999988877653    47899999999999999887665433110            0                   


Q ss_pred             --------CccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887          137 --------SAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus       137 --------~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                              .-++..|-+-|.....|+.+++++....
T Consensus       101 ~e~~~~~~~ipkIyyaSRTHsQltQvvrElrrT~Y~  136 (945)
T KOG1132|consen  101 GEPIACYTGIPKIYYASRTHSQLTQVVRELRRTGYR  136 (945)
T ss_pred             cCccccccCCceEEEecchHHHHHHHHHHHhhcCCC
Confidence                    1245666667777777777777766544

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

Probab=93.27  E-value=0.16  Score=48.56  Aligned_cols=52  Identities=13%  Similarity=0.204  Sum_probs=41.4

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      .-.++.+|-|||||.+..-++-+.+..  ...++|+++..++|+.+..++++..
T Consensus        50 ~V~vVRSpMGTGKTtaLi~wLk~~l~~--~~~~VLvVShRrSL~~sL~~rf~~~  101 (824)
T PF02399_consen   50 GVLVVRSPMGTGKTTALIRWLKDALKN--PDKSVLVVSHRRSLTKSLAERFKKA  101 (824)
T ss_pred             CeEEEECCCCCCcHHHHHHHHHHhccC--CCCeEEEEEhHHHHHHHHHHHHhhc
Confidence            347899999999998887766555422  2338999999999999999999754

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

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

Probab=93.25  E-value=0.077  Score=47.59  Aligned_cols=51  Identities=20%  Similarity=0.257  Sum_probs=39.4

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      .++++.|+||||||..+++|.+-  ....   .++|.=|--||........++.+.
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll--~~~~---s~iV~D~KgEl~~~t~~~r~~~G~   95 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLL--NYPG---SMIVTDPKGELYEKTAGYRKKRGY   95 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHH--hccC---CEEEEECCCcHHHHHHHHHHHCCC
Confidence            46999999999999999999763  2222   577778999998887776666553

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

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=93.19  E-value=0.28  Score=39.45  Aligned_cols=52  Identities=15%  Similarity=0.204  Sum_probs=35.9

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      |.-+++.|++|+|||...+--+...+..+.   .++++.-. +-..++.+.+..+.
T Consensus        16 g~~~li~G~~G~GKt~~~~~~~~~~~~~g~---~~~y~s~e-~~~~~l~~~~~~~~   67 (224)
T TIGR03880        16 GHVIVVIGEYGTGKTTFSLQFLYQGLKNGE---KAMYISLE-EREERILGYAKSKG   67 (224)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhCCC---eEEEEECC-CCHHHHHHHHHHcC
Confidence            467899999999999876555555565554   67776544 34667666666654

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.

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=93.02  E-value=0.95  Score=45.08  Aligned_cols=76  Identities=20%  Similarity=0.099  Sum_probs=51.2

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHhHHc-CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHH
Q 028887           77 VPEHVLRRMEETGYVLPTDIQREALPVLFS-SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVT  155 (202)
Q Consensus        77 l~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~-g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~  155 (202)
                      +.+..+......++ .+++.|..++..+.. ++-+++.|..|+|||.+.- ++.+.+..  .+.+++.++||---+..+.
T Consensus       367 v~~~~l~a~~~~~~-~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~l~-~~~~~~e~--~G~~V~g~ApTgkAA~~L~  442 (1102)
T PRK13826        367 VREAVLAATFARHA-RLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMMK-AAREAWEA--AGYRVVGGALAGKAAEGLE  442 (1102)
T ss_pred             CCHHHHHHHHhcCC-CCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHHH-HHHHHHHH--cCCeEEEEcCcHHHHHHHH
Confidence            44444444444444 689999999998764 4668999999999996543 34444433  2337888999966665544


Q ss_pred             H
Q 028887          156 K  156 (202)
Q Consensus       156 ~  156 (202)
                      +
T Consensus       443 e  443 (1102)
T PRK13826        443 K  443 (1102)
T ss_pred             H
Confidence            3

>PF12846 AAA_10: AAA-like domain

Probab=92.88  E-value=0.23  Score=41.02  Aligned_cols=42  Identities=26%  Similarity=0.336  Sum_probs=29.2

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHH
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGM  152 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~  152 (202)
                      .++++.|.||+|||......+.+.+..+.   .++++=|.-+...
T Consensus         2 ~h~~i~G~tGsGKT~~~~~l~~~~~~~g~---~~~i~D~~g~~~~   43 (304)
T PF12846_consen    2 PHTLILGKTGSGKTTLLKNLLEQLIRRGP---RVVIFDPKGDYSP   43 (304)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHcCC---CEEEEcCCchHHH
Confidence            57899999999999877755555555443   6666666655444

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=92.86  E-value=3  Score=36.87  Aligned_cols=21  Identities=48%  Similarity=0.447  Sum_probs=17.1

Q ss_pred             CcEEEeccCCCchHHHHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLLLI  128 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~  128 (202)
                      ..+++.||||+|||.+..--.
T Consensus       175 ~vi~lvGptGvGKTTT~aKLA  195 (388)
T PRK12723        175 RVFILVGPTGVGKTTTIAKLA  195 (388)
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            468899999999998875444

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=92.85  E-value=0.21  Score=45.32  Aligned_cols=54  Identities=22%  Similarity=0.316  Sum_probs=39.5

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHh-cCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNA-QRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~-~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      .|+.+++.|++|+|||...+--+.+.+.+ +.   .+++++-. |-..++.+.+..++-
T Consensus        20 ~g~~~Li~G~pGsGKT~la~qfl~~g~~~~ge---~~lyvs~e-E~~~~l~~~~~~~G~   74 (484)
T TIGR02655        20 IGRSTLVSGTSGTGKTLFSIQFLYNGIIHFDE---PGVFVTFE-ESPQDIIKNARSFGW   74 (484)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCC---CEEEEEEe-cCHHHHHHHHHHcCC
Confidence            35779999999999998877666666655 45   67777754 666777777776653

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.

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

Probab=92.85  E-value=0.33  Score=45.56  Aligned_cols=54  Identities=20%  Similarity=0.242  Sum_probs=40.6

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHH--hHHHHHHHHHHhhcC
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRE--LGMQVTKVARVLAAK  164 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~--La~Q~~~~~~~l~~~  164 (202)
                      .++++.|+||+|||..+...+.+.+..+.   .++++=|--+  |...+...++..+..
T Consensus       177 ~H~lv~G~TGsGKT~l~~~l~~q~i~~g~---~viv~DpKgD~~l~~~~~~~~~~~G~~  232 (634)
T TIGR03743       177 GHTLVLGTTGVGKTRLAELLITQDIRRGD---VVIVIDPKGDADLKRRMRAEAKRAGRP  232 (634)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHcCC---eEEEEeCCCchHHHHHHHHHHHHhCCC
Confidence            57999999999999888666666676554   6777777754  777777777776543

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.

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=92.81  E-value=0.23  Score=41.00  Aligned_cols=54  Identities=19%  Similarity=0.257  Sum_probs=40.1

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      .|+.+++.|++|||||...+--+.+.+..+.   .++++ -+.+...++.+.+..++-
T Consensus        22 ~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge---~vlyv-s~~e~~~~l~~~~~~~g~   75 (260)
T COG0467          22 RGSVVLITGPPGTGKTIFALQFLYEGAREGE---PVLYV-STEESPEELLENARSFGW   75 (260)
T ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHHHhcCC---cEEEE-EecCCHHHHHHHHHHcCC
Confidence            4578999999999999877766666666644   56654 567777788887776543

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=92.79  E-value=0.43  Score=42.19  Aligned_cols=57  Identities=26%  Similarity=0.187  Sum_probs=33.6

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCC-HHhHHHHHHHHHHhh
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPT-RELGMQVTKVARVLA  162 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Pt-r~La~Q~~~~~~~l~  162 (202)
                      .++.+.+.||||.|||....-.........+...-+||-.=| |-=|..+.+.+-++.
T Consensus       202 ~~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA~EQLk~Ya~im  259 (407)
T COG1419         202 QKRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVEQLKTYADIM  259 (407)
T ss_pred             cCcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhHHHHHHHHHHHh
Confidence            367899999999999988765554444223333245555443 444444444444443

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=92.78  E-value=0.42  Score=37.19  Aligned_cols=58  Identities=19%  Similarity=0.223  Sum_probs=37.5

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhc-------CCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQ-------RSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~-------~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .|.-+++.|++|+|||...+--+.......       ....++|++..+-. ..++.+++..+...
T Consensus        31 ~g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~~~~   95 (193)
T PF13481_consen   31 RGELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRALLQD   95 (193)
T ss_dssp             TTSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHHHHTT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHHHhcc
Confidence            566789999999999987665555554311       13447888877766 56777888777654

>PRK10436 hypothetical protein; Provisional

Probab=92.77  E-value=0.28  Score=44.29  Aligned_cols=39  Identities=26%  Similarity=0.276  Sum_probs=25.5

Q ss_pred             cHHHHHHHHhHHc--CCcEEEeccCCCchHHHHHHHHHHHHH
Q 028887           94 TDIQREALPVLFS--SRDCILHAQTGSGKTLTYLLLIFSLVN  133 (202)
Q Consensus        94 t~~Q~~~i~~i~~--g~~~l~~a~TGsGKT~~~l~~~l~~l~  133 (202)
                      .+.|.+.+..+..  +--+++.||||||||... ..++..+.
T Consensus       203 ~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL-~a~l~~~~  243 (462)
T PRK10436        203 TPAQLAQFRQALQQPQGLILVTGPTGSGKTVTL-YSALQTLN  243 (462)
T ss_pred             CHHHHHHHHHHHHhcCCeEEEECCCCCChHHHH-HHHHHhhC
Confidence            4555555655443  345899999999999765 34555553

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=92.76  E-value=0.27  Score=45.53  Aligned_cols=45  Identities=20%  Similarity=0.376  Sum_probs=29.3

Q ss_pred             HHHCCCCCCcHHHHHHHHhHHcC--CcEEEeccCCCchHHHHHHHHHHHHH
Q 028887           85 MEETGYVLPTDIQREALPVLFSS--RDCILHAQTGSGKTLTYLLLIFSLVN  133 (202)
Q Consensus        85 l~~~g~~~~t~~Q~~~i~~i~~g--~~~l~~a~TGsGKT~~~l~~~l~~l~  133 (202)
                      +.++|+   .+.|.+.+..+...  --++++||||||||... ..++..+.
T Consensus       295 l~~lg~---~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl-~a~l~~~~  341 (564)
T TIGR02538       295 IDKLGF---EPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL-YTALNILN  341 (564)
T ss_pred             HHHcCC---CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHHhhC
Confidence            344554   45666666655442  35789999999999774 45556554

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.

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

Probab=92.73  E-value=0.14  Score=42.37  Aligned_cols=51  Identities=20%  Similarity=0.127  Sum_probs=32.7

Q ss_pred             HHcCCcEEEeccCCCchHHHHHHHHHHHHHh-cCCccEEEEecCCHHhHHHHHHHH
Q 028887          104 LFSSRDCILHAQTGSGKTLTYLLLIFSLVNA-QRSAVQAVIVVPTRELGMQVTKVA  158 (202)
Q Consensus       104 i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~-~~~~~~~Lil~Ptr~La~Q~~~~~  158 (202)
                      +..|.-+++.|++|+|||...+.-+.+.... +.   .+++++-+- -..++.+++
T Consensus        27 ~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~g~---~vl~iS~E~-~~~~~~~r~   78 (271)
T cd01122          27 LRKGELIILTAGTGVGKTTFLREYALDLITQHGV---RVGTISLEE-PVVRTARRL   78 (271)
T ss_pred             EcCCcEEEEEcCCCCCHHHHHHHHHHHHHHhcCc---eEEEEEccc-CHHHHHHHH
Confidence            4556789999999999997766555554443 33   677776432 233444444

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

>KOG1131 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 5'-3' helicase subunit RAD3 [Transcription; Replication, recombination and repair]

Probab=92.70  E-value=1.1  Score=41.20  Aligned_cols=75  Identities=20%  Similarity=0.167  Sum_probs=47.1

Q ss_pred             CCCCCcHHHHHHHHhHH----cCCcEEEeccCCCchHHHHHHHHHHHHHhcC-CccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887           89 GYVLPTDIQREALPVLF----SSRDCILHAQTGSGKTLTYLLLIFSLVNAQR-SAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus        89 g~~~~t~~Q~~~i~~i~----~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~-~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      .|...+|.|-.-+-.+.    ++-+.++..|+|+|||.+.+..++.....-. ...+.++-+-|..-......+++.+..
T Consensus        13 PY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~~~~KliYCSRTvpEieK~l~El~~l~~   92 (755)
T KOG1131|consen   13 PYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEIEKALEELKRLMD   92 (755)
T ss_pred             CCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCcccceEEEecCcchHHHHHHHHHHHHHH
Confidence            45677899988776653    3567999999999999998877766543322 223455544444434444444444433

>PRK07952 DNA replication protein DnaC; Validated

Probab=92.68  E-value=0.63  Score=38.44  Aligned_cols=57  Identities=16%  Similarity=0.191  Sum_probs=33.1

Q ss_pred             cHHHHHHHHhHHc-------C-CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHH
Q 028887           94 TDIQREALPVLFS-------S-RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQV  154 (202)
Q Consensus        94 t~~Q~~~i~~i~~-------g-~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~  154 (202)
                      +..|..++..+..       + ..+++.|++|+|||.....-.-+....+.   .++++ +..++...+
T Consensus        78 ~~~q~~al~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~aia~~l~~~g~---~v~~i-t~~~l~~~l  142 (244)
T PRK07952         78 CEGQMNALSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNELLLRGK---SVLII-TVADIMSAM  142 (244)
T ss_pred             CchHHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHHhcCC---eEEEE-EHHHHHHHH
Confidence            4556556544321       1 46899999999999766544333333333   55554 455555443

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=92.68  E-value=0.35  Score=41.92  Aligned_cols=47  Identities=21%  Similarity=0.233  Sum_probs=30.7

Q ss_pred             HHHHHCCCCCCcHHHHHHHHhH-HcCCcEEEeccCCCchHHHHHHHHHHHH
Q 028887           83 RRMEETGYVLPTDIQREALPVL-FSSRDCILHAQTGSGKTLTYLLLIFSLV  132 (202)
Q Consensus        83 ~~l~~~g~~~~t~~Q~~~i~~i-~~g~~~l~~a~TGsGKT~~~l~~~l~~l  132 (202)
                      ..+.+.|+  +++.+...+..+ ..+.++++.|+||+|||... -.++..+
T Consensus       155 ~~l~~~g~--~~~~~~~~L~~~v~~~~~ili~G~tGsGKTTll-~al~~~i  202 (340)
T TIGR03819       155 DELVASGT--FPPGVARLLRAIVAARLAFLISGGTGSGKTTLL-SALLALV  202 (340)
T ss_pred             HHHHHcCC--CCHHHHHHHHHHHhCCCeEEEECCCCCCHHHHH-HHHHccC
Confidence            34445554  456666666554 45689999999999998654 3334333

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.

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=92.68  E-value=0.12  Score=36.88  Aligned_cols=39  Identities=15%  Similarity=0.101  Sum_probs=24.0

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCH
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTR  148 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr  148 (202)
                      +..+++.||+|+|||.....-+ ..+....  ..++++.+..
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~-~~~~~~~--~~~~~~~~~~   40 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALA-RELGPPG--GGVIYIDGED   40 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHH-hccCCCC--CCEEEECCEE
Confidence            4678999999999997764443 2222111  1366666553

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.

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=92.55  E-value=0.51  Score=42.96  Aligned_cols=86  Identities=23%  Similarity=0.263  Sum_probs=59.1

Q ss_pred             CcHHHHHHHHhHHcC-----CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCC
Q 028887           93 PTDIQREALPVLFSS-----RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLD  167 (202)
Q Consensus        93 ~t~~Q~~~i~~i~~g-----~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~  167 (202)
                      +-|.|.+.+--+...     ...++.-.-|.|||.-.+..++..+..    -..||++|+.+|. ||.+++..+..+.  
T Consensus       185 LL~fQkE~l~Wl~~QE~Ss~~GGiLADEMGMGKTIQtIaLllae~~r----a~tLVvaP~VAlm-QW~nEI~~~T~gs--  257 (791)
T KOG1002|consen  185 LLPFQKEGLAWLTSQEESSVAGGILADEMGMGKTIQTIALLLAEVDR----APTLVVAPTVALM-QWKNEIERHTSGS--  257 (791)
T ss_pred             chhhhHHHHHHHHHhhhhhhccceehhhhccchHHHHHHHHHhcccc----CCeeEEccHHHHH-HHHHHHHHhccCc--
Confidence            456777766544322     235677789999998876666653332    2489999999875 7788887777653  


Q ss_pred             cccccccceEEEEEeCCccHHHHHHH
Q 028887          168 TDLEHKLCTVMALLDGGMLRRHKSWL  193 (202)
Q Consensus       168 ~~~~~~~~~~~~~~~g~~~~~~~~~l  193 (202)
                              ..+.+|||.......+.|
T Consensus       258 --------lkv~~YhG~~R~~nikel  275 (791)
T KOG1002|consen  258 --------LKVYIYHGAKRDKNIKEL  275 (791)
T ss_pred             --------eEEEEEecccccCCHHHh
Confidence                    447889997766655544

>PRK08727 hypothetical protein; Validated

Probab=92.38  E-value=0.65  Score=37.84  Aligned_cols=52  Identities=19%  Similarity=0.176  Sum_probs=31.4

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      ..+++.|++|+|||.......-+....+   .+++++ |..++.....+.++.+..
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~~~~~~---~~~~y~-~~~~~~~~~~~~~~~l~~   93 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAAAEQAG---RSSAYL-PLQAAAGRLRDALEALEG   93 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcC---CcEEEE-eHHHhhhhHHHHHHHHhc
Confidence            3499999999999966543333333333   256665 455555555555555544

>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=92.36  E-value=0.2  Score=44.11  Aligned_cols=47  Identities=23%  Similarity=0.345  Sum_probs=29.8

Q ss_pred             HcCCcEEEeccCCCchHHHHHHHHHHHHH-hcCCccEEEEecCCHHhHHHHH
Q 028887          105 FSSRDCILHAQTGSGKTLTYLLLIFSLVN-AQRSAVQAVIVVPTRELGMQVT  155 (202)
Q Consensus       105 ~~g~~~l~~a~TGsGKT~~~l~~~l~~l~-~~~~~~~~Lil~Ptr~La~Q~~  155 (202)
                      ...+++++.|.||||||.+ +..++..+. ++.   +++|.=|.-+.....+
T Consensus        13 ~e~~~~li~G~~GsGKT~~-i~~ll~~~~~~g~---~~iI~D~kg~~~~~f~   60 (386)
T PF10412_consen   13 SENRHILIIGATGSGKTQA-IRHLLDQIRARGD---RAIIYDPKGEFTERFY   60 (386)
T ss_dssp             GGGG-EEEEE-TTSSHHHH-HHHHHHHHHHTT----EEEEEEETTHHHHHH-
T ss_pred             hhhCcEEEECCCCCCHHHH-HHHHHHHHHHcCC---EEEEEECCchHHHHhc
Confidence            4567899999999999974 455665553 333   6777777766654433

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.

>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=92.31  E-value=0.79  Score=32.81  Aligned_cols=18  Identities=28%  Similarity=0.453  Sum_probs=15.5

Q ss_pred             CCcEEEeccCCCchHHHH
Q 028887          107 SRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~  124 (202)
                      +..+++.|++|+|||...
T Consensus        19 ~~~v~i~G~~G~GKT~l~   36 (151)
T cd00009          19 PKNLLLYGPPGTGKTTLA   36 (151)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            678999999999999643

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.

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

Probab=92.28  E-value=0.5  Score=44.31  Aligned_cols=71  Identities=23%  Similarity=0.112  Sum_probs=57.7

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCC-ccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS-AVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~-~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .+++.|.+++...  ...++|.|..|||||.+-..=+.+.+..+.- .-++|.++=|+--|..+.+++.++.+.
T Consensus         2 ~Ln~~Q~~av~~~--~gp~lV~AGaGsGKT~vlt~Ria~li~~~~v~p~~Il~vTFTnkAA~em~~Rl~~~~~~   73 (655)
T COG0210           2 KLNPEQREAVLHP--DGPLLVLAGAGSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKAAAEMRERLLKLLGL   73 (655)
T ss_pred             CCCHHHHHHHhcC--CCCeEEEECCCCCchhhHHHHHHHHHHcCCcChHHeeeeechHHHHHHHHHHHHHHhCc
Confidence            5788999988665  4568888999999999988888888776533 335788888999999999999999874

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.28  E-value=0.82  Score=41.88  Aligned_cols=75  Identities=21%  Similarity=0.316  Sum_probs=56.7

Q ss_pred             CCCcHHHHHHHHhHHcCCcEEEeccC-CCch--HHHHHHHHHHHHHh----------------------------cCCcc
Q 028887           91 VLPTDIQREALPVLFSSRDCILHAQT-GSGK--TLTYLLLIFSLVNA----------------------------QRSAV  139 (202)
Q Consensus        91 ~~~t~~Q~~~i~~i~~g~~~l~~a~T-GsGK--T~~~l~~~l~~l~~----------------------------~~~~~  139 (202)
                      ..+|+.|.+.+-.+.+-+|++.-..| +.|+  +-+|++-+++++.+                            |-..|
T Consensus       215 ~pltalQ~~L~~~m~~YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~~IL~Nn~r~~Sqk~g~~~~~~frDQG~tRp  294 (698)
T KOG2340|consen  215 EPLTALQKELFKIMFNYRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRDLILGNNRRLASQKEGENPDESFRDQGFTRP  294 (698)
T ss_pred             CcchHHHHHHHHHHHhhhhhccccccccccchhhhhHHHHHHHHHHHHHHHHhcchHhhhhhhcCCCCchhhhhcCCCCc
Confidence            36799999999999999998654433 3454  55688888877631                            11358


Q ss_pred             EEEEecCCHHhHHHHHHHHHHhhcCC
Q 028887          140 QAVIVVPTRELGMQVTKVARVLAAKP  165 (202)
Q Consensus       140 ~~Lil~Ptr~La~Q~~~~~~~l~~~~  165 (202)
                      ++||+||+|+-|..+.+.+..+..+.
T Consensus       295 kVLivvpfRe~A~riVn~lis~l~G~  320 (698)
T KOG2340|consen  295 KVLIVVPFRESAYRIVNLLISLLSGD  320 (698)
T ss_pred             eEEEEecchHHHHHHHHHHHHHhcCc
Confidence            99999999999999999998885543

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=92.26  E-value=0.93  Score=44.75  Aligned_cols=74  Identities=19%  Similarity=0.147  Sum_probs=55.0

Q ss_pred             CcHHHHHHHHhHHc--------CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           93 PTDIQREALPVLFS--------SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        93 ~t~~Q~~~i~~i~~--------g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      -+..|..|+..+..        |--++-.|.||+|||.+=.-- +..+...+.+++..|-.-.|.|..|..+.+++-.+-
T Consensus       409 rF~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aNARI-myaLsd~~~g~RfsiALGLRTLTLQTGda~r~rL~L  487 (1110)
T TIGR02562       409 RFRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLANARA-MYALRDDKQGARFAIALGLRSLTLQTGHALKTRLNL  487 (1110)
T ss_pred             CcchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHHHHH-HHHhCCCCCCceEEEEccccceeccchHHHHHhcCC
Confidence            36689999987643        335777899999999884333 233445566778888889999999999999988765


Q ss_pred             CCC
Q 028887          165 PLD  167 (202)
Q Consensus       165 ~~~  167 (202)
                      ..|
T Consensus       488 ~~d  490 (1110)
T TIGR02562       488 SDD  490 (1110)
T ss_pred             Ccc
Confidence            433

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.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=92.26  E-value=0.47  Score=38.41  Aligned_cols=52  Identities=8%  Similarity=0.229  Sum_probs=35.7

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      |.-+++.|++|+|||...+.-+...+..+.   +++++.-. +-..++.+.+.++.
T Consensus        25 g~~~~i~G~~GsGKt~l~~~~~~~~~~~g~---~~~y~~~e-~~~~~~~~~~~~~g   76 (234)
T PRK06067         25 PSLILIEGDHGTGKSVLSQQFVYGALKQGK---KVYVITTE-NTSKSYLKQMESVK   76 (234)
T ss_pred             CcEEEEECCCCCChHHHHHHHHHHHHhCCC---EEEEEEcC-CCHHHHHHHHHHCC
Confidence            466899999999999877666666665555   67777654 33455666666554

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=92.26  E-value=0.29  Score=44.42  Aligned_cols=52  Identities=19%  Similarity=0.198  Sum_probs=38.1

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      |.-+++.|++|+|||...+--+...+.++.   +++|++ .-|-..|+.++++.++
T Consensus       263 gs~~li~G~~G~GKt~l~~~f~~~~~~~ge---~~~y~s-~eEs~~~i~~~~~~lg  314 (484)
T TIGR02655       263 DSIILATGATGTGKTLLVSKFLENACANKE---RAILFA-YEESRAQLLRNAYSWG  314 (484)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHCCC---eEEEEE-eeCCHHHHHHHHHHcC
Confidence            357999999999999876666655555554   678766 4566677777777765

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.

>PRK08116 hypothetical protein; Validated

Probab=92.23  E-value=1.4  Score=36.81  Aligned_cols=44  Identities=20%  Similarity=0.209  Sum_probs=27.9

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVT  155 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~  155 (202)
                      ..+++.|++|+|||.... ++.+.+....  ..+++ .+..++...+.
T Consensus       115 ~gl~l~G~~GtGKThLa~-aia~~l~~~~--~~v~~-~~~~~ll~~i~  158 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAA-CIANELIEKG--VPVIF-VNFPQLLNRIK  158 (268)
T ss_pred             ceEEEECCCCCCHHHHHH-HHHHHHHHcC--CeEEE-EEHHHHHHHHH
Confidence            349999999999997655 4555554332  24444 45566665554

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=92.21  E-value=0.35  Score=43.99  Aligned_cols=45  Identities=27%  Similarity=0.299  Sum_probs=28.8

Q ss_pred             HHHCCCCCCcHHHHHHHHhHHcC-C-cEEEeccCCCchHHHHHHHHHHHHH
Q 028887           85 MEETGYVLPTDIQREALPVLFSS-R-DCILHAQTGSGKTLTYLLLIFSLVN  133 (202)
Q Consensus        85 l~~~g~~~~t~~Q~~~i~~i~~g-~-~~l~~a~TGsGKT~~~l~~~l~~l~  133 (202)
                      +.++|+   .+.|.+.+..+... . -+++.||||||||... ..++..+.
T Consensus       221 l~~Lg~---~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL-~a~L~~l~  267 (486)
T TIGR02533       221 LETLGM---SPELLSRFERLIRRPHGIILVTGPTGSGKTTTL-YAALSRLN  267 (486)
T ss_pred             HHHcCC---CHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH-HHHHhccC
Confidence            344554   56666666665543 3 3789999999999764 33455554

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.

>KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]

Probab=92.21  E-value=0.69  Score=44.99  Aligned_cols=66  Identities=17%  Similarity=0.233  Sum_probs=51.7

Q ss_pred             cHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHH
Q 028887           94 TDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVAR  159 (202)
Q Consensus        94 t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~  159 (202)
                      +..+++.+..+.+...+++.|.||+|||.-.---+++.....+..++.++-=|-|--|.-+.+++.
T Consensus       175 ~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIsvAeRVa  240 (924)
T KOG0920|consen  175 YKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAISVAERVA  240 (924)
T ss_pred             HHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcCCCCeEEecCCchHHHHHHHHHHH
Confidence            667788888899999999999999999988766666665444466676666698888888877764

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=92.16  E-value=0.17  Score=42.11  Aligned_cols=28  Identities=32%  Similarity=0.304  Sum_probs=22.0

Q ss_pred             HHHHhHHcCCcEEEeccCCCchHHHHHH
Q 028887           99 EALPVLFSSRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus        99 ~~i~~i~~g~~~l~~a~TGsGKT~~~l~  126 (202)
                      .++..+..|.++++.|++|+|||.....
T Consensus        13 ~~l~~l~~g~~vLL~G~~GtGKT~lA~~   40 (262)
T TIGR02640        13 RALRYLKSGYPVHLRGPAGTGKTTLAMH   40 (262)
T ss_pred             HHHHHHhcCCeEEEEcCCCCCHHHHHHH
Confidence            3344456789999999999999988643

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).

>PRK09183 transposase/IS protein; Provisional

Probab=92.14  E-value=0.3  Score=40.64  Aligned_cols=46  Identities=22%  Similarity=0.270  Sum_probs=30.3

Q ss_pred             HHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHH
Q 028887          104 LFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQ  153 (202)
Q Consensus       104 i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q  153 (202)
                      +..|.++++.||+|+|||.....-.......+.   .++++ +..+|..+
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~al~~~a~~~G~---~v~~~-~~~~l~~~  144 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAIALGYEAVRAGI---KVRFT-TAADLLLQ  144 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHHHHHHHHHHcCC---eEEEE-eHHHHHHH
Confidence            456789999999999999776554444344343   56554 44555544

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=92.06  E-value=1.4  Score=35.35  Aligned_cols=38  Identities=18%  Similarity=0.205  Sum_probs=28.4

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCC
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPT  147 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Pt  147 (202)
                      |.-+.+.|++|+|||...+..+.+.+..+.   +++++.-+
T Consensus        23 g~i~~i~G~~GsGKT~l~~~la~~~~~~~~---~v~yi~~e   60 (225)
T PRK09361         23 GTITQIYGPPGSGKTNICLQLAVEAAKNGK---KVIYIDTE   60 (225)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCC---eEEEEECC
Confidence            456899999999999887766666655444   67777655

>PRK13764 ATPase; Provisional

Probab=91.96  E-value=0.44  Score=44.44  Aligned_cols=28  Identities=11%  Similarity=0.216  Sum_probs=21.3

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHh
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNA  134 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~  134 (202)
                      .+.+++++|+||||||.. +.+++..+..
T Consensus       256 ~~~~ILIsG~TGSGKTTl-l~AL~~~i~~  283 (602)
T PRK13764        256 RAEGILIAGAPGAGKSTF-AQALAEFYAD  283 (602)
T ss_pred             cCCEEEEECCCCCCHHHH-HHHHHHHHhh
Confidence            457799999999999964 4566666654

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=91.93  E-value=0.5  Score=34.98  Aligned_cols=39  Identities=28%  Similarity=0.344  Sum_probs=25.0

Q ss_pred             EEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhH
Q 028887          110 CILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELG  151 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La  151 (202)
                      +++.|++|+|||.....-+......+.   .++++.......
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~~~---~v~~~~~e~~~~   40 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATKGG---KVVYVDIEEEIE   40 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhcCC---EEEEEECCcchH
Confidence            678999999999876555444433333   566666554433

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.

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

Probab=91.89  E-value=0.58  Score=40.34  Aligned_cols=41  Identities=20%  Similarity=0.102  Sum_probs=28.8

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHh
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTREL  150 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~L  150 (202)
                      |+-+.+.||+|+|||...+..+.+....+.   .++++..+..+
T Consensus        55 G~iteI~Gp~GsGKTtLal~~~~~~~~~g~---~~vyId~E~~~   95 (325)
T cd00983          55 GRIIEIYGPESSGKTTLALHAIAEAQKLGG---TVAFIDAEHAL   95 (325)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCC---CEEEECccccH
Confidence            456889999999999887776666555444   56666554433

RecA couples ATP hydrolysis to DNA strand exchange.

>cd01394 radB RadB

Probab=91.77  E-value=1.1  Score=35.63  Aligned_cols=36  Identities=14%  Similarity=0.151  Sum_probs=26.4

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEec
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVV  145 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~  145 (202)
                      |.-+++.|++|+|||...+.-+.+....+.   .++++.
T Consensus        19 g~i~~i~G~~GsGKT~l~~~~a~~~~~~g~---~v~yi~   54 (218)
T cd01394          19 GTVTQVYGPPGTGKTNIAIQLAVETAGQGK---KVAYID   54 (218)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcCC---eEEEEE
Confidence            456899999999999887666655554444   677774

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

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=91.77  E-value=0.6  Score=38.95  Aligned_cols=39  Identities=28%  Similarity=0.267  Sum_probs=24.8

Q ss_pred             cHHHHHHHHhHHc--CCcEEEeccCCCchHHHHHHHHHHHHH
Q 028887           94 TDIQREALPVLFS--SRDCILHAQTGSGKTLTYLLLIFSLVN  133 (202)
Q Consensus        94 t~~Q~~~i~~i~~--g~~~l~~a~TGsGKT~~~l~~~l~~l~  133 (202)
                      .+.|.+.+..++.  +..+++.|+||||||... ..++..+.
T Consensus        65 ~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l-~all~~i~  105 (264)
T cd01129          65 KPENLEIFRKLLEKPHGIILVTGPTGSGKTTTL-YSALSELN  105 (264)
T ss_pred             CHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHH-HHHHhhhC
Confidence            4445555554443  345899999999999764 44444443

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.

>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=91.75  E-value=0.97  Score=37.02  Aligned_cols=83  Identities=23%  Similarity=0.344  Sum_probs=54.7

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHhHHc---CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHH
Q 028887           77 VPEHVLRRMEETGYVLPTDIQREALPVLFS---SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQ  153 (202)
Q Consensus        77 l~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~---g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q  153 (202)
                      .++.++=.+. .++ -..+.|.+....+.+   |.+.+.+.-.|.|||.+.+ |++..+..++.. -+.+++| ++|..|
T Consensus        10 ~P~wLl~E~e-~~i-liR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsVI~-Pmla~~LAdg~~-LvrviVp-k~Ll~q   84 (229)
T PF12340_consen   10 YPDWLLFEIE-SNI-LIRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSVIV-PMLALALADGSR-LVRVIVP-KALLEQ   84 (229)
T ss_pred             ChHHHHHHHH-cCc-eeeHHHHHHHHHHhCCCCCCCeEeeecccCCccchHH-HHHHHHHcCCCc-EEEEEcC-HHHHHH
Confidence            4444444432 344 579999999988765   5789999999999997764 554444333322 3445555 468888


Q ss_pred             HHHHHHHhhcC
Q 028887          154 VTKVARVLAAK  164 (202)
Q Consensus       154 ~~~~~~~l~~~  164 (202)
                      ..+.++.-.+.
T Consensus        85 ~~~~L~~~lg~   95 (229)
T PF12340_consen   85 MRQMLRSRLGG   95 (229)
T ss_pred             HHHHHHHHHHH
Confidence            88887655543

There are two conserved sequence motifs: LLE and NMG.

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

Probab=91.67  E-value=0.11  Score=44.72  Aligned_cols=21  Identities=43%  Similarity=0.518  Sum_probs=17.0

Q ss_pred             HcCCcEEEeccCCCchHHHHH
Q 028887          105 FSSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       105 ~~g~~~l~~a~TGsGKT~~~l  125 (202)
                      +...++++.||||||||+..-
T Consensus        95 L~KSNILLiGPTGsGKTlLAq  115 (408)
T COG1219          95 LSKSNILLIGPTGSGKTLLAQ  115 (408)
T ss_pred             eeeccEEEECCCCCcHHHHHH
Confidence            344689999999999998653

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

Probab=91.65  E-value=0.076  Score=46.50  Aligned_cols=49  Identities=20%  Similarity=0.228  Sum_probs=37.1

Q ss_pred             cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          109 DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      ++++.|+||||||..+++|-+-..  ..   .++|.=|--|+........+..+
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~~--~~---s~vv~D~Kge~~~~t~~~r~~~G   49 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLTW--PG---SVVVLDPKGENFELTSEHRRALG   49 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhcC--CC---CEEEEccchhHHHHHHHHHHHcC
Confidence            478999999999999998876532  22   57888888888877766655543

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.

>PRK04296 thymidine kinase; Provisional

Probab=91.63  E-value=0.33  Score=38.32  Aligned_cols=37  Identities=14%  Similarity=0.220  Sum_probs=26.4

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecC
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP  146 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~P  146 (202)
                      |.-.++.|+.|+|||...+--+......+.   +++++-|
T Consensus         2 g~i~litG~~GsGKTT~~l~~~~~~~~~g~---~v~i~k~   38 (190)
T PRK04296          2 AKLEFIYGAMNSGKSTELLQRAYNYEERGM---KVLVFKP   38 (190)
T ss_pred             cEEEEEECCCCCHHHHHHHHHHHHHHHcCC---eEEEEec
Confidence            445788999999999777665555544444   7777766

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=91.58  E-value=0.55  Score=37.97  Aligned_cols=40  Identities=15%  Similarity=0.110  Sum_probs=28.6

Q ss_pred             HcCCcEEEeccCCCchHHHHHHHHHHHHHh-cCCccEEEEecCC
Q 028887          105 FSSRDCILHAQTGSGKTLTYLLLIFSLVNA-QRSAVQAVIVVPT  147 (202)
Q Consensus       105 ~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~-~~~~~~~Lil~Pt  147 (202)
                      ..|.-+++.|++|+|||...+--+.+.... +.   .+++++.+
T Consensus        11 ~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~---~vly~s~E   51 (242)
T cd00984          11 QPGDLIIIAARPSMGKTAFALNIAENIAKKQGK---PVLFFSLE   51 (242)
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCC---ceEEEeCC
Confidence            345678999999999997766555555554 44   67887743

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.

>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=91.48  E-value=0.71  Score=39.52  Aligned_cols=60  Identities=22%  Similarity=0.284  Sum_probs=37.2

Q ss_pred             chHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHH-HhHHcCCcEEEeccCCCchHHHHHHHHHHHH
Q 028887           67 LTLRELCQGHVPEHVLRRMEETGYVLPTDIQREAL-PVLFSSRDCILHAQTGSGKTLTYLLLIFSLV  132 (202)
Q Consensus        67 ~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i-~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l  132 (202)
                      .+++.+....+...-   +.+.|  .+++.|..-+ -.+.++++++++|+||||||.. +.+++..+
T Consensus       107 ~~IRk~~~~~~t~~~---l~~~g--t~~~~~~ayL~~~ie~~~siii~G~t~sGKTt~-lnall~~I  167 (312)
T COG0630         107 FTIRKFSDEPITPED---LIEYG--TISPEQAAYLWLAIEARKSIIICGGTASGKTTL-LNALLDFI  167 (312)
T ss_pred             EEEEcCCCCCCCHHH---HhhcC--CCCHHHHHHHHHHHHcCCcEEEECCCCCCHHHH-HHHHHHhC
Confidence            455555544454432   22233  4666665554 4567889999999999999954 44554443

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=91.35  E-value=1.3  Score=39.15  Aligned_cols=67  Identities=24%  Similarity=0.197  Sum_probs=40.0

Q ss_pred             chHHHHHhCCCCHHHHHHHHHC--------CCCCCcHHHHHHHHhH------------HcCCcEEEeccCCCchHHHHHH
Q 028887           67 LTLRELCQGHVPEHVLRRMEET--------GYVLPTDIQREALPVL------------FSSRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus        67 ~~~~~l~~~gl~~~l~~~l~~~--------g~~~~t~~Q~~~i~~i------------~~g~~~l~~a~TGsGKT~~~l~  126 (202)
                      .-.+.|.+.|+.+.+...+-+.        +..++..+...+.+.+            ..++.+++.||+|+|||.....
T Consensus       146 ~~~~~L~~~gV~~~~~~~l~~~~~~~~~~~~~~~~~~v~~~~~~~L~~~l~~~~~~~~~~~~ii~lvGptGvGKTTt~ak  225 (407)
T PRK12726        146 DFVKFLKGRGISDTYVADFMQAGRKQFKQVETAHLDDITDWFVPYLSGKLAVEDSFDLSNHRIISLIGQTGVGKTTTLVK  225 (407)
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHhccccccccHHHHHHHHHHHhcCcEeeCCCceecCCeEEEEECCCCCCHHHHHHH
Confidence            3466777888888776665321        1112233344444333            1245688999999999987665


Q ss_pred             HHHHHHH
Q 028887          127 LIFSLVN  133 (202)
Q Consensus       127 ~~l~~l~  133 (202)
                      -......
T Consensus       226 LA~~l~~  232 (407)
T PRK12726        226 LGWQLLK  232 (407)
T ss_pred             HHHHHHH
Confidence            5544333

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=91.33  E-value=0.43  Score=43.35  Aligned_cols=70  Identities=13%  Similarity=-0.002  Sum_probs=48.4

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      .+...|..+.-..-.|+- .++|-.|||||.....-..+ +...+..-+.++-+=|+.|+.++.+.+.+++-
T Consensus       162 nfD~~Q~kaa~~~~~G~q-rIrGLAGSGKT~~La~Kaa~-lh~knPd~~I~~Tfftk~L~s~~r~lv~~F~f  231 (660)
T COG3972         162 NFDTDQTKAAFQSGFGKQ-RIRGLAGSGKTELLAHKAAE-LHSKNPDSRIAFTFFTKILASTMRTLVPEFFF  231 (660)
T ss_pred             cccchhheeeeecCCchh-hhhcccCCCchhHHHHHHHH-HhcCCCCceEEEEeehHHHHHHHHHHHHHHHH
Confidence            344455554433344544 57889999999886654433 33344445899999999999999999888874

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]

Probab=91.32  E-value=0.79  Score=43.71  Aligned_cols=69  Identities=25%  Similarity=0.253  Sum_probs=50.2

Q ss_pred             CCcHHHHHHHHhHH----cCCcEEEeccCCCchHHH---HHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLF----SSRDCILHAQTGSGKTLT---YLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~----~g~~~l~~a~TGsGKT~~---~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .+.+.|++++.-+.    ++...|+--.-|-|||.-   |+.++.+.   ++-.-.+||+||. .+..||.++|..+.+.
T Consensus       205 ~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQiisFLaaL~~S---~k~~~paLIVCP~-Tii~qW~~E~~~w~p~  280 (923)
T KOG0387|consen  205 KLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQIISFLAALHHS---GKLTKPALIVCPA-TIIHQWMKEFQTWWPP  280 (923)
T ss_pred             HhhHHHHHHHHHHHHHHhccCCCeecccccCccchhHHHHHHHHhhc---ccccCceEEEccH-HHHHHHHHHHHHhCcc
Confidence            46899999998763    455677888899999965   44343332   1222369999996 6778999999999875

>TIGR02012 tigrfam_recA protein RecA

Probab=91.31  E-value=0.53  Score=40.53  Aligned_cols=37  Identities=24%  Similarity=0.126  Sum_probs=26.2

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecC
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP  146 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~P  146 (202)
                      |+-+.+.|++|+|||...+..+.+....+.   .++++-.
T Consensus        55 G~iteI~G~~GsGKTtLaL~~~~~~~~~g~---~v~yId~   91 (321)
T TIGR02012        55 GRIIEIYGPESSGKTTLALHAIAEAQKAGG---TAAFIDA   91 (321)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCC---cEEEEcc
Confidence            366889999999999887776666655443   4554433

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=91.20  E-value=0.23  Score=42.32  Aligned_cols=21  Identities=38%  Similarity=0.517  Sum_probs=18.1

Q ss_pred             HHcCCcEEEeccCCCchHHHH
Q 028887          104 LFSSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       104 i~~g~~~l~~a~TGsGKT~~~  124 (202)
                      +..|.++++.|+||||||...
T Consensus       141 v~~~~~ili~G~tGsGKTTll  161 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTTFL  161 (308)
T ss_pred             hhCCCEEEEECCCCCCHHHHH
Confidence            457889999999999999764

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.

>PRK09354 recA recombinase A; Provisional

Probab=91.13  E-value=0.78  Score=39.94  Aligned_cols=39  Identities=23%  Similarity=0.133  Sum_probs=27.9

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCH
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTR  148 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr  148 (202)
                      |+-+.+.|++|+|||...+..+.+....+.   .++++-.+.
T Consensus        60 G~IteI~G~~GsGKTtLal~~~~~~~~~G~---~~~yId~E~   98 (349)
T PRK09354         60 GRIVEIYGPESSGKTTLALHAIAEAQKAGG---TAAFIDAEH   98 (349)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCC---cEEEECCcc
Confidence            356889999999999988877776665544   455554443

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=91.13  E-value=0.57  Score=40.92  Aligned_cols=27  Identities=22%  Similarity=0.255  Sum_probs=20.2

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVN  133 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~  133 (202)
                      .+.-+++.||||||||... -.++..+.
T Consensus       133 ~~glilI~GpTGSGKTTtL-~aLl~~i~  159 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLL-AAIIRELA  159 (358)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHh
Confidence            4567999999999999764 55555553

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.

>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family

Probab=91.11  E-value=0.76  Score=43.16  Aligned_cols=53  Identities=19%  Similarity=0.154  Sum_probs=41.2

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCH--HhHHHHHHHHHHhhc
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTR--ELGMQVTKVARVLAA  163 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr--~La~Q~~~~~~~l~~  163 (202)
                      .+.++.|+||+|||......+.+.+..+.   .++++=|-.  ++...++..++..+.
T Consensus       181 gHtlV~GtTGsGKT~l~~~li~q~i~~g~---~vi~fDpkgD~el~~~~~~~~~~~GR  235 (643)
T TIGR03754       181 GHTLVLGTTRVGKTRLAELLITQDIRRGD---VVIVFDPKGDADLLKRMYAEAKRAGR  235 (643)
T ss_pred             CceEEECCCCCCHHHHHHHHHHHHHHcCC---eEEEEeCCCCHHHHHHHHHHHHHhCC
Confidence            57899999999999998888888887655   677777875  566666666666655

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.

>KOG1805 consensus DNA replication helicase [Replication, recombination and repair]

Probab=91.00  E-value=0.77  Score=44.70  Aligned_cols=68  Identities=24%  Similarity=0.245  Sum_probs=51.5

Q ss_pred             CCCcHHHHHHHHhHHcCCc-EEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887           91 VLPTDIQREALPVLFSSRD-CILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus        91 ~~~t~~Q~~~i~~i~~g~~-~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      ..++..|++|+-.++..+| .++.|=+|+|||...+..+--.+..++   ++|+.+=|..-+.-+.-.++.+
T Consensus       668 ~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~~LIkiL~~~gk---kVLLtsyThsAVDNILiKL~~~  736 (1100)
T KOG1805|consen  668 LRLNNDQRQALLKALAAEDYALILGMPGTGKTTTISLLIKILVALGK---KVLLTSYTHSAVDNILIKLKGF  736 (1100)
T ss_pred             hhcCHHHHHHHHHHHhccchheeecCCCCCchhhHHHHHHHHHHcCC---eEEEEehhhHHHHHHHHHHhcc
Confidence            3689999999999888766 688999999999988777655566666   7887777766555555555444

>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=90.87  E-value=1.1  Score=35.57  Aligned_cols=50  Identities=22%  Similarity=0.143  Sum_probs=28.5

Q ss_pred             cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEec--CCHHhHHHHHHHHHHh
Q 028887          109 DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVV--PTRELGMQVTKVARVL  161 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~--Ptr~La~Q~~~~~~~l  161 (202)
                      -+++.||||+|||....--.......++   ++.+++  ..|.=+.++.+.+-+.
T Consensus         3 vi~lvGptGvGKTTt~aKLAa~~~~~~~---~v~lis~D~~R~ga~eQL~~~a~~   54 (196)
T PF00448_consen    3 VIALVGPTGVGKTTTIAKLAARLKLKGK---KVALISADTYRIGAVEQLKTYAEI   54 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTT-----EEEEEESTSSTHHHHHHHHHHHH
T ss_pred             EEEEECCCCCchHhHHHHHHHHHhhccc---cceeecCCCCCccHHHHHHHHHHH
Confidence            3688999999999987665544444422   333333  3454454444444333

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 ....

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=90.76  E-value=0.29  Score=43.41  Aligned_cols=49  Identities=18%  Similarity=0.285  Sum_probs=31.4

Q ss_pred             HHhHHcCCcEEEeccCCCchHHHHHHHHHHHHH-hcCCccEEEEecCCHHhHHH
Q 028887          101 LPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVN-AQRSAVQAVIVVPTRELGMQ  153 (202)
Q Consensus       101 i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~-~~~~~~~~Lil~Ptr~La~Q  153 (202)
                      ++.-...+++++.|+||+|||.+ +..++..+. .+.   +++|+=|..++...
T Consensus        36 ~~~~~~~~h~~i~g~tGsGKt~~-i~~l~~~~~~~~~---~~vi~D~kg~~~~~   85 (410)
T cd01127          36 FPKDAEEAHTMIIGTTGTGKTTQ-IRELLASIRARGD---RAIIYDPNGGFVSK   85 (410)
T ss_pred             CCcchhhccEEEEcCCCCCHHHH-HHHHHHHHHhcCC---CEEEEeCCcchhHh
Confidence            33344567899999999999976 333444333 233   56777777666543

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.

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=90.69  E-value=1.2  Score=42.12  Aligned_cols=85  Identities=25%  Similarity=0.241  Sum_probs=58.6

Q ss_pred             CCcHHHHHHHHhHH-----cCCcEEEeccCCCchHHHHHHHHHHHHH-----hcC--CccEEEEecCCHHhHHHHHHHHH
Q 028887           92 LPTDIQREALPVLF-----SSRDCILHAQTGSGKTLTYLLLIFSLVN-----AQR--SAVQAVIVVPTRELGMQVTKVAR  159 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~-----~g~~~l~~a~TGsGKT~~~l~~~l~~l~-----~~~--~~~~~Lil~Ptr~La~Q~~~~~~  159 (202)
                      ++-++|..++..+.     .+...|+...-|-|||+.-+..+++.-.     .++  .....||+||- +|..||..++.
T Consensus       325 ~LmpHQkaal~Wl~wRE~q~~~GGILaddmGLGKTlsmislil~qK~~~~~~~~~~~~a~~TLII~Pa-Sli~qW~~Ev~  403 (901)
T KOG4439|consen  325 ELMPHQKAALRWLLWRESQPPSGGILADDMGLGKTLSMISLILHQKAARKAREKKGESASKTLIICPA-SLIHQWEAEVA  403 (901)
T ss_pred             ecchhhhhhhhhhcccccCCCCCcccccccccccchHHHHHHHHHHHHHHhhcccccccCCeEEeCcH-HHHHHHHHHHH
Confidence            35689999887764     2345777888899999977666655422     111  11248999995 78889998886


Q ss_pred             HhhcCCCCcccccccceEEEEEeCCcc
Q 028887          160 VLAAKPLDTDLEHKLCTVMALLDGGML  186 (202)
Q Consensus       160 ~l~~~~~~~~~~~~~~~~~~~~~g~~~  186 (202)
                      +-....         ...+++|||.+.
T Consensus       404 ~rl~~n---------~LsV~~~HG~n~  421 (901)
T KOG4439|consen  404 RRLEQN---------ALSVYLYHGPNK  421 (901)
T ss_pred             HHHhhc---------ceEEEEecCCcc
Confidence            655542         455789999874

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=90.59  E-value=0.87  Score=45.63  Aligned_cols=57  Identities=14%  Similarity=0.112  Sum_probs=45.8

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      .++++|.|.-|||||.+..--++..+..+...-..++|+-|+.=|..+.+++.+...
T Consensus        10 ~~~~~~~a~agsgkt~~l~~~~~~~~~~~~~~~~i~~~t~t~~aa~em~~Ri~~~L~   66 (1141)
T TIGR02784        10 KTSAWVSANAGSGKTHVLTQRVIRLLLNGVPPSKILCLTYTKAAAAEMQNRVFDRLG   66 (1141)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHHcCCCCCeEEEEecCHHHHHHHHHHHHHHHH
Confidence            467999999999999998888877776655455899999999988888877665543

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.

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=90.58  E-value=0.36  Score=46.29  Aligned_cols=44  Identities=32%  Similarity=0.479  Sum_probs=32.8

Q ss_pred             cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHH
Q 028887          109 DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQ  153 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q  153 (202)
                      ++=|...||+|||.+|+-.|.+.-. .-.-.+-+|+||+.+.-.-
T Consensus        76 NiDI~METGTGKTy~YlrtmfeLhk-~YG~~KFIivVPs~AIkeG  119 (985)
T COG3587          76 NIDILMETGTGKTYTYLRTMFELHK-KYGLFKFIIVVPSLAIKEG  119 (985)
T ss_pred             eeeEEEecCCCceeeHHHHHHHHHH-HhCceeEEEEeccHHHHhh
Confidence            5667899999999999988876432 2233478999999876443

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

Probab=90.51  E-value=0.4  Score=44.01  Aligned_cols=48  Identities=23%  Similarity=0.241  Sum_probs=39.1

Q ss_pred             EEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887          110 CILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      ++-+|||.||||.-.    ++++...+   .+++--|.|-||..++++++..+-.
T Consensus       194 i~H~GPTNSGKTy~A----Lqrl~~ak---sGvycGPLrLLA~EV~~r~na~gip  241 (700)
T KOG0953|consen  194 IMHVGPTNSGKTYRA----LQRLKSAK---SGVYCGPLRLLAHEVYDRLNALGIP  241 (700)
T ss_pred             EEEeCCCCCchhHHH----HHHHhhhc---cceecchHHHHHHHHHHHhhhcCCC
Confidence            566789999999655    56666666   6889899999999999999987653

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=90.32  E-value=0.49  Score=38.26  Aligned_cols=37  Identities=24%  Similarity=0.241  Sum_probs=26.2

Q ss_pred             cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecC
Q 028887          109 DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP  146 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~P  146 (202)
                      .++++|++|+|||- .+.++.+.+.....+.+++++..
T Consensus        36 ~l~l~G~~G~GKTH-LL~Ai~~~~~~~~~~~~v~y~~~   72 (219)
T PF00308_consen   36 PLFLYGPSGLGKTH-LLQAIANEAQKQHPGKRVVYLSA   72 (219)
T ss_dssp             EEEEEESTTSSHHH-HHHHHHHHHHHHCTTS-EEEEEH
T ss_pred             ceEEECCCCCCHHH-HHHHHHHHHHhccccccceeecH
Confidence            48999999999998 46666666655444557887753

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=90.15  E-value=1.4  Score=45.60  Aligned_cols=61  Identities=20%  Similarity=0.245  Sum_probs=44.0

Q ss_pred             CCcHHHHHHHHhHHcC--CcEEEeccCCCchHHHH--HHHHHHHHHhcCCccEEEEecCCHHhHHH
Q 028887           92 LPTDIQREALPVLFSS--RDCILHAQTGSGKTLTY--LLLIFSLVNAQRSAVQAVIVVPTRELGMQ  153 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g--~~~l~~a~TGsGKT~~~--l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q  153 (202)
                      .+++.|.+++..++.+  +.++++|..|+|||...  ++.++..+.. ..+.+++.++||---+..
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            6899999999999865  67999999999999774  2333333322 223468889999655544

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=90.09  E-value=2.3  Score=37.40  Aligned_cols=52  Identities=19%  Similarity=0.171  Sum_probs=35.2

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      |.-+++.|++|+|||...+.-.......+.   +++|+.-+ +-..|+..+..++.
T Consensus        82 GslvLI~G~pG~GKStLllq~a~~~a~~g~---~VlYvs~E-Es~~qi~~Ra~rlg  133 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLLQVAARLAKRGG---KVLYVSGE-ESPEQIKLRADRLG  133 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHhcCC---eEEEEECC-cCHHHHHHHHHHcC
Confidence            466899999999999876655444443333   68888755 34567766666654

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=89.82  E-value=0.67  Score=42.19  Aligned_cols=52  Identities=19%  Similarity=0.185  Sum_probs=37.0

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      |..+++.|++|+|||...+--+.+.+..+.   ++++++-+ +-..++.+.+..++
T Consensus       273 g~~~li~G~~G~GKT~l~~~~~~~~~~~g~---~~~yis~e-~~~~~i~~~~~~~g  324 (509)
T PRK09302        273 GSIILVSGATGTGKTLLASKFAEAACRRGE---RCLLFAFE-ESRAQLIRNARSWG  324 (509)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhCCC---cEEEEEec-CCHHHHHHHHHHcC
Confidence            466889999999999887666666665555   67777544 44667777766654

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=89.66  E-value=0.24  Score=41.53  Aligned_cols=22  Identities=32%  Similarity=0.422  Sum_probs=18.6

Q ss_pred             HHcCCcEEEeccCCCchHHHHH
Q 028887          104 LFSSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       104 i~~g~~~l~~a~TGsGKT~~~l  125 (202)
                      +.+++.+++.|++|+|||...-
T Consensus        30 ~~~~~pvLl~G~~GtGKT~li~   51 (272)
T PF12775_consen   30 LSNGRPVLLVGPSGTGKTSLIQ   51 (272)
T ss_dssp             HHCTEEEEEESSTTSSHHHHHH
T ss_pred             HHcCCcEEEECCCCCchhHHHH
Confidence            4578899999999999997643

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=89.63  E-value=0.27  Score=45.89  Aligned_cols=50  Identities=18%  Similarity=0.151  Sum_probs=40.1

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      .++++.||||||||..+++|-+-..  +.   .++|+=|--|+........++.+
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~~--~~---S~VV~DpKGEl~~~Ta~~R~~~G  208 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLFW--ED---SVVVHDIKLENYELTSGWREKQG  208 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHhC--CC---CEEEEeCcHHHHHHHHHHHHHCC
Confidence            4789999999999999999987653  22   47778899999888777776654

>cd01131 PilT Pilus retraction ATPase PilT

Probab=89.62  E-value=0.71  Score=36.61  Aligned_cols=23  Identities=30%  Similarity=0.535  Sum_probs=17.1

Q ss_pred             EEEeccCCCchHHHHHHHHHHHHH
Q 028887          110 CILHAQTGSGKTLTYLLLIFSLVN  133 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~l~~~l~~l~  133 (202)
                      +++.||||||||... ..++..+.
T Consensus         4 ilI~GptGSGKTTll-~~ll~~~~   26 (198)
T cd01131           4 VLVTGPTGSGKSTTL-AAMIDYIN   26 (198)
T ss_pred             EEEECCCCCCHHHHH-HHHHHHhh
Confidence            689999999999774 44455554

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.

>PRK05642 DNA replication initiation factor; Validated

Probab=89.57  E-value=1.4  Score=35.98  Aligned_cols=50  Identities=18%  Similarity=0.092  Sum_probs=29.2

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      ..++++|++|+|||-. +.++.+.+...  +.+++++. ..++.....+..+.+
T Consensus        46 ~~l~l~G~~G~GKTHL-l~a~~~~~~~~--~~~v~y~~-~~~~~~~~~~~~~~~   95 (234)
T PRK05642         46 SLIYLWGKDGVGRSHL-LQAACLRFEQR--GEPAVYLP-LAELLDRGPELLDNL   95 (234)
T ss_pred             CeEEEECCCCCCHHHH-HHHHHHHHHhC--CCcEEEee-HHHHHhhhHHHHHhh
Confidence            4588999999999976 33444444322  23667654 455554433333333

>PRK13700 conjugal transfer protein TraD; Provisional

Probab=89.51  E-value=0.54  Score=44.61  Aligned_cols=45  Identities=18%  Similarity=0.169  Sum_probs=29.9

Q ss_pred             HcCCcEEEeccCCCchHHHHHHHHHHHH-HhcCCccEEEEecCCHHhHHH
Q 028887          105 FSSRDCILHAQTGSGKTLTYLLLIFSLV-NAQRSAVQAVIVVPTRELGMQ  153 (202)
Q Consensus       105 ~~g~~~l~~a~TGsGKT~~~l~~~l~~l-~~~~~~~~~Lil~Ptr~La~Q  153 (202)
                      ...+++++.|.||||||.+. .-++..+ .++.   +++|.=|.-+.+..
T Consensus       183 ~E~~H~li~GttGSGKS~~i-~~LL~~ir~RGd---rAIIyD~~GeFv~~  228 (732)
T PRK13700        183 SEIQNFCLHGTVGAGKSEVI-RRLANYARQRGD---MVVIYDRSGEFVKS  228 (732)
T ss_pred             hhhcceEEeCCCCCCHHHHH-HHHHHHHHHcCC---eEEEEeCCCchHHH
Confidence            45578999999999999866 4444444 3344   56666666555543

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=89.44  E-value=0.33  Score=31.42  Aligned_cols=18  Identities=22%  Similarity=0.377  Sum_probs=15.3

Q ss_pred             CCcEEEeccCCCchHHHH
Q 028887          107 SRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~  124 (202)
                      |...++.|++|+|||..+
T Consensus        23 g~~tli~G~nGsGKSTll   40 (62)
T PF13555_consen   23 GDVTLITGPNGSGKSTLL   40 (62)
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            456999999999999764

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=89.34  E-value=5.5  Score=38.33  Aligned_cols=62  Identities=21%  Similarity=0.037  Sum_probs=35.5

Q ss_pred             HHHHHhCCCCHHHHHHHHH-CC-CCCCcHHHHHHHHhH------H--------cCCcEEEeccCCCchHHHHHHHHHH
Q 028887           69 LRELCQGHVPEHVLRRMEE-TG-YVLPTDIQREALPVL------F--------SSRDCILHAQTGSGKTLTYLLLIFS  130 (202)
Q Consensus        69 ~~~l~~~gl~~~l~~~l~~-~g-~~~~t~~Q~~~i~~i------~--------~g~~~l~~a~TGsGKT~~~l~~~l~  130 (202)
                      .+.|.+.|+.+.+.+.+-+ .. -..+..........+      +        .|+-+.+.||||+|||.....-.-.
T Consensus       131 ~~~Ll~~dv~~~la~~l~~~l~~~~~~~~~~~~l~~~L~~~l~il~~~~~~~~~g~Vi~lVGpnGvGKTTTiaKLA~~  208 (767)
T PRK14723        131 FRWLLGAGFSGQLARALLERLPVGYDRPAAMAWIRNELATHLPVLRDEDALLAQGGVLALVGPTGVGKTTTTAKLAAR  208 (767)
T ss_pred             HHHHHHCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhhccCCCcccCCCeEEEEECCCCCcHHHHHHHHHhh
Confidence            4667788888877777633 11 012222222222221      1        2445789999999999886654433

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=89.33  E-value=2.1  Score=38.39  Aligned_cols=34  Identities=21%  Similarity=0.258  Sum_probs=25.2

Q ss_pred             HhHHcCCcEEEeccCCCchHHHHHHHHHH-HHHhc
Q 028887          102 PVLFSSRDCILHAQTGSGKTLTYLLLIFS-LVNAQ  135 (202)
Q Consensus       102 ~~i~~g~~~l~~a~TGsGKT~~~l~~~l~-~l~~~  135 (202)
                      +.+..+.+++..||+|+|||-.|..-... .+..+
T Consensus       204 ~fve~~~Nli~lGp~GTGKThla~~l~~~~a~~sG  238 (449)
T TIGR02688       204 PLVEPNYNLIELGPKGTGKSYIYNNLSPYVILISG  238 (449)
T ss_pred             HHHhcCCcEEEECCCCCCHHHHHHHHhHHHHHHcC
Confidence            55667899999999999999887754434 44444

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.

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

Probab=89.33  E-value=0.87  Score=45.69  Aligned_cols=57  Identities=16%  Similarity=0.236  Sum_probs=44.5

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcC--CccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQR--SAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~--~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      .+.+++|.|..|||||.+-..-++..+..+.  .-.+.|+++-|+.=+..+..++.+-.
T Consensus        15 ~~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~~v~~ILvvTFT~aAa~Emk~RI~~~L   73 (1139)
T COG1074          15 PGQSVLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRDRL   73 (1139)
T ss_pred             CCCcEEEEEcCCCCchhHHHHHHHHHHhhcCCCChhHeeeeeccHHHHHHHHHHHHHHH
Confidence            4578999999999999998888888877642  34478999999888777776655433

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=89.30  E-value=1.9  Score=45.06  Aligned_cols=62  Identities=26%  Similarity=0.270  Sum_probs=43.7

Q ss_pred             CCcHHHHHHHHhHHcC--CcEEEeccCCCchHHHHHHHHHHHHHh--cCCccEEEEecCCHHhHHHH
Q 028887           92 LPTDIQREALPVLFSS--RDCILHAQTGSGKTLTYLLLIFSLVNA--QRSAVQAVIVVPTRELGMQV  154 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g--~~~l~~a~TGsGKT~~~l~~~l~~l~~--~~~~~~~Lil~Ptr~La~Q~  154 (202)
                      .+++.|.+++..++.+  +-+++.|..|+|||... -.++..+..  ...+.+++.++||---+..+
T Consensus       967 ~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l-~~v~~~~~~l~~~~~~~V~glAPTgrAAk~L 1032 (1747)
T PRK13709        967 GLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQF-RAVMSAVNTLPESERPRVVGLGPTHRAVGEM 1032 (1747)
T ss_pred             CCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHH-HHHHHHHHHhhcccCceEEEECCcHHHHHHH
Confidence            6899999999999875  56899999999999764 233333321  12234688899997555443

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

Probab=89.29  E-value=1.6  Score=42.29  Aligned_cols=67  Identities=21%  Similarity=0.157  Sum_probs=42.6

Q ss_pred             cHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887           94 TDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus        94 t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      +....+.+..+.+..-+++.|+||||||...-.-+++.-..+  .....+.=|-|-=|.-+.+++.+-.
T Consensus        52 ~~~~~~i~~ai~~~~vvii~getGsGKTTqlP~~lle~g~~~--~g~I~~tQPRRlAArsvA~RvAeel  118 (845)
T COG1643          52 TAVRDEILKAIEQNQVVIIVGETGSGKTTQLPQFLLEEGLGI--AGKIGCTQPRRLAARSVAERVAEEL  118 (845)
T ss_pred             HHHHHHHHHHHHhCCEEEEeCCCCCChHHHHHHHHHhhhccc--CCeEEecCchHHHHHHHHHHHHHHh
Confidence            455566666777888899999999999987655555443311  1134444477655566666654433

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=89.28  E-value=5.9  Score=33.25  Aligned_cols=23  Identities=30%  Similarity=0.375  Sum_probs=18.5

Q ss_pred             CcEEEeccCCCchHHHHHHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFS  130 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~  130 (202)
                      ..+.+.|++|+|||..+..-...
T Consensus        76 ~~i~~~G~~g~GKTtl~~~l~~~   98 (270)
T PRK06731         76 QTIALIGPTGVGKTTTLAKMAWQ   98 (270)
T ss_pred             CEEEEECCCCCcHHHHHHHHHHH
Confidence            57899999999999987655444

>PRK11823 DNA repair protein RadA; Provisional

Probab=89.11  E-value=0.91  Score=40.82  Aligned_cols=52  Identities=21%  Similarity=0.211  Sum_probs=35.3

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      |.-+++.|++|+|||...+.-.......+.   +++|+.-+ +-..|+..+.+++.
T Consensus        80 Gs~~lI~G~pG~GKTtL~lq~a~~~a~~g~---~vlYvs~E-es~~qi~~ra~rlg  131 (446)
T PRK11823         80 GSVVLIGGDPGIGKSTLLLQVAARLAAAGG---KVLYVSGE-ESASQIKLRAERLG  131 (446)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhcCC---eEEEEEcc-ccHHHHHHHHHHcC
Confidence            456899999999999876655544443333   78887754 44567766666654

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=89.00  E-value=1.6  Score=46.17  Aligned_cols=61  Identities=21%  Similarity=0.254  Sum_probs=44.7

Q ss_pred             CCcHHHHHHHHhHHcC--CcEEEeccCCCchHHHHH---HHHHHHHHhcCCccEEEEecCCHHhHHHH
Q 028887           92 LPTDIQREALPVLFSS--RDCILHAQTGSGKTLTYL---LLIFSLVNAQRSAVQAVIVVPTRELGMQV  154 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g--~~~l~~a~TGsGKT~~~l---~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~  154 (202)
                      .+++.|+.++..++.+  +-+++.|..|+|||...-   -++.+.+..  .+.+++.++||-.-+..+
T Consensus      1019 ~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~--~g~~v~glApT~~Aa~~L 1084 (1960)
T TIGR02760      1019 RLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFES--EQLQVIGLAPTHEAVGEL 1084 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHHh--cCCeEEEEeChHHHHHHH
Confidence            6899999999998875  557889999999997762   344444432  234788899996666544

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.

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=88.86  E-value=0.85  Score=32.85  Aligned_cols=23  Identities=35%  Similarity=0.358  Sum_probs=14.5

Q ss_pred             cCCcEEEeccCCCchHHHHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLI  128 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~  128 (202)
                      .++.+++.|++|+|||...-.-.
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~~   25 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRLA   25 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHHHHH
Confidence            34668999999999998754433

>TIGR00416 sms DNA repair protein RadA

Probab=88.81  E-value=0.91  Score=40.92  Aligned_cols=52  Identities=21%  Similarity=0.176  Sum_probs=35.2

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      |.-+++.|++|+|||...+.-+.+....+.   +++|+..+ |-..|+..+..++.
T Consensus        94 GsvilI~G~pGsGKTTL~lq~a~~~a~~g~---kvlYvs~E-Es~~qi~~ra~rlg  145 (454)
T TIGR00416        94 GSLILIGGDPGIGKSTLLLQVACQLAKNQM---KVLYVSGE-ESLQQIKMRAIRLG  145 (454)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHHhcCC---cEEEEECc-CCHHHHHHHHHHcC
Confidence            466899999999999877665544443333   68888765 34566666665553

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=88.75  E-value=0.99  Score=34.46  Aligned_cols=28  Identities=25%  Similarity=0.434  Sum_probs=16.7

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhc
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQ  135 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~  135 (202)
                      ++.+++.|+.|+|||... -.++..+...
T Consensus        24 ~~~~ll~G~~G~GKT~ll-~~~~~~~~~~   51 (185)
T PF13191_consen   24 PRNLLLTGESGSGKTSLL-RALLDRLAER   51 (185)
T ss_dssp             ---EEE-B-TTSSHHHHH-HHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHH-HHHHHHHHhc
Confidence            467999999999999663 3455555544

>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown

Probab=88.70  E-value=0.71  Score=37.11  Aligned_cols=26  Identities=35%  Similarity=0.474  Sum_probs=20.0

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLV  132 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l  132 (202)
                      ++++.+.|.||||||...-.-+.+.+
T Consensus        23 ~~H~~I~G~TGsGKS~~~~~ll~~l~   48 (229)
T PF01935_consen   23 NRHIAIFGTTGSGKSNTVKVLLEELL   48 (229)
T ss_pred             cceEEEECCCCCCHHHHHHHHHHHHH
Confidence            57899999999999977655554444

It contains several conserved aspartates and histidines that could be metal ligands.

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=88.64  E-value=0.88  Score=36.27  Aligned_cols=21  Identities=29%  Similarity=0.317  Sum_probs=17.0

Q ss_pred             cCCcEEEeccCCCchHHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~  126 (202)
                      .+..+++.|++|+|||.....
T Consensus        37 ~~~~lll~G~~G~GKT~la~~   57 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSHLLQA   57 (226)
T ss_pred             CCCeEEEECCCCCCHHHHHHH
Confidence            356799999999999976544

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.

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

Probab=88.63  E-value=0.45  Score=46.60  Aligned_cols=69  Identities=25%  Similarity=0.286  Sum_probs=49.3

Q ss_pred             CCcHHHHHHHHhHHc-CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887           92 LPTDIQREALPVLFS-SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~-g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      ...|+|.+.+-...+ ..++++-+|||+|||++|.+++...+.... +.++.+++|-++|+....+.....
T Consensus       927 ~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~p-~~kvvyIap~kalvker~~Dw~~r  996 (1230)
T KOG0952|consen  927 YFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYYP-GSKVVYIAPDKALVKERSDDWSKR  996 (1230)
T ss_pred             ccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccCC-CccEEEEcCCchhhcccccchhhh
Confidence            345555554433322 356888999999999999999988776433 358999999999987766555433

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=88.51  E-value=2.5  Score=33.68  Aligned_cols=43  Identities=21%  Similarity=0.119  Sum_probs=28.8

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhc---CCccEEEEecCCHH
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQ---RSAVQAVIVVPTRE  149 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~---~~~~~~Lil~Ptr~  149 (202)
                      |.-+.+.|++|+|||...+.-+......+   .....++++.....
T Consensus        19 g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~~   64 (226)
T cd01393          19 GRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGA   64 (226)
T ss_pred             CcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCCC
Confidence            46789999999999987776555544333   01136788876543

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=88.49  E-value=12  Score=33.42  Aligned_cols=81  Identities=20%  Similarity=0.077  Sum_probs=42.6

Q ss_pred             chHHHHHhCCCCHHHHHHHHHC--CCCCCcHHH-------HHHHHh------HHcCCcEEEeccCCCchHHHHHHHHHHH
Q 028887           67 LTLRELCQGHVPEHVLRRMEET--GYVLPTDIQ-------REALPV------LFSSRDCILHAQTGSGKTLTYLLLIFSL  131 (202)
Q Consensus        67 ~~~~~l~~~gl~~~l~~~l~~~--g~~~~t~~Q-------~~~i~~------i~~g~~~l~~a~TGsGKT~~~l~~~l~~  131 (202)
                      .-++.|.+.|+.+.+.+.+-+.  +........       ...++.      +..|.-+.+.|+||+|||.......-..
T Consensus       136 ~~~~~L~~~~v~~~la~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~g~vi~lvGpnG~GKTTtlakLA~~~  215 (420)
T PRK14721        136 KVLRTLLSAGFSPLLSRHLLEKLPADRDFEQSLKKTISLLTLNLRTIGGDEIIEQGGVYALIGPTGVGKTTTTAKLAARA  215 (420)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhcCCccccCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            3457888889888877776331  000111111       111111      1235568999999999998876444333


Q ss_pred             HHhcCCccEEEEecCC
Q 028887          132 VNAQRSAVQAVIVVPT  147 (202)
Q Consensus       132 l~~~~~~~~~Lil~Pt  147 (202)
                      +.......-+++...+
T Consensus       216 ~~~~~~~~v~~i~~d~  231 (420)
T PRK14721        216 VIRHGADKVALLTTDS  231 (420)
T ss_pred             HHhcCCCeEEEEecCC
Confidence            2221111235555555

>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=88.47  E-value=0.35  Score=34.78  Aligned_cols=17  Identities=35%  Similarity=0.477  Sum_probs=13.9

Q ss_pred             EEEeccCCCchHHHHHH
Q 028887          110 CILHAQTGSGKTLTYLL  126 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~l~  126 (202)
                      ++++||.|+|||...-.
T Consensus         1 ill~G~~G~GKT~l~~~   17 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARA   17 (132)
T ss_dssp             EEEESSTTSSHHHHHHH
T ss_pred             CEEECcCCCCeeHHHHH
Confidence            58999999999976543

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 ....

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

Probab=88.38  E-value=1.5  Score=43.28  Aligned_cols=57  Identities=23%  Similarity=0.280  Sum_probs=45.3

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCC
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKP  165 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~  165 (202)
                      +..++.=-+|||||+.-+...-..+.. ...+.+++++=.++|-.|+.+.|..+....
T Consensus       274 ~~G~IWHtqGSGKTlTm~~~A~~l~~~-~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~  330 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMFKLARLLLEL-PKNPKVLFVVDRKDLDDQTSDEFQSFGKVA  330 (962)
T ss_pred             CceEEEeecCCchHHHHHHHHHHHHhc-cCCCeEEEEechHHHHHHHHHHHHHHHHhh
Confidence            457888889999999865554333333 566799999999999999999999988764

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=88.27  E-value=1.1  Score=40.72  Aligned_cols=52  Identities=19%  Similarity=0.302  Sum_probs=36.8

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHh-cCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNA-QRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~-~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      |.-+++.|++|+|||...+--+.+.+.. +.   .+++++ +-+-..|+.+.+..++
T Consensus        31 Gs~~li~G~pGsGKT~l~~qf~~~~~~~~ge---~~lyis-~ee~~~~i~~~~~~~g   83 (509)
T PRK09302         31 GRPTLVSGTAGTGKTLFALQFLVNGIKRFDE---PGVFVT-FEESPEDIIRNVASFG   83 (509)
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHhcCC---CEEEEE-ccCCHHHHHHHHHHcC
Confidence            5679999999999998776656666655 44   577764 4455666667776664

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=88.24  E-value=0.34  Score=45.80  Aligned_cols=49  Identities=12%  Similarity=0.126  Sum_probs=36.1

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      .++++.|+||||||..|++|-+-..  ..   .++|+=|--|+........++.
T Consensus       140 ~hvlviApTgSGKgvg~VIPnLL~~--~g---S~VV~DpKGE~~~~Ta~~R~~~  188 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIPTLLTF--KG---SVIALDVKGELFELTSRARKAS  188 (670)
T ss_pred             ceEEEEecCCCCceeeehHhHHhcC--CC---CEEEEeCCchHHHHHHHHHHhC
Confidence            4799999999999999999986543  12   4677777777776665555444

>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=88.19  E-value=1  Score=35.61  Aligned_cols=27  Identities=30%  Similarity=0.404  Sum_probs=17.7

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVN  133 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~  133 (202)
                      ..++++.|.||||||.+....+...+.
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            358999999999999876654444443

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.

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=87.92  E-value=1.2  Score=37.59  Aligned_cols=19  Identities=26%  Similarity=0.368  Sum_probs=16.2

Q ss_pred             CCcEEEeccCCCchHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l  125 (202)
                      +.++++.|++|+|||.+..
T Consensus        58 ~~~vll~G~pGTGKT~lA~   76 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVAL   76 (284)
T ss_pred             CceEEEEcCCCCCHHHHHH
Confidence            4579999999999998763

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.

>PRK08084 DNA replication initiation factor; Provisional

Probab=87.85  E-value=1.1  Score=36.53  Aligned_cols=20  Identities=20%  Similarity=0.243  Sum_probs=16.0

Q ss_pred             CCcEEEeccCCCchHHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~  126 (202)
                      +..++++||+|+|||.....
T Consensus        45 ~~~l~l~Gp~G~GKThLl~a   64 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLLHA   64 (235)
T ss_pred             CCeEEEECCCCCCHHHHHHH
Confidence            35789999999999966543

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=87.79  E-value=1.8  Score=38.93  Aligned_cols=46  Identities=15%  Similarity=0.191  Sum_probs=30.0

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVT  155 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~  155 (202)
                      ..++++|++|+|||.. +.++.+.+.....+.+++++.. .++..++.
T Consensus       142 npl~i~G~~G~GKTHL-l~Ai~~~l~~~~~~~~v~yv~~-~~f~~~~~  187 (450)
T PRK14087        142 NPLFIYGESGMGKTHL-LKAAKNYIESNFSDLKVSYMSG-DEFARKAV  187 (450)
T ss_pred             CceEEECCCCCcHHHH-HHHHHHHHHHhCCCCeEEEEEH-HHHHHHHH
Confidence            4589999999999944 3566666654444457777654 45554443

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=87.74  E-value=0.37  Score=35.52  Aligned_cols=17  Identities=29%  Similarity=0.352  Sum_probs=14.4

Q ss_pred             cEEEeccCCCchHHHHH
Q 028887          109 DCILHAQTGSGKTLTYL  125 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l  125 (202)
                      ++++.|++|+|||...-
T Consensus         1 ~vlL~G~~G~GKt~l~~   17 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLAR   17 (139)
T ss_dssp             EEEEEESSSSSHHHHHH
T ss_pred             CEEEECCCCCCHHHHHH
Confidence            47999999999997743

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.

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

Probab=87.74  E-value=0.83  Score=42.85  Aligned_cols=50  Identities=20%  Similarity=0.154  Sum_probs=36.7

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      .++++.||||+|||..+++|.+-  .-+.   .++|+=|.-|+...+...-++.+
T Consensus       212 ~H~lv~ApTgsGKgvg~VIPnLL--~~~g---S~VV~DpKgE~~~~Ta~~R~~~G  261 (623)
T TIGR02767       212 THMIFFAGSGGFKTTSVVVPTAL--KYGG---PLVCLDPSTEVAPMVCEHRRQAG  261 (623)
T ss_pred             ceEEEEeCCCCCccceeehhhhh--cCCC---CEEEEEChHHHHHHHHHHHHHcC
Confidence            57999999999999999999743  2222   46777788888776665555444

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.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=87.65  E-value=1.1  Score=38.78  Aligned_cols=27  Identities=26%  Similarity=0.373  Sum_probs=19.7

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVN  133 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~  133 (202)
                      .+..++++||||||||... ..++..+.
T Consensus       121 ~~g~ili~G~tGSGKTT~l-~al~~~i~  147 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTL-ASMIDYIN  147 (343)
T ss_pred             cCcEEEEECCCCCCHHHHH-HHHHHhhC
Confidence            3567899999999999765 44455554

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.

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=87.44  E-value=0.42  Score=34.14  Aligned_cols=17  Identities=29%  Similarity=0.321  Sum_probs=14.0

Q ss_pred             EEEeccCCCchHHHHHH
Q 028887          110 CILHAQTGSGKTLTYLL  126 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~l~  126 (202)
                      +++.|++|||||...-.
T Consensus         2 I~I~G~~gsGKST~a~~   18 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKE   18 (121)
T ss_dssp             EEEEESTTSSHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            68999999999976543

...

>PRK06893 DNA replication initiation factor; Validated

Probab=87.36  E-value=0.97  Score=36.69  Aligned_cols=21  Identities=14%  Similarity=0.036  Sum_probs=15.8

Q ss_pred             CcEEEeccCCCchHHHHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLLLI  128 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~  128 (202)
                      ..++++|++|+|||.......
T Consensus        40 ~~l~l~G~~G~GKThL~~ai~   60 (229)
T PRK06893         40 PFFYIWGGKSSGKSHLLKAVS   60 (229)
T ss_pred             CeEEEECCCCCCHHHHHHHHH
Confidence            347899999999996554433

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=87.31  E-value=1.2  Score=35.85  Aligned_cols=19  Identities=26%  Similarity=0.352  Sum_probs=15.7

Q ss_pred             CCcEEEeccCCCchHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l  125 (202)
                      +..++++|++|+|||....
T Consensus        42 ~~~~~l~G~~G~GKT~La~   60 (227)
T PRK08903         42 DRFFYLWGEAGSGRSHLLQ   60 (227)
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            4579999999999996544

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=87.28  E-value=1.9  Score=42.39  Aligned_cols=69  Identities=26%  Similarity=0.171  Sum_probs=45.8

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCC
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKP  165 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~  165 (202)
                      .|+++|-..=-.+..|  -|....||-|||++..+|+.-....|+   .+=|++..=-||..=.+++..+....
T Consensus       138 ~~ydVQLiGgivLh~G--~IAEM~TGEGKTLvatlp~yLnAL~G~---gVHvVTvNDYLA~RDaewm~p~y~fl  206 (1025)
T PRK12900        138 VPYDVQLIGGIVLHSG--KISEMATGEGKTLVSTLPTFLNALTGR---GVHVVTVNDYLAQRDKEWMNPVFEFH  206 (1025)
T ss_pred             cccchHHhhhHHhhcC--CccccCCCCCcchHhHHHHHHHHHcCC---CcEEEeechHhhhhhHHHHHHHHHHh
Confidence            4778886554444444  467899999999999998865555455   45566666667775555555554444

>TIGR02773 addB_Gpos ATP-dependent nuclease subunit B

Probab=87.25  E-value=2.1  Score=43.02  Aligned_cols=52  Identities=13%  Similarity=0.189  Sum_probs=40.3

Q ss_pred             EEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887          111 ILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus       111 l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      ++.|+.|||||.+.+--+.+.+..+..+++.+++||+.. ..+..+++....+
T Consensus         5 fi~G~aGSGKT~~l~~ri~~~l~~~~~~~~~illVPeq~-TF~~e~rl~~~~~   56 (1158)
T TIGR02773         5 FIYGRAGTGKSTFCIDEIKQKIKENPLGKPIILIVPDQM-TFQMEQALLNDIE   56 (1158)
T ss_pred             EEEeCCCCChHHHHHHHHHHHHhhCCCCCcEEEEcCCcc-cHHHHHHHHHhcc
Confidence            578999999999988888888876666778999999873 5566666655443

DNA repair is accomplished by several different systems in prokaryotes. Recombinational repair of double-stranded DNA breaks involves the RecBCD pathway in some lineages, and AddAB (also called RexAB) in other. The AddA protein is conserved between the firmicutes and the alphaproteobacteria, while the partner protein is not. Nevertheless, the partner is designated AddB in both systems. This model describes the AddB protein as found Bacillus subtilis and related species. Although the RexB protein of Streptococcus and Lactococcus is considered to be orthologous, functionally equivalent, and merely named differently, all members of this protein family have a P-loop nucleotide binding motif GxxGxGK[ST] at the N-terminus, unlike RexB proteins, and a CxxCxxxxxC motif at the C-terminus, both of which may be relevant to function.

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=87.21  E-value=1.2  Score=34.52  Aligned_cols=44  Identities=30%  Similarity=0.452  Sum_probs=32.5

Q ss_pred             HHHHHHHHCCCCC-----CcHHHHHHHHhHHcCCcEEEeccCCCchHHH
Q 028887           80 HVLRRMEETGYVL-----PTDIQREALPVLFSSRDCILHAQTGSGKTLT  123 (202)
Q Consensus        80 ~l~~~l~~~g~~~-----~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~  123 (202)
                      ++++...+.||.-     -+......+...+.++.+++.|++|.||+..
T Consensus         3 ~~~~~y~~~gy~v~~~S~~~~~g~~~l~~~l~~k~~vl~G~SGvGKSSL   51 (161)
T PF03193_consen    3 ELLEQYEKLGYPVFFISAKTGEGIEELKELLKGKTSVLLGQSGVGKSSL   51 (161)
T ss_dssp             HHHHHHHHTTSEEEE-BTTTTTTHHHHHHHHTTSEEEEECSTTSSHHHH
T ss_pred             HHHHHHHHcCCcEEEEeCCCCcCHHHHHHHhcCCEEEEECCCCCCHHHH
Confidence            4556667777752     2445556666778889999999999999965

RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.

>KOG4150 consensus Predicted ATP-dependent RNA helicase [RNA processing and modification]

Probab=87.14  E-value=0.3  Score=45.15  Aligned_cols=98  Identities=11%  Similarity=-0.108  Sum_probs=66.2

Q ss_pred             HCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCC
Q 028887           87 ETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPL  166 (202)
Q Consensus        87 ~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~  166 (202)
                      .+.-+....+|.+++..+-.|+++++...|-+||.++|.......+.... ....+++.|+.+++....+-++...... 
T Consensus       281 ~~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~~-~s~~~~~~~~~~~~~~~~~~~~V~~~~I-  358 (1034)
T KOG4150|consen  281 KNTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLCH-ATNSLLPSEMVEHLRNGSKGQVVHVEVI-  358 (1034)
T ss_pred             cccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcCc-ccceecchhHHHHhhccCCceEEEEEeh-
Confidence            34445678899999999999999999999999999999988877654332 3367888999999876444333222111 


Q ss_pred             CcccccccceEEEEEeCCccHHHH
Q 028887          167 DTDLEHKLCTVMALLDGGMLRRHK  190 (202)
Q Consensus       167 ~~~~~~~~~~~~~~~~g~~~~~~~  190 (202)
                          +.....++.++.|.......
T Consensus       359 ----~~~K~A~V~~~D~~sE~~~~  378 (1034)
T KOG4150|consen  359 ----KARKSAYVEMSDKLSETTKS  378 (1034)
T ss_pred             ----hhhhcceeecccCCCchhHH
Confidence                11123446666665555443

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=86.92  E-value=0.87  Score=41.02  Aligned_cols=33  Identities=27%  Similarity=0.354  Sum_probs=26.1

Q ss_pred             CcHHHHHHHHhHHcCCcEEEeccCCCchHHHHH
Q 028887           93 PTDIQREALPVLFSSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus        93 ~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l  125 (202)
                      +-......+..+..++++++.|++|+|||....
T Consensus       180 ~e~~le~l~~~L~~~~~iil~GppGtGKT~lA~  212 (459)
T PRK11331        180 PETTIETILKRLTIKKNIILQGPPGVGKTFVAR  212 (459)
T ss_pred             CHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHH
Confidence            344555666677789999999999999997764

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=86.70  E-value=1.9  Score=38.65  Aligned_cols=44  Identities=16%  Similarity=0.169  Sum_probs=26.9

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHH
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQ  153 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q  153 (202)
                      ..++++|++|+|||... .++...+.....+.+++++ +..++..+
T Consensus       149 ~~l~l~G~~G~GKThL~-~ai~~~~~~~~~~~~v~yi-~~~~~~~~  192 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLL-HAIGNYILEKNPNAKVVYV-TSEKFTND  192 (450)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHHHhCCCCeEEEE-EHHHHHHH
Confidence            45899999999999664 3444444433234466666 33444443

>CHL00181 cbbX CbbX; Provisional

Probab=86.68  E-value=1.5  Score=37.10  Aligned_cols=22  Identities=23%  Similarity=0.292  Sum_probs=17.8

Q ss_pred             CCcEEEeccCCCchHHHHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYLLLI  128 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~  128 (202)
                      |.++++.|++|+|||.+.-.-.
T Consensus        59 ~~~ill~G~pGtGKT~lAr~la   80 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVALKMA   80 (287)
T ss_pred             CceEEEECCCCCCHHHHHHHHH
Confidence            4568999999999998865543

>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=86.64  E-value=0.5  Score=33.79  Aligned_cols=17  Identities=29%  Similarity=0.155  Sum_probs=14.2

Q ss_pred             EEEeccCCCchHHHHHH
Q 028887          110 CILHAQTGSGKTLTYLL  126 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~l~  126 (202)
                      +++.|.+|||||.+.-.
T Consensus         1 I~i~G~~GsGKtTia~~   17 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKE   17 (129)
T ss_dssp             EEEEESTTSSHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHH
Confidence            57899999999988543

...

>PRK08939 primosomal protein DnaI; Reviewed

Probab=86.61  E-value=1.8  Score=37.00  Aligned_cols=26  Identities=19%  Similarity=0.220  Sum_probs=19.1

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLV  132 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l  132 (202)
                      ++.+++.|++|+|||.......-+..
T Consensus       156 ~~gl~L~G~~G~GKThLa~Aia~~l~  181 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYLLAAIANELA  181 (306)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            46799999999999976654433333

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=86.53  E-value=5.4  Score=34.16  Aligned_cols=63  Identities=11%  Similarity=0.043  Sum_probs=38.1

Q ss_pred             HHHhHHcC-----CcEEEeccCCCchHHHHHHHHHHHHHh---cCCccEEEEecCCHHh-HHHHHHHHHHhh
Q 028887          100 ALPVLFSS-----RDCILHAQTGSGKTLTYLLLIFSLVNA---QRSAVQAVIVVPTREL-GMQVTKVARVLA  162 (202)
Q Consensus       100 ~i~~i~~g-----~~~l~~a~TGsGKT~~~l~~~l~~l~~---~~~~~~~Lil~Ptr~L-a~Q~~~~~~~l~  162 (202)
                      .+..++.|     .-+.+.|++|+|||...+.........   +..+.+++|+.-+-.. ..++.+.+..+.
T Consensus        84 ~LD~lLgGGi~~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~~~a~~~g  155 (313)
T TIGR02238        84 ALDGILGGGIESMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRAIAERFG  155 (313)
T ss_pred             HHHHHhCCCCcCCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHHHHHHHcC
Confidence            34455554     457899999999998776544433221   2233479999866543 444555554443

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>PF02374 ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_A 3IBG_B 3SJA_A 3H84_B 3SJD_A 3ZS9_A 3A37_A 2WOJ_A 3SJC_B 3A36_B

Probab=86.48  E-value=1.6  Score=37.25  Aligned_cols=41  Identities=22%  Similarity=0.331  Sum_probs=31.3

Q ss_pred             cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEec--CCHHhHH
Q 028887          109 DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVV--PTRELGM  152 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~--Ptr~La~  152 (202)
                      -+++.|+-|.|||.+.....+.....|+   ++|+++  |..+|..
T Consensus         3 ~~~~~GKGGVGKTT~aaA~A~~~A~~G~---rtLlvS~Dpa~~L~d   45 (305)
T PF02374_consen    3 ILFFGGKGGVGKTTVAAALALALARRGK---RTLLVSTDPAHSLSD   45 (305)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTTS----EEEEESSTTTHHHH
T ss_pred             EEEEecCCCCCcHHHHHHHHHHHhhCCC---CeeEeecCCCccHHH
Confidence            4688999999999998887777776666   778775  7666654

...

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=86.46  E-value=0.69  Score=43.49  Aligned_cols=46  Identities=20%  Similarity=0.083  Sum_probs=35.0

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVA  158 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~  158 (202)
                      .++++.|+||||||..+++|.+-..  +.   .++|+=|--|+........
T Consensus       176 ~HvlviapTgSGKgvg~ViPnLL~~--~~---S~VV~D~KGE~~~~Tag~R  221 (636)
T PRK13880        176 EHVLTYAPTRSGKGVGLVVPTLLSW--GH---SSVITDLKGELWALTAGWR  221 (636)
T ss_pred             ceEEEEecCCCCCceEEEccchhhC--CC---CEEEEeCcHHHHHHHHHHH
Confidence            5799999999999999999986532  22   5788888888876554443

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=86.37  E-value=3.3  Score=43.94  Aligned_cols=63  Identities=19%  Similarity=0.273  Sum_probs=45.5

Q ss_pred             CCcHHHHHHHHhHHcC--CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHH
Q 028887           92 LPTDIQREALPVLFSS--RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKV  157 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g--~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~  157 (202)
                      .+++.|.+++..++..  +-.++.|+.|+|||... -.+.+.+..  .+.+++.++||-.-+..+.+.
T Consensus       429 ~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~l-~~l~~~~~~--~G~~V~~lAPTgrAA~~L~e~  493 (1960)
T TIGR02760       429 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEIA-QLLLHLASE--QGYEIQIITAGSLSAQELRQK  493 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHHH-HHHHHHHHh--cCCeEEEEeCCHHHHHHHHHH
Confidence            5789999999998875  56899999999999663 333344433  233799999997665554443

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.

>PF05729 NACHT: NACHT domain

Probab=86.29  E-value=1.6  Score=32.45  Aligned_cols=25  Identities=16%  Similarity=0.169  Sum_probs=17.6

Q ss_pred             cEEEeccCCCchHHHHHHHHHHHHHh
Q 028887          109 DCILHAQTGSGKTLTYLLLIFSLVNA  134 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~~~l~~l~~  134 (202)
                      -+++.|+.|+|||.... -+...+..
T Consensus         2 ~l~I~G~~G~GKStll~-~~~~~~~~   26 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLR-KLAQQLAE   26 (166)
T ss_pred             EEEEECCCCCChHHHHH-HHHHHHHh
Confidence            47899999999997654 44444443

>KOG1807 consensus Helicases [Replication, recombination and repair]

Probab=86.08  E-value=3.8  Score=39.35  Aligned_cols=68  Identities=18%  Similarity=0.077  Sum_probs=52.9

Q ss_pred             CcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC---CccEEEEecCCHHhHHHHHHHHHH
Q 028887           93 PTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR---SAVQAVIVVPTRELGMQVTKVARV  160 (202)
Q Consensus        93 ~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~---~~~~~Lil~Ptr~La~Q~~~~~~~  160 (202)
                      +..-|+.|....+.-+-.+++||+|+|||.+-+..+-..+....   .....|+.|=|..-..|....+..
T Consensus       379 ldsSq~~A~qs~ltyelsliqgppGTgkt~vtlkav~tLL~n~s~~~~~epIlvvC~Tnhavdq~ligiy~  449 (1025)
T KOG1807|consen  379 LDSSQQFAKQSKLTYELSLIQGPPGTGKTLVTLKAVDTLLLNSSGYTEPEPILVVCLTNHAVDQYLIGIYY  449 (1025)
T ss_pred             ecHHHHHHHHHHhhhhhheeecCCCCCceeehHHHHHHHHhcccccccccceeeeehhhHHHHHHHHHHHh
Confidence            34468888888888888999999999999999888766665431   123478899998888888777765

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=86.07  E-value=0.56  Score=44.97  Aligned_cols=25  Identities=28%  Similarity=0.388  Sum_probs=19.4

Q ss_pred             HHHHhHHcCCcEEEeccCCCchHHH
Q 028887           99 EALPVLFSSRDCILHAQTGSGKTLT  123 (202)
Q Consensus        99 ~~i~~i~~g~~~l~~a~TGsGKT~~  123 (202)
                      +.+.+|..+.-+|+||.||||||.-
T Consensus       263 ~IMEaIn~n~vvIIcGeTGsGKTTQ  287 (1172)
T KOG0926|consen  263 RIMEAINENPVVIICGETGSGKTTQ  287 (1172)
T ss_pred             HHHHHhhcCCeEEEecCCCCCcccc
Confidence            3445556667799999999999975

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=86.04  E-value=0.71  Score=43.44  Aligned_cols=50  Identities=18%  Similarity=0.160  Sum_probs=36.5

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      .++++.|+||+|||..+++|-+-  ..+.   .++|+=|--|+...+....++.+
T Consensus       225 ~H~Lv~ApTgsGKt~g~VIPnLL--~~~g---S~VV~DpKgEl~~~Ta~~R~~~G  274 (641)
T PRK13822        225 THGLVFAGSGGFKTTSVVVPTAL--KWGG---PLVVLDPSTEVAPMVSEHRRDAG  274 (641)
T ss_pred             ceEEEEeCCCCCccceEehhhhh--cCCC---CEEEEeCcHHHHHHHHHHHHHCC
Confidence            57899999999999999999753  2222   46666688888776666555543

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=85.96  E-value=2.3  Score=37.52  Aligned_cols=44  Identities=16%  Similarity=0.125  Sum_probs=27.3

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHH
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQ  153 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q  153 (202)
                      ..++++|++|+|||... ..+.+.+.....+..++++.. .++..+
T Consensus       137 n~l~l~G~~G~GKThL~-~ai~~~l~~~~~~~~v~yi~~-~~~~~~  180 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLL-HAIGNEILENNPNAKVVYVSS-EKFTND  180 (405)
T ss_pred             CeEEEECCCCCcHHHHH-HHHHHHHHHhCCCCcEEEEEH-HHHHHH
Confidence            35899999999999765 445555544333346777643 344433

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>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=85.95  E-value=0.56  Score=34.47  Aligned_cols=15  Identities=40%  Similarity=0.474  Sum_probs=13.2

Q ss_pred             EEEeccCCCchHHHH
Q 028887          110 CILHAQTGSGKTLTY  124 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~  124 (202)
                      ++++|++|||||...
T Consensus         2 ii~~G~pgsGKSt~a   16 (143)
T PF13671_consen    2 IILCGPPGSGKSTLA   16 (143)
T ss_dssp             EEEEESTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            689999999999774

...

>cd01363 Motor_domain Myosin and Kinesin motor domain

Probab=85.82  E-value=0.6  Score=36.63  Aligned_cols=25  Identities=36%  Similarity=0.388  Sum_probs=19.7

Q ss_pred             HHHHhHHcCCc--EEEeccCCCchHHH
Q 028887           99 EALPVLFSSRD--CILHAQTGSGKTLT  123 (202)
Q Consensus        99 ~~i~~i~~g~~--~l~~a~TGsGKT~~  123 (202)
                      .++..++.|.|  ++..|+||||||..
T Consensus        14 ~~v~~~~~G~n~~i~~yG~tGsGKT~T   40 (186)
T cd01363          14 PLLQSALDGYNVCIFAYGQTGSGKTYT   40 (186)
T ss_pred             HHHHHHhCCcceeEEEECCCCCcceEe
Confidence            55666778865  78899999999955

These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=85.74  E-value=1.7  Score=33.80  Aligned_cols=45  Identities=9%  Similarity=0.018  Sum_probs=29.7

Q ss_pred             EEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHH
Q 028887          110 CILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARV  160 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~  160 (202)
                      +++.|++|||||.....-+..   .+   .+++|+......-..+.+++..
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~---~~---~~~~y~at~~~~d~em~~rI~~   46 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAE---LG---GPVTYIATAEAFDDEMAERIAR   46 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHh---cC---CCeEEEEccCcCCHHHHHHHHH
Confidence            578999999999776543322   22   2688888777765555555433

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=85.73  E-value=2.9  Score=36.59  Aligned_cols=54  Identities=17%  Similarity=0.159  Sum_probs=38.8

Q ss_pred             cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHH-hHHHHHHHHHHhh
Q 028887          109 DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRE-LGMQVTKVARVLA  162 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~-La~Q~~~~~~~l~  162 (202)
                      -.++.|..|||||.+...-++..+.....+.+++++-++.. +-.-++..+....
T Consensus         3 ~~i~~GgrgSGKS~~~~~~~~~~~~~~~~~~~~~~~r~~~~sl~~sv~~~l~~~i   57 (396)
T TIGR01547         3 EIIAKGGRRSGKTFAIALKLVEKLAINKKQQNILAARKVQNSIRDSVFKDIENLL   57 (396)
T ss_pred             eEEEeCCCCcccHHHHHHHHHHHHHhcCCCcEEEEEehhhhHHHHHHHHHHHHHH
Confidence            36789999999999988877777665423458898888866 5555555555443

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.

>PHA02533 17 large terminase protein; Provisional

Probab=85.61  E-value=6.7  Score=36.20  Aligned_cols=72  Identities=14%  Similarity=0.145  Sum_probs=54.2

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .+.|.|...+..+..++-.++.-+-..|||.+...-.+..... ..+.++++++|+++.|..+.+.++.+...
T Consensus        59 ~L~p~Q~~i~~~~~~~R~~ii~~aRq~GKStl~a~~al~~a~~-~~~~~v~i~A~~~~QA~~vF~~ik~~ie~  130 (534)
T PHA02533         59 QMRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCF-NKDKNVGILAHKASMAAEVLDRTKQAIEL  130 (534)
T ss_pred             CCcHHHHHHHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHh-CCCCEEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            5789999998877666767788888899999877544433322 22348999999999999999888866553

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]

Probab=85.52  E-value=7.8  Score=37.27  Aligned_cols=83  Identities=19%  Similarity=0.237  Sum_probs=56.5

Q ss_pred             CCcHHHHHHHHhH----HcCCcEEEeccCCCchHHHHHHHHHHHHH--hcCCccEEEEecCCHHhHHHHHHHHHHhhcCC
Q 028887           92 LPTDIQREALPVL----FSSRDCILHAQTGSGKTLTYLLLIFSLVN--AQRSAVQAVIVVPTRELGMQVTKVARVLAAKP  165 (202)
Q Consensus        92 ~~t~~Q~~~i~~i----~~g~~~l~~a~TGsGKT~~~l~~~l~~l~--~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~  165 (202)
                      .+.+.|-+.+.-+    .+|-+.|+.-.-|-|||+--+ +++..+.  .+..+| -||++|---|. .|.++|+++++..
T Consensus       167 ~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQtI-s~l~yl~~~~~~~GP-fLVi~P~StL~-NW~~Ef~rf~P~l  243 (971)
T KOG0385|consen  167 ELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQTI-SLLGYLKGRKGIPGP-FLVIAPKSTLD-NWMNEFKRFTPSL  243 (971)
T ss_pred             ccchhhhccHHHHHHHHhcCcccEeehhcccchHHHHH-HHHHHHHHhcCCCCC-eEEEeeHhhHH-HHHHHHHHhCCCc
Confidence            5778887776654    468889999999999997643 2333332  222343 78999976664 5788899998764


Q ss_pred             CCcccccccceEEEEEeCCccHH
Q 028887          166 LDTDLEHKLCTVMALLDGGMLRR  188 (202)
Q Consensus       166 ~~~~~~~~~~~~~~~~~g~~~~~  188 (202)
                                . +.+|+|....+
T Consensus       244 ----------~-~~~~~Gdk~eR  255 (971)
T KOG0385|consen  244 ----------N-VVVYHGDKEER  255 (971)
T ss_pred             ----------c-eEEEeCCHHHH
Confidence                      3 55677765443

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=85.52  E-value=2.7  Score=39.88  Aligned_cols=61  Identities=23%  Similarity=0.286  Sum_probs=38.2

Q ss_pred             HHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEec--CCHHhHHHHHHHHH
Q 028887           95 DIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVV--PTRELGMQVTKVAR  159 (202)
Q Consensus        95 ~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~--Ptr~La~Q~~~~~~  159 (202)
                      ..+.+.+..+..++.+++.|.||||||.-.    -+.+...+-+...+|-|  |-|--|.-+.+++.
T Consensus       359 ~~R~~ll~~ir~n~vvvivgETGSGKTTQl----~QyL~edGY~~~GmIGcTQPRRvAAiSVAkrVa  421 (1042)
T KOG0924|consen  359 ACRDQLLSVIRENQVVVIVGETGSGKTTQL----AQYLYEDGYADNGMIGCTQPRRVAAISVAKRVA  421 (1042)
T ss_pred             HHHHHHHHHHhhCcEEEEEecCCCCchhhh----HHHHHhcccccCCeeeecCchHHHHHHHHHHHH
Confidence            344455555566788999999999999753    23333333222334444  77877777776654

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=85.52  E-value=3.4  Score=35.23  Aligned_cols=54  Identities=19%  Similarity=0.129  Sum_probs=33.0

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHh---cCCccEEEEecCCHHh-HHHHHHHHHHh
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNA---QRSAVQAVIVVPTREL-GMQVTKVARVL  161 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~---~~~~~~~Lil~Ptr~L-a~Q~~~~~~~l  161 (202)
                      .-+.+.|++|+|||...+-.+.....+   +..+.+++|+.-.-.. ..++.+.+..+
T Consensus       103 ~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~~~~~~~  160 (317)
T PRK04301        103 SITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQMAEAL  160 (317)
T ss_pred             cEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHHHHHHHc
Confidence            567899999999998776665554332   1123378888755432 34444444444

>PTZ00035 Rad51 protein; Provisional

Probab=85.31  E-value=4.8  Score=34.81  Aligned_cols=39  Identities=13%  Similarity=-0.003  Sum_probs=23.7

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHH---hcCCccEEEEecC
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVN---AQRSAVQAVIVVP  146 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~---~~~~~~~~Lil~P  146 (202)
                      .-+.+.|++|+|||............   .+..+-+++++.-
T Consensus       119 ~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdt  160 (337)
T PTZ00035        119 SITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDT  160 (337)
T ss_pred             eEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEc
Confidence            45789999999999876544433221   1222336777653

>PRK13876 conjugal transfer coupling protein TraG; Provisional

Probab=85.28  E-value=0.62  Score=43.98  Aligned_cols=45  Identities=16%  Similarity=0.053  Sum_probs=31.7

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKV  157 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~  157 (202)
                      .++++.||||||||..+++|-+-..  ..   .++|+=|--|+.......
T Consensus       145 ~hvLviApTrSGKgvg~VIPnLL~~--~~---S~VV~D~KGEl~~~Ta~~  189 (663)
T PRK13876        145 EHVLCFAPTRSGKGVGLVVPTLLTW--PG---SAIVHDIKGENWQLTAGF  189 (663)
T ss_pred             ceEEEEecCCCCcceeEehhhHHhC--CC---CEEEEeCcchHHHHHHHH
Confidence            5799999999999999999986643  11   355555666655544443

>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD

Probab=85.20  E-value=1.2  Score=41.44  Aligned_cols=42  Identities=19%  Similarity=0.392  Sum_probs=26.1

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHh
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTREL  150 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~L  150 (202)
                      ..+++++.|+||||||.+ +-.++..+...  +-+++|+=|.-+.
T Consensus       175 e~~h~li~G~tGsGKs~~-i~~ll~~~~~~--g~~~ii~D~~g~~  216 (566)
T TIGR02759       175 ETQHILIHGTTGSGKSVA-IRKLLRWIRQR--GDRAIIYDKGCTF  216 (566)
T ss_pred             cccceEEEcCCCCCHHHH-HHHHHHHHHhc--CCeEEEEECCCCe
Confidence            346899999999999964 44455554322  1245555555443

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).

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=85.19  E-value=1.8  Score=32.22  Aligned_cols=52  Identities=15%  Similarity=0.112  Sum_probs=29.0

Q ss_pred             EEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEe-----cCCHHhHHHHHHHHHHh
Q 028887          110 CILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIV-----VPTRELGMQVTKVARVL  161 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil-----~Ptr~La~Q~~~~~~~l  161 (202)
                      +-++|+||+||+.+.-+-.-+....+-....+...     .|..+.+.+-.+.++..
T Consensus        56 lSfHG~tGtGKn~v~~liA~~ly~~G~~S~~V~~f~~~~hFP~~~~v~~Yk~~L~~~  112 (127)
T PF06309_consen   56 LSFHGWTGTGKNFVSRLIAEHLYKSGMKSPFVHQFIATHHFPHNSNVDEYKEQLKSW  112 (127)
T ss_pred             EEeecCCCCcHHHHHHHHHHHHHhcccCCCceeeecccccCCCchHHHHHHHHHHHH
Confidence            44899999999988766554434433333333332     35555555444444433

Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor

>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=85.01  E-value=0.81  Score=36.11  Aligned_cols=24  Identities=29%  Similarity=0.416  Sum_probs=17.4

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFS  130 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~  130 (202)
                      ...+++.||.|||||..|....-.
T Consensus         3 ~~~vlL~Gps~SGKTaLf~~L~~~   26 (181)
T PF09439_consen    3 RPTVLLVGPSGSGKTALFSQLVNG   26 (181)
T ss_dssp             --EEEEE-STTSSHHHHHHHHHHS
T ss_pred             CceEEEEcCCCCCHHHHHHHHhcC
Confidence            456899999999999988765543

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.

>PRK14974 cell division protein FtsY; Provisional

Probab=84.87  E-value=3.7  Score=35.60  Aligned_cols=51  Identities=24%  Similarity=0.243  Sum_probs=28.3

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCC--H-HhHHHHHHHHHHh
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPT--R-ELGMQVTKVARVL  161 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Pt--r-~La~Q~~~~~~~l  161 (202)
                      .-+++.|++|+|||........ .+...  +.+++++...  | .-..|+......+
T Consensus       141 ~vi~~~G~~GvGKTTtiakLA~-~l~~~--g~~V~li~~Dt~R~~a~eqL~~~a~~l  194 (336)
T PRK14974        141 VVIVFVGVNGTGKTTTIAKLAY-YLKKN--GFSVVIAAGDTFRAGAIEQLEEHAERL  194 (336)
T ss_pred             eEEEEEcCCCCCHHHHHHHHHH-HHHHc--CCeEEEecCCcCcHHHHHHHHHHHHHc
Confidence            3588999999999987554443 23322  2245555432  3 3344554444443

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=84.70  E-value=2.8  Score=41.51  Aligned_cols=68  Identities=22%  Similarity=0.130  Sum_probs=44.2

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .|+++|-..--.+..|  -+....||-|||++..+|+.-....|+   .+-|++..=-||..=.+++..+...
T Consensus       169 ~~yDVQliGgivLh~G--~IAEM~TGEGKTLvAtlp~yLnAL~Gk---gVHvVTVNDYLA~RDaewmgply~f  236 (1112)
T PRK12901        169 VHYDVQLIGGVVLHQG--KIAEMATGEGKTLVATLPVYLNALTGN---GVHVVTVNDYLAKRDSEWMGPLYEF  236 (1112)
T ss_pred             cccchHHhhhhhhcCC--ceeeecCCCCchhHHHHHHHHHHHcCC---CcEEEEechhhhhccHHHHHHHHHH
Confidence            4677775443333333  578899999999999998866555555   4666666667776444444444433

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=84.42  E-value=1.3  Score=36.21  Aligned_cols=35  Identities=20%  Similarity=0.265  Sum_probs=24.3

Q ss_pred             CCcHHHHHHHHhHH----cCC-cEEEeccCCCchHHHHHH
Q 028887           92 LPTDIQREALPVLF----SSR-DCILHAQTGSGKTLTYLL  126 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~----~g~-~~l~~a~TGsGKT~~~l~  126 (202)
                      -+++.+.+++..+.    .+. .+++.|++|+|||...-.
T Consensus        23 ~~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~~   62 (269)
T TIGR03015        23 YPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIRN   62 (269)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHHH
Confidence            35666666766543    233 588999999999976543

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.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=84.41  E-value=4.1  Score=34.12  Aligned_cols=35  Identities=20%  Similarity=0.227  Sum_probs=22.8

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEec
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVV  145 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~  145 (202)
                      +-+++.|++|+|||....-........+.   +++++.
T Consensus        73 ~vi~l~G~~G~GKTTt~akLA~~l~~~g~---~V~li~  107 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIAKLANKLKKQGK---SVLLAA  107 (272)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHHhcCC---EEEEEe
Confidence            45778899999999876655544333333   555554

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=84.39  E-value=2  Score=32.85  Aligned_cols=20  Identities=35%  Similarity=0.358  Sum_probs=15.5

Q ss_pred             EEEeccCCCchHHHHHHHHH
Q 028887          110 CILHAQTGSGKTLTYLLLIF  129 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~l~~~l  129 (202)
                      +++.|++|+|||.....-..
T Consensus         3 ~~~~G~~G~GKTt~~~~la~   22 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLAL   22 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57889999999988654443

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>KOG1533 consensus Predicted GTPase [General function prediction only]

Probab=84.36  E-value=1.2  Score=36.83  Aligned_cols=36  Identities=28%  Similarity=0.342  Sum_probs=23.7

Q ss_pred             EEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecC
Q 028887          110 CILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP  146 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~P  146 (202)
                      -++.||+||||| .|+..+.+.+..-++...++=|=|
T Consensus         5 qvVIGPPgSGKs-TYc~g~~~fls~~gr~~~vVNLDP   40 (290)
T KOG1533|consen    5 QVVIGPPGSGKS-TYCNGMSQFLSAIGRPVAVVNLDP   40 (290)
T ss_pred             eEEEcCCCCCcc-chhhhHHHHHHHhCCceEEEecCC
Confidence            478899999999 677777776655443333333333

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=84.27  E-value=3.7  Score=36.78  Aligned_cols=24  Identities=29%  Similarity=0.306  Sum_probs=18.2

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSL  131 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~  131 (202)
                      .-+++.||+|+|||.....-....
T Consensus       224 ~vi~lvGptGvGKTTtaaKLA~~~  247 (432)
T PRK12724        224 KVVFFVGPTGSGKTTSIAKLAAKY  247 (432)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            347889999999998876655443

>PF02456 Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR003389 Va2 protein can interact with the adenoviral packaging signal and this interaction involves DNA sequences that have previously been demonstrated to be required for packaging []

Probab=84.14  E-value=1.2  Score=38.19  Aligned_cols=42  Identities=21%  Similarity=0.316  Sum_probs=26.1

Q ss_pred             EEEeccCCCchHHHHHHHHH-HHHHhcCCccEEEEecCCHHhHHH
Q 028887          110 CILHAQTGSGKTLTYLLLIF-SLVNAQRSAVQAVIVVPTRELGMQ  153 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~l~~~l-~~l~~~~~~~~~Lil~Ptr~La~Q  153 (202)
                      .+|.||||+||+-..--.+- +.+.  ...-.+++++|++....-
T Consensus        90 ~~VYGPTG~GKSqLlRNLis~~lI~--P~PETVfFItP~~~mIpp  132 (369)
T PF02456_consen   90 GVVYGPTGSGKSQLLRNLISCQLIQ--PPPETVFFITPQKDMIPP  132 (369)
T ss_pred             EEEECCCCCCHHHHHHHhhhcCccc--CCCCceEEECCCCCCCCH
Confidence            68899999999954321111 1111  122368999999887653

During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter [].; GO: 0019083 viral transcription

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=84.12  E-value=1.8  Score=35.70  Aligned_cols=19  Identities=26%  Similarity=0.399  Sum_probs=15.9

Q ss_pred             CcEEEeccCCCchHHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~  126 (202)
                      .++++.||+|+|||...-.
T Consensus        43 ~~vll~GppGtGKTtlA~~   61 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVARI   61 (261)
T ss_pred             ceEEEEcCCCCCHHHHHHH
Confidence            4689999999999987533

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>PHA02244 ATPase-like protein

Probab=84.12  E-value=1.5  Score=38.64  Aligned_cols=22  Identities=23%  Similarity=0.317  Sum_probs=18.5

Q ss_pred             hHHcCCcEEEeccCCCchHHHH
Q 028887          103 VLFSSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       103 ~i~~g~~~l~~a~TGsGKT~~~  124 (202)
                      .+..+.++++.||||+|||...
T Consensus       115 ~l~~~~PVLL~GppGtGKTtLA  136 (383)
T PHA02244        115 IVNANIPVFLKGGAGSGKNHIA  136 (383)
T ss_pred             HHhcCCCEEEECCCCCCHHHHH
Confidence            3456889999999999999664

>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional

Probab=84.01  E-value=0.69  Score=39.45  Aligned_cols=20  Identities=15%  Similarity=0.247  Sum_probs=16.3

Q ss_pred             CcEEEeccCCCchHHHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLLL  127 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~  127 (202)
                      +-+++.||||||||...+-.
T Consensus         5 ~ii~I~GpTasGKS~LAl~L   24 (300)
T PRK14729          5 KIVFIFGPTAVGKSNILFHF   24 (300)
T ss_pred             cEEEEECCCccCHHHHHHHH
Confidence            45899999999999876643

>PRK13531 regulatory ATPase RavA; Provisional

Probab=83.98  E-value=1.1  Score=40.79  Aligned_cols=28  Identities=25%  Similarity=0.252  Sum_probs=22.3

Q ss_pred             HHHHHhHHcCCcEEEeccCCCchHHHHH
Q 028887           98 REALPVLFSSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus        98 ~~~i~~i~~g~~~l~~a~TGsGKT~~~l  125 (202)
                      ..++-.++.|.++++.|++|+|||...-
T Consensus        30 ~lll~aalag~hVLL~GpPGTGKT~LAr   57 (498)
T PRK13531         30 RLCLLAALSGESVFLLGPPGIAKSLIAR   57 (498)
T ss_pred             HHHHHHHccCCCEEEECCCChhHHHHHH
Confidence            3344456789999999999999998763

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=83.91  E-value=28  Score=30.24  Aligned_cols=42  Identities=12%  Similarity=0.019  Sum_probs=26.9

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHH---HhcCCccEEEEecCCHH
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLV---NAQRSAVQAVIVVPTRE  149 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l---~~~~~~~~~Lil~Ptr~  149 (202)
                      .-+.+.|++|+|||...+.......   ..+....+++|+.-+-.
T Consensus       124 ~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~  168 (342)
T PLN03186        124 SITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGT  168 (342)
T ss_pred             eEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCC
Confidence            3478999999999987754443322   12222337888876654

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=83.75  E-value=1.7  Score=32.17  Aligned_cols=21  Identities=29%  Similarity=0.422  Sum_probs=16.7

Q ss_pred             HHcCCcEEEeccCCCchHHHH
Q 028887          104 LFSSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       104 i~~g~~~l~~a~TGsGKT~~~  124 (202)
                      ...+..+++.|+.|+||+.+.
T Consensus        18 a~~~~pvli~GE~GtGK~~~A   38 (138)
T PF14532_consen   18 AKSSSPVLITGEPGTGKSLLA   38 (138)
T ss_dssp             HCSSS-EEEECCTTSSHHHHH
T ss_pred             hCCCCcEEEEcCCCCCHHHHH
Confidence            345678999999999999864

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=83.50  E-value=3.1  Score=35.77  Aligned_cols=24  Identities=21%  Similarity=0.378  Sum_probs=17.6

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLV  132 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l  132 (202)
                      ..++++||+|+|||...- .+++.+
T Consensus        41 ~~i~I~G~~GtGKT~l~~-~~~~~l   64 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVTK-YVMKEL   64 (365)
T ss_pred             CcEEEECCCCCCHHHHHH-HHHHHH
Confidence            579999999999997643 333333

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=83.47  E-value=1.5  Score=35.34  Aligned_cols=27  Identities=26%  Similarity=0.416  Sum_probs=17.5

Q ss_pred             HHHHHh-HHcCCcEEEeccCCCchHHHH
Q 028887           98 REALPV-LFSSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus        98 ~~~i~~-i~~g~~~l~~a~TGsGKT~~~  124 (202)
                      +.++.. +..+.++++.|+.|+|||+..
T Consensus        12 KrAL~iAAaG~h~lLl~GppGtGKTmlA   39 (206)
T PF01078_consen   12 KRALEIAAAGGHHLLLIGPPGTGKTMLA   39 (206)
T ss_dssp             HHHHHHHHHCC--EEEES-CCCTHHHHH
T ss_pred             HHHHHHHHcCCCCeEEECCCCCCHHHHH
Confidence            344443 345689999999999999875

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=83.46  E-value=0.89  Score=35.49  Aligned_cols=20  Identities=25%  Similarity=0.227  Sum_probs=16.5

Q ss_pred             CCcEEEeccCCCchHHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~  126 (202)
                      |..+++.||+|+|||...-.
T Consensus         2 g~~i~l~G~sGsGKsTl~~~   21 (186)
T PRK10078          2 GKLIWLMGPSGSGKDSLLAA   21 (186)
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            56789999999999987543

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=83.41  E-value=0.85  Score=38.43  Aligned_cols=18  Identities=22%  Similarity=0.532  Sum_probs=15.9

Q ss_pred             CCcEEEeccCCCchHHHH
Q 028887          107 SRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~  124 (202)
                      .++++..||+|+|||+..
T Consensus       151 PknVLFyGppGTGKTm~A  168 (368)
T COG1223         151 PKNVLFYGPPGTGKTMMA  168 (368)
T ss_pred             cceeEEECCCCccHHHHH
Confidence            379999999999999865

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=83.29  E-value=0.8  Score=40.04  Aligned_cols=17  Identities=35%  Similarity=0.563  Sum_probs=15.3

Q ss_pred             CcEEEeccCCCchHHHH
Q 028887          108 RDCILHAQTGSGKTLTY  124 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~  124 (202)
                      +-++++||+|+|||+..
T Consensus       186 KGVLLYGPPGTGKTLLA  202 (406)
T COG1222         186 KGVLLYGPPGTGKTLLA  202 (406)
T ss_pred             CceEeeCCCCCcHHHHH
Confidence            67999999999999865

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=83.03  E-value=0.93  Score=40.14  Aligned_cols=23  Identities=30%  Similarity=0.622  Sum_probs=18.2

Q ss_pred             HhHHcC-----CcEEEeccCCCchHHHH
Q 028887          102 PVLFSS-----RDCILHAQTGSGKTLTY  124 (202)
Q Consensus       102 ~~i~~g-----~~~l~~a~TGsGKT~~~  124 (202)
                      |..++|     +.++..||+|+|||+..
T Consensus       235 Pe~F~GirrPWkgvLm~GPPGTGKTlLA  262 (491)
T KOG0738|consen  235 PEFFKGIRRPWKGVLMVGPPGTGKTLLA  262 (491)
T ss_pred             HHHHhhcccccceeeeeCCCCCcHHHHH
Confidence            344555     67999999999999764

>PRK00131 aroK shikimate kinase; Reviewed

Probab=82.93  E-value=0.84  Score=34.58  Aligned_cols=21  Identities=19%  Similarity=0.253  Sum_probs=17.4

Q ss_pred             HcCCcEEEeccCCCchHHHHH
Q 028887          105 FSSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       105 ~~g~~~l~~a~TGsGKT~~~l  125 (202)
                      ..+..+++.|++|||||...-
T Consensus         2 ~~~~~i~l~G~~GsGKstla~   22 (175)
T PRK00131          2 LKGPNIVLIGFMGAGKSTIGR   22 (175)
T ss_pred             CCCCeEEEEcCCCCCHHHHHH
Confidence            356789999999999998754

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=82.72  E-value=7  Score=33.67  Aligned_cols=70  Identities=20%  Similarity=0.163  Sum_probs=42.4

Q ss_pred             CcHHHHHHHHhHHcC-C---cEEEeccCCCchHHHHHHHHHHHHHh------------------cCCccEEEEecCCH--
Q 028887           93 PTDIQREALPVLFSS-R---DCILHAQTGSGKTLTYLLLIFSLVNA------------------QRSAVQAVIVVPTR--  148 (202)
Q Consensus        93 ~t~~Q~~~i~~i~~g-~---~~l~~a~TGsGKT~~~l~~~l~~l~~------------------~~~~~~~Lil~Ptr--  148 (202)
                      .+|.|...+..+... +   -++++||.|.||+.....-.-..+..                  .+..|...++.|..  
T Consensus         4 ~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~~~   83 (328)
T PRK05707          4 IYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEEAD   83 (328)
T ss_pred             CCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccCCC
Confidence            468888888777643 2   48899999999997654422222211                  12245677787852  


Q ss_pred             --HhHHHHHHHHHHhh
Q 028887          149 --ELGMQVTKVARVLA  162 (202)
Q Consensus       149 --~La~Q~~~~~~~l~  162 (202)
                        --+.|+.+....+.
T Consensus        84 ~~i~id~iR~l~~~~~   99 (328)
T PRK05707         84 KTIKVDQVRELVSFVV   99 (328)
T ss_pred             CCCCHHHHHHHHHHHh
Confidence              23556665544444

>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=82.70  E-value=2.1  Score=35.30  Aligned_cols=23  Identities=22%  Similarity=0.404  Sum_probs=16.6

Q ss_pred             cEEEeccCCCchHHHHHHHHHHHH
Q 028887          109 DCILHAQTGSGKTLTYLLLIFSLV  132 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~~~l~~l  132 (202)
                      .+++.|++|||||.. +.-++..+
T Consensus        15 r~viIG~sGSGKT~l-i~~lL~~~   37 (241)
T PF04665_consen   15 RMVIIGKSGSGKTTL-IKSLLYYL   37 (241)
T ss_pred             eEEEECCCCCCHHHH-HHHHHHhh
Confidence            688999999999954 44444433

This is thought to be an ATPase involved in viral DNA packaging [].

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=82.69  E-value=1.8  Score=36.70  Aligned_cols=18  Identities=28%  Similarity=0.392  Sum_probs=15.3

Q ss_pred             cEEEeccCCCchHHHHHH
Q 028887          109 DCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~  126 (202)
                      .++++||+|+|||.....
T Consensus        38 ~lll~Gp~GtGKT~la~~   55 (337)
T PRK12402         38 HLLVQGPPGSGKTAAVRA   55 (337)
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            699999999999976543

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=82.59  E-value=0.92  Score=35.31  Aligned_cols=16  Identities=31%  Similarity=0.434  Sum_probs=13.7

Q ss_pred             cEEEeccCCCchHHHH
Q 028887          109 DCILHAQTGSGKTLTY  124 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~  124 (202)
                      ++++.||||+|||...
T Consensus         5 ~~ll~GpsGvGKT~la   20 (171)
T PF07724_consen    5 NFLLAGPSGVGKTELA   20 (171)
T ss_dssp             EEEEESSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5789999999999754

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=82.50  E-value=0.84  Score=40.97  Aligned_cols=19  Identities=42%  Similarity=0.555  Sum_probs=15.8

Q ss_pred             cCCcEEEeccCCCchHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~  124 (202)
                      ...++++.||||||||+..
T Consensus       225 eKSNvLllGPtGsGKTlla  243 (564)
T KOG0745|consen  225 EKSNVLLLGPTGSGKTLLA  243 (564)
T ss_pred             ecccEEEECCCCCchhHHH
Confidence            3457999999999999764

>PRK08506 replicative DNA helicase; Provisional

Probab=82.16  E-value=4  Score=37.01  Aligned_cols=49  Identities=16%  Similarity=0.114  Sum_probs=30.8

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVA  158 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~  158 (202)
                      .|.-+++.|.+|.|||...+--+.+....+.   .+++++.+ .-..|+..++
T Consensus       191 ~G~LivIaarpg~GKT~fal~ia~~~~~~g~---~V~~fSlE-Ms~~ql~~Rl  239 (472)
T PRK08506        191 KGDLIIIAARPSMGKTTLCLNMALKALNQDK---GVAFFSLE-MPAEQLMLRM  239 (472)
T ss_pred             CCceEEEEcCCCCChHHHHHHHHHHHHhcCC---cEEEEeCc-CCHHHHHHHH
Confidence            3456888999999999776666555544333   56777644 2334444443

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=82.15  E-value=1.4  Score=39.74  Aligned_cols=27  Identities=26%  Similarity=0.441  Sum_probs=20.4

Q ss_pred             HHHHHh-HHcCCcEEEeccCCCchHHHH
Q 028887           98 REALPV-LFSSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus        98 ~~~i~~-i~~g~~~l~~a~TGsGKT~~~  124 (202)
                      ++++.. ...|.++++.||.|||||+..
T Consensus       188 KrAleiAAAGgHnLl~~GpPGtGKTmla  215 (490)
T COG0606         188 KRALEIAAAGGHNLLLVGPPGTGKTMLA  215 (490)
T ss_pred             HHHHHHHHhcCCcEEEecCCCCchHHhh
Confidence            334433 346799999999999999874

>PRK10867 signal recognition particle protein; Provisional

Probab=82.09  E-value=4.6  Score=36.25  Aligned_cols=41  Identities=22%  Similarity=0.226  Sum_probs=25.1

Q ss_pred             cEEEeccCCCchHHHHHHHHHHHHHh-cCCccEEEEec--CCHHhHH
Q 028887          109 DCILHAQTGSGKTLTYLLLIFSLVNA-QRSAVQAVIVV--PTRELGM  152 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~~~l~~l~~-~~~~~~~Lil~--Ptr~La~  152 (202)
                      -+++.|++|+|||....--....... +.   +++++.  +.|.-+.
T Consensus       102 vI~~vG~~GsGKTTtaakLA~~l~~~~G~---kV~lV~~D~~R~aa~  145 (433)
T PRK10867        102 VIMMVGLQGAGKTTTAGKLAKYLKKKKKK---KVLLVAADVYRPAAI  145 (433)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHhcCC---cEEEEEccccchHHH
Confidence            37889999999998765554433333 33   455544  3454443

>TIGR02746 TraC-F-type type-IV secretion system protein TraC

Probab=82.08  E-value=2.4  Score=40.65  Aligned_cols=38  Identities=16%  Similarity=0.204  Sum_probs=26.2

Q ss_pred             cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHH
Q 028887          109 DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRE  149 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~  149 (202)
                      ++++.|+||+|||...-.-+.+.+..+   .+++|+=|..+
T Consensus       432 n~~I~G~tGsGKS~~~~~l~~~~~~~g---~~v~iiD~~~s  469 (797)
T TIGR02746       432 NIAVVGGSGAGKSFFMQELIVDNLSRG---GKVWVIDVGRS  469 (797)
T ss_pred             ceEEEcCCCCCHHHHHHHHHHHHHhCC---CEEEEEeCCCC
Confidence            689999999999987655444444433   36666666544

The protein family described here is common among the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The protein conyains the Walker A and B motifs and so is a putative nucleotide triphosphatase.

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=82.01  E-value=2.6  Score=37.82  Aligned_cols=38  Identities=16%  Similarity=0.167  Sum_probs=25.0

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecC
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP  146 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~P  146 (202)
                      ..++++|++|+|||... .++.+.+.....+.+++++..
T Consensus       131 n~l~lyG~~G~GKTHLl-~ai~~~l~~~~~~~~v~yi~~  168 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLL-QSIGNYVVQNEPDLRVMYITS  168 (440)
T ss_pred             CeEEEEcCCCCcHHHHH-HHHHHHHHHhCCCCeEEEEEH
Confidence            35899999999999654 344455544333446777653

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=81.99  E-value=1.7  Score=37.24  Aligned_cols=23  Identities=30%  Similarity=0.446  Sum_probs=19.9

Q ss_pred             HhHHcCCcEEEeccCCCchHHHH
Q 028887          102 PVLFSSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       102 ~~i~~g~~~l~~a~TGsGKT~~~  124 (202)
                      -.++.|..+++.|++|+|||...
T Consensus        38 ~a~~~~~~vll~G~PG~gKT~la   60 (329)
T COG0714          38 LALLAGGHVLLEGPPGVGKTLLA   60 (329)
T ss_pred             HHHHcCCCEEEECCCCccHHHHH
Confidence            35678999999999999999765

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=81.88  E-value=1.7  Score=37.56  Aligned_cols=26  Identities=15%  Similarity=0.203  Sum_probs=20.6

Q ss_pred             HHHhHHcCCcEEEeccCCCchHHHHH
Q 028887          100 ALPVLFSSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       100 ~i~~i~~g~~~l~~a~TGsGKT~~~l  125 (202)
                      .+-.+..++++++.|++|+|||...-
T Consensus        57 vl~~l~~~~~ilL~G~pGtGKTtla~   82 (327)
T TIGR01650        57 ICAGFAYDRRVMVQGYHGTGKSTHIE   82 (327)
T ss_pred             HHHHHhcCCcEEEEeCCCChHHHHHH
Confidence            33445668899999999999998754

This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=81.53  E-value=1.5  Score=35.15  Aligned_cols=42  Identities=19%  Similarity=0.101  Sum_probs=27.0

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhc---CCccEEEEecCC
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQ---RSAVQAVIVVPT  147 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~---~~~~~~Lil~Pt  147 (202)
                      .|.-+.+.|++|+|||...+.-+......+   ...-.++++.-.
T Consensus        18 ~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e   62 (235)
T cd01123          18 TGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTE   62 (235)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCC
Confidence            346689999999999988766555433221   112357777643

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=81.52  E-value=2.8  Score=35.99  Aligned_cols=21  Identities=29%  Similarity=0.161  Sum_probs=16.2

Q ss_pred             CcEEEeccCCCchHHHHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLLLI  128 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~  128 (202)
                      .-+.+.||+|+|||.....-.
T Consensus       115 ~vi~lvGpnGsGKTTt~~kLA  135 (318)
T PRK10416        115 FVILVVGVNGVGKTTTIGKLA  135 (318)
T ss_pred             eEEEEECCCCCcHHHHHHHHH
Confidence            457889999999998765433

>PLN02165 adenylate isopentenyltransferase

Probab=81.15  E-value=1.3  Score=38.44  Aligned_cols=21  Identities=24%  Similarity=0.324  Sum_probs=17.4

Q ss_pred             cCCcEEEeccCCCchHHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~  126 (202)
                      .|..+++.||||||||.....
T Consensus        42 ~g~iivIiGPTGSGKStLA~~   62 (334)
T PLN02165         42 KDKVVVIMGATGSGKSRLSVD   62 (334)
T ss_pred             CCCEEEEECCCCCcHHHHHHH
Confidence            356689999999999988754

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=81.02  E-value=6.4  Score=33.87  Aligned_cols=23  Identities=26%  Similarity=0.327  Sum_probs=19.0

Q ss_pred             CcEEEeccCCCchHHHHHHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFS  130 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~  130 (202)
                      .+++.+||.|+|||-+.++..-+
T Consensus        58 p~~LFyGPpGTGKTStalafar~   80 (346)
T KOG0989|consen   58 PHYLFYGPPGTGKTSTALAFARA   80 (346)
T ss_pred             ceEEeeCCCCCcHhHHHHHHHHH
Confidence            56899999999999988765544

>PRK04220 2-phosphoglycerate kinase; Provisional

Probab=80.95  E-value=3.7  Score=35.08  Aligned_cols=85  Identities=14%  Similarity=0.057  Sum_probs=47.4

Q ss_pred             CCCCCchHHHHHhccCCCCHHHHHcccCCCcchHHHHHhCC--------CCHHHHHHHHHCCCCCCcHHHHHHHHhHHcC
Q 028887           36 PVSISLKPLRAVLSSSAVSTEELAAGTGNNSLTLRELCQGH--------VPEHVLRRMEETGYVLPTDIQREALPVLFSS  107 (202)
Q Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~g--------l~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g  107 (202)
                      ..+++.-.+.+.+...+..+++..+-   ...-.+.|.+.|        +.+.+.+.|.+.++..+.+- -..+..+...
T Consensus        14 ~~pfSrgiL~rsL~~~g~~~~~A~~i---A~~i~~~L~~~g~~~i~~~el~~~V~~~L~~~~~~~~~~~-y~~~~~i~~~   89 (301)
T PRK04220         14 EMPFSKGILARSLTAAGMKPSIAYEI---ASEIEEELKKEGIKEITKEELRRRVYYKLIEKDYEEVAEK-YLLWRRIRKS   89 (301)
T ss_pred             cCCCcHHHHHHHHHHcCCChhHHHHH---HHHHHHHHHHcCCEEeeHHHHHHHHHHHHHHhCcHhHHHH-HHHHHHHhcC
Confidence            34566666777777666665543221   122334444444        22345566666676654432 2333333332


Q ss_pred             ---CcEEEeccCCCchHHHH
Q 028887          108 ---RDCILHAQTGSGKTLTY  124 (202)
Q Consensus       108 ---~~~l~~a~TGsGKT~~~  124 (202)
                         .-+++.|++|+|||...
T Consensus        90 ~~p~iIlI~G~sgsGKStlA  109 (301)
T PRK04220         90 KEPIIILIGGASGVGTSTIA  109 (301)
T ss_pred             CCCEEEEEECCCCCCHHHHH
Confidence               24889999999999854

>cd01367 KISc_KIF2_like Kinesin motor domain, KIF2-like group

Probab=80.84  E-value=1.3  Score=37.96  Aligned_cols=24  Identities=50%  Similarity=0.740  Sum_probs=18.2

Q ss_pred             HhHHcCCc--EEEeccCCCchHHHHH
Q 028887          102 PVLFSSRD--CILHAQTGSGKTLTYL  125 (202)
Q Consensus       102 ~~i~~g~~--~l~~a~TGsGKT~~~l  125 (202)
                      ..++.|.+  ++..|+||||||....
T Consensus        78 ~~~~~G~n~~i~ayGqtGSGKTyTm~  103 (322)
T cd01367          78 PHVFEGGVATCFAYGQTGSGKTYTML  103 (322)
T ss_pred             HHHhCCCceEEEeccCCCCCCceEec
Confidence            34567765  7888999999997754

KIF2 is a protein expressed in neurons, which has been associated with axonal transport and neuron development; alternative splice forms have been implicated in lysosomal translocation. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this subgroup the motor domain is found in the middle (M-type) of the protein chain. M-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second (KIF2 may be slower). To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and lo

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=80.79  E-value=1.2  Score=34.27  Aligned_cols=18  Identities=22%  Similarity=0.213  Sum_probs=15.2

Q ss_pred             CcEEEeccCCCchHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l  125 (202)
                      +-+++.|++|||||...-
T Consensus         2 ~~~~i~G~sGsGKttl~~   19 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLD   19 (179)
T ss_pred             cEEEEECCCCCCHHHHHH
Confidence            457899999999998764

Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=80.79  E-value=4.9  Score=38.77  Aligned_cols=30  Identities=23%  Similarity=0.120  Sum_probs=22.3

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcC
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQR  136 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~  136 (202)
                      |.-+.+.|++|+|||...+..+......+.
T Consensus        60 GsiteI~G~~GsGKTtLal~~~~~a~~~G~   89 (790)
T PRK09519         60 GRVIEIYGPESSGKTTVALHAVANAQAAGG   89 (790)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCC
Confidence            456889999999999887766665554433

>cd01370 KISc_KIP3_like Kinesin motor domain, KIP3-like subgroup

Probab=80.72  E-value=1.7  Score=37.54  Aligned_cols=22  Identities=27%  Similarity=0.350  Sum_probs=17.5

Q ss_pred             hHHcCCc--EEEeccCCCchHHHH
Q 028887          103 VLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       103 ~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      .++.|.+  ++.+|+||||||...
T Consensus        82 ~~~~G~n~~i~ayGqtGSGKTyTm  105 (338)
T cd01370          82 GVLNGYNATVFAYGATGAGKTHTM  105 (338)
T ss_pred             HHHCCCCceEEeeCCCCCCCeEEE
Confidence            3467755  788999999999874

The yeast kinesin KIP3 plays a role in positioning the mitotic spindle. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a sec

>cd01368 KISc_KIF23_like Kinesin motor domain, KIF23-like subgroup

Probab=80.71  E-value=1.3  Score=38.30  Aligned_cols=23  Identities=30%  Similarity=0.335  Sum_probs=17.5

Q ss_pred             HhHHcCCc--EEEeccCCCchHHHH
Q 028887          102 PVLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       102 ~~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      ..++.|.+  ++.+|+||||||...
T Consensus        82 ~~~l~G~n~ti~aYGqtGSGKTyTm  106 (345)
T cd01368          82 QDLLKGKNSLLFTYGVTNSGKTYTM  106 (345)
T ss_pred             HHHhCCCceEEEEeCCCCCCCeEEe
Confidence            33467755  788999999999763

Members of this group may play a role in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, a

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=80.71  E-value=1.3  Score=34.12  Aligned_cols=19  Identities=26%  Similarity=0.284  Sum_probs=16.4

Q ss_pred             CCcEEEeccCCCchHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l  125 (202)
                      |+-+++.|++|||||...-
T Consensus         2 ~~~i~l~G~~gsGKst~a~   20 (175)
T cd00227           2 GRIIILNGGSSAGKSSIAR   20 (175)
T ss_pred             CCEEEEECCCCCCHHHHHH
Confidence            5678999999999998754

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PTZ00301 uridine kinase; Provisional

Probab=80.62  E-value=3.6  Score=33.13  Aligned_cols=15  Identities=27%  Similarity=0.304  Sum_probs=12.8

Q ss_pred             EEEeccCCCchHHHH
Q 028887          110 CILHAQTGSGKTLTY  124 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~  124 (202)
                      +-+.|++|||||...
T Consensus         6 IgIaG~SgSGKTTla   20 (210)
T PTZ00301          6 IGISGASGSGKSSLS   20 (210)
T ss_pred             EEEECCCcCCHHHHH
Confidence            567899999999765

>PRK00300 gmk guanylate kinase; Provisional

Probab=80.37  E-value=1.4  Score=34.73  Aligned_cols=18  Identities=22%  Similarity=0.335  Sum_probs=15.7

Q ss_pred             cCCcEEEeccCCCchHHH
Q 028887          106 SSRDCILHAQTGSGKTLT  123 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~  123 (202)
                      .|+-+++.|++|||||..
T Consensus         4 ~g~~i~i~G~sGsGKstl   21 (205)
T PRK00300          4 RGLLIVLSGPSGAGKSTL   21 (205)
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            567799999999999964

>cd01373 KISc_KLP2_like Kinesin motor domain, KLP2-like subgroup

Probab=80.23  E-value=1.3  Score=38.18  Aligned_cols=21  Identities=43%  Similarity=0.420  Sum_probs=16.4

Q ss_pred             hHHcCCc--EEEeccCCCchHHH
Q 028887          103 VLFSSRD--CILHAQTGSGKTLT  123 (202)
Q Consensus       103 ~i~~g~~--~l~~a~TGsGKT~~  123 (202)
                      .++.|.+  ++.+|.||||||..
T Consensus        69 ~~~~G~n~ti~aYGqTGSGKTyT   91 (337)
T cd01373          69 DCLSGYNGSIFAYGQTGSGKTYT   91 (337)
T ss_pred             HHhCCCceeEEEeCCCCCCceEE
Confidence            3467765  78899999999954

Members of this subgroup seem to play a role in mitosis and meiosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second

>KOG2373 consensus Predicted mitochondrial DNA helicase twinkle [Replication, recombination and repair]

Probab=80.20  E-value=2.9  Score=36.70  Aligned_cols=46  Identities=22%  Similarity=0.250  Sum_probs=30.9

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHH
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQ  153 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q  153 (202)
                      .-.++.||||||||....--.++...+|-+...+=+=.|..-|+.-
T Consensus       274 ElTvlTGpTGsGKTTFlsEYsLDL~~QGVnTLwgSFEi~n~rla~~  319 (514)
T KOG2373|consen  274 ELTVLTGPTGSGKTTFLSEYSLDLFTQGVNTLWGSFEIPNKRLAHW  319 (514)
T ss_pred             ceEEEecCCCCCceeEehHhhHHHHhhhhhheeeeeecchHHHHHH
Confidence            4589999999999987666666666555543344444577666654

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=80.14  E-value=11  Score=32.15  Aligned_cols=84  Identities=21%  Similarity=0.235  Sum_probs=50.8

Q ss_pred             HHHHHhccCCCCHHHHHcccCCCcchHHHHHhCCCCH--HHHHHH-HHCCC-----------------------CCCcHH
Q 028887           43 PLRAVLSSSAVSTEELAAGTGNNSLTLRELCQGHVPE--HVLRRM-EETGY-----------------------VLPTDI   96 (202)
Q Consensus        43 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~gl~~--~l~~~l-~~~g~-----------------------~~~t~~   96 (202)
                      .++.+......+.+++.+..+.+...+..|+...-.+  ..+..+ ..+|.                       ..+++.
T Consensus        32 rl~~~R~~~gltq~~lA~~~gvs~~~i~~~E~g~~~ps~~~l~~ia~~l~v~~~~l~~~~~~~~~~~~~l~~~l~~l~~~  111 (309)
T PRK08154         32 RVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADLLGDVDTSSPDWLLIRELLEQASPA  111 (309)
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHHHHhCCCCCCChHHHHHHHHHhcCCHH
Confidence            4555666777788888887777777777776554222  222222 11121                       134555


Q ss_pred             HHHHHHhHH-----------cCCcEEEeccCCCchHHHHHH
Q 028887           97 QREALPVLF-----------SSRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus        97 Q~~~i~~i~-----------~g~~~l~~a~TGsGKT~~~l~  126 (202)
                      |.+.+-.++           .+..+++.|..|+|||.+.-.
T Consensus       112 ~~~~~~~~l~~~~~~~~~~~~~~~I~l~G~~GsGKStvg~~  152 (309)
T PRK08154        112 QLARVRDALSGMLGAGRRAARRRRIALIGLRGAGKSTLGRM  152 (309)
T ss_pred             HHHHHHHHHHHHHhhhhhccCCCEEEEECCCCCCHHHHHHH
Confidence            555544332           235799999999999988654

>PF00225 Kinesin: Kinesin motor domain; InterPro: IPR001752 Kinesin [, , ] is a microtubule-associated force-producing protein that may play a role in organelle transport

Probab=80.12  E-value=1.8  Score=36.98  Aligned_cols=25  Identities=32%  Similarity=0.356  Sum_probs=18.1

Q ss_pred             HhHHcCCc--EEEeccCCCchHHHHHH
Q 028887          102 PVLFSSRD--CILHAQTGSGKTLTYLL  126 (202)
Q Consensus       102 ~~i~~g~~--~l~~a~TGsGKT~~~l~  126 (202)
                      ..++.|.+  ++..|+||||||....-
T Consensus        68 ~~~l~G~n~~i~ayG~tgSGKT~Tm~G   94 (335)
T PF00225_consen   68 DSVLDGYNATIFAYGQTGSGKTYTMFG   94 (335)
T ss_dssp             HHHHTT-EEEEEEEESTTSSHHHHHTB
T ss_pred             HHhhcCCceEEEeeccccccccccccc
Confidence            34567865  78899999999976543

The kinesin motor activity is directed toward the microtubule's plus end. Kinesin is an oligomeric complex composed of two heavy chains and two light chains. The maintenance of the quaternary structure does not require interchain disulphide bonds. The heavy chain is composed of three structural domains: a large globular N-terminal domain which is responsible for the motor activity of kinesin (it is known to hydrolyse ATP, to bind and move on microtubules), a central alpha-helical coiled coil domain that mediates the heavy chain dimerisation; and a small globular C-terminal domain which interacts with other proteins (such as the kinesin light chains), vesicles and membranous organelles. A number of proteins have been recently found that contain a domain similar to that of the kinesin 'motor' domain [, ]: Drosophila melanogaster claret segregational protein (ncd). Ncd is required for normal chromosomal segregation in meiosis, in females, and in early mitotic divisions of the embryo. The ncd motor activity is directed toward the microtubule's minus end. Homo sapiens CENP-E []. CENP-E is a protein that associates with kinetochores during chromosome congression, relocates to the spindle midzone at anaphase, and is quantitatively discarded at the end of the cell division. CENP-E is probably an important motor molecule in chromosome movement and/or spindle elongation. H. sapiens mitotic kinesin-like protein-1 (MKLP-1), a motor protein whose activity is directed toward the microtubule's plus end. Saccharomyces cerevisiae KAR3 protein, which is essential for nuclear fusion during mating. KAR3 may mediate microtubule sliding during nuclear fusion and possibly mitosis. S. cerevisiae CIN8 and KIP1 proteins which are required for the assembly of the mitotic spindle. Both proteins seem to interact with spindle microtubules to produce an outwardly directed force acting upon the poles. Emericella nidulans (Aspergillus nidulans) bimC, which plays an important role in nuclear division. A. nidulans klpA. Caenorhabditis elegans unc-104, which may be required for the transport of substances needed for neuronal cell differentiation. C. elegans osm-3. Xenopus laevis Eg5, which may be involved in mitosis. Arabidopsis thaliana KatA, KatB and katC. Chlamydomonas reinhardtii FLA10/KHP1 and KLP1. Both proteins seem to play a role in the rotation or twisting of the microtubules of the flagella. C. elegans hypothetical protein T09A5.2. The kinesin motor domain is located in the N-terminal part of most of the above proteins, with the exception of KAR3, klpA, and ncd where it is located in the C-terminal section. The kinesin motor domain contains about 330 amino acids. An ATP-binding motif of type A is found near position 80 to 90, the C-terminal half of the domain is involved in microtubule-binding.; GO: 0003777 microtubule motor activity, 0005524 ATP binding, 0007018 microtubule-based movement; PDB: 3NWN_A 2Y5W_A 2Y65_C 3BFN_A 2WBE_C 2ZFL_A 2ZFI_A 1I6I_A 2ZFM_A 1IA0_K ....

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=80.06  E-value=10  Score=31.08  Aligned_cols=40  Identities=15%  Similarity=0.132  Sum_probs=29.1

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCC
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPT  147 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Pt  147 (202)
                      .|.-+++.|.+|.|||...+--+.+....++  ..+++++.+
T Consensus        18 ~g~L~vi~a~pg~GKT~~~l~ia~~~a~~~~--~~vly~SlE   57 (259)
T PF03796_consen   18 PGELTVIAARPGVGKTAFALQIALNAALNGG--YPVLYFSLE   57 (259)
T ss_dssp             TT-EEEEEESTTSSHHHHHHHHHHHHHHTTS--SEEEEEESS
T ss_pred             cCcEEEEEecccCCchHHHHHHHHHHHHhcC--CeEEEEcCC
Confidence            3456889999999999877777766665532  378888865

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>cd01376 KISc_KID_like Kinesin motor domain, KIF22/Kid-like subgroup

Probab=80.05  E-value=1.6  Score=37.28  Aligned_cols=24  Identities=38%  Similarity=0.569  Sum_probs=18.3

Q ss_pred             HHhHHcCCc--EEEeccCCCchHHHH
Q 028887          101 LPVLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       101 i~~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      ++.++.|.+  ++.+|.||||||...
T Consensus        73 v~~~~~G~n~~i~ayG~tgSGKTyTm   98 (319)
T cd01376          73 VPHLLSGQNATVFAYGSTGAGKTHTM   98 (319)
T ss_pred             HHHHhCCCceEEEEECCCCCCCcEEE
Confidence            334577765  788899999999854

Members of this group might play a role in regulating chromosomal movement along microtubules in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	202
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		9e-12
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		1e-11
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		5e-11
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		4e-10
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		1e-09
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		1e-09
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		1e-09
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-09
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-09
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		1e-09
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		4e-09
3ly5_A	262	Ddx18 Dead-Domain Length = 262		5e-09
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		5e-09
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		7e-09
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		1e-08
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		2e-08
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		2e-08
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		2e-08
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		2e-08
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		2e-08
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		3e-08
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		3e-08
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		3e-08
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		5e-08
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		8e-08
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		1e-07
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		1e-07
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		2e-07
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		3e-07
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		3e-07
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		3e-07
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		5e-07
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		1e-06
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		1e-06
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		2e-06
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		2e-06
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		2e-06
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		2e-06
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		6e-06
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		7e-06
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		1e-05
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		1e-05
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		1e-05
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		1e-05
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		1e-05
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		3e-05
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		5e-05
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		5e-05
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		5e-05

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 66.6 bits (161), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 48/76 (63%)
Query: 87  ETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP 146
           E G+  P+ IQ EA+PV  + RD +  A+ G+GKT  +++     V  + + +QA+I+VP
Sbjct: 38  EAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVP 97
Query: 147 TRELGMQVTKVARVLA 162
           TREL +Q ++V R L 
Sbjct: 98  TRELALQTSQVVRTLG 113

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score = 66.2 bits (160), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 49/71 (69%)
Query: 87  ETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP 146
           E G+  P+ IQ E++P+  S RD +  A+ G+GK+  YL+ +   ++ ++  +QA+++VP
Sbjct: 20  EMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVP 79
Query: 147 TRELGMQVTKV 157
           TREL +QV+++
Sbjct: 80  TRELALQVSQI 90

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score = 64.3 bits (155), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 36/87 (41%), Positives = 52/87 (59%), Gaps = 5/87 (5%)
Query: 81  VLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLV-----NAQ 135
           ++  + ++GY +PT IQ+ ++PV+ S RD +  AQTGSGKT  +LL I S +       +
Sbjct: 67  IIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELE 126
Query: 136 RSAVQAVIVVPTRELGMQVTKVARVLA 162
               Q VIV PTREL +Q+   AR  A
Sbjct: 127 LGRPQVVIVSPTRELAIQIFNEARKFA 153

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score = 60.8 bits (146), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/104 (28%), Positives = 59/104 (56%), Gaps = 14/104 (13%)
Query: 76  HVPEHVLRRMEETGYVLPTDIQREALPVLFSSR-DCILHAQTGSGKTLTYLLLIFSLVNA 134
           ++ +++L  +   G+  PTDIQ + +P+  +   + +  A+TGSGKT ++ + +  LVN 
Sbjct: 12  NLSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVN- 70
Query: 135 QRSAVQAVIVVPTRELGMQVT------------KVARVLAAKPL 166
           + + ++A+I+ PTREL +QV             K+A++   K +
Sbjct: 71  ENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAI 114

>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 = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 47/78 (60%)
Query: 79  EHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSA 138
           E +LR +   G+  P+ IQ+ A+  +   RD I  +Q+G+GKT T+ + +   ++ Q   
Sbjct: 47  EDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRE 106
Query: 139 VQAVIVVPTRELGMQVTK 156
            QA+I+ PTREL +Q+ K
Sbjct: 107 TQALILAPTRELAVQIQK 124

>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 = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 47/78 (60%)
Query: 79  EHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSA 138
           E +LR +   G+  P+ IQ+ A+  +   RD I  +Q+G+GKT T+ + +   ++ Q   
Sbjct: 47  EDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRE 106
Query: 139 VQAVIVVPTRELGMQVTK 156
            QA+I+ PTREL +Q+ K
Sbjct: 107 TQALILAPTRELAVQIQK 124

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 47/78 (60%)
Query: 79  EHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSA 138
           E +LR +   G+  P+ IQ+ A+  +   RD I  +Q+G+GKT T+ + +   ++ Q   
Sbjct: 46  EDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRE 105
Query: 139 VQAVIVVPTRELGMQVTK 156
            QA+I+ PTREL +Q+ K
Sbjct: 106 TQALILAPTRELAVQIQK 123

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 59.3 bits (142), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/78 (37%), Positives = 47/78 (60%)
Query: 79  EHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSA 138
           E +LR +   G+  P+ IQ+ A+  +   RD I  +Q+G+GKT T+ + +   ++ Q   
Sbjct: 10  EDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCLDIQVRE 69
Query: 139 VQAVIVVPTRELGMQVTK 156
            QA+I+ PTREL +QV K
Sbjct: 70  TQALILAPTRELAVQVQK 87

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 59.3 bits (142), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/78 (37%), Positives = 47/78 (60%)
Query: 79  EHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSA 138
           E +LR +   G+  P+ IQ+ A+  +   RD I  +Q+G+GKT T+ + +   ++ Q   
Sbjct: 10  EDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCLDIQVRE 69
Query: 139 VQAVIVVPTRELGMQVTK 156
            QA+I+ PTREL +QV K
Sbjct: 70  TQALILAPTRELAVQVQK 87

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 59.3 bits (142), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 47/78 (60%)
Query: 79  EHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSA 138
           E +LR +   G+  P+ IQ+ A+  +   RD I  +Q+G+GKT T+ + +   ++ Q   
Sbjct: 25  EDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRE 84
Query: 139 VQAVIVVPTRELGMQVTK 156
            QA+I+ PTREL +Q+ K
Sbjct: 85  TQALILAPTRELAVQIQK 102

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 57.8 bits (138), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 30/89 (33%), Positives = 53/89 (59%), Gaps = 2/89 (2%)
Query: 68  TLRELCQGH-VPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLL 126
           T ++L Q + +   +L+ + + G+ +PT IQ +A+PV+   R+ +  A TGSGKTL + +
Sbjct: 26  TFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSI 85
Query: 127 -LIFSLVNAQRSAVQAVIVVPTRELGMQV 154
            ++  L        +A+I+ PTREL  Q+
Sbjct: 86  PILMQLKQPANKGFRALIISPTRELASQI 114

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score = 57.4 bits (137), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 34/89 (38%), Positives = 51/89 (57%), Gaps = 4/89 (4%)
Query: 77  VPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLL----LIFSLV 132
           V E+ L+ ++E G+   T+IQ +++  L   RD +  A+TGSGKTL +L+    LI  L 
Sbjct: 61  VNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLR 120
Query: 133 NAQRSAVQAVIVVPTRELGMQVTKVARVL 161
              R+    +I+ PTREL MQ   V + L
Sbjct: 121 FMPRNGTGVLILSPTRELAMQTFGVLKEL 149

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 57.4 bits (137), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 30/87 (34%), Positives = 47/87 (54%)
Query: 76  HVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ 135
           ++ E +LR +   G+  P+ IQ+ A+       D I  AQ+G+GKT T+ + I   +   
Sbjct: 46  NLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELD 105
Query: 136 RSAVQAVIVVPTRELGMQVTKVARVLA 162
             A QA+++ PTREL  Q+ KV   L 
Sbjct: 106 LKATQALVLAPTRELAQQIQKVVMALG 132

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 57.0 bits (136), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 30/87 (34%), Positives = 47/87 (54%)
Query: 76  HVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ 135
           ++ E +LR +   G+  P+ IQ+ A+       D I  AQ+G+GKT T+ + I   +   
Sbjct: 20  NLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELD 79
Query: 136 RSAVQAVIVVPTRELGMQVTKVARVLA 162
             A QA+++ PTREL  Q+ KV   L 
Sbjct: 80  LKATQALVLAPTRELAQQIQKVVMALG 106

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 27/65 (41%), Positives = 37/65 (56%)
Query: 90  YVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRE 149
           +  PT+IQ   +P        +  +QTG+GKT  YLL I   +  +R+ VQAVI  PTRE
Sbjct: 24  FYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLPIXEKIKPERAEVQAVITAPTRE 83
Query: 150 LGMQV 154
           L  Q+
Sbjct: 84  LATQI 88

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score = 55.8 bits (133), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 46/82 (56%)
Query: 76  HVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ 135
           ++ E +LR +   G+  P+ IQ+ A+       D I  AQ+G+GKT T+ + I   +  +
Sbjct: 36  NLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIE 95
Query: 136 RSAVQAVIVVPTRELGMQVTKV 157
               QA+++ PTREL  Q+ KV
Sbjct: 96  FKETQALVLAPTRELAQQIQKV 117

>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 = 55.5 bits (132), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/87 (33%), Positives = 50/87 (57%)
Query: 76  HVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ 135
            + E++LR +   G+  P+ IQ+ A+  +    D +  AQ+G+GKT T+ +     ++  
Sbjct: 20  ELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS 79
Query: 136 RSAVQAVIVVPTRELGMQVTKVARVLA 162
             A QA+++ PTREL +Q+ KV   LA
Sbjct: 80  VKAPQALMLAPTRELALQIQKVVMALA 106

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score = 55.5 bits (132), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 48/84 (57%)
Query: 79  EHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSA 138
           E +LR +   G+  P+ IQ+ A+  +    D +  AQ+G+GKT T+ +     ++    A
Sbjct: 30  EQLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKA 89
Query: 139 VQAVIVVPTRELGMQVTKVARVLA 162
            QA+++ PTREL +Q+ KV   LA
Sbjct: 90  PQALMLAPTRELALQIQKVVMALA 113

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 55.5 bits (132), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/87 (33%), Positives = 49/87 (56%)
Query: 76  HVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ 135
            + E++LR +   G+  P+ IQ+ A+  +    D +  AQ+G+GKT T+ +     ++  
Sbjct: 27  ELDENLLRGVFGYGFEEPSAIQQRAIXPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS 86
Query: 136 RSAVQAVIVVPTRELGMQVTKVARVLA 162
             A QA+ + PTREL +Q+ KV   LA
Sbjct: 87  VKAPQALXLAPTRELALQIQKVVXALA 113

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 55.5 bits (132), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/87 (33%), Positives = 50/87 (57%)
Query: 76  HVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ 135
            + E++LR +   G+  P+ IQ+ A+  +    D +  AQ+G+GKT T+ +     ++  
Sbjct: 28  ELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS 87
Query: 136 RSAVQAVIVVPTRELGMQVTKVARVLA 162
             A QA+++ PTREL +Q+ KV   LA
Sbjct: 88  VKAPQALMLAPTRELALQIQKVVMALA 114

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 55.1 bits (131), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 37/126 (29%), Positives = 62/126 (49%), Gaps = 19/126 (15%)
Query: 58  LAAGTGNNSLT-LRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQT 116
           +   TGNN    +       + E ++  +E T Y  PT +Q+ A+P++   RD +  AQT
Sbjct: 2   MVEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQT 61
Query: 117 GSGKTLTYLLLIFSLV--NAQRSAVQAV----------------IVVPTRELGMQVTKVA 158
           GSGKT  +LL I S +  +    A++A+                ++ PTREL +Q+ + A
Sbjct: 62  GSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEA 121
Query: 159 RVLAAK 164
           R  + +
Sbjct: 122 RKFSYR 127

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 55.1 bits (131), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 33/90 (36%), Positives = 47/90 (52%), Gaps = 5/90 (5%)
Query: 74  QGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVN 133
           + + P +V+  +    +  PT IQ +  PV  S  D +  AQTGSGKTL+YLL     +N
Sbjct: 33  EANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHIN 92
Query: 134 AQ-----RSAVQAVIVVPTRELGMQVTKVA 158
            Q           +++ PTREL  QV +VA
Sbjct: 93  HQPFLERGDGPICLVLAPTRELAQQVQQVA 122

>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 = 54.7 bits (130), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 33/90 (36%), Positives = 47/90 (52%), Gaps = 5/90 (5%)
Query: 74  QGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVN 133
           + + P +V+  +    +  PT IQ +  PV  S  D +  AQTGSGKTL+YLL     +N
Sbjct: 47  EANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHIN 106
Query: 134 AQ-----RSAVQAVIVVPTRELGMQVTKVA 158
            Q           +++ PTREL  QV +VA
Sbjct: 107 HQPFLERGDGPICLVLAPTRELAQQVQQVA 136

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score = 54.3 bits (129), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 45/78 (57%)
Query: 86  EETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVV 145
           ++ G+  PT IQ EA+P+    RD I  A+TGSGKT  + L I + +      + A+++ 
Sbjct: 59  DQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLT 118
Query: 146 PTRELGMQVTKVARVLAA 163
           PTREL  Q+++    L +
Sbjct: 119 PTRELAFQISEQFEALGS 136

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score = 53.5 bits (127), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 46/81 (56%), Gaps = 6/81 (7%)
Query: 80  HVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIF------SLVN 133
            +L+ +   G + PT IQ +A P++    D I+ AQTG+GKTL+YL+  F       +  
Sbjct: 30  DLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISR 89
Query: 134 AQRSAVQAVIVVPTRELGMQV 154
            QR+    +++ PTREL + V
Sbjct: 90  EQRNGPGMLVLTPTRELALHV 110

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/87 (32%), Positives = 45/87 (51%)
Query: 76  HVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ 135
           ++ E +LR +   G+  P+ IQ+ A+       D I  AQ+G+G T T+ + I   +   
Sbjct: 21  NLSESLLRGIYAYGFEXPSAIQQRAILPCIXGYDVIAQAQSGTGXTATFAISILQQIELD 80
Query: 136 RSAVQAVIVVPTRELGMQVTKVARVLA 162
             A QA+++ PTREL  Q+  V   L 
Sbjct: 81  LXATQALVLAPTRELAQQIQXVVMALG 107

>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 = 52.8 bits (125), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/74 (40%), Positives = 43/74 (58%), Gaps = 9/74 (12%)
Query: 90  YVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLL-----LIFSLVNAQRSAVQA--- 141
           Y  PT IQ+ A+P +   RD +  AQTGSGKT  +L+     L+   +N QR +  A   
Sbjct: 43  YQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPK 102
Query: 142 -VIVVPTRELGMQV 154
            +I+ PTREL +Q+
Sbjct: 103 CLILAPTRELAIQI 116

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/90 (32%), Positives = 52/90 (57%), Gaps = 3/90 (3%)
Query: 75  GHVPEHVLRRMEETGYVLPTDIQREALPVLFSS--RDCILHAQTGSGKTLTYLLLIFSLV 132
           G  PE +L+ +    +  P+ IQ  ALP+L  +  R+ I  +Q+G+GKT  + L + + V
Sbjct: 28  GLAPE-LLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRV 86
Query: 133 NAQRSAVQAVIVVPTRELGMQVTKVARVLA 162
           N + ++ QA+ + P+REL  Q  +V + + 
Sbjct: 87  NPEDASPQAICLAPSRELARQTLEVVQEMG 116

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 30/99 (30%), Positives = 51/99 (51%), Gaps = 18/99 (18%)
Query: 79  EHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSA 138
           E + + + E G+   T++Q + +P++   ++ ++ A+TGSGKT  Y + I  L       
Sbjct: 3   EKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL------G 56
Query: 139 VQAVIVVPTRELGMQV------------TKVARVLAAKP 165
           +++++V PTREL  QV            TKVA V    P
Sbjct: 57  MKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMP 95

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/90 (32%), Positives = 52/90 (57%), Gaps = 3/90 (3%)
Query: 75  GHVPEHVLRRMEETGYVLPTDIQREALPVLFSS--RDCILHAQTGSGKTLTYLLLIFSLV 132
           G  PE +L+ +    +  P+ IQ  ALP+L  +  R+ I  +Q+G+GKT  + L + + V
Sbjct: 11  GLAPE-LLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRV 69
Query: 133 NAQRSAVQAVIVVPTRELGMQVTKVARVLA 162
           N + ++ QA+ + P+REL  Q  +V + + 
Sbjct: 70  NPEDASPQAICLAPSRELARQTLEVVQEMG 99

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 51.2 bits (121), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/90 (32%), Positives = 52/90 (57%), Gaps = 3/90 (3%)
Query: 75  GHVPEHVLRRMEETGYVLPTDIQREALPVLFSS--RDCILHAQTGSGKTLTYLLLIFSLV 132
           G  PE +L+ +    +  P+ IQ  ALP+L  +  R+ I  +Q+G+GKT  + L + + V
Sbjct: 11  GLAPE-LLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRV 69
Query: 133 NAQRSAVQAVIVVPTRELGMQVTKVARVLA 162
           N + ++ QA+ + P+REL  Q  +V + + 
Sbjct: 70  NPEDASPQAICLAPSRELARQTLEVVQEMG 99

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score = 50.8 bits (120), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 43/78 (55%), Gaps = 3/78 (3%)
Query: 80  HVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFS-LVNAQRSA 138
            +L  +   G   PT IQ  ALP+    +D I  A+TG+GKTL + L I   L  +Q   
Sbjct: 11  EILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERG 70
Query: 139 VQ--AVIVVPTRELGMQV 154
            +  A+++ PTREL +QV
Sbjct: 71  RKPRALVLTPTRELALQV 88

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/78 (37%), Positives = 43/78 (55%), Gaps = 3/78 (3%)
Query: 80  HVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFS-LVNAQRSA 138
            +L  +   G   PT I+  ALP+    +D I  A+TG+GKTL + L I   L  +Q   
Sbjct: 11  EILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERG 70
Query: 139 VQ--AVIVVPTRELGMQV 154
            +  A+++ PTREL +QV
Sbjct: 71  RKPRALVLTPTRELALQV 88

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 27/82 (32%), Positives = 46/82 (56%), Gaps = 4/82 (4%)
Query: 82  LRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLL----LIFSLVNAQRS 137
           L+ ++E  Y L T+IQ++ + +    +D +  A+TGSGKTL +L+     ++ L      
Sbjct: 37  LKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTD 96
Query: 138 AVQAVIVVPTRELGMQVTKVAR 159
            +  +I+ PTREL  Q  +V R
Sbjct: 97  GLGVLIISPTRELAYQTFEVLR 118

>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 = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 31/77 (40%), Positives = 47/77 (61%), Gaps = 9/77 (11%)
Query: 84  RMEETGYVLPTDIQREALPVLFSSRD--CILHAQTGSGKTLTYLLLIFS-LVNAQRSA-- 138
           RME  G    T +Q++ +  + SS D   I  A+TG+GKT  +L+ IF  L+N +  +  
Sbjct: 38  RMEFPGL---TPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQY 94
Query: 139 -VQAVIVVPTRELGMQV 154
            V+AVIV PTR+L +Q+
Sbjct: 95  MVKAVIVAPTRDLALQI 111

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 38/110 (34%), Positives = 60/110 (54%), Gaps = 13/110 (11%)
Query: 84  RMEETGYVLPTDIQREALPVLFSSRD--CILHAQTGSGKTLTYLLLIFS-LVNAQRSA-- 138
           RME  G    T +Q++ +  + SS D   I  A+TG+GKT  +L+ IF  L+N +  +  
Sbjct: 38  RMEFPGL---TPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQY 94
Query: 139 -VQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLR 187
            V+AVIV PTR+L +Q+   A V     ++  L+   C  ++L+ G   R
Sbjct: 95  MVKAVIVAPTRDLALQIE--AEVKKIHDMNYGLKKYAC--VSLVGGTDFR 140

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 31/77 (40%), Positives = 47/77 (61%), Gaps = 9/77 (11%)
Query: 84  RMEETGYVLPTDIQREALPVLFSSRD--CILHAQTGSGKTLTYLLLIFS-LVNAQRSA-- 138
           RME  G    T +Q++ +  + SS D   I  A+TG+GKT  +L+ IF  L+N +  +  
Sbjct: 89  RMEFPGL---TPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQY 145
Query: 139 -VQAVIVVPTRELGMQV 154
            V+AVIV PTR+L +Q+
Sbjct: 146 MVKAVIVAPTRDLALQI 162

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score = 47.0 bits (110), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 89  GYVLPTDIQREALPVLFSS--RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP 146
           G+  P+ IQ  ALP++ +   ++ I  +Q+G+GKT  ++L + S V       Q + + P
Sbjct: 111 GFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSP 170
Query: 147 TRELGMQVTKV 157
           T EL +Q  KV
Sbjct: 171 TYELALQTGKV 181

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 47.0 bits (110), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 89  GYVLPTDIQREALPVLFSS--RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP 146
           G+  P+ IQ  ALP++ +   ++ I  +Q+G+GKT  ++L + S V       Q + + P
Sbjct: 111 GFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSP 170
Query: 147 TRELGMQVTKV 157
           T EL +Q  KV
Sbjct: 171 TYELALQTGKV 181

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 89  GYVLPTDIQREALPVLFSS--RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP 146
           G+  P+ IQ  ALP++ +   ++ I  +Q+G+GKT  ++L + S V       Q + + P
Sbjct: 44  GFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSP 103
Query: 147 TRELGMQVTKV 157
           T EL +Q  KV
Sbjct: 104 TYELALQTGKV 114

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 89  GYVLPTDIQREALPVLFSS--RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP 146
           G+  P+ IQ  ALP++ +   ++ I  +Q+G+GKT  ++L + S V       Q + + P
Sbjct: 44  GFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSP 103
Query: 147 TRELGMQVTKV 157
           T EL +Q  KV
Sbjct: 104 TYELALQTGKV 114

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 89  GYVLPTDIQREALPVLFSS--RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP 146
           G+  P+ IQ  ALP++ +   ++ I  +Q+G+GKT  ++L + S V       Q + + P
Sbjct: 60  GFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSP 119
Query: 147 TRELGMQVTKV 157
           T EL +Q  KV
Sbjct: 120 TYELALQTGKV 130

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 89  GYVLPTDIQREALPVLFSS--RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP 146
           G+  P+ IQ  ALP++ +   ++ I  +Q+G+GKT  ++L + S V       Q + + P
Sbjct: 81  GFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSP 140
Query: 147 TRELGMQVTKV 157
           T EL +Q  KV
Sbjct: 141 TYELALQTGKV 151

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 31/114 (27%), Positives = 57/114 (50%), Gaps = 7/114 (6%)
Query: 81  VLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQ 140
           VL  +   G+  P+ +Q +A+P+     D I+ A++G+GKT  +  +    +  +  + Q
Sbjct: 35  VLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQ 94
Query: 141 AVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK 194
            +I+ PTRE+ +Q+  V   +  K     +E   C V   + G  L + K+ LK
Sbjct: 95  ILILAPTREIAVQIHSVITAIGIK-----MEGLECHV--FIGGTPLSQDKTRLK 141

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/79 (29%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS 137
           PE +LR + + G+  P+++Q E +P      D +  A++G GKT  ++L     +     
Sbjct: 23  PE-LLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTG 81
Query: 138 AVQAVIVVPTRELGMQVTK 156
            V  +++  TREL  Q++K
Sbjct: 82  QVSVLVMCHTRELAFQISK 100

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 23/79 (29%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS 137
           PE +LR + + G+  P+++Q E +P      D +  A++G GKT  ++L     +     
Sbjct: 17  PE-LLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTG 75
Query: 138 AVQAVIVVPTRELGMQVTK 156
            V  +++  TREL  Q++K
Sbjct: 76  QVSVLVMCHTRELAFQISK 94

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 23/79 (29%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS 137
           PE +LR + + G+  P+++Q E +P      D +  A++G GKT  ++L     +     
Sbjct: 17  PE-LLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTG 75
Query: 138 AVQAVIVVPTRELGMQVTK 156
            V  +++  TREL  Q++K
Sbjct: 76  QVSVLVMCHTRELAFQISK 94

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 23/79 (29%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS 137
           PE +LR + + G+  P+++Q E +P      D +  A++G GKT  ++L     +     
Sbjct: 16  PE-LLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTG 74
Query: 138 AVQAVIVVPTRELGMQVTK 156
            V  +++  TREL  Q++K
Sbjct: 75  QVSVLVMCHTRELAFQISK 93

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	202
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	8e-24
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	1e-23
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	2e-23
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	3e-23
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	2e-22
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	1e-21
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	3e-21
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	3e-21
3bor_A	237	Human initiation factor 4A-II; translation initiat	3e-21
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	5e-21
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	6e-21
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	6e-21
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	6e-21
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	8e-21
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	9e-21
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	1e-20
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	3e-20
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	4e-20
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	8e-20
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	1e-19
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	1e-19
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	2e-19
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	3e-19
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	4e-19
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	5e-19
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	6e-19
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	7e-19
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	8e-19
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	2e-18
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	1e-17
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	2e-16
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	2e-06
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	5e-06
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	2e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	7e-05
3b6e_A	216	Interferon-induced helicase C domain-containing P;	1e-04
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	4e-04
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	5e-04
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	7e-04

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score = 93.0 bits (232), Expect = 8e-24
 Identities = 27/85 (31%), Positives = 42/85 (49%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS 137
              ++  ++   +  PT+IQ   +P        +  +QTG+GKT  YLL I   +  +R+
Sbjct: 12  QPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERA 71

Query: 138 AVQAVIVVPTRELGMQVTKVARVLA 162
            VQAVI  PTREL  Q+      + 
Sbjct: 72  EVQAVITAPTRELATQIYHETLKIT 96

>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 = 93.0 bits (232), Expect = 1e-23
 Identities = 27/87 (31%), Positives = 50/87 (57%), Gaps = 1/87 (1%)

Query: 77  VPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR 136
           +   +L+ + + G+ +PT IQ +A+PV+   R+ +  A TGSGKTL + + I   +    
Sbjct: 36  INSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPA 95

Query: 137 SA-VQAVIVVPTRELGMQVTKVARVLA 162
           +   +A+I+ PTREL  Q+ +    ++
Sbjct: 96  NKGFRALIISPTRELASQIHRELIKIS 122

>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 = 92.2 bits (230), Expect = 2e-23
 Identities = 33/91 (36%), Positives = 48/91 (52%), Gaps = 5/91 (5%)

Query: 74  QGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVN 133
           + + P +V+  +    +  PT IQ +  PV  S  D +  AQTGSGKTL+YLL     +N
Sbjct: 33  EANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHIN 92

Query: 134 AQRSAVQ-----AVIVVPTRELGMQVTKVAR 159
            Q    +      +++ PTREL  QV +VA 
Sbjct: 93  HQPFLERGDGPICLVLAPTRELAQQVQQVAA 123

>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 = 91.5 bits (228), Expect = 3e-23
 Identities = 30/95 (31%), Positives = 51/95 (53%), Gaps = 6/95 (6%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS 137
              +L+ +   G + PT IQ +A P++    D I+ AQTG+GKTL+YL+  F  +++Q  
Sbjct: 28  YPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPI 87

Query: 138 AVQ------AVIVVPTRELGMQVTKVARVLAAKPL 166
           + +       +++ PTREL + V       + K L
Sbjct: 88  SREQRNGPGMLVLTPTRELALHVEAECSKYSYKGL 122

>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 = 89.1 bits (222), Expect = 2e-22
 Identities = 27/86 (31%), Positives = 55/86 (63%)

Query: 77  VPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR 136
           +   +L  + E G+  P+ IQ E++P+  S RD +  A+ G+GK+  YL+ +   ++ ++
Sbjct: 10  LKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKK 69

Query: 137 SAVQAVIVVPTRELGMQVTKVARVLA 162
             +QA+++VPTREL +QV+++   ++
Sbjct: 70  DNIQAMVIVPTRELALQVSQICIQVS 95

>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 = 90.3 bits (225), Expect = 1e-21
 Identities = 35/91 (38%), Positives = 53/91 (58%), Gaps = 5/91 (5%)

Query: 74  QGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVN 133
              + + ++  + ++GY +PT IQ+ ++PV+ S RD +  AQTGSGKT  +LL I S + 
Sbjct: 60  SADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLL 119

Query: 134 AQRSAV-----QAVIVVPTRELGMQVTKVAR 159
                +     Q VIV PTREL +Q+   AR
Sbjct: 120 EDPHELELGRPQVVIVSPTRELAIQIFNEAR 150

>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 = 86.5 bits (215), Expect = 3e-21
 Identities = 29/85 (34%), Positives = 49/85 (57%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS 137
            E++LR +   G+  P+ IQ+ A+  +    D +  AQ+G+GKT T+ +     ++    
Sbjct: 22  DENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVK 81

Query: 138 AVQAVIVVPTRELGMQVTKVARVLA 162
           A QA+++ PTREL +Q+ KV   LA
Sbjct: 82  APQALMLAPTRELALQIQKVVMALA 106

>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 = 89.9 bits (223), Expect = 3e-21
 Identities = 28/120 (23%), Positives = 56/120 (46%), Gaps = 8/120 (6%)

Query: 49  SSSAVSTEELAAGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSS- 107
           SS  +   +          +L E  +G + + + + +    +   T +Q++ +  + SS 
Sbjct: 2   SSKLIHVPKEDNSKEVTLDSLLE--EGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSE 59

Query: 108 -RDCILHAQTGSGKTLTYLL----LIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA 162
             D I  A+TG+GKT  +L+     + +     +  V+AVIV PTR+L +Q+    + + 
Sbjct: 60  DHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIH 119

>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 = 86.5 bits (215), Expect = 3e-21
 Identities = 29/85 (34%), Positives = 45/85 (52%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS 137
            E +LR +   G+  P+ IQ+ A+       D I  AQ+G+GKT T+ + I   +  +  
Sbjct: 38  KESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFK 97

Query: 138 AVQAVIVVPTRELGMQVTKVARVLA 162
             QA+++ PTREL  Q+ KV   L 
Sbjct: 98  ETQALVLAPTRELAQQIQKVILALG 122

>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 = 88.4 bits (220), Expect = 5e-21
 Identities = 32/101 (31%), Positives = 54/101 (53%), Gaps = 3/101 (2%)

Query: 62  TGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKT 121
                 T  +     +   +L  + E G+  P+ IQ EA+PV  + RD +  A+ G+GKT
Sbjct: 16  LNTKGNTFEDFY---LKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKT 72

Query: 122 LTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA 162
             +++     V  + + +QA+I+VPTREL +Q ++V R L 
Sbjct: 73  AAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLG 113

>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 = 88.7 bits (220), Expect = 6e-21
 Identities = 23/90 (25%), Positives = 46/90 (51%), Gaps = 6/90 (6%)

Query: 79  EHVLRRMEETGYVLPTDIQREALPVLFSS--RDCILHAQTGSGKTLTYLL----LIFSLV 132
           + + + +    +   T +Q++ +  + SS   D I  A+TG+GKT  +L+     + +  
Sbjct: 81  KEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTK 140

Query: 133 NAQRSAVQAVIVVPTRELGMQVTKVARVLA 162
              +  V+AVIV PTR+L +Q+    + + 
Sbjct: 141 FDSQYMVKAVIVAPTRDLALQIEAEVKKIH 170

>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 = 85.7 bits (213), Expect = 6e-21
 Identities = 22/85 (25%), Positives = 44/85 (51%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS 137
              VL  +   G+  P+ +Q +A+P+     D I+ A++G+GKT  +  +    +  +  
Sbjct: 32  SRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENL 91

Query: 138 AVQAVIVVPTRELGMQVTKVARVLA 162
           + Q +I+ PTRE+ +Q+  V   + 
Sbjct: 92  STQILILAPTREIAVQIHSVITAIG 116

>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 = 88.0 bits (219), Expect = 6e-21
 Identities = 29/85 (34%), Positives = 49/85 (57%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS 137
            E++LR +   G+  P+ IQ+ A+  +    D +  AQ+G+GKT T+ +     ++    
Sbjct: 29  DENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVK 88

Query: 138 AVQAVIVVPTRELGMQVTKVARVLA 162
           A QA+++ PTREL +Q+ KV   LA
Sbjct: 89  APQALMLAPTRELALQIQKVVMALA 113

>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 = 88.0 bits (219), Expect = 8e-21
 Identities = 30/85 (35%), Positives = 45/85 (52%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS 137
            E +LR +   G+  P+ IQ+ A+       D I  AQ+G+GKT T+ + I   +     
Sbjct: 48  SESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLK 107

Query: 138 AVQAVIVVPTRELGMQVTKVARVLA 162
           A QA+++ PTREL  Q+ KV   L 
Sbjct: 108 ATQALVLAPTRELAQQIQKVVMALG 132

>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 = 85.4 bits (212), Expect = 9e-21
 Identities = 31/111 (27%), Positives = 54/111 (48%), Gaps = 13/111 (11%)

Query: 79  EHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLL----LIFSLVNA 134
           +  L+ ++E  Y L T+IQ++ + +    +D +  A+TGSGKTL +L+     ++ L   
Sbjct: 34  KKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWT 93

Query: 135 QRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGM 185
               +  +I+ PTREL  Q  +V R +     + D          L+ GG 
Sbjct: 94  STDGLGVLIISPTRELAYQTFEVLRKVGK---NHDFSA------GLIIGGK 135

>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 = 87.6 bits (218), Expect = 1e-20
 Identities = 29/85 (34%), Positives = 48/85 (56%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS 137
            E +LR +   G+  P+ IQ+ A+  +   RD I  +Q+G+GKT T+ + +   ++ Q  
Sbjct: 45  REDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVR 104

Query: 138 AVQAVIVVPTRELGMQVTKVARVLA 162
             QA+I+ PTREL +Q+ K    L 
Sbjct: 105 ETQALILAPTRELAVQIQKGLLALG 129

>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 = 84.1 bits (209), Expect = 3e-20
 Identities = 27/91 (29%), Positives = 44/91 (48%), Gaps = 9/91 (9%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS 137
              +   +    Y  PT IQ+ A+P +   RD +  AQTGSGKT  +L+ I + +  Q  
Sbjct: 31  DPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDL 90

Query: 138 AV---------QAVIVVPTRELGMQVTKVAR 159
                      + +I+ PTREL +Q+   ++
Sbjct: 91  NQQRYSKTAYPKCLILAPTRELAIQILSESQ 121

>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 = 84.3 bits (209), Expect = 4e-20
 Identities = 33/89 (37%), Positives = 50/89 (56%), Gaps = 4/89 (4%)

Query: 79  EHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLL----LIFSLVNA 134
           E+ L+ ++E G+   T+IQ +++  L   RD +  A+TGSGKTL +L+    LI  L   
Sbjct: 63  ENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFM 122

Query: 135 QRSAVQAVIVVPTRELGMQVTKVARVLAA 163
            R+    +I+ PTREL MQ   V + L  
Sbjct: 123 PRNGTGVLILSPTRELAMQTFGVLKELMT 151

>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 = 83.1 bits (206), Expect = 8e-20
 Identities = 31/115 (26%), Positives = 55/115 (47%), Gaps = 3/115 (2%)

Query: 49  SSSAVSTEELAAGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSR 108
              + +           + T ++L    V + +    ++ G+  PT IQ EA+P+    R
Sbjct: 25  EHDSPTEASQPIVEEEETKTFKDL---GVTDVLCEACDQLGWTKPTKIQIEAIPLALQGR 81

Query: 109 DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA 163
           D I  A+TGSGKT  + L I + +      + A+++ PTREL  Q+++    L +
Sbjct: 82  DIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTPTRELAFQISEQFEALGS 136

>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 = 81.9 bits (203), Expect = 1e-19
 Identities = 23/101 (22%), Positives = 46/101 (45%), Gaps = 3/101 (2%)

Query: 62  TGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKT 121
              +S   R+     +   +LR + + G+  P+++Q E +P      D +  A++G GKT
Sbjct: 9   VSIHSSGFRDF---LLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKT 65

Query: 122 LTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA 162
             ++L     +      V  +++  TREL  Q++K     +
Sbjct: 66  AVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFS 106

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 84.4 bits (209), Expect = 1e-19
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 79  EHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSA 138
           E      ++      T  QR     +   +   + A TG GKT   ++    L    +  
Sbjct: 8   EDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGK-- 65

Query: 139 VQAVIVVPTRELGMQVTKVARVLAAKPL 166
            ++ +V PT  L  Q  +  + LA + +
Sbjct: 66  -KSALVFPTVTLVKQTLERLQKLADEKV 92

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score = 84.1 bits (209), Expect = 2e-19
 Identities = 31/100 (31%), Positives = 50/100 (50%), Gaps = 18/100 (18%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS 137
            E ++  +E T Y  PT +Q+ A+P++   RD +  AQTGSGKT  +LL I S + +   
Sbjct: 23  GEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGP 82

Query: 138 AV------------------QAVIVVPTRELGMQVTKVAR 159
                                ++++ PTREL +Q+ + AR
Sbjct: 83  GEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEAR 122

>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 = 82.1 bits (203), Expect = 3e-19
 Identities = 25/87 (28%), Positives = 45/87 (51%), Gaps = 2/87 (2%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFS--SRDCILHAQTGSGKTLTYLLLIFSLVNAQ 135
              +L+ +   G+  P+ IQ  ALP++ +   ++ I  +Q+G+GKT  ++L + S V   
Sbjct: 100 KPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA 159

Query: 136 RSAVQAVIVVPTRELGMQVTKVARVLA 162
               Q + + PT EL +Q  KV   + 
Sbjct: 160 NKYPQCLCLSPTYELALQTGKVIEQMG 186

>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 = 82.6 bits (205), Expect = 4e-19
 Identities = 30/102 (29%), Positives = 54/102 (52%), Gaps = 5/102 (4%)

Query: 65  NSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSR-DCILHAQTGSGKTLT 123
             +   EL   ++ +++L  +   G+  PTDIQ + +P+  +   + +  A+TGSGKT +
Sbjct: 4   EYMNFNEL---NLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTAS 60

Query: 124 YLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKP 165
           + + +  LVN     ++A+I+ PTREL +QV      L    
Sbjct: 61  FAIPLIELVNENN-GIEAIILTPTRELAIQVADEIESLKGNK 101

>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 = 83.0 bits (206), Expect = 5e-19
 Identities = 25/87 (28%), Positives = 45/87 (51%), Gaps = 2/87 (2%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFS--SRDCILHAQTGSGKTLTYLLLIFSLVNAQ 135
              +L+ +   G+  P+ IQ  ALP++ +   ++ I  +Q+G+GKT  ++L + S V   
Sbjct: 33  KPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA 92

Query: 136 RSAVQAVIVVPTRELGMQVTKVARVLA 162
               Q + + PT EL +Q  KV   + 
Sbjct: 93  NKYPQCLCLSPTYELALQTGKVIEQMG 119

>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 = 82.7 bits (205), Expect = 6e-19
 Identities = 25/87 (28%), Positives = 45/87 (51%), Gaps = 2/87 (2%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFS--SRDCILHAQTGSGKTLTYLLLIFSLVNAQ 135
              +L+ +   G+  P+ IQ  ALP++ +   ++ I  +Q+G+GKT  ++L + S V   
Sbjct: 100 KPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA 159

Query: 136 RSAVQAVIVVPTRELGMQVTKVARVLA 162
               Q + + PT EL +Q  KV   + 
Sbjct: 160 NKYPQCLCLSPTYELALQTGKVIEQMG 186

>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 = 82.2 bits (204), Expect = 7e-19
 Identities = 26/89 (29%), Positives = 49/89 (55%), Gaps = 2/89 (2%)

Query: 76  HVPEHVLRRMEETGYVLPTDIQREALPVLFS--SRDCILHAQTGSGKTLTYLLLIFSLVN 133
            +   +L+ +    +  P+ IQ  ALP+L     R+ I  +Q+G+GKT  + L + + VN
Sbjct: 11  GLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVN 70

Query: 134 AQRSAVQAVIVVPTRELGMQVTKVARVLA 162
            + ++ QA+ + P+REL  Q  +V + + 
Sbjct: 71  PEDASPQAICLAPSRELARQTLEVVQEMG 99

>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 = 82.2 bits (204), Expect = 8e-19
 Identities = 21/85 (24%), Positives = 41/85 (48%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS 137
              +LR + + G+  P+++Q E +P      D +  A++G GKT  ++L     +     
Sbjct: 16  KPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTG 75

Query: 138 AVQAVIVVPTRELGMQVTKVARVLA 162
            V  +++  TREL  Q++K     +
Sbjct: 76  QVSVLVMCHTRELAFQISKEYERFS 100

>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 = 78.3 bits (194), Expect = 2e-18
 Identities = 28/80 (35%), Positives = 42/80 (52%), Gaps = 3/80 (3%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS 137
              +L  +   G   PT IQ  ALP+    +D I  A+TG+GKTL + L I   +   + 
Sbjct: 9   KPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQE 68

Query: 138 ---AVQAVIVVPTRELGMQV 154
                +A+++ PTREL +QV
Sbjct: 69  RGRKPRALVLTPTRELALQV 88

>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 = 75.2 bits (186), Expect = 2e-16
 Identities = 21/77 (27%), Positives = 45/77 (58%), Gaps = 6/77 (7%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS 137
            E + + + E G+   T++Q + +P++   ++ ++ A+TGSGKT       +++   +  
Sbjct: 2   NEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAA-----YAIPILEL- 55

Query: 138 AVQAVIVVPTRELGMQV 154
            +++++V PTREL  QV
Sbjct: 56  GMKSLVVTPTRELTRQV 72

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19 Length = 494

 Score = 46.3 bits (109), Expect = 2e-06
 Identities = 14/67 (20%), Positives = 28/67 (41%), Gaps = 3/67 (4%)

Query: 93  PTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGM 152
           P   Q           +C++   TG GKTL  +++        +   + +++ PT+ L +
Sbjct: 10  PRIYQEVIYAKCKE-TNCLIVLPTGLGKTLIAMMIAEYR--LTKYGGKVLMLAPTKPLVL 66

Query: 153 QVTKVAR 159
           Q  +  R
Sbjct: 67  QHAESFR 73

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A* Length = 472

 Score = 45.2 bits (107), Expect = 5e-06
 Identities = 18/59 (30%), Positives = 24/59 (40%), Gaps = 6/59 (10%)

Query: 95  DIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQ 153
           D Q +AL      +   +   TGSGKT   +  I         +   +IVVPT  L  Q
Sbjct: 96  DYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAI------NELSTPTLIVVPTLALAEQ 148

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19 Length = 237

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 21/91 (23%), Positives = 31/91 (34%), Gaps = 12/91 (13%)

Query: 69  LRELCQGHVPEHVLRRMEETGYVLPT------DIQREALPVLFSSRDCILHAQTGSGKTL 122
           + E  + +  E V    +              D Q +AL      +   +   TGSGKT 
Sbjct: 64  IIEYFESNGIEFVDNAADPIPTPYFDAEISLRDYQEKALERWLVDKRGCIVLPTGSGKTH 123

Query: 123 TYLLLIFSLVNAQRSAVQAVIVVPTRELGMQ 153
             +  I         +   +IVVPT  L  Q
Sbjct: 124 VAMAAI------NELSTPTLIVVPTLALAEQ 148

>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 = 42.5 bits (99), Expect = 4e-05
 Identities = 35/224 (15%), Positives = 66/224 (29%), Gaps = 56/224 (25%)

Query: 11  PILVTR-VNHKLSSPNSIDFTNRAFLPVSISLKPLRAVLSSSAVSTEE------LAAGTG 63
            IL    ++H + S +++  T R F   ++  K    V     V          L +   
Sbjct: 44  SILSKEEIDHIIMSKDAVSGTLRLF--WTLLSKQEEMV--QKFVEEVLRINYKFLMS--- 96

Query: 64  NNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQ----------------REALPVLFSS 107
                ++   +   P  + R   E    L  D Q                R+AL  L  +
Sbjct: 97  ----PIKTEQRQ--PSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPA 150

Query: 108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRE-------LGMQVTKVARV 160
           ++ ++    GSGKT         +         +  V    +       L    +    +
Sbjct: 151 KNVLIDGVLGSGKT--------WVAL---DVCLSYKVQCKMDFKIFWLNLKNCNSPETVL 199

Query: 161 LAAKPLDTDLEHKLCTVMALLDGGMLRRH--KSWLKVLYSLTSY 202
              + L   ++    +         LR H  ++ L+ L     Y
Sbjct: 200 EMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPY 243

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A Length = 702

 Score = 41.7 bits (98), Expect = 7e-05
 Identities = 20/84 (23%), Positives = 39/84 (46%), Gaps = 4/84 (4%)

Query: 67  LTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLL 126
           + + EL +  +  + +  ++E G       Q EA+  +FS ++ +L   T +GKTL   +
Sbjct: 1   MKVEELAES-ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEM 59

Query: 127 LIFSLVNAQRSAVQAVIVVPTREL 150
            +           +++ VVP R L
Sbjct: 60  AMVREAIKGG---KSLYVVPLRAL 80

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens} Length = 216

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 16/79 (20%), Positives = 31/79 (39%), Gaps = 3/79 (3%)

Query: 78  PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS 137
            E+V  R      +     Q E        ++ I+   TGSGKT   + +    ++ ++ 
Sbjct: 19  EENVAARASPEPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKK 78

Query: 138 AVQ---AVIVVPTRELGMQ 153
           A +    +++V    L  Q
Sbjct: 79  ASEPGKVIVLVNKVLLVEQ 97

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 39.6 bits (91), Expect = 4e-04
 Identities = 15/69 (21%), Positives = 23/69 (33%), Gaps = 2/69 (2%)

Query: 93  PTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAV--QAVIVVPTREL 150
           P + Q E        ++ I+ A TG GKT   LL+    +         + V       +
Sbjct: 14  PRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPV 73

Query: 151 GMQVTKVAR 159
             Q   V  
Sbjct: 74  YEQNKSVFS 82

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A* Length = 556

 Score = 39.5 bits (91), Expect = 5e-04
 Identities = 13/69 (18%), Positives = 24/69 (34%), Gaps = 2/69 (2%)

Query: 93  PTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLV--NAQRSAVQAVIVVPTREL 150
               Q E      + ++ ++ A TGSGKT   +L+              + V +     +
Sbjct: 8   ARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPV 67

Query: 151 GMQVTKVAR 159
             Q   V +
Sbjct: 68  YEQQKNVFK 76

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Length = 720

 Score = 38.7 bits (90), Expect = 7e-04
 Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 3/75 (4%)

Query: 77  VPEHVLRRMEETGYVLPTDIQREALPVLF-SSRDCILHAQTGSGKTLTYLLLIFSLVNAQ 135
           V E +   ++E G       Q EAL       ++ ++   T SGKTL   + +   +  Q
Sbjct: 8   VDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQ 67

Query: 136 RSAVQAVIVVPTREL 150
               +AV +VP + L
Sbjct: 68  GG--KAVYIVPLKAL 80

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	202
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.89
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.87
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.87
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.86
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.85
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.85
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.85
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.85
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.85
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.84
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.84
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.84
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.84
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.83
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.83
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.83
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.82
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.82
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.8
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.8
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.8
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.79
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.78
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.78
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.78
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.77
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.76
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.75
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.72
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.66
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.62
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.6
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.58
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.58
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.58
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.57
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.57
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.57
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.57
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.56
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.55
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.55
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.54
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.54
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.48
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.47
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.46
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.45
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.41
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.41
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.4
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.4
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.4
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.38
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.37
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.36
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.35
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.34
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.29
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.27
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.26
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.23
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.22
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.2
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.19
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.17
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.15
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.02
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.02
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.0
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	98.89
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	98.89
3h1t_A	590	Type I site-specific restriction-modification syst	98.86
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	98.83
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	98.83
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	98.67
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	98.63
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	98.52
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.31
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	98.25
3jux_A	822	Protein translocase subunit SECA; protein transloc	98.23
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.17
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	97.92
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	97.66
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	97.64
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	97.55
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	97.43
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	97.42
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	97.23
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.17
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.16
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	97.05
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	97.03
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	96.31
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	95.11
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	95.04
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	94.91
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	93.11
3co5_A	143	Putative two-component system transcriptional RES	92.8
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	92.52
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	92.38
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	92.17
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	91.3
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	90.98
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	90.95
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	90.58
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	90.45
2qgz_A	308	Helicase loader, putative primosome component; str	90.14
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	90.0
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	89.98
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	89.95
2z43_A	324	DNA repair and recombination protein RADA; archaea	88.71
3bos_A	242	Putative DNA replication factor; P-loop containing	88.67
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	88.27
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	87.34
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	87.0
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	86.95
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	86.92
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	86.81
2r44_A	331	Uncharacterized protein; putative ATPase, structur	86.8
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	86.72
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	86.27
2chg_A	226	Replication factor C small subunit; DNA-binding pr	85.94
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	85.86
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	85.86
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	85.75
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	85.67
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	85.64
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	85.44
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	85.42
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	85.31
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	84.98
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	84.95
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	84.9
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	84.87
1u94_A	356	RECA protein, recombinase A; homologous recombinat	84.72
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	84.7
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	84.67
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	84.66
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	84.66
3nwn_A	359	Kinesin-like protein KIF9; motor domain, ADP, stru	84.65
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	84.62
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	84.61
2cvh_A	220	DNA repair and recombination protein RADB; filamen	84.59
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	84.57
3io5_A	333	Recombination and repair protein; storage dimer, i	84.51
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	84.47
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	84.25
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	84.24
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	84.18
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	84.13
1p9r_A	418	General secretion pathway protein E; bacterial typ	84.12
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	84.02
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	83.86
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	83.86
1bg2_A	325	Kinesin; motor protein, ATPase, microtubule associ	83.86
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	83.84
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	83.57
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	83.42
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	83.34
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	83.34
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	83.33
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	83.01
2eyu_A	261	Twitching motility protein PILT; pilus retraction	82.96
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	82.83
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	82.83
3dc4_A	344	Kinesin-like protein NOD; catalytic domain, ATPase	82.8
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	82.79
4a14_A	344	Kinesin, kinesin-like protein KIF7; motor protein,	82.78
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	82.71
2y65_A	365	Kinesin, kinesin heavy chain; motor protein; HET:	82.63
2vvg_A	350	Kinesin-2; motor protein, nucleotide-binding, micr	82.59
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	82.55
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	82.53
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	82.47
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	82.44
2h58_A	330	Kinesin-like protein KIFC3 variant; motor domain,	82.36
3b6u_A	372	Kinesin-like protein KIF3B; structural genomics co	82.3
3gbj_A	354	KIF13B protein; kinesin, motor domain, ADP, struct	82.3
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	82.23
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	82.19
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	82.17
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	82.17
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	82.04
1goj_A	355	Kinesin, kinesin heavy chain; motor protein, ATPas	82.01
2nr8_A	358	Kinesin-like protein KIF9; motor domain, ADP, stru	81.99
1t5c_A	349	CENP-E protein, centromeric protein E; kinesin mot	81.93
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	81.93
2zfi_A	366	Kinesin-like protein KIF1A, kinesin heavy chain is	81.89
3lre_A	355	Kinesin-like protein KIF18A; motor protein, nucleo	81.78
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	81.74
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	81.69
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	81.66
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	81.63
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	81.61
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	81.6
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	81.56
1x88_A	359	Kinesin-like protein KIF11; switch II, motor domai	81.47
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	81.46
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	81.44
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	81.39
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	81.13
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	81.1
3t0q_A	349	AGR253WP; kinesin, alpha and beta proteins, P-loop	81.05
1v8k_A	410	Kinesin-like protein KIF2C; microtubule destabiliz	81.0
1xp8_A	366	RECA protein, recombinase A; recombination, radior	80.99
3u06_A	412	Protein claret segregational; motor domain, stalk	80.94
2wbe_C	373	Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mit	80.71
3cob_A	369	Kinesin heavy chain-like protein; motor, switch II	80.69
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	80.66
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	80.58
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	80.4
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	80.38
2heh_A	387	KIF2C protein; kinesin, motor domain, ADP, structu	80.34
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	80.28
1f9v_A	347	Kinesin-like protein KAR3; kinesin-related protein	80.23
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	80.23

>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=99.89  E-value=3e-23  Score=174.25  Aligned_cols=120  Identities=23%  Similarity=0.363  Sum_probs=102.2

Q ss_pred             cccCCCcchHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcC--CcEEEeccCCCchHHHHHHHHHHHHHhcCC
Q 028887           60 AGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSS--RDCILHAQTGSGKTLTYLLLIFSLVNAQRS  137 (202)
Q Consensus        60 ~~~~~~~~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g--~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~  137 (202)
                      .+.+.+..++..|.+.++++.+++.+.++||..||++|.++||.++.|  +|++++++||||||++|++|+++.+.....
T Consensus        82 ~~~~~p~~~~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~  161 (300)
T 3fmo_B           82 RDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANK  161 (300)
T ss_dssp             SSTTCCCCCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTSC
T ss_pred             CCCCCCcCCcCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccCC
Confidence            344444456677888899999999999999999999999999999987  999999999999999999999999987777


Q ss_pred             ccEEEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCcc
Q 028887          138 AVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGML  186 (202)
Q Consensus       138 ~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~  186 (202)
                      ++++|||+|||+||.|++++++.++....       .+.+..+++|...
T Consensus       162 ~~~~lil~PtreLa~Q~~~~~~~l~~~~~-------~~~~~~~~~~~~~  203 (300)
T 3fmo_B          162 YPQCLCLSPTYELALQTGKVIEQMGKFYP-------ELKLAYAVRGNKL  203 (300)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTST-------TCCEEEESTTCCC
T ss_pred             CceEEEEcCcHHHHHHHHHHHHHHHhhCC-------CcEEEEEeCCccH
Confidence            78999999999999999999999987532       3455555555543

>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=99.87  E-value=6.3e-22  Score=160.56  Aligned_cols=121  Identities=29%  Similarity=0.378  Sum_probs=104.3

Q ss_pred             cchHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhc-----CCccE
Q 028887           66 SLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ-----RSAVQ  140 (202)
Q Consensus        66 ~~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~-----~~~~~  140 (202)
                      ..++..|.+.++++.+++.+.+.||..|+++|.++++.++.|+|+++++|||+|||++|++|++..+...     ..+++
T Consensus        25 p~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~~~~~  104 (242)
T 3fe2_A           25 PKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPI  104 (242)
T ss_dssp             CCCCSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCCCCTTCCCS
T ss_pred             CCccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhccccccCCCCE
Confidence            3456667777999999999999999999999999999999999999999999999999999999998743     24668


Q ss_pred             EEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          141 AVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       141 ~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      +||++||++|+.|+++.+++++...        ++.+..++||.....+.+.++
T Consensus       105 ~lil~Pt~~L~~Q~~~~~~~~~~~~--------~~~~~~~~g~~~~~~~~~~~~  150 (242)
T 3fe2_A          105 CLVLAPTRELAQQVQQVAAEYCRAC--------RLKSTCIYGGAPKGPQIRDLE  150 (242)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHHHT--------TCCEEEECTTSCHHHHHHHHH
T ss_pred             EEEEeCcHHHHHHHHHHHHHHHhhc--------CceEEEEECCCChHHHHHHhc
Confidence            9999999999999999999998765        467777777777766655544

>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=99.87  E-value=9e-22  Score=172.62  Aligned_cols=120  Identities=32%  Similarity=0.504  Sum_probs=105.0

Q ss_pred             chHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC-----CccEE
Q 028887           67 LTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR-----SAVQA  141 (202)
Q Consensus        67 ~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~-----~~~~~  141 (202)
                      .++..|.+.++++.+++++.++||.+||++|.++||.++.|+|++++++||||||++|++|+++.+....     .++++
T Consensus        53 ~~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~~~~  132 (434)
T 2db3_A           53 QPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQV  132 (434)
T ss_dssp             CCCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTCCSE
T ss_pred             CCcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccccccCCccE
Confidence            4566788889999999999999999999999999999999999999999999999999999999987543     36789


Q ss_pred             EEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          142 VIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       142 Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      |||+|||+|+.|+++++++++...        .+++..++||.....|.+.++
T Consensus       133 lil~PtreLa~Q~~~~~~~~~~~~--------~~~~~~~~gg~~~~~~~~~l~  177 (434)
T 2db3_A          133 VIVSPTRELAIQIFNEARKFAFES--------YLKIGIVYGGTSFRHQNECIT  177 (434)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTS--------SCCCCEECTTSCHHHHHHHHT
T ss_pred             EEEecCHHHHHHHHHHHHHHhccC--------CcEEEEEECCCCHHHHHHHhh
Confidence            999999999999999999998765        466777788877776665543

>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=99.86  E-value=3.3e-21  Score=157.46  Aligned_cols=117  Identities=26%  Similarity=0.327  Sum_probs=101.7

Q ss_pred             hHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCC
Q 028887           68 TLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPT  147 (202)
Q Consensus        68 ~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Pt  147 (202)
                      ....|.+.++++.+++.+.++||..|+++|.++++.++.|++++++++||+|||++|++|+++.+.....++++||++||
T Consensus        41 ~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~~~~~~lil~Pt  120 (249)
T 3ber_A           41 ETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTPT  120 (249)
T ss_dssp             HHCCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCCSSCEEEECSS
T ss_pred             ccCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCCCCceEEEEeCC
Confidence            45567777999999999999999999999999999999999999999999999999999999998877777789999999


Q ss_pred             HHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHH
Q 028887          148 RELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSW  192 (202)
Q Consensus       148 r~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~  192 (202)
                      ++|+.|+.+++++++...        ++.+..++||.....+...
T Consensus       121 r~L~~q~~~~~~~~~~~~--------~~~~~~~~g~~~~~~~~~~  157 (249)
T 3ber_A          121 RELAFQISEQFEALGSSI--------GVQSAVIVGGIDSMSQSLA  157 (249)
T ss_dssp             HHHHHHHHHHHHHHHGGG--------TCCEEEECTTSCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccC--------CeeEEEEECCCChHHHHHH
Confidence            999999999999998754        3566666666665555443

>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=99.85  E-value=5.2e-21  Score=150.78  Aligned_cols=113  Identities=30%  Similarity=0.489  Sum_probs=96.7

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHh
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTREL  150 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~L  150 (202)
                      +|++.++++.+++.+.++||..|+++|.++++.+++|+++++.+|||+|||++|++|+++.+.....++++||++|+++|
T Consensus         4 ~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L   83 (206)
T 1vec_A            4 EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTREL   83 (206)
T ss_dssp             SGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHHH
T ss_pred             ChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhcccCCCeeEEEEeCcHHH
Confidence            36667999999999999999999999999999999999999999999999999999999988766666789999999999


Q ss_pred             HHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHH
Q 028887          151 GMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHK  190 (202)
Q Consensus       151 a~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~  190 (202)
                      +.|+++.+++++....       ++.+..++||.....+.
T Consensus        84 ~~q~~~~~~~~~~~~~-------~~~~~~~~g~~~~~~~~  116 (206)
T 1vec_A           84 ALQVSQICIQVSKHMG-------GAKVMATTGGTNLRDDI  116 (206)
T ss_dssp             HHHHHHHHHHHTTTSS-------SCCEEEECSSSCHHHHH
T ss_pred             HHHHHHHHHHHHhhcC-------CceEEEEeCCccHHHHH
Confidence            9999999999986542       24555556665554443

>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=99.85  E-value=4.6e-21  Score=154.37  Aligned_cols=113  Identities=22%  Similarity=0.353  Sum_probs=95.7

Q ss_pred             HHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHH
Q 028887           70 RELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRE  149 (202)
Q Consensus        70 ~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~  149 (202)
                      ..|.+.++++.+++.+.+.||..|+++|.++++.++.|+|++++++||+|||++|++|+++.+.....+.++||++||++
T Consensus        24 ~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~  103 (230)
T 2oxc_A           24 ADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTRE  103 (230)
T ss_dssp             CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             CCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEeCCHH
Confidence            34566699999999999999999999999999999999999999999999999999999998866555678999999999


Q ss_pred             hHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHH
Q 028887          150 LGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRH  189 (202)
Q Consensus       150 La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~  189 (202)
                      |+.|+++++++++....       ++.+..++||.....+
T Consensus       104 L~~q~~~~~~~~~~~~~-------~~~~~~~~g~~~~~~~  136 (230)
T 2oxc_A          104 IAVQIHSVITAIGIKME-------GLECHVFIGGTPLSQD  136 (230)
T ss_dssp             HHHHHHHHHHHHTTTST-------TCCEEEECTTSCHHHH
T ss_pred             HHHHHHHHHHHHhcccC-------CceEEEEeCCCCHHHH
Confidence            99999999999986531       2455555555554443

>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=99.85  E-value=2.1e-21  Score=157.11  Aligned_cols=115  Identities=29%  Similarity=0.395  Sum_probs=94.2

Q ss_pred             HHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCH
Q 028887           69 LRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTR  148 (202)
Q Consensus        69 ~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr  148 (202)
                      ...|++.++++.+++.+.++||..|+++|.++++.++.|+|++++++||+|||++|++|+++.+.....+.++||++||+
T Consensus        29 ~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~  108 (237)
T 3bor_A           29 VDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTR  108 (237)
T ss_dssp             CCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSH
T ss_pred             cCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEECcH
Confidence            34567779999999999999999999999999999999999999999999999999999999887655567899999999


Q ss_pred             HhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHH
Q 028887          149 ELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKS  191 (202)
Q Consensus       149 ~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~  191 (202)
                      +|+.|+.+++++++...        ++.+..+++|.....+.+
T Consensus       109 ~L~~q~~~~~~~~~~~~--------~~~~~~~~g~~~~~~~~~  143 (237)
T 3bor_A          109 ELAQQIQKVILALGDYM--------GATCHACIGGTNVRNEMQ  143 (237)
T ss_dssp             HHHHHHHHHHHHHTTTT--------TCCEEEECC---------
T ss_pred             HHHHHHHHHHHHHhhhc--------CceEEEEECCCchHHHHH
Confidence            99999999999998754        355666666665555433

>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=99.85  E-value=5.1e-21  Score=153.50  Aligned_cols=114  Identities=27%  Similarity=0.389  Sum_probs=91.3

Q ss_pred             HHHh-CCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhc------CCccEEEE
Q 028887           71 ELCQ-GHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ------RSAVQAVI  143 (202)
Q Consensus        71 ~l~~-~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~------~~~~~~Li  143 (202)
                      .|.+ .++++.+++++.+.||..|+++|.++++.+++|+|+++++|||+|||++|++|++..+...      ..++++||
T Consensus        20 ~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~~~~~li   99 (228)
T 3iuy_A           20 RFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLV   99 (228)
T ss_dssp             SHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC---------CCCSEEE
T ss_pred             hHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchhhccCCCcEEE
Confidence            3444 4899999999999999999999999999999999999999999999999999999887532      24568999


Q ss_pred             ecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHH
Q 028887          144 VVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWL  193 (202)
Q Consensus       144 l~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l  193 (202)
                      ++||++|+.|+.++++++...         ++.+..++||.....+.+.+
T Consensus       100 l~Pt~~L~~q~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~  140 (228)
T 3iuy_A          100 LTPTRELALHVEAECSKYSYK---------GLKSICIYGGRNRNGQIEDI  140 (228)
T ss_dssp             ECSSHHHHHHHHHHHHHHCCT---------TCCEEEECC------CHHHH
T ss_pred             EeCCHHHHHHHHHHHHHhccc---------CceEEEEECCCChHHHHHHh
Confidence            999999999999999998743         36677777777666554443

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.85  E-value=1.6e-20  Score=151.32  Aligned_cols=117  Identities=24%  Similarity=0.400  Sum_probs=97.8

Q ss_pred             chHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhc----CCccEEE
Q 028887           67 LTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ----RSAVQAV  142 (202)
Q Consensus        67 ~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~----~~~~~~L  142 (202)
                      .+...|.+.++++.+++.+.+.||..|+++|.++++.+++|++++++++||+|||++|++|+++.+...    ..+.++|
T Consensus        22 ~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~l  101 (236)
T 2pl3_A           22 NEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVL  101 (236)
T ss_dssp             GGCSBGGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEE
T ss_pred             cccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceEE
Confidence            345567778999999999999999999999999999999999999999999999999999999988642    2345899


Q ss_pred             EecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHH
Q 028887          143 IVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKS  191 (202)
Q Consensus       143 il~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~  191 (202)
                      |++||++|+.|+.+++++++...        ++.+..++||.....+.+
T Consensus       102 il~Pt~~L~~q~~~~~~~~~~~~--------~~~~~~~~g~~~~~~~~~  142 (236)
T 2pl3_A          102 IISPTRELAYQTFEVLRKVGKNH--------DFSAGLIIGGKDLKHEAE  142 (236)
T ss_dssp             EECSSHHHHHHHHHHHHHHTTTS--------SCCEEEECCC--CHHHHH
T ss_pred             EEeCCHHHHHHHHHHHHHHhCCC--------CeeEEEEECCCCHHHHHH
Confidence            99999999999999999998764        356666666665555443

>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=99.84  E-value=1.8e-20  Score=149.33  Aligned_cols=116  Identities=21%  Similarity=0.361  Sum_probs=98.0

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHh
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTREL  150 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~L  150 (202)
                      .|.+.++++.+++.+.+.||..|+++|.++++.+++|++++++++||+|||++|++|+++.+.......++||++|+++|
T Consensus        15 ~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L   94 (220)
T 1t6n_A           15 GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTREL   94 (220)
T ss_dssp             CSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHH
T ss_pred             CHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEeCCHHH
Confidence            46667999999999999999999999999999999999999999999999999999999988665556689999999999


Q ss_pred             HHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHH
Q 028887          151 GMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWL  193 (202)
Q Consensus       151 a~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l  193 (202)
                      +.|+.++++++.....       ++.+..++||.....+.+.+
T Consensus        95 ~~q~~~~~~~~~~~~~-------~~~v~~~~g~~~~~~~~~~~  130 (220)
T 1t6n_A           95 AFQISKEYERFSKYMP-------NVKVAVFFGGLSIKKDEEVL  130 (220)
T ss_dssp             HHHHHHHHHHHTTTST-------TCCEEEESCCSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhCC-------CceEEEEeCCCChHHHHHHH
Confidence            9999999999986532       24555555655555554444

>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=99.84  E-value=5.9e-21  Score=152.45  Aligned_cols=113  Identities=28%  Similarity=0.402  Sum_probs=94.0

Q ss_pred             HHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCH
Q 028887           69 LRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTR  148 (202)
Q Consensus        69 ~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr  148 (202)
                      ...|.+.++++.+++.+.++||..|+++|.++++.+++|+++++.+|||+|||++|++|+++.+.....+.++||++|++
T Consensus        13 ~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~   92 (224)
T 1qde_A           13 VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTR   92 (224)
T ss_dssp             CCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSH
T ss_pred             cCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccCCCceEEEEECCH
Confidence            34566669999999999999999999999999999999999999999999999999999999887666677999999999


Q ss_pred             HhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHH
Q 028887          149 ELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRH  189 (202)
Q Consensus       149 ~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~  189 (202)
                      +|+.|+++.+++++...        ++.+..++||.....+
T Consensus        93 ~L~~q~~~~~~~~~~~~--------~~~~~~~~g~~~~~~~  125 (224)
T 1qde_A           93 ELALQIQKVVMALAFHM--------DIKVHACIGGTSFVED  125 (224)
T ss_dssp             HHHHHHHHHHHHHTTTS--------CCCEEEECC-------
T ss_pred             HHHHHHHHHHHHHhccc--------CceEEEEeCCcchHHH
Confidence            99999999999998764        3555556665554443

>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=99.84  E-value=4.8e-21  Score=156.07  Aligned_cols=118  Identities=24%  Similarity=0.365  Sum_probs=100.2

Q ss_pred             hHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC---------Cc
Q 028887           68 TLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR---------SA  138 (202)
Q Consensus        68 ~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~---------~~  138 (202)
                      ++..|.+.++++.+++++.++||..|+++|.++++.++.|+|++++++||+|||++|++|+++.+....         .+
T Consensus        21 ~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~  100 (253)
T 1wrb_A           21 VIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAY  100 (253)
T ss_dssp             CCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBC
T ss_pred             ccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccCC
Confidence            344566669999999999999999999999999999999999999999999999999999999886432         24


Q ss_pred             cEEEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHH
Q 028887          139 VQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWL  193 (202)
Q Consensus       139 ~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l  193 (202)
                      +++||++||++|+.|+++++++++...        .+.+..++||.....+.+.+
T Consensus       101 ~~~lil~Pt~~L~~q~~~~~~~~~~~~--------~~~~~~~~g~~~~~~~~~~~  147 (253)
T 1wrb_A          101 PKCLILAPTRELAIQILSESQKFSLNT--------PLRSCVVYGGADTHSQIREV  147 (253)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHTTS--------SCCEEEECSSSCSHHHHHHH
T ss_pred             ceEEEEECCHHHHHHHHHHHHHHhccC--------CceEEEEECCCCHHHHHHHh
Confidence            689999999999999999999998764        46667777777766655443

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.84  E-value=1.4e-20  Score=150.16  Aligned_cols=113  Identities=26%  Similarity=0.394  Sum_probs=95.1

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHh
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTREL  150 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~L  150 (202)
                      .|.+.++++.+++.+.++||..|+++|.++++.++.|++++++++||+|||++|++|+++.+.....+.++||++||++|
T Consensus         5 ~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L   84 (219)
T 1q0u_A            5 QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTREL   84 (219)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHH
T ss_pred             CHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhCcCCceEEEEcCcHHH
Confidence            46667999999999999999999999999999999999999999999999999999999988765566789999999999


Q ss_pred             HHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccH
Q 028887          151 GMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLR  187 (202)
Q Consensus       151 a~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~  187 (202)
                      +.|+++++++++....+    ...+.+..++||....
T Consensus        85 ~~q~~~~~~~~~~~~~~----~~~~~~~~~~g~~~~~  117 (219)
T 1q0u_A           85 ATQIYHETLKITKFCPK----DRMIVARCLIGGTDKQ  117 (219)
T ss_dssp             HHHHHHHHHHHHTTSCG----GGCCCEEEECCCSHHH
T ss_pred             HHHHHHHHHHHhhhccc----ccceEEEEEeCCCCHH
Confidence            99999999999875421    0124455555555433

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.83  E-value=2.8e-20  Score=160.45  Aligned_cols=118  Identities=28%  Similarity=0.429  Sum_probs=99.8

Q ss_pred             hHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC-----------
Q 028887           68 TLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR-----------  136 (202)
Q Consensus        68 ~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~-----------  136 (202)
                      ++..|.+.++++.+++++..+||..|+++|.++|+.++.|+|+++++|||+|||++|++|+++.+....           
T Consensus        13 ~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~~~   92 (417)
T 2i4i_A           13 HIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKEN   92 (417)
T ss_dssp             CCSSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHHHC
T ss_pred             ccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhccccc
Confidence            344566679999999999999999999999999999999999999999999999999999998876432           


Q ss_pred             -------CccEEEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHH
Q 028887          137 -------SAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWL  193 (202)
Q Consensus       137 -------~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l  193 (202)
                             .++++||++||++|+.|+++++++++...        ++.+..++||.....+.+.+
T Consensus        93 ~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~--------~~~~~~~~g~~~~~~~~~~~  148 (417)
T 2i4i_A           93 GRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRS--------RVRPCVVYGGADIGQQIRDL  148 (417)
T ss_dssp             BTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTS--------SCCEEEECSSSCHHHHHHHH
T ss_pred             cccccccCCccEEEECCcHHHHHHHHHHHHHHhCcC--------CceEEEEECCCCHHHHHHHh
Confidence                   13679999999999999999999998764        46667777776666554443

>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=99.83  E-value=3.2e-20  Score=152.64  Aligned_cols=109  Identities=32%  Similarity=0.462  Sum_probs=94.2

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC----CccEEEEecCCHHhHH
Q 028887           77 VPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR----SAVQAVIVVPTRELGM  152 (202)
Q Consensus        77 l~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~----~~~~~Lil~Ptr~La~  152 (202)
                      +++.+++.+.++||..|+++|.++++.++.|+|++++++||+|||++|++|+++.+...+    .+.++||++||++|+.
T Consensus        61 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~lil~Pt~~La~  140 (262)
T 3ly5_A           61 VNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAM  140 (262)
T ss_dssp             CCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHH
T ss_pred             cCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceEEEEeCCHHHHH
Confidence            999999999999999999999999999999999999999999999999999999887532    3458999999999999


Q ss_pred             HHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHH
Q 028887          153 QVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWL  193 (202)
Q Consensus       153 Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l  193 (202)
                      |+++.+++++...        +..+..++||.....+...+
T Consensus       141 q~~~~~~~~~~~~--------~~~~~~~~g~~~~~~~~~~~  173 (262)
T 3ly5_A          141 QTFGVLKELMTHH--------VHTYGLIMGGSNRSAEAQKL  173 (262)
T ss_dssp             HHHHHHHHHTTTC--------CSCEEEECSSSCHHHHHHHH
T ss_pred             HHHHHHHHHHhhc--------CceEEEEECCCCHHHHHHHh
Confidence            9999999998765        35566666666666554443

>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=99.83  E-value=6.4e-20  Score=144.42  Aligned_cols=112  Identities=30%  Similarity=0.434  Sum_probs=95.4

Q ss_pred             HHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhc---CCccEEEEecCCH
Q 028887           72 LCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ---RSAVQAVIVVPTR  148 (202)
Q Consensus        72 l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~---~~~~~~Lil~Ptr  148 (202)
                      |.+.++++.+++.+.+.||..|+++|.++++.+++|+++++.+|||+|||++|++|+++.+...   ..++++||++|++
T Consensus         3 f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~~   82 (207)
T 2gxq_A            3 FKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTR   82 (207)
T ss_dssp             GGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSSH
T ss_pred             hhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEECCH
Confidence            5667999999999999999999999999999999999999999999999999999999987532   2456899999999


Q ss_pred             HhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHH
Q 028887          149 ELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWL  193 (202)
Q Consensus       149 ~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l  193 (202)
                      +|+.|+.+.+++++..          +.+..++||.....+.+.+
T Consensus        83 ~L~~q~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~  117 (207)
T 2gxq_A           83 ELALQVASELTAVAPH----------LKVVAVYGGTGYGKQKEAL  117 (207)
T ss_dssp             HHHHHHHHHHHHHCTT----------SCEEEECSSSCSHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhc----------ceEEEEECCCChHHHHHHh
Confidence            9999999999999764          3456666666655554443

>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=99.82  E-value=1.8e-20  Score=151.78  Aligned_cols=103  Identities=28%  Similarity=0.493  Sum_probs=89.9

Q ss_pred             CCCcchHHHHH-hCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhc-CCccE
Q 028887           63 GNNSLTLRELC-QGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ-RSAVQ  140 (202)
Q Consensus        63 ~~~~~~~~~l~-~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~-~~~~~  140 (202)
                      +.+..+|.++. +.++++.+++.+.++||..|+++|.++++.++.|+++++.+|||+|||++|++|+++.+... ..+++
T Consensus        21 p~~~~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~  100 (245)
T 3dkp_A           21 PDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFR  100 (245)
T ss_dssp             CCCCSSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHCSCCSSSCC
T ss_pred             CCcccCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHhhcccCCce
Confidence            34445566653 35899999999999999999999999999999999999999999999999999999988642 34568


Q ss_pred             EEEecCCHHhHHHHHHHHHHhhcCC
Q 028887          141 AVIVVPTRELGMQVTKVARVLAAKP  165 (202)
Q Consensus       141 ~Lil~Ptr~La~Q~~~~~~~l~~~~  165 (202)
                      +||++||++|+.|+++++++++...
T Consensus       101 ~lil~Pt~~L~~q~~~~~~~~~~~~  125 (245)
T 3dkp_A          101 ALIISPTRELASQIHRELIKISEGT  125 (245)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTS
T ss_pred             EEEEeCCHHHHHHHHHHHHHHhccc
Confidence            9999999999999999999997654

>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=99.82  E-value=8.1e-20  Score=157.60  Aligned_cols=117  Identities=27%  Similarity=0.377  Sum_probs=101.0

Q ss_pred             HHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHH
Q 028887           70 RELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRE  149 (202)
Q Consensus        70 ~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~  149 (202)
                      ..|.+.++++.+++.+.+.||..|+++|.++++.++.|++++++++||+|||++|++|+++.+.....+.++||++||++
T Consensus        37 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~Pt~~  116 (410)
T 2j0s_A           37 PTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRE  116 (410)
T ss_dssp             CSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHH
T ss_pred             CCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhccCCceEEEEcCcHH
Confidence            35666699999999999999999999999999999999999999999999999999999998765555668999999999


Q ss_pred             hHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          150 LGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       150 La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      |+.|+.+++++++...        ++.+..++||.....+.+.++
T Consensus       117 L~~q~~~~~~~~~~~~--------~~~~~~~~g~~~~~~~~~~~~  153 (410)
T 2j0s_A          117 LAVQIQKGLLALGDYM--------NVQCHACIGGTNVGEDIRKLD  153 (410)
T ss_dssp             HHHHHHHHHHHHTTTT--------TCCEEEECTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccC--------CeEEEEEECCCCHHHHHHHhh
Confidence            9999999999998765        466667777776666555443

>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=99.80  E-value=2e-19  Score=154.55  Aligned_cols=111  Identities=24%  Similarity=0.402  Sum_probs=96.9

Q ss_pred             HHHHHcccCCCcchHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcC--CcEEEeccCCCchHHHHHHHHHHHH
Q 028887           55 TEELAAGTGNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSS--RDCILHAQTGSGKTLTYLLLIFSLV  132 (202)
Q Consensus        55 ~~~l~~~~~~~~~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g--~~~l~~a~TGsGKT~~~l~~~l~~l  132 (202)
                      .+........+..++..|.+.++++.+++.+.+.||..|+++|.++++.++.+  +++++++|||+|||++|++|+++.+
T Consensus        10 ~~~~~~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~   89 (412)
T 3fht_A           10 VEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV   89 (412)
T ss_dssp             HHHHTTCTTSTTCCSSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             ceeecccCCCCccccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHh
Confidence            33343444445566777888899999999999999999999999999999987  9999999999999999999999998


Q ss_pred             HhcCCccEEEEecCCHHhHHHHHHHHHHhhcCC
Q 028887          133 NAQRSAVQAVIVVPTRELGMQVTKVARVLAAKP  165 (202)
Q Consensus       133 ~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~  165 (202)
                      ..+..++++||++|+++|+.|+.++++++....
T Consensus        90 ~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~  122 (412)
T 3fht_A           90 EPANKYPQCLCLSPTYELALQTGKVIEQMGKFY  122 (412)
T ss_dssp             CTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTS
T ss_pred             hhcCCCCCEEEECCCHHHHHHHHHHHHHHHhhc
Confidence            777777789999999999999999999998653

>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=99.80  E-value=6.8e-20  Score=161.91  Aligned_cols=103  Identities=24%  Similarity=0.416  Sum_probs=92.6

Q ss_pred             CCCcchHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcC--CcEEEeccCCCchHHHHHHHHHHHHHhcCCccE
Q 028887           63 GNNSLTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSS--RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQ  140 (202)
Q Consensus        63 ~~~~~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g--~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~  140 (202)
                      +.+..++..|.+.++++.+++.+.++||..|+++|.++++.++.|  ++++++|+||||||++|++|+++.+..+..+++
T Consensus        85 ~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~~~~~  164 (479)
T 3fmp_B           85 NSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQ  164 (479)
T ss_dssp             TSCCCCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTTSCSCC
T ss_pred             CCCccCcCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhcCCCCc
Confidence            334345667777899999999999999999999999999999987  999999999999999999999998877777779


Q ss_pred             EEEecCCHHhHHHHHHHHHHhhcCC
Q 028887          141 AVIVVPTRELGMQVTKVARVLAAKP  165 (202)
Q Consensus       141 ~Lil~Ptr~La~Q~~~~~~~l~~~~  165 (202)
                      +|||+||++|+.|++++++++....
T Consensus       165 ~lil~Pt~~La~Q~~~~~~~~~~~~  189 (479)
T 3fmp_B          165 CLCLSPTYELALQTGKVIEQMGKFY  189 (479)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHTTS
T ss_pred             EEEEeChHHHHHHHHHHHHHHHhhC
Confidence            9999999999999999999988753

>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=99.80  E-value=5e-19  Score=151.24  Aligned_cols=118  Identities=21%  Similarity=0.363  Sum_probs=98.6

Q ss_pred             HHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHH
Q 028887           70 RELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRE  149 (202)
Q Consensus        70 ~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~  149 (202)
                      ..|++.++++.+++.+.++||..|+++|.++++.++.|+++++.+|||+|||++|++|++..+.....+.++||++|+++
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~   87 (391)
T 1xti_A            8 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE   87 (391)
T ss_dssp             -CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSCHH
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCCHH
Confidence            34566699999999999999999999999999999999999999999999999999999998765555668999999999


Q ss_pred             hHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          150 LGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       150 La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      |+.|+.++++++.....       ++.+..++||.....+.+.++
T Consensus        88 L~~q~~~~~~~~~~~~~-------~~~~~~~~g~~~~~~~~~~~~  125 (391)
T 1xti_A           88 LAFQISKEYERFSKYMP-------NVKVAVFFGGLSIKKDEEVLK  125 (391)
T ss_dssp             HHHHHHHHHHHHTTTCT-------TCCEEEECTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhCC-------CeEEEEEeCCCCHHHHHHHHh
Confidence            99999999999987542       355565666666555544443

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.79  E-value=1.7e-18  Score=156.80  Aligned_cols=128  Identities=23%  Similarity=0.393  Sum_probs=105.2

Q ss_pred             CCCcchHHHHHhCC-CCHHHHHHHHHCCCCCCcHHHHHHHHhHH--cCCcEEEeccCCCchHHHHHHHHHHHHHhcC---
Q 028887           63 GNNSLTLRELCQGH-VPEHVLRRMEETGYVLPTDIQREALPVLF--SSRDCILHAQTGSGKTLTYLLLIFSLVNAQR---  136 (202)
Q Consensus        63 ~~~~~~~~~l~~~g-l~~~l~~~l~~~g~~~~t~~Q~~~i~~i~--~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~---  136 (202)
                      +....++.+|.+.+ +++.+++++.++||..|+++|.++|+.++  .|+|+++++|||+|||++|++|+++.+..++   
T Consensus        13 ~~~~~~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~   92 (579)
T 3sqw_A           13 NSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDS   92 (579)
T ss_dssp             SCCCCCHHHHHHTTSSCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSS
T ss_pred             CCCCcCHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccccc
Confidence            44566888888776 99999999999999999999999999999  7899999999999999999999999987653   


Q ss_pred             -CccEEEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          137 -SAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       137 -~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                       ..+++|||+||++|+.|+.+++++++....    ....+.+..+++|.....+.+.+.
T Consensus        93 ~~~~~~lvl~Ptr~La~Q~~~~~~~~~~~~~----~~~~~~~~~~~gg~~~~~~~~~l~  147 (579)
T 3sqw_A           93 QYMVKAVIVAPTRDLALQIEAEVKKIHDMNY----GLKKYACVSLVGGTDFRAAMNKMN  147 (579)
T ss_dssp             TTSCCEEEECSSHHHHHHHHHHHHHHHHHCG----GGTTSCEEEECTTSCHHHHHHHHH
T ss_pred             cCCCeEEEEcchHHHHHHHHHHHHHHHhhcc----cccceEEEEEECCccHHHHHHHHh
Confidence             346899999999999999999999864310    001356677788877766655543

>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=99.78  E-value=7.4e-19  Score=150.94  Aligned_cols=112  Identities=31%  Similarity=0.481  Sum_probs=96.3

Q ss_pred             HHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHH
Q 028887           70 RELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRE  149 (202)
Q Consensus        70 ~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~  149 (202)
                      ..|++.++++.+++.+.++||..|+++|.++++.++.|+++++.+|||+|||++|++|++..+.....+.++||++|+++
T Consensus        21 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  100 (400)
T 1s2m_A           21 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRE  100 (400)
T ss_dssp             CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcCCHH
Confidence            34666699999999999999999999999999999999999999999999999999999998866555668999999999


Q ss_pred             hHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHH
Q 028887          150 LGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRH  189 (202)
Q Consensus       150 La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~  189 (202)
                      |+.|+.+++++++...        ++.+..++++.....+
T Consensus       101 L~~q~~~~~~~~~~~~--------~~~~~~~~g~~~~~~~  132 (400)
T 1s2m_A          101 LALQTSQVVRTLGKHC--------GISCMVTTGGTNLRDD  132 (400)
T ss_dssp             HHHHHHHHHHHHTTTT--------TCCEEEECSSSCHHHH
T ss_pred             HHHHHHHHHHHHhccc--------CceEEEEeCCcchHHH
Confidence            9999999999998764        3555555555554443

>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=99.78  E-value=8.2e-19  Score=149.85  Aligned_cols=114  Identities=28%  Similarity=0.386  Sum_probs=98.2

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHh
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTREL  150 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~L  150 (202)
                      .|++.++++.+++.+.+.||..|+++|.++++.++.|+++++.+|||+|||++|++|+++.+.....+.++||++|+++|
T Consensus        22 ~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L  101 (394)
T 1fuu_A           22 KFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTREL  101 (394)
T ss_dssp             SSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEECSSHHH
T ss_pred             ChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEEcCCHHH
Confidence            35556999999999999999999999999999999999999999999999999999999988766566789999999999


Q ss_pred             HHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHH
Q 028887          151 GMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSW  192 (202)
Q Consensus       151 a~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~  192 (202)
                      +.|+.+++++++...        ++.+..++||.....+.+.
T Consensus       102 ~~q~~~~~~~~~~~~--------~~~~~~~~g~~~~~~~~~~  135 (394)
T 1fuu_A          102 ALQIQKVVMALAFHM--------DIKVHACIGGTSFVEDAEG  135 (394)
T ss_dssp             HHHHHHHHHHHTTTS--------CCCEEEECSSCCHHHHHHH
T ss_pred             HHHHHHHHHHHhccC--------CeeEEEEeCCCchHHHHhh
Confidence            999999999998764        3566666666665554443

>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=99.78  E-value=1e-18  Score=150.31  Aligned_cols=117  Identities=28%  Similarity=0.386  Sum_probs=100.3

Q ss_pred             hHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCC
Q 028887           68 TLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPT  147 (202)
Q Consensus        68 ~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Pt  147 (202)
                      ....|.+.++++.+++.+.+.||..|+++|.++++.++.|+++++.++||+|||++|++|+++.+.....+.++||++|+
T Consensus        38 ~~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~  117 (414)
T 3eiq_A           38 IVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPT  117 (414)
T ss_dssp             CCCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTSCSCCEEEECSS
T ss_pred             hhcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcCCceeEEEEeCh
Confidence            34556677999999999999999999999999999999999999999999999999999999988765566689999999


Q ss_pred             HHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHH
Q 028887          148 RELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSW  192 (202)
Q Consensus       148 r~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~  192 (202)
                      ++|+.|+.+++++++...        +..+..+++|.....+.+.
T Consensus       118 ~~L~~q~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~  154 (414)
T 3eiq_A          118 RELAQQIQKVVMALGDYM--------GASCHACIGGTNVRAEVQK  154 (414)
T ss_dssp             HHHHHHHHHHHHHHGGGS--------CCCEEECCCCTTHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccc--------CceEEEEECCcchHHHHHH
Confidence            999999999999998764        3566666666665555433

>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=99.77  E-value=3.8e-18  Score=153.40  Aligned_cols=126  Identities=24%  Similarity=0.396  Sum_probs=103.2

Q ss_pred             CCcchHHHHHhCC-CCHHHHHHHHHCCCCCCcHHHHHHHHhHH--cCCcEEEeccCCCchHHHHHHHHHHHHHhcC----
Q 028887           64 NNSLTLRELCQGH-VPEHVLRRMEETGYVLPTDIQREALPVLF--SSRDCILHAQTGSGKTLTYLLLIFSLVNAQR----  136 (202)
Q Consensus        64 ~~~~~~~~l~~~g-l~~~l~~~l~~~g~~~~t~~Q~~~i~~i~--~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~----  136 (202)
                      ....++.+|.+.+ +++.+++.+.+.||..|+++|.++|+.++  .|+|+++++|||+|||++|++|+++.+..++    
T Consensus        65 ~~~~~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~  144 (563)
T 3i5x_A           65 SKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQ  144 (563)
T ss_dssp             CCCCCHHHHHHTTSSCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSST
T ss_pred             CCCcCHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhcccccc
Confidence            3456788887776 99999999999999999999999999999  6789999999999999999999999987654    


Q ss_pred             CccEEEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHH
Q 028887          137 SAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWL  193 (202)
Q Consensus       137 ~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l  193 (202)
                      ..+++|||+||++|+.|++++++++.....    ......+..++||.....+.+.+
T Consensus       145 ~~~~~lil~Ptr~La~Q~~~~~~~~~~~~~----~~~~~~~~~~~g~~~~~~~~~~~  197 (563)
T 3i5x_A          145 YMVKAVIVAPTRDLALQIEAEVKKIHDMNY----GLKKYACVSLVGGTDFRAAMNKM  197 (563)
T ss_dssp             TSCCEEEECSSHHHHHHHHHHHHHHHHHCG----GGTTSCEEEECTTSCHHHHHHHH
T ss_pred             CCeeEEEEcCcHHHHHHHHHHHHHHHhhcc----ccCceeEEEEECCcCHHHHHHHH
Confidence            245899999999999999999999865321    01134567778887766665444

>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=99.76  E-value=2.1e-18  Score=146.99  Aligned_cols=96  Identities=27%  Similarity=0.469  Sum_probs=88.0

Q ss_pred             HHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcC--CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCC
Q 028887           70 RELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSS--RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPT  147 (202)
Q Consensus        70 ~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g--~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Pt  147 (202)
                      .+|.+.|+++.+++.+.+.||..|+++|.++++.++.+  +++++++|||+|||++|++|++..+.....+.++||++|+
T Consensus         5 ~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~   84 (395)
T 3pey_A            5 KSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPS   84 (395)
T ss_dssp             CSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEECSS
T ss_pred             cCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEECCC
Confidence            45667799999999999999999999999999999998  9999999999999999999999988766566789999999


Q ss_pred             HHhHHHHHHHHHHhhcCC
Q 028887          148 RELGMQVTKVARVLAAKP  165 (202)
Q Consensus       148 r~La~Q~~~~~~~l~~~~  165 (202)
                      ++|+.|+.+++++++...
T Consensus        85 ~~L~~q~~~~~~~~~~~~  102 (395)
T 3pey_A           85 RELARQTLEVVQEMGKFT  102 (395)
T ss_dssp             HHHHHHHHHHHHHHTTTS
T ss_pred             HHHHHHHHHHHHHHhccc
Confidence            999999999999988654

>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=99.75  E-value=9.6e-18  Score=141.55  Aligned_cols=113  Identities=26%  Similarity=0.489  Sum_probs=95.7

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcC-CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHH
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSS-RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRE  149 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g-~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~  149 (202)
                      .|.+.++++.+++.+.+.||..|+++|.++++.++.| +++++.+|||+|||++|++|++..+... .+.++||++|+++
T Consensus         7 ~f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~-~~~~~lil~P~~~   85 (367)
T 1hv8_A            7 NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN-NGIEAIILTPTRE   85 (367)
T ss_dssp             CGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS-SSCCEEEECSCHH
T ss_pred             chhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhccc-CCCcEEEEcCCHH
Confidence            4666799999999999999999999999999999988 7999999999999999999998877542 3458999999999


Q ss_pred             hHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHH
Q 028887          150 LGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSW  192 (202)
Q Consensus       150 La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~  192 (202)
                      |+.|+.++++++++..        .+.+..+++|.....+...
T Consensus        86 L~~q~~~~~~~~~~~~--------~~~v~~~~~~~~~~~~~~~  120 (367)
T 1hv8_A           86 LAIQVADEIESLKGNK--------NLKIAKIYGGKAIYPQIKA  120 (367)
T ss_dssp             HHHHHHHHHHHHHCSS--------CCCEEEECTTSCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCC--------CceEEEEECCcchHHHHhh
Confidence            9999999999998764        3566666666665554443

>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=99.72  E-value=6.3e-17  Score=135.18  Aligned_cols=100  Identities=27%  Similarity=0.447  Sum_probs=85.2

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHH
Q 028887           77 VPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTK  156 (202)
Q Consensus        77 l~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~  156 (202)
                      +++.+.+.+.++||..|+++|.++++.+++|+++++.+|||+|||++|++|+++.   +.   ++||++|+++|+.|+.+
T Consensus         1 l~~~i~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~---~~---~~liv~P~~~L~~q~~~   74 (337)
T 2z0m_A            1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL---GM---KSLVVTPTRELTRQVAS   74 (337)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH---TC---CEEEECSSHHHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhh---cC---CEEEEeCCHHHHHHHHH
Confidence            5688999999999999999999999999999999999999999999999998763   33   79999999999999999


Q ss_pred             HHHHhhcCCCCcccccccceEEEEEeCCccHHHH
Q 028887          157 VARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHK  190 (202)
Q Consensus       157 ~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~  190 (202)
                      ++++++...        ++.+..+++|.....+.
T Consensus        75 ~~~~~~~~~--------~~~~~~~~~~~~~~~~~  100 (337)
T 2z0m_A           75 HIRDIGRYM--------DTKVAEVYGGMPYKAQI  100 (337)
T ss_dssp             HHHHHTTTS--------CCCEEEECTTSCHHHHH
T ss_pred             HHHHHhhhc--------CCcEEEEECCcchHHHH
Confidence            999998764        34555555555554443

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.66  E-value=2.8e-16  Score=136.08  Aligned_cols=91  Identities=20%  Similarity=0.151  Sum_probs=76.3

Q ss_pred             HHHHH-CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887           83 RRMEE-TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus        83 ~~l~~-~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      +.+.+ .|| .|+++|.++++.++.|+|+++++|||+|||++|+++++..+..+   .++|||+||++|+.|+.++++++
T Consensus        12 ~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~~~~---~~~lil~Pt~~L~~q~~~~~~~~   87 (414)
T 3oiy_A           12 SFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKG---KKSALVFPTVTLVKQTLERLQKL   87 (414)
T ss_dssp             HHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHHTTT---CCEEEEESSHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHhcCC---CEEEEEECCHHHHHHHHHHHHHH
Confidence            34433 477 79999999999999999999999999999999999998877444   48999999999999999999998


Q ss_pred             hcCCCCcccccccceEEEEEeCCcc
Q 028887          162 AAKPLDTDLEHKLCTVMALLDGGML  186 (202)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~~g~~~  186 (202)
                      +. .        ++.+..++||...
T Consensus        88 ~~-~--------~~~v~~~~g~~~~  103 (414)
T 3oiy_A           88 AD-E--------KVKIFGFYSSMKK  103 (414)
T ss_dssp             CC-S--------SCCEEECCTTSCH
T ss_pred             cc-C--------CceEEEEECCCCh
Confidence            76 3        4566666666655

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.60  E-value=3.7e-15  Score=136.89  Aligned_cols=101  Identities=16%  Similarity=0.063  Sum_probs=80.8

Q ss_pred             HHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCC--ccEEEEecCCHHhHHHHHHHHHH
Q 028887           83 RRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS--AVQAVIVVPTRELGMQVTKVARV  160 (202)
Q Consensus        83 ~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~--~~~~Lil~Ptr~La~Q~~~~~~~  160 (202)
                      ..+..+||..|+++|.++++.++.|++++++++||+|||++|++|+++.+.....  +.++||++||++|+.|+.+++++
T Consensus         4 ~~l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L~~Q~~~~~~~   83 (696)
T 2ykg_A            4 SDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVFSK   83 (696)
T ss_dssp             ---CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHHHHHHHHHHHH
T ss_pred             CcccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHHHHHHHHHHHH
Confidence            4566789999999999999999999999999999999999999999998876532  25899999999999999999999


Q ss_pred             hhcCCCCcccccccceEEEEEeCCccHHHHH
Q 028887          161 LAAKPLDTDLEHKLCTVMALLDGGMLRRHKS  191 (202)
Q Consensus       161 l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~  191 (202)
                      ++...        ++.+..++||.....+.+
T Consensus        84 ~~~~~--------~~~v~~~~g~~~~~~~~~  106 (696)
T 2ykg_A           84 YFERH--------GYRVTGISGATAENVPVE  106 (696)
T ss_dssp             HTTTT--------TCCEEEECSSSCSSSCHH
T ss_pred             HhccC--------CceEEEEeCCccccccHH
Confidence            98654        456666666655544433

>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=99.58  E-value=5.6e-15  Score=136.88  Aligned_cols=89  Identities=21%  Similarity=0.237  Sum_probs=81.0

Q ss_pred             HHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHh-HHcCCcEEEeccCCCchHHHHHHHHHHHHH-hcCCccEEEEecCCHH
Q 028887           72 LCQGHVPEHVLRRMEETGYVLPTDIQREALPV-LFSSRDCILHAQTGSGKTLTYLLLIFSLVN-AQRSAVQAVIVVPTRE  149 (202)
Q Consensus        72 l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~-i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~-~~~~~~~~Lil~Ptr~  149 (202)
                      |.+.++++.+.+.+.+.||..|+++|.++++. +..|+++++++|||||||++|.+++++.+. .+.   +++|++|+++
T Consensus         3 f~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~---~~l~i~P~ra   79 (720)
T 2zj8_A            3 VDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQGG---KAVYIVPLKA   79 (720)
T ss_dssp             GGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHHCS---EEEEECSSGG
T ss_pred             HhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhCCC---EEEEEcCcHH
Confidence            56679999999999999999999999999998 889999999999999999999999998876 343   8999999999


Q ss_pred             hHHHHHHHHHHhhc
Q 028887          150 LGMQVTKVARVLAA  163 (202)
Q Consensus       150 La~Q~~~~~~~l~~  163 (202)
                      |+.|++++++.+..
T Consensus        80 La~q~~~~~~~l~~   93 (720)
T 2zj8_A           80 LAEEKFQEFQDWEK   93 (720)
T ss_dssp             GHHHHHHHTGGGGG
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999976654

>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=99.58  E-value=9.2e-15  Score=133.04  Aligned_cols=82  Identities=20%  Similarity=0.210  Sum_probs=75.0

Q ss_pred             hCCCCHHHHHHHHH-CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHH
Q 028887           74 QGHVPEHVLRRMEE-TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGM  152 (202)
Q Consensus        74 ~~gl~~~l~~~l~~-~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~  152 (202)
                      +.++++.+.+.|.+ +||..|+++|.++|+.++.|+|+++.+|||+|||++|++|++.   ..   .++||++|+++|+.
T Consensus        25 ~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~---~~---g~~lVisP~~~L~~   98 (591)
T 2v1x_A           25 DFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALC---SD---GFTLVICPLISLME   98 (591)
T ss_dssp             CSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHT---SS---SEEEEECSCHHHHH
T ss_pred             cCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHH---cC---CcEEEEeCHHHHHH
Confidence            35788999999988 6999999999999999999999999999999999999999965   22   38999999999999


Q ss_pred             HHHHHHHHh
Q 028887          153 QVTKVARVL  161 (202)
Q Consensus       153 Q~~~~~~~l  161 (202)
                      |+.+.++++
T Consensus        99 q~~~~l~~~  107 (591)
T 2v1x_A           99 DQLMVLKQL  107 (591)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHhc
Confidence            999999987

>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=99.58  E-value=3.4e-15  Score=133.95  Aligned_cols=86  Identities=23%  Similarity=0.298  Sum_probs=77.5

Q ss_pred             HHHhCCCCHHHHHHHHH-CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHH
Q 028887           71 ELCQGHVPEHVLRRMEE-TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRE  149 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~-~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~  149 (202)
                      +|++.++++.+.+.+.+ +||..|+++|.++|+.+++|+|+++.+|||+|||++|++|++..   .+   .+||++|+++
T Consensus         3 ~fe~l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~---~g---~~lvi~P~~a   76 (523)
T 1oyw_A            3 QAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL---NG---LTVVVSPLIS   76 (523)
T ss_dssp             CCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS---SS---EEEEECSCHH
T ss_pred             ChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHh---CC---CEEEECChHH
Confidence            46677899999999988 89999999999999999999999999999999999999998742   23   7999999999


Q ss_pred             hHHHHHHHHHHhh
Q 028887          150 LGMQVTKVARVLA  162 (202)
Q Consensus       150 La~Q~~~~~~~l~  162 (202)
                      |+.|+.+.++.++
T Consensus        77 L~~q~~~~l~~~g   89 (523)
T 1oyw_A           77 LMKDQVDQLQANG   89 (523)
T ss_dssp             HHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcC
Confidence            9999999998863

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.57  E-value=1.1e-14  Score=129.17  Aligned_cols=90  Identities=17%  Similarity=0.082  Sum_probs=76.7

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCC--ccEEEEecCCHHhHHHHHHHHHHhhcCCCCcc
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS--AVQAVIVVPTRELGMQVTKVARVLAAKPLDTD  169 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~--~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~  169 (202)
                      .|+++|.++++.++.|+++++.++||+|||++|++|+++.+.....  +.++||++||++|+.|+.+++++++...    
T Consensus         4 ~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~----   79 (555)
T 3tbk_A            4 KPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFERL----   79 (555)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTT----
T ss_pred             CCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhccC----
Confidence            6999999999999999999999999999999999999999876432  5589999999999999999999998765    


Q ss_pred             cccccceEEEEEeCCccHHH
Q 028887          170 LEHKLCTVMALLDGGMLRRH  189 (202)
Q Consensus       170 ~~~~~~~~~~~~~g~~~~~~  189 (202)
                          ++.+..++|+.....+
T Consensus        80 ----~~~~~~~~g~~~~~~~   95 (555)
T 3tbk_A           80 ----GYNIASISGATSDSVS   95 (555)
T ss_dssp             ----TCCEEEECTTTGGGSC
T ss_pred             ----CcEEEEEcCCCcchhh
Confidence                3566666666544443

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.57  E-value=7.2e-15  Score=135.88  Aligned_cols=90  Identities=24%  Similarity=0.272  Sum_probs=80.5

Q ss_pred             HHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHh-HHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHh
Q 028887           72 LCQGHVPEHVLRRMEETGYVLPTDIQREALPV-LFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTREL  150 (202)
Q Consensus        72 l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~-i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~L  150 (202)
                      |.+.++++.+.+.+.+.||..|+++|.++++. +..+++++++||||||||++|.+++++.+...  +.+++|++|+++|
T Consensus        10 ~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~--~~~il~i~P~r~L   87 (715)
T 2va8_A           10 IEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKN--GGKAIYVTPLRAL   87 (715)
T ss_dssp             GGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHS--CSEEEEECSCHHH
T ss_pred             HHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHC--CCeEEEEeCcHHH
Confidence            55569999999999999999999999999999 78899999999999999999999999887632  2389999999999


Q ss_pred             HHHHHHHHHHhhc
Q 028887          151 GMQVTKVARVLAA  163 (202)
Q Consensus       151 a~Q~~~~~~~l~~  163 (202)
                      +.|+.++++.+..
T Consensus        88 a~q~~~~~~~~~~  100 (715)
T 2va8_A           88 TNEKYLTFKDWEL  100 (715)
T ss_dssp             HHHHHHHHGGGGG
T ss_pred             HHHHHHHHHHhhc
Confidence            9999999965543

>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=99.57  E-value=1.5e-14  Score=135.22  Aligned_cols=103  Identities=20%  Similarity=0.157  Sum_probs=82.9

Q ss_pred             HHHHHHHCCCCCCcHHHHHHHHhHHcC------CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHH
Q 028887           81 VLRRMEETGYVLPTDIQREALPVLFSS------RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQV  154 (202)
Q Consensus        81 l~~~l~~~g~~~~t~~Q~~~i~~i~~g------~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~  154 (202)
                      +.+.+..+|| .||++|.++++.++.+      ++++++|+||||||++|++|+++.+..+.   +++|++||++|+.|+
T Consensus       358 ~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~g~---qvlvlaPtr~La~Q~  433 (780)
T 1gm5_A          358 AEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGF---QTAFMVPTSILAIQH  433 (780)
T ss_dssp             HHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTS---CEEEECSCHHHHHHH
T ss_pred             HHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHcCC---eEEEEeCcHHHHHHH
Confidence            3344578899 8999999999998765      58999999999999999999999998766   899999999999999


Q ss_pred             HHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHHH
Q 028887          155 TKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKV  195 (202)
Q Consensus       155 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~  195 (202)
                      ++.+++++...        ++.+..++|+....++.+.++.
T Consensus       434 ~~~l~~~~~~~--------gi~v~~l~G~~~~~~r~~~~~~  466 (780)
T 1gm5_A          434 YRRTVESFSKF--------NIHVALLIGATTPSEKEKIKSG  466 (780)
T ss_dssp             HHHHHHHHTCS--------SCCEEECCSSSCHHHHHHHHHH
T ss_pred             HHHHHHHhhhc--------CceEEEEeCCCCHHHHHHHHHH
Confidence            99999998754        3555555555554444444443

>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=99.57  E-value=9.2e-15  Score=130.10  Aligned_cols=93  Identities=15%  Similarity=0.119  Sum_probs=72.7

Q ss_pred             CCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCC--ccEEEEecCCHHhHHHHHHHHHHhhcCCC
Q 028887           89 GYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS--AVQAVIVVPTRELGMQVTKVARVLAAKPL  166 (202)
Q Consensus        89 g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~--~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~  166 (202)
                      +...|+++|.++++.++.|+++++.++||+|||++|++|+++.+.....  +.++||++||++|+.|+.+++++++... 
T Consensus         4 ~~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~-   82 (556)
T 4a2p_A            4 ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQ-   82 (556)
T ss_dssp             ----CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGG-
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhccc-
Confidence            3457999999999999999999999999999999999999999876432  5589999999999999999999998754 


Q ss_pred             CcccccccceEEEEEeCCccHHH
Q 028887          167 DTDLEHKLCTVMALLDGGMLRRH  189 (202)
Q Consensus       167 ~~~~~~~~~~~~~~~~g~~~~~~  189 (202)
                             ++.+..++|+.....+
T Consensus        83 -------~~~~~~~~g~~~~~~~   98 (556)
T 4a2p_A           83 -------GYSVQGISGENFSNVS   98 (556)
T ss_dssp             -------TCCEEECCCC-----C
T ss_pred             -------CceEEEEeCCCCcchh
Confidence                   3555555555544433

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.56  E-value=1e-14  Score=140.86  Aligned_cols=87  Identities=21%  Similarity=0.163  Sum_probs=75.4

Q ss_pred             HCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCC
Q 028887           87 ETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPL  166 (202)
Q Consensus        87 ~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~  166 (202)
                      ..|| .|+++|.++++.++.|+|++++|+||||||++|+.+++..+..+   .++|||+||++|+.|+++++++++ .. 
T Consensus        74 ~~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~~~---~~~Lil~PtreLa~Q~~~~l~~l~-~~-  147 (1104)
T 4ddu_A           74 KFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKG---KKSALVFPTVTLVKQTLERLQKLA-DE-  147 (1104)
T ss_dssp             HSSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHTTT---CCEEEEESSHHHHHHHHHHHHTTS-CT-
T ss_pred             hcCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHhcC---CeEEEEechHHHHHHHHHHHHHhh-CC-
Confidence            4688 69999999999999999999999999999999999998887444   489999999999999999999977 33 


Q ss_pred             CcccccccceEEEEEeCCcc
Q 028887          167 DTDLEHKLCTVMALLDGGML  186 (202)
Q Consensus       167 ~~~~~~~~~~~~~~~~g~~~  186 (202)
                             ++.+..++||.+.
T Consensus       148 -------~i~v~~l~Gg~~~  160 (1104)
T 4ddu_A          148 -------KVKIFGFYSSMKK  160 (1104)
T ss_dssp             -------TSCEEEECTTCCT
T ss_pred             -------CCeEEEEeCCCCH
Confidence                   4666666766666

>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=99.55  E-value=1.3e-14  Score=135.16  Aligned_cols=89  Identities=21%  Similarity=0.134  Sum_probs=77.0

Q ss_pred             HCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCC
Q 028887           87 ETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPL  166 (202)
Q Consensus        87 ~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~  166 (202)
                      .+|| .||++|..++|.++.|+  ++.++||+|||++|.+|++.....+.   +++||+||++||.|+.+++..++... 
T Consensus        79 ~lG~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL~g~---~vlVltptreLA~qd~e~~~~l~~~l-  151 (844)
T 1tf5_A           79 VTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALTGK---GVHVVTVNEYLASRDAEQMGKIFEFL-  151 (844)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTTSS---CEEEEESSHHHHHHHHHHHHHHHHHT-
T ss_pred             HcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHHcCC---CEEEEeCCHHHHHHHHHHHHHHHhhc-
Confidence            4799 99999999999999999  99999999999999999985433333   89999999999999999999998876 


Q ss_pred             CcccccccceEEEEEeCCccHHH
Q 028887          167 DTDLEHKLCTVMALLDGGMLRRH  189 (202)
Q Consensus       167 ~~~~~~~~~~~~~~~~g~~~~~~  189 (202)
                             ++++.+++||.+...+
T Consensus       152 -------gl~v~~i~gg~~~~~r  167 (844)
T 1tf5_A          152 -------GLTVGLNLNSMSKDEK  167 (844)
T ss_dssp             -------TCCEEECCTTSCHHHH
T ss_pred             -------CCeEEEEeCCCCHHHH
Confidence                   5788888888765443

>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=99.55  E-value=2.3e-14  Score=137.95  Aligned_cols=100  Identities=19%  Similarity=0.172  Sum_probs=82.2

Q ss_pred             HHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCC
Q 028887           86 EETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKP  165 (202)
Q Consensus        86 ~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~  165 (202)
                      ..+||. | ++|.++|+.++.|+|++++|+||||||+ |.+|++..+..  .++++|||+||++|+.|+++++++++...
T Consensus        52 ~~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~--~~~~~lil~PtreLa~Q~~~~l~~l~~~~  126 (1054)
T 1gku_B           52 KCVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLAL--KGKRCYVIFPTSLLVIQAAETIRKYAEKA  126 (1054)
T ss_dssp             TTTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHT--TSCCEEEEESCHHHHHHHHHHHHHHHTTT
T ss_pred             HhcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhh--cCCeEEEEeccHHHHHHHHHHHHHHHhhc
Confidence            357998 9 9999999999999999999999999998 88888887754  34589999999999999999999999765


Q ss_pred             CCcccccccc----eEEEEEeCCccHHHHHHHHHhcC
Q 028887          166 LDTDLEHKLC----TVMALLDGGMLRRHKSWLKVLYS  198 (202)
Q Consensus       166 ~~~~~~~~~~----~~~~~~~g~~~~~~~~~l~~l~~  198 (202)
                              ++    .+..++||.....+.++++.+++
T Consensus       127 --------~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~  155 (1054)
T 1gku_B          127 --------GVGTENLIGYYHGRIPKREKENFMQNLRN  155 (1054)
T ss_dssp             --------CCSGGGSEEECCSSCCSHHHHHHHHSGGG
T ss_pred             --------CCCccceEEEEeCCCChhhHHHHHhhccC
Confidence                    34    55666666666666555555543

>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=99.54  E-value=2.5e-14  Score=133.99  Aligned_cols=95  Identities=15%  Similarity=0.103  Sum_probs=74.3

Q ss_pred             HCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCC--ccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           87 ETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS--AVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        87 ~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~--~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      -+|+..|+++|.++++.++.|++++++++||+|||++|++|+++.+.....  +.++|||+||++|+.|+.+++++++..
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            357889999999999999999999999999999999999999999876432  558999999999999999999999875


Q ss_pred             CCCcccccccceEEEEEeCCccHHH
Q 028887          165 PLDTDLEHKLCTVMALLDGGMLRRH  189 (202)
Q Consensus       165 ~~~~~~~~~~~~~~~~~~g~~~~~~  189 (202)
                      .        ++.+..++||.....+
T Consensus       323 ~--------~~~v~~~~g~~~~~~~  339 (797)
T 4a2q_A          323 Q--------GYSVQGISGENFSNVS  339 (797)
T ss_dssp             G--------TCCEEEECCC-----C
T ss_pred             C--------CceEEEEeCCcchhhh
Confidence            4        3566666666544443

>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=99.54  E-value=2.4e-15  Score=138.92  Aligned_cols=84  Identities=21%  Similarity=0.228  Sum_probs=74.6

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHH
Q 028887           77 VPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTK  156 (202)
Q Consensus        77 l~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~  156 (202)
                      +++.+.+.+.+.||..|+++|.++++.+..|+++++++|||||||++|.+++++.+..+.   +++|++|+++|+.|+.+
T Consensus        10 l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~---~~l~i~P~r~La~q~~~   86 (702)
T 2p6r_A           10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGG---KSLYVVPLRALAGEKYE   86 (702)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTTC---CEEEEESSHHHHHHHHH
T ss_pred             cCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHhCC---cEEEEeCcHHHHHHHHH
Confidence            889999999999999999999999999999999999999999999999999999887544   89999999999999999


Q ss_pred             HHHHhhc
Q 028887          157 VARVLAA  163 (202)
Q Consensus       157 ~~~~l~~  163 (202)
                      +++.+..
T Consensus        87 ~~~~~~~   93 (702)
T 2p6r_A           87 SFKKWEK   93 (702)
T ss_dssp             HHTTTTT
T ss_pred             HHHHHHh
Confidence            9965543

>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=99.48  E-value=3.1e-14  Score=137.53  Aligned_cols=86  Identities=16%  Similarity=0.138  Sum_probs=74.1

Q ss_pred             CCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHH
Q 028887           75 GHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQV  154 (202)
Q Consensus        75 ~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~  154 (202)
                      .++.+.+...+...++..|+++|.++|+.+..|++++++|+||||||++|++|++..+..+.   ++||++||++|+.|+
T Consensus       167 ~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~g~---rvlvl~PtraLa~Q~  243 (1108)
T 3l9o_A          167 TPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQ---RVIYTSPIKALSNQK  243 (1108)
T ss_dssp             STTTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHTTC---EEEEEESSHHHHHHH
T ss_pred             CCCChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhcCC---eEEEEcCcHHHHHHH
Confidence            34444444444445555799999999999999999999999999999999999999987666   999999999999999


Q ss_pred             HHHHHHhhc
Q 028887          155 TKVARVLAA  163 (202)
Q Consensus       155 ~~~~~~l~~  163 (202)
                      ++.+++++.
T Consensus       244 ~~~l~~~~~  252 (1108)
T 3l9o_A          244 YRELLAEFG  252 (1108)
T ss_dssp             HHHHHHHTS
T ss_pred             HHHHHHHhC
Confidence            999999876

>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=99.47  E-value=1.2e-13  Score=108.56  Aligned_cols=76  Identities=18%  Similarity=0.152  Sum_probs=65.8

Q ss_pred             CCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhc---CCccEEEEecCCHHhHHH-HHHHHHHhhcC
Q 028887           89 GYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ---RSAVQAVIVVPTRELGMQ-VTKVARVLAAK  164 (202)
Q Consensus        89 g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~---~~~~~~Lil~Ptr~La~Q-~~~~~~~l~~~  164 (202)
                      +...|+++|.++++.++.++++++.++||+|||++|+.++++.+...   ....++||++|+++|+.| +.+.++.+...
T Consensus        30 ~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~~~~~~~~~~  109 (216)
T 3b6e_A           30 PELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKK  109 (216)
T ss_dssp             CCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTHHHHHTT
T ss_pred             CCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHHHHHHHHhcc
Confidence            34479999999999999999999999999999999999998877542   224589999999999999 77889888765

>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=99.46  E-value=9.1e-14  Score=129.44  Aligned_cols=86  Identities=26%  Similarity=0.092  Sum_probs=74.9

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCC
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLD  167 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~  167 (202)
                      +|. .|+++|..+++.++.|+  ++.++||+|||++|++|++.....+.   +++||+||++||.|+.+++..++...  
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--IAEMRTGEGKTLTATLPAYLNALTGK---GVHVVTVNDYLAQRDAENNRPLFEFL--  142 (853)
T ss_dssp             HSC-CCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHTTSS---CCEEEESSHHHHHHHHHHHHHHHHHT--
T ss_pred             cCC-CCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHHcCC---cEEEEcCCHHHHHHHHHHHHHHHHhc--
Confidence            465 89999999999999998  89999999999999999986554443   89999999999999999999999876  


Q ss_pred             cccccccceEEEEEeCCccH
Q 028887          168 TDLEHKLCTVMALLDGGMLR  187 (202)
Q Consensus       168 ~~~~~~~~~~~~~~~g~~~~  187 (202)
                            ++++.+++||.+..
T Consensus       143 ------gl~v~~i~GG~~~~  156 (853)
T 2fsf_A          143 ------GLTVGINLPGMPAP  156 (853)
T ss_dssp             ------TCCEEECCTTCCHH
T ss_pred             ------CCeEEEEeCCCCHH
Confidence                  57888888886643

>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=99.45  E-value=1.5e-13  Score=130.99  Aligned_cols=94  Identities=15%  Similarity=0.111  Sum_probs=73.9

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCC--ccEEEEecCCHHhHHHHHHHHHHhhcCC
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS--AVQAVIVVPTRELGMQVTKVARVLAAKP  165 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~--~~~~Lil~Ptr~La~Q~~~~~~~l~~~~  165 (202)
                      .|+..|+++|.++++.++.|+++++.++||+|||++|++|+++.+.....  +.++|||+||++|+.|+++++++++...
T Consensus       244 ~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~  323 (936)
T 4a2w_A          244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQ  323 (936)
T ss_dssp             ----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTT
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHHhccc
Confidence            36778999999999999999999999999999999999999988765321  4589999999999999999999998764


Q ss_pred             CCcccccccceEEEEEeCCccHHH
Q 028887          166 LDTDLEHKLCTVMALLDGGMLRRH  189 (202)
Q Consensus       166 ~~~~~~~~~~~~~~~~~g~~~~~~  189 (202)
                              ++.+..++||.....+
T Consensus       324 --------~~~v~~~~G~~~~~~~  339 (936)
T 4a2w_A          324 --------GYSVQGISGENFSNVS  339 (936)
T ss_dssp             --------TCCEEEECCC-----C
T ss_pred             --------CceEEEEECCcchhhH
Confidence                    3566666666544443

>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=99.41  E-value=5.2e-13  Score=124.84  Aligned_cols=87  Identities=21%  Similarity=0.099  Sum_probs=75.3

Q ss_pred             HCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCC
Q 028887           87 ETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPL  166 (202)
Q Consensus        87 ~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~  166 (202)
                      .+|+ .|+++|..++|.++.|+  ++.++||+|||++|.+|++.....+.   +++||+||++||.|+.+++..++... 
T Consensus       107 ~lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~g~---~v~VvTpTreLA~Qdae~m~~l~~~l-  179 (922)
T 1nkt_A          107 VLDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALAGN---GVHIVTVNDYLAKRDSEWMGRVHRFL-  179 (922)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTTTS---CEEEEESSHHHHHHHHHHHHHHHHHT-
T ss_pred             HcCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHhCC---CeEEEeCCHHHHHHHHHHHHHHHhhc-
Confidence            3688 89999999999999998  99999999999999999975444444   79999999999999999999998876 


Q ss_pred             CcccccccceEEEEEeCCccH
Q 028887          167 DTDLEHKLCTVMALLDGGMLR  187 (202)
Q Consensus       167 ~~~~~~~~~~~~~~~~g~~~~  187 (202)
                             ++++.+++||.+..
T Consensus       180 -------GLsv~~i~gg~~~~  193 (922)
T 1nkt_A          180 -------GLQVGVILATMTPD  193 (922)
T ss_dssp             -------TCCEEECCTTCCHH
T ss_pred             -------CCeEEEEeCCCCHH
Confidence                   57877778776643

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.41  E-value=5.6e-13  Score=124.64  Aligned_cols=85  Identities=19%  Similarity=0.094  Sum_probs=74.8

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCC
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLD  167 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~  167 (202)
                      +|+ .|+++|..++|.++.|+  ++++.||+|||++|.+|++.....+.   +++|++||++||.|..+++..++...  
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--IAEMKTGEGKTLVATLAVALNALTGK---GVHVVTVNDYLARRDAEWMGPVYRGL--  147 (997)
T ss_dssp             TCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTTCS---CCEEEESSHHHHHHHHHHHHHHHHTT--
T ss_pred             hCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHhCC---CEEEEeCCHHHHHHHHHHHHHHHHhc--
Confidence            699 89999999999999998  89999999999999999965444444   79999999999999999999999877  


Q ss_pred             cccccccceEEEEEeCCcc
Q 028887          168 TDLEHKLCTVMALLDGGML  186 (202)
Q Consensus       168 ~~~~~~~~~~~~~~~g~~~  186 (202)
                            ++++..++||.+.
T Consensus       148 ------GLsv~~i~Gg~~~  160 (997)
T 2ipc_A          148 ------GLSVGVIQHASTP  160 (997)
T ss_dssp             ------TCCEEECCTTCCH
T ss_pred             ------CCeEEEEeCCCCH
Confidence                  5787777777663

>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=99.40  E-value=6.5e-13  Score=132.82  Aligned_cols=77  Identities=19%  Similarity=0.259  Sum_probs=68.5

Q ss_pred             CCCCCcHHHHHHHHhHHc-CCcEEEeccCCCchHHHHHHHHHHHHHhc--------CCccEEEEecCCHHhHHHHHHHHH
Q 028887           89 GYVLPTDIQREALPVLFS-SRDCILHAQTGSGKTLTYLLLIFSLVNAQ--------RSAVQAVIVVPTRELGMQVTKVAR  159 (202)
Q Consensus        89 g~~~~t~~Q~~~i~~i~~-g~~~l~~a~TGsGKT~~~l~~~l~~l~~~--------~~~~~~Lil~Ptr~La~Q~~~~~~  159 (202)
                      ||++++++|.+++|.++. +++++++||||||||+++.+++++.+.+.        ..+.++||++|+|+|+.|+++.++
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            799999999999999875 78999999999999999999999998652        235689999999999999999998


Q ss_pred             HhhcCC
Q 028887          160 VLAAKP  165 (202)
Q Consensus       160 ~l~~~~  165 (202)
                      +.+...
T Consensus       156 ~~~~~~  161 (1724)
T 4f92_B          156 KRLATY  161 (1724)
T ss_dssp             HHHTTT
T ss_pred             HHHhhC
Confidence            877654

>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=99.40  E-value=6.7e-13  Score=132.73  Aligned_cols=87  Identities=18%  Similarity=0.237  Sum_probs=74.5

Q ss_pred             CCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcC-CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHH
Q 028887           76 HVPEHVLRRMEETGYVLPTDIQREALPVLFSS-RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQV  154 (202)
Q Consensus        76 gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g-~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~  154 (202)
                      .+.+...+.+...+|..++|+|.++++.++++ ++++++||||||||++|.+|+++.+.... +.+++|++|+|+|+.|+
T Consensus       910 ~L~~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~~-~~kavyi~P~raLa~q~  988 (1724)
T 4f92_B          910 ALRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSS-EGRCVYITPMEALAEQV  988 (1724)
T ss_dssp             GSCCHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHCT-TCCEEEECSCHHHHHHH
T ss_pred             cccCHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhCC-CCEEEEEcChHHHHHHH
Confidence            34556677787889999999999999999764 67999999999999999999999987643 33799999999999999


Q ss_pred             HHHHHHhhc
Q 028887          155 TKVARVLAA  163 (202)
Q Consensus       155 ~~~~~~l~~  163 (202)
                      ++.+++.+.
T Consensus       989 ~~~~~~~f~  997 (1724)
T 4f92_B          989 YMDWYEKFQ  997 (1724)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHhc
Confidence            999876554

>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=1.1e-12  Score=125.78  Aligned_cols=73  Identities=15%  Similarity=0.179  Sum_probs=67.5

Q ss_pred             HCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887           87 ETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus        87 ~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      ..+|. |+++|.++++.+..|+++++++|||+|||++|.++++..+..+.   ++||++|+++|+.|+++.++++++
T Consensus        82 ~~~f~-L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~~g~---rvL~l~PtkaLa~Q~~~~l~~~~~  154 (1010)
T 2xgj_A           82 TYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQ---RVIYTSPIKALSNQKYRELLAEFG  154 (1010)
T ss_dssp             CCSSC-CCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHTTC---EEEEEESSHHHHHHHHHHHHHHHS
T ss_pred             hCCCC-CCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhccCC---eEEEECChHHHHHHHHHHHHHHhC
Confidence            45774 99999999999999999999999999999999999999887655   999999999999999999999876

>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=99.38  E-value=4.9e-13  Score=122.84  Aligned_cols=87  Identities=18%  Similarity=0.180  Sum_probs=70.6

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC---CccEEEEecCCHHhHHHH-HHHHHHhhcCCCC
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR---SAVQAVIVVPTRELGMQV-TKVARVLAAKPLD  167 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~---~~~~~Lil~Ptr~La~Q~-~~~~~~l~~~~~~  167 (202)
                      .|+++|.++++.++.|+++++.++||+|||++|++|+++.+..+.   .+.++||++|+++|+.|+ .++++++++..  
T Consensus         7 ~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~~--   84 (699)
T 4gl2_A            7 QLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKW--   84 (699)
T ss_dssp             CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHHTHHHHHTTT--
T ss_pred             CccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHHHHHHHcCcC--
Confidence            699999999999999999999999999999999999999876542   124799999999999999 99999998752  


Q ss_pred             cccccccceEEEEEeCCccH
Q 028887          168 TDLEHKLCTVMALLDGGMLR  187 (202)
Q Consensus       168 ~~~~~~~~~~~~~~~g~~~~  187 (202)
                             +.+..+.|+....
T Consensus        85 -------~~v~~~~g~~~~~   97 (699)
T 4gl2_A           85 -------YRVIGLSGDTQLK   97 (699)
T ss_dssp             -------SCEEEEC----CC
T ss_pred             -------ceEEEEeCCcchh
Confidence                   4455555554443

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.37  E-value=1.4e-12  Score=115.73  Aligned_cols=71  Identities=24%  Similarity=0.205  Sum_probs=64.6

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .|++.|.++++.++.+++++++++||+|||++|+.++...+..++  .++|||+|+++|+.|+.+.+++++..
T Consensus       113 ~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~--~~vlvl~P~~~L~~Q~~~~~~~~~~~  183 (510)
T 2oca_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYE--GKILIIVPTTALTTQMADDFVDYRLF  183 (510)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHCS--SEEEEEESSHHHHHHHHHHHHHTTSS
T ss_pred             CCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCCC--CeEEEEECcHHHHHHHHHHHHHhhcC
Confidence            799999999999999999999999999999999999988886433  38999999999999999999988654

>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=99.36  E-value=2.1e-12  Score=106.57  Aligned_cols=71  Identities=24%  Similarity=0.205  Sum_probs=63.2

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .|+++|.++++.++.+.+.+++++||+|||++++.++...+..+.  .++||++|+++|+.|+.+++++++..
T Consensus       113 ~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~--~~~lil~Pt~~L~~q~~~~l~~~~~~  183 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYE--GKILIIVPTTALTTQMADDFVDYRLF  183 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHCS--SEEEEECSSHHHHHHHHHHHHHHTSC
T ss_pred             CccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHcCC--CeEEEEECCHHHHHHHHHHHHHhccc
Confidence            799999999999988888999999999999999998887776432  37999999999999999999998754

>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=99.35  E-value=8.3e-12  Score=121.11  Aligned_cols=86  Identities=22%  Similarity=0.206  Sum_probs=72.4

Q ss_pred             CCCHHHHHHH-HHCCCCCCcHHHHHHHHhHHc----CC--cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCH
Q 028887           76 HVPEHVLRRM-EETGYVLPTDIQREALPVLFS----SR--DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTR  148 (202)
Q Consensus        76 gl~~~l~~~l-~~~g~~~~t~~Q~~~i~~i~~----g~--~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr  148 (202)
                      +.++...+.+ ..+||+ +|++|.++++.++.    |+  |++++++||+|||++|+.+++..+..+.   +++|++||+
T Consensus       587 ~~~~~~~~~~~~~f~~~-~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~g~---~vlvlvPt~  662 (1151)
T 2eyq_A          587 KHDREQYQLFCDSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHK---QVAVLVPTT  662 (1151)
T ss_dssp             CCCHHHHHHHHHTCCSC-CCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTTC---EEEEECSSH
T ss_pred             CCCHHHHHHHHHhCCCC-CCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHhCC---eEEEEechH
Confidence            3455555555 456885 79999999999876    65  9999999999999999999988876655   999999999


Q ss_pred             HhHHHHHHHHHHhhcCC
Q 028887          149 ELGMQVTKVARVLAAKP  165 (202)
Q Consensus       149 ~La~Q~~~~~~~l~~~~  165 (202)
                      +|+.|+++.+++.+...
T Consensus       663 ~La~Q~~~~~~~~~~~~  679 (1151)
T 2eyq_A          663 LLAQQHYDNFRDRFANW  679 (1151)
T ss_dssp             HHHHHHHHHHHHHSTTT
T ss_pred             HHHHHHHHHHHHHhhcC
Confidence            99999999999887654

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.34  E-value=3.4e-12  Score=122.26  Aligned_cols=73  Identities=18%  Similarity=0.126  Sum_probs=65.8

Q ss_pred             HCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887           87 ETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus        87 ~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      ..+| .|+++|.++|+.++.|+++++.+|||+|||++|++++...+..+.   ++||++|+++|+.|+++++++++.
T Consensus        35 ~~~f-~l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~~g~---~vlvl~PtraLa~Q~~~~l~~~~~  107 (997)
T 4a4z_A           35 SWPF-ELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRNMT---KTIYTSPIKALSNQKFRDFKETFD  107 (997)
T ss_dssp             CCSS-CCCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHHTTC---EEEEEESCGGGHHHHHHHHHTTC-
T ss_pred             hCCC-CCCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHhcCC---eEEEEeCCHHHHHHHHHHHHHHcC
Confidence            3566 489999999999999999999999999999999999988876655   899999999999999999998764

>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=99.29  E-value=1.6e-11  Score=106.20  Aligned_cols=86  Identities=21%  Similarity=0.254  Sum_probs=70.5

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCCcccc
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLE  171 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~  171 (202)
                      .|+++|.++++.++.+ ++++.++||+|||++++.+++..+..  .+.++||++|+++|+.|+.++++++++..      
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~~--~~~~~liv~P~~~L~~q~~~~~~~~~~~~------   79 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLTK--YGGKVLMLAPTKPLVLQHAESFRRLFNLP------   79 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHHH--SCSCEEEECSSHHHHHHHHHHHHHHBCSC------
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHhc--CCCeEEEEECCHHHHHHHHHHHHHHhCcc------
Confidence            6899999999999999 99999999999999999999888762  23479999999999999999999997542      


Q ss_pred             cccceEEEEEeCCccHHH
Q 028887          172 HKLCTVMALLDGGMLRRH  189 (202)
Q Consensus       172 ~~~~~~~~~~~g~~~~~~  189 (202)
                        ... +.+++|.....+
T Consensus        80 --~~~-v~~~~g~~~~~~   94 (494)
T 1wp9_A           80 --PEK-IVALTGEKSPEE   94 (494)
T ss_dssp             --GGG-EEEECSCSCHHH
T ss_pred             --hhh-eEEeeCCcchhh
Confidence              123 455566554443

>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=99.27  E-value=1.3e-11  Score=108.42  Aligned_cols=64  Identities=30%  Similarity=0.303  Sum_probs=58.9

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      .|++.|.++++.++.+++++++++||+|||++|+.++...   +.   ++||++|+++|+.|+.++++++
T Consensus        93 ~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~---~~---~~Lvl~P~~~L~~Q~~~~~~~~  156 (472)
T 2fwr_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL---ST---PTLIVVPTLALAEQWKERLGIF  156 (472)
T ss_dssp             CBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH---CS---CEEEEESSHHHHHHHHHHGGGG
T ss_pred             CcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc---CC---CEEEEECCHHHHHHHHHHHHhC
Confidence            6999999999999999999999999999999999998764   33   7999999999999999999884

>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=99.26  E-value=9.9e-13  Score=115.80  Aligned_cols=70  Identities=21%  Similarity=0.279  Sum_probs=60.8

Q ss_pred             CCCCCcHHHHHHHHhHHcCCcE-EEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887           89 GYVLPTDIQREALPVLFSSRDC-ILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus        89 g~~~~t~~Q~~~i~~i~~g~~~-l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      |+..|+++|+ +||.++.|+++ +++++||||||++|++|++..+..  .+.++||++|||+|+.|+.+.++.+
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~--~~~~~lvl~Ptr~La~Q~~~~l~g~   71 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALL--RRLRTLILAPTRVVAAEMEEALRGL   71 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTTTS
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHh--cCCcEEEECCCHHHHHHHHHHhcCc
Confidence            7888999986 79999999887 999999999999999999887654  2358999999999999999988643

>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=99.23  E-value=3.4e-11  Score=96.93  Aligned_cols=87  Identities=16%  Similarity=0.193  Sum_probs=69.1

Q ss_pred             CHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCC--ccEEEEecCCHHhHHHHH
Q 028887           78 PEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS--AVQAVIVVPTRELGMQVT  155 (202)
Q Consensus        78 ~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~--~~~~Lil~Ptr~La~Q~~  155 (202)
                      .+.+.+.....+.-.++++|.++++.+..|+++++.|+||||||.++.+++++.....+.  .++++++.|+++|+.|+.
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            334333333333335799999999999999999999999999999999999887665443  568999999999999999


Q ss_pred             HHHHHhhcC
Q 028887          156 KVARVLAAK  164 (202)
Q Consensus       156 ~~~~~l~~~  164 (202)
                      +.+......
T Consensus       127 ~~~~~~~~~  135 (235)
T 3llm_A          127 ERVAFERGE  135 (235)
T ss_dssp             HHHHHTTTC
T ss_pred             HHHHHHhcc
Confidence            888766543

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.22  E-value=5.3e-13  Score=123.07  Aligned_cols=75  Identities=21%  Similarity=0.353  Sum_probs=62.5

Q ss_pred             HHHCCCC-----CCcHHHH-----HHHHhHH------cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCH
Q 028887           85 MEETGYV-----LPTDIQR-----EALPVLF------SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTR  148 (202)
Q Consensus        85 l~~~g~~-----~~t~~Q~-----~~i~~i~------~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr  148 (202)
                      +..+||.     .||++|+     ++||.++      .|+|++++++||||||++|++|+++.+..  .+.++|||+||+
T Consensus       203 l~~~Gf~~~~~~~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~--~~~~~lilaPTr  280 (673)
T 2wv9_A          203 LYGNGVILGNGAYVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQ--KRLRTAVLAPTR  280 (673)
T ss_dssp             EEEEEEECSSSCEEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHH--TTCCEEEEESSH
T ss_pred             eeeccccccCCCccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHh--CCCcEEEEccHH
Confidence            3455666     8999999     9999988      89999999999999999999999988654  235899999999


Q ss_pred             HhHHHHHHHHHHh
Q 028887          149 ELGMQVTKVARVL  161 (202)
Q Consensus       149 ~La~Q~~~~~~~l  161 (202)
                      +||.|+++.++.+
T Consensus       281 ~La~Q~~~~l~~~  293 (673)
T 2wv9_A          281 VVAAEMAEALRGL  293 (673)
T ss_dssp             HHHHHHHHHTTTS
T ss_pred             HHHHHHHHHHhcC
Confidence            9999999988755

>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=99.20  E-value=2.2e-12  Score=117.90  Aligned_cols=80  Identities=16%  Similarity=0.190  Sum_probs=64.1

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHH
Q 028887           77 VPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTK  156 (202)
Q Consensus        77 l~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~  156 (202)
                      +.+.+++.+... ...++|+|+.+++.+++|+|+++.++||||||++|++|+++.+..  .+.++|||+|||+|+.|+.+
T Consensus       157 ~~~~~~~~l~~~-~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~--~~~~vLvl~PtreLa~Qi~~  233 (618)
T 2whx_A          157 KSGDYVSAITQA-ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALK--RRLRTLILAPTRVVAAEMEE  233 (618)
T ss_dssp             -----CEECBCC-CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHH
T ss_pred             chHHHHHHHhhc-cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHh--CCCeEEEEcChHHHHHHHHH
Confidence            444444444332 478899988889999999999999999999999999999988765  34589999999999999998


Q ss_pred             HHH
Q 028887          157 VAR  159 (202)
Q Consensus       157 ~~~  159 (202)
                      .++
T Consensus       234 ~l~  236 (618)
T 2whx_A          234 ALR  236 (618)
T ss_dssp             HTT
T ss_pred             Hhc
Confidence            886

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.19  E-value=2.2e-11  Score=109.73  Aligned_cols=70  Identities=26%  Similarity=0.174  Sum_probs=60.3

Q ss_pred             CCCCCcHHHHHHHHh----HHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           89 GYVLPTDIQREALPV----LFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        89 g~~~~t~~Q~~~i~~----i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      || .+++.|.+.+..    +..|+++++.+|||+|||++|++|++.   .+   .+++|++||++|+.|+.+.++.+...
T Consensus         1 ~~-~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~---~~---~~v~i~~pt~~l~~q~~~~~~~l~~~   73 (551)
T 3crv_A            1 MV-KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLE---VK---PKVLFVVRTHNEFYPIYRDLTKIREK   73 (551)
T ss_dssp             CC-SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHH---HC---SEEEEEESSGGGHHHHHHHHTTCCCS
T ss_pred             CC-CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHh---CC---CeEEEEcCCHHHHHHHHHHHHHHhhh
Confidence            45 689999997765    457999999999999999999999987   23   38999999999999999999888655


Q ss_pred             C
Q 028887          165 P  165 (202)
Q Consensus       165 ~  165 (202)
                      .
T Consensus        74 ~   74 (551)
T 3crv_A           74 R   74 (551)
T ss_dssp             S
T ss_pred             c
Confidence            3

>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=99.17  E-value=1.3e-10  Score=93.98  Aligned_cols=64  Identities=30%  Similarity=0.304  Sum_probs=57.5

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      .|+++|.+++..++.+++++++++||+|||.+++.++...   +   .+++|++|+++|+.|+.+.++++
T Consensus        93 ~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~---~---~~~liv~P~~~L~~q~~~~~~~~  156 (237)
T 2fz4_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL---S---TPTLIVVPTLALAEQWKERLGIF  156 (237)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS---C---SCEEEEESSHHHHHHHHHHHGGG
T ss_pred             CcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc---C---CCEEEEeCCHHHHHHHHHHHHhC
Confidence            7899999999999999999999999999999998887653   2   37999999999999999999874

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.15  E-value=3.9e-11  Score=109.70  Aligned_cols=84  Identities=24%  Similarity=0.210  Sum_probs=67.3

Q ss_pred             CCcHHHHHHHHh----HHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCC
Q 028887           92 LPTDIQREALPV----LFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLD  167 (202)
Q Consensus        92 ~~t~~Q~~~i~~----i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~  167 (202)
                      .|++.|.+.+..    +.+|+++++.+|||+|||++|++|++..+...  +.+++|++||++|+.|+.+.++.+....  
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            578999888864    56899999999999999999999999987642  2489999999999999999999887643  


Q ss_pred             cccccccceEEEEEeCCc
Q 028887          168 TDLEHKLCTVMALLDGGM  185 (202)
Q Consensus       168 ~~~~~~~~~~~~~~~g~~  185 (202)
                            .++++.+.|+.+
T Consensus        79 ------~~~~~~l~gr~~   90 (620)
T 4a15_A           79 ------KIRAIPMQGRVN   90 (620)
T ss_dssp             ------CCCEEECCCHHH
T ss_pred             ------CeEEEEEECCCc
Confidence                  355555555543

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.02  E-value=5.1e-10  Score=100.68  Aligned_cols=67  Identities=25%  Similarity=0.253  Sum_probs=54.3

Q ss_pred             CCCCCCcHHHHHHHHh----HHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887           88 TGYVLPTDIQREALPV----LFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~----i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      .|| .|+++|.+++..    +..|+++++.+|||+|||++|++|++..   +.   +++|++||++|+.|+.+.++.+
T Consensus         4 ~~~-~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~---~~---~~~~~~~t~~l~~q~~~~~~~l   74 (540)
T 2vl7_A            4 LKL-QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQL---KK---KVLIFTRTHSQLDSIYKNAKLL   74 (540)
T ss_dssp             ------CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH---TC---EEEEEESCHHHHHHHHHHHGGG
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC---CC---cEEEEcCCHHHHHHHHHHHHhc
Confidence            467 799999998754    4688999999999999999999998652   33   8999999999999999888775

>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=99.02  E-value=1.1e-10  Score=102.93  Aligned_cols=57  Identities=23%  Similarity=0.306  Sum_probs=49.2

Q ss_pred             HhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHH
Q 028887          102 PVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARV  160 (202)
Q Consensus       102 ~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~  160 (202)
                      ..+..|++++++++||||||++|++|+++.+..  .+.++||++|||+|+.|+.++++.
T Consensus        16 ~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~--~~~~~lvl~Ptr~La~Q~~~~l~g   72 (459)
T 2z83_A           16 NMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQ--QRLRTAVLAPTRVVAAEMAEALRG   72 (459)
T ss_dssp             GGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHH--TTCCEEEEECSHHHHHHHHHHTTT
T ss_pred             HHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHh--CCCcEEEECchHHHHHHHHHHhcC
Confidence            345678999999999999999999999988764  235899999999999999998873

>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=99.00  E-value=1.5e-10  Score=101.61  Aligned_cols=57  Identities=21%  Similarity=0.338  Sum_probs=50.1

Q ss_pred             hHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887          103 VLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus       103 ~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      .+++|+|++++|+||||||++|++|+++.+..+  +.+++|++||++|+.|+++.++.+
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~--~~~~lil~Ptr~La~Q~~~~l~~~   60 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECARR--RLRTLVLAPTRVVLSEMKEAFHGL   60 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTTTS
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhc--CCeEEEEcchHHHHHHHHHHHhcC
Confidence            357899999999999999999999999977653  358999999999999999988754

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=98.89  E-value=9.7e-10  Score=96.18  Aligned_cols=52  Identities=23%  Similarity=0.332  Sum_probs=44.3

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVAR  159 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~  159 (202)
                      .|++++++++||||||++|++|+++.+...  +.+++|++||++|+.|+++.++
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~~--g~~~lvl~Pt~~La~Q~~~~~~   52 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVKK--RLRTVILAPTRVVASEMYEALR   52 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTT
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHhC--CCCEEEECcHHHHHHHHHHHhC
Confidence            378999999999999999999999655432  2489999999999999998875

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=98.89  E-value=2e-09  Score=100.67  Aligned_cols=91  Identities=20%  Similarity=0.270  Sum_probs=71.2

Q ss_pred             HHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHc-CCcEEEeccCCCchHHHHHHHHHHHHH--hcCCccEEEEec
Q 028887           69 LRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFS-SRDCILHAQTGSGKTLTYLLLIFSLVN--AQRSAVQAVIVV  145 (202)
Q Consensus        69 ~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~-g~~~l~~a~TGsGKT~~~l~~~l~~l~--~~~~~~~~Lil~  145 (202)
                      ...|.+.++++.+.+.+...| ..|+++|+++|+.++. |+++++.|+||+|||+  ++|++-...  ....+.++++++
T Consensus        71 ~~~f~~~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTt--llp~ll~~~~~~~~~g~~ilvl~  147 (773)
T 2xau_A           71 INPFTGREFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTT--QIPQFVLFDEMPHLENTQVACTQ  147 (773)
T ss_dssp             BCTTTCSBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHH--HHHHHHHHHHCGGGGTCEEEEEE
T ss_pred             CCCccccCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHH--HHHHHHHHhccccCCCceEEecC
Confidence            445677799999999998888 6899999999988765 5789999999999999  455542221  111245799999


Q ss_pred             CCHHhHHHHHHHHHHhh
Q 028887          146 PTRELGMQVTKVARVLA  162 (202)
Q Consensus       146 Ptr~La~Q~~~~~~~l~  162 (202)
                      |+++|+.|+.+++....
T Consensus       148 P~r~La~q~~~~l~~~~  164 (773)
T 2xau_A          148 PRRVAAMSVAQRVAEEM  164 (773)
T ss_dssp             SCHHHHHHHHHHHHHHT
T ss_pred             chHHHHHHHHHHHHHHh
Confidence            99999999998876554

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=98.86  E-value=1.3e-09  Score=98.59  Aligned_cols=72  Identities=17%  Similarity=0.199  Sum_probs=47.4

Q ss_pred             CCcHHHHHHHHhHHc----C-CcEEEeccCCCchHHHHHHHHHHHHHhc------CCccEEEEecCCHHhHHHHH-HHHH
Q 028887           92 LPTDIQREALPVLFS----S-RDCILHAQTGSGKTLTYLLLIFSLVNAQ------RSAVQAVIVVPTRELGMQVT-KVAR  159 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~----g-~~~l~~a~TGsGKT~~~l~~~l~~l~~~------~~~~~~Lil~Ptr~La~Q~~-~~~~  159 (202)
                      .|+++|.++++.++.    | ++++++++||+|||++++..+...+..+      ....++|||+|+++|+.|+. +.++
T Consensus       178 ~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~~~  257 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKTFT  257 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHHHHTTCCSSCSSSCCCEEEEEC-----------CCT
T ss_pred             CchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHHHHHHHHhcccccccccCCCeEEEEeCCHHHHHHHHHHHHH
Confidence            699999999998865    4 6689999999999999766554444432      14568999999999999999 7777


Q ss_pred             Hhhc
Q 028887          160 VLAA  163 (202)
Q Consensus       160 ~l~~  163 (202)
                      .++.
T Consensus       258 ~~~~  261 (590)
T 3h1t_A          258 PFGD  261 (590)
T ss_dssp             TTCS
T ss_pred             hcch
Confidence            6653

>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=98.83  E-value=4.5e-09  Score=100.95  Aligned_cols=72  Identities=22%  Similarity=0.188  Sum_probs=59.8

Q ss_pred             CCcHHHHHHHHhHHc--------------CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHH
Q 028887           92 LPTDIQREALPVLFS--------------SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKV  157 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~--------------g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~  157 (202)
                      .|+++|..|++.++.              ++++++.++||||||+++ ++++..+.......++|||+|+++|+.|+.+.
T Consensus       271 ~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~~~~~~rvLvlvpr~eL~~Q~~~~  349 (1038)
T 2w00_A          271 VMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATELDFIDKVFFVVDRKDLDYQTMKE  349 (1038)
T ss_dssp             ECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTTCTTCCEEEEEECGGGCCHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHhcCCCceEEEEeCcHHHHHHHHHH
Confidence            599999999998765              368999999999999997 56666554433345899999999999999999


Q ss_pred             HHHhhcC
Q 028887          158 ARVLAAK  164 (202)
Q Consensus       158 ~~~l~~~  164 (202)
                      ++.++..
T Consensus       350 f~~f~~~  356 (1038)
T 2w00_A          350 YQRFSPD  356 (1038)
T ss_dssp             HHTTSTT
T ss_pred             HHHhccc
Confidence            9988753

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=98.83  E-value=7.2e-10  Score=101.80  Aligned_cols=66  Identities=17%  Similarity=0.071  Sum_probs=53.4

Q ss_pred             CcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           93 PTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        93 ~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      +...|+++++.+.++++++++|+||||||.+|.+++++   .+   .++||++|||+||.|+.+++.+..+.
T Consensus       218 ~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~---~g---~~vLVl~PTReLA~Qia~~l~~~~g~  283 (666)
T 3o8b_A          218 VFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAA---QG---YKVLVLNPSVAATLGFGAYMSKAHGI  283 (666)
T ss_dssp             SCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHH---TT---CCEEEEESCHHHHHHHHHHHHHHHSC
T ss_pred             cHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHH---CC---CeEEEEcchHHHHHHHHHHHHHHhCC
Confidence            34455555555668899999999999999999999876   23   38999999999999999988776653

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=98.67  E-value=3e-08  Score=91.41  Aligned_cols=51  Identities=16%  Similarity=0.160  Sum_probs=42.1

Q ss_pred             HcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          105 FSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       105 ~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      +.|++++++||||||||+    ++++.+...+   +++|++|||+||.|+++++++++
T Consensus       153 l~rk~vlv~apTGSGKT~----~al~~l~~~~---~gl~l~PtR~LA~Qi~~~l~~~g  203 (677)
T 3rc3_A          153 MQRKIIFHSGPTNSGKTY----HAIQKYFSAK---SGVYCGPLKLLAHEIFEKSNAAG  203 (677)
T ss_dssp             SCCEEEEEECCTTSSHHH----HHHHHHHHSS---SEEEEESSHHHHHHHHHHHHHTT
T ss_pred             cCCCEEEEEcCCCCCHHH----HHHHHHHhcC---CeEEEeCHHHHHHHHHHHHHhcC
Confidence            578899999999999998    4444554444   46999999999999999998863

>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=98.63  E-value=1.2e-07  Score=83.61  Aligned_cols=71  Identities=13%  Similarity=0.091  Sum_probs=57.0

Q ss_pred             CCcHHHHHHHHhH----HcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVL----FSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i----~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .|+|+|.++++.+    ..+.++++..+||+|||+..+..+...... ....++||+|| .+|+.||.++++++++.
T Consensus        37 ~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i~~~~~~-~~~~~~LIv~P-~~l~~qw~~e~~~~~~~  111 (500)
T 1z63_A           37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKE-NELTPSLVICP-LSVLKNWEEELSKFAPH  111 (500)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHHHT-TCCSSEEEEEC-STTHHHHHHHHHHHCTT
T ss_pred             cchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHHHHHHhc-CCCCCEEEEcc-HHHHHHHHHHHHHHCCC
Confidence            6899999999876    457899999999999999976655444433 33347999999 57999999999998754

>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=98.52  E-value=1.7e-07  Score=89.54  Aligned_cols=70  Identities=16%  Similarity=0.083  Sum_probs=59.3

Q ss_pred             CCcHHHHHHHHhHHc--CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887           92 LPTDIQREALPVLFS--SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~--g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      .|+|+|.+++..++.  +..+++..+||+|||.+++..+...+..+.. .++|||||+ +|+.||.+.+.+.++
T Consensus       153 ~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g~~-~rvLIVvP~-sLl~Qw~~E~~~~f~  224 (968)
T 3dmq_A          153 SLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGAA-ERVLIIVPE-TLQHQWLVEMLRRFN  224 (968)
T ss_dssp             CCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTSSC-CCEEEECCT-TTHHHHHHHHHHHSC
T ss_pred             CCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhCCC-CeEEEEeCH-HHHHHHHHHHHHHhC
Confidence            689999999998776  4579999999999999998888777765443 369999999 999999999977664

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=98.31  E-value=2.2e-06  Score=80.35  Aligned_cols=72  Identities=24%  Similarity=0.199  Sum_probs=59.5

Q ss_pred             CCcHHHHHHHHhHH----cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLF----SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~----~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .+.+.|.+++..+.    .+.++++..++|.|||+..+..+...+........+||+|| .+|+.||.+.+.++++.
T Consensus       236 ~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P-~sll~qW~~E~~~~~p~  311 (800)
T 3mwy_W          236 ELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVP-LSTMPAWLDTFEKWAPD  311 (800)
T ss_dssp             CCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECC-TTTHHHHHHHHHHHSTT
T ss_pred             CcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEEC-chHHHHHHHHHHHHCCC
Confidence            57899999998765    78899999999999999987777665544443346899999 88999999999999854

>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19

Probab=98.25  E-value=4.8e-06  Score=76.25  Aligned_cols=72  Identities=25%  Similarity=0.381  Sum_probs=58.4

Q ss_pred             CCcHHHHHHHHhHH---------cCCcEEEeccCCCchHHHHHHHHHHHHHhcC----CccEEEEecCCHHhHHHHHHHH
Q 028887           92 LPTDIQREALPVLF---------SSRDCILHAQTGSGKTLTYLLLIFSLVNAQR----SAVQAVIVVPTRELGMQVTKVA  158 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~---------~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~----~~~~~Lil~Ptr~La~Q~~~~~  158 (202)
                      .+.|+|.+++..+.         .+...++..++|.|||+..+..+...+..+.    ...++||++|+ +|+.||.+++
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            68999999998863         4567899999999999998887776665432    12358999996 8999999999


Q ss_pred             HHhhcC
Q 028887          159 RVLAAK  164 (202)
Q Consensus       159 ~~l~~~  164 (202)
                      .++++.
T Consensus       134 ~~~~~~  139 (644)
T 1z3i_X          134 GKWLGG  139 (644)
T ss_dssp             HHHHGG
T ss_pred             HHHcCC
Confidence            999864

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=98.23  E-value=4.2e-06  Score=77.44  Aligned_cols=81  Identities=19%  Similarity=0.100  Sum_probs=68.6

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCC
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLD  167 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~  167 (202)
                      +|. .|+++|-...-.+..|+  +....||+|||+++.+|++-....++   .+.|++|+..||.|-.+++..+....  
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--VAEMKTGEGKTLAATMPIYLNALIGK---GVHLVTVNDYLARRDALWMGPVYLFL--  143 (822)
T ss_dssp             TSC-CCCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTTSS---CEEEEESSHHHHHHHHHHHHHHHHHT--
T ss_pred             hCC-CCcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhcCC---ceEEEeccHHHHHhHHHHHHHHHHHh--
Confidence            576 68999999988888887  88999999999999999975544455   79999999999999999998888876  


Q ss_pred             cccccccceEEEEEe
Q 028887          168 TDLEHKLCTVMALLD  182 (202)
Q Consensus       168 ~~~~~~~~~~~~~~~  182 (202)
                            ++++.++++
T Consensus       144 ------glsvg~i~~  152 (822)
T 3jux_A          144 ------GLRVGVINS  152 (822)
T ss_dssp             ------TCCEEEEET
T ss_pred             ------CCEEEEEcC
Confidence                  577777776

>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=98.17  E-value=2.3e-06  Score=77.91  Aligned_cols=67  Identities=19%  Similarity=0.265  Sum_probs=56.1

Q ss_pred             cHHHHHHHHhHHcCCcEEEeccCCCchH--HHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887           94 TDIQREALPVLFSSRDCILHAQTGSGKT--LTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus        94 t~~Q~~~i~~i~~g~~~l~~a~TGsGKT--~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      ++.|+.+++.++.++++++.|++|||||  ++++++.+..+.. ..+.++++++||.+.+.++.+.+...
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~-~~~~~vll~APTg~AA~~L~e~~~~~  219 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMAD-GERCRIRLAAPTGKAAARLTESLGKA  219 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCS-SCCCCEEEEBSSHHHHHHHHHHHTHH
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhh-cCCCeEEEEeCChhHHHHHHHHHHHH
Confidence            7899999999999999999999999999  6677777765532 23458999999999999998877654

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=97.92  E-value=3.6e-05  Score=70.41  Aligned_cols=68  Identities=21%  Similarity=0.282  Sum_probs=57.5

Q ss_pred             CCcHHHHHHHHhHHcCCc-EEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887           92 LPTDIQREALPVLFSSRD-CILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~-~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      .+++.|.+|+..++..++ .+++||+|||||.+....+.+.+..+.   ++|+.+||..=+.++.+++....
T Consensus       189 ~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~~I~~l~~~~~---~ILv~a~TN~AvD~i~erL~~~~  257 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQGL---KVLCCAPSNIAVDNLVERLALCK  257 (646)
T ss_dssp             TCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHHHHHHHHHTTC---CEEEEESSHHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHHHHHHHHhCCC---eEEEEcCchHHHHHHHHHHHhcC
Confidence            478999999999887654 799999999999998777777776655   89999999999999988886654

>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=97.66  E-value=0.00013  Score=66.55  Aligned_cols=70  Identities=16%  Similarity=0.185  Sum_probs=55.5

Q ss_pred             CCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887           90 YVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus        90 ~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      ...+++.|..++..++.+..++++||+|||||.+....+...+..  .+.++|+++||..-+.++.+++.+.
T Consensus       178 ~~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~~~i~~l~~~--~~~~ilv~a~tn~A~~~l~~~l~~~  247 (624)
T 2gk6_A          178 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ--GNGPVLVCAPSNIAVDQLTEKIHQT  247 (624)
T ss_dssp             SCCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHHHHHHHHHTS--SSCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             cCCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHHHHHHHHHHc--CCCeEEEEeCcHHHHHHHHHHHHhc
Confidence            346899999999998888889999999999998765544333321  2337999999999999998888754

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=97.64  E-value=0.00018  Score=67.52  Aligned_cols=70  Identities=16%  Similarity=0.289  Sum_probs=56.9

Q ss_pred             CCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHH-hcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887           90 YVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVN-AQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus        90 ~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~-~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      +..+++.|.+|+..++.+..++++||.|||||.+....+...+. .+.   ++|+++||..-+.++.+++.+.+
T Consensus       358 ~~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~~~i~~l~~~~~~---~ILv~a~tn~A~d~l~~rL~~~g  428 (802)
T 2xzl_A          358 FAQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKIHKD---RILVCAPSNVAVDHLAAKLRDLG  428 (802)
T ss_dssp             SCCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHHHHHHHHHHHCC---CEEEEESSHHHHHHHHHHHHHTT
T ss_pred             cccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHHhCCCC---eEEEEcCcHHHHHHHHHHHHhhC
Confidence            34689999999999988778899999999999886555444443 334   79999999999999999987753

>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=97.55  E-value=0.00024  Score=64.36  Aligned_cols=72  Identities=24%  Similarity=0.217  Sum_probs=59.0

Q ss_pred             CCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC-CccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           91 VLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR-SAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        91 ~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~-~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      ..+++.|.+++..  .+..++|.|+.|||||.+.+.-+...+..++ ..-++|++++|+..+.++.+++.++.+.
T Consensus         8 ~~Ln~~Q~~av~~--~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~aa~e~~~rl~~~~~~   80 (647)
T 3lfu_A            8 DSLNDKQREAVAA--PRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLMGT   80 (647)
T ss_dssp             TTCCHHHHHHHTC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHHHHHHHHHHHHHHCS
T ss_pred             hcCCHHHHHHHhC--CCCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEeccHHHHHHHHHHHHHHhcc
Confidence            4689999999973  3567999999999999998887777776533 3347999999999999999999888653

>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=97.43  E-value=0.00025  Score=65.16  Aligned_cols=69  Identities=29%  Similarity=0.362  Sum_probs=54.2

Q ss_pred             CCCCCcHHHHHHHHhHH----cCC-cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887           89 GYVLPTDIQREALPVLF----SSR-DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus        89 g~~~~t~~Q~~~i~~i~----~g~-~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      +| .|++.|..++..+.    .|. ..++.|.||||||.+..-.+ ...  ++   .+|||+|+..+|.|+++.++.+++
T Consensus         6 ~~-~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a~~~-~~~--~~---~~lvv~~~~~~A~ql~~el~~~~~   78 (664)
T 1c4o_A            6 GP-SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAKVI-EAL--GR---PALVLAPNKILAAQLAAEFRELFP   78 (664)
T ss_dssp             SC-CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHH-HHH--TC---CEEEEESSHHHHHHHHHHHHHHCT
T ss_pred             CC-CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHHHHH-HHh--CC---CEEEEecCHHHHHHHHHHHHHHCC
Confidence            56 79999999988654    343 46788999999998775433 322  23   489999999999999999999975


Q ss_pred             C
Q 028887          164 K  164 (202)
Q Consensus       164 ~  164 (202)
                      .
T Consensus        79 ~   79 (664)
T 1c4o_A           79 E   79 (664)
T ss_dssp             T
T ss_pred             C
Confidence            4

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=97.42  E-value=0.00038  Score=65.31  Aligned_cols=69  Identities=16%  Similarity=0.188  Sum_probs=54.4

Q ss_pred             CCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887           91 VLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus        91 ~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      ..+++.|.+++..++.+...+++||+|||||.+....+...+..  .+.++|+++||..-+.++.+.+...
T Consensus       355 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti~~~i~~l~~~--~~~~ilv~a~tn~A~~~l~~~l~~~  423 (800)
T 2wjy_A          355 PDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ--GNGPVLVCAPSNIAVDQLTEKIHQT  423 (800)
T ss_dssp             CCCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHHHHHHHHHHTT--CSSCEEEEESSHHHHHHHHHHHHTT
T ss_pred             cCCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHHHHHHHHHHHc--CCCcEEEEcCcHHHHHHHHHHHHHh
Confidence            46799999999998888889999999999998765444333321  2337999999999999988887654

>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=97.23  E-value=0.00075  Score=61.79  Aligned_cols=71  Identities=20%  Similarity=0.172  Sum_probs=57.9

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHh-cCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNA-QRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~-~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .+++.|.+++..  .+..++|.|..|||||.+...-+...+.. +-...++|+++.|+..+.++.+++..+.+.
T Consensus         2 ~L~~~Q~~av~~--~~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lTfT~~Aa~em~~Rl~~~l~~   73 (673)
T 1uaa_A            2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLGR   73 (673)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSCT
T ss_pred             CCCHHHHHHHhC--CCCCEEEEeCCCCChHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHcCc
Confidence            478999999865  35678999999999999988777777765 323457999999999999999999887653

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=97.17  E-value=0.0011  Score=57.98  Aligned_cols=70  Identities=14%  Similarity=0.261  Sum_probs=50.5

Q ss_pred             HCCCCCCcHHHHHHHHhHHcC----C-cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHH
Q 028887           87 ETGYVLPTDIQREALPVLFSS----R-DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVA  158 (202)
Q Consensus        87 ~~g~~~~t~~Q~~~i~~i~~g----~-~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~  158 (202)
                      .+.|..+++.|++++..++..    . .+++.|+.|||||.+. ..++..+...+. ..+++++||...+..+.+.+
T Consensus        20 p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll-~~~~~~l~~~~~-~~il~~a~T~~Aa~~l~~~~   94 (459)
T 3upu_A           20 HMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLT-KFIIEALISTGE-TGIILAAPTHAAKKILSKLS   94 (459)
T ss_dssp             -CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHH-HHHHHHHHHTTC-CCEEEEESSHHHHHHHHHHH
T ss_pred             CCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHH-HHHHHHHHhcCC-ceEEEecCcHHHHHHHHhhh
Confidence            457889999999999876432    3 8999999999999654 344444443322 25889999988887666543

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=97.16  E-value=0.0013  Score=59.53  Aligned_cols=63  Identities=21%  Similarity=0.254  Sum_probs=48.9

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHH
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKV  157 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~  157 (202)
                      .+++.|..++..++.+..+++.|+.|+|||.... .++..+...  +.++++++||...+..+.+.
T Consensus       189 ~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i~-~l~~~l~~~--g~~Vl~~ApT~~Aa~~L~e~  251 (574)
T 3e1s_A          189 GLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTK-AVADLAESL--GLEVGLCAPTGKAARRLGEV  251 (574)
T ss_dssp             TCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHHH-HHHHHHHHT--TCCEEEEESSHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHHH-HHHHHHHhc--CCeEEEecCcHHHHHHhHhh
Confidence            4789999999999999999999999999997643 333433332  23789999999888877653

>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=97.05  E-value=0.0012  Score=64.64  Aligned_cols=69  Identities=20%  Similarity=0.184  Sum_probs=58.0

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC---CccEEEEecCCHHhHHHHHHHHHHhh
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR---SAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~---~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      .+|+.|.++|..-  +.+++|.|..|||||.+.+-=++..+..+.   ..-++|++++|+..+..+.+++....
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            5899999998653  789999999999999998888888776643   34479999999999999998887643

>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=97.03  E-value=0.0022  Score=59.37  Aligned_cols=71  Identities=18%  Similarity=0.178  Sum_probs=57.9

Q ss_pred             CCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC-CccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887           91 VLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR-SAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus        91 ~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~-~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      ..+++.|.+++..  .+..++|.|..|||||.+...-+...+...+ ..-++|+++.|+..|.++.+++..+.+
T Consensus        10 ~~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~vTFTnkAA~Em~~Rl~~~l~   81 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLG   81 (724)
T ss_dssp             TTSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHHG
T ss_pred             hhCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHhc
Confidence            4689999999865  3567899999999999998877777776432 344799999999999999999988754

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B*

Probab=96.31  E-value=0.0079  Score=55.16  Aligned_cols=67  Identities=24%  Similarity=0.302  Sum_probs=51.6

Q ss_pred             CCcHHHHHHHHhHH----cCC-cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLF----SSR-DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~----~g~-~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .|+..|..++..+.    .|. ..++.|.||||||.+..-.+ ...  ++   .+|||+|+..+|.|+++.++.+++.
T Consensus        12 ~p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~a~~~-~~~--~~---~~lvv~~~~~~A~~l~~el~~~~~~   83 (661)
T 2d7d_A           12 QPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSNLI-KEV--NK---PTLVIAHNKTLAGQLYSEFKEFFPN   83 (661)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHH-HHH--CC---CEEEECSSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHHHHHH-HHh--CC---CEEEEECCHHHHHHHHHHHHHHcCC
Confidence            68999998887654    343 46788999999997764333 322  23   4899999999999999999999754

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=95.11  E-value=0.057  Score=40.41  Aligned_cols=33  Identities=21%  Similarity=0.185  Sum_probs=24.4

Q ss_pred             cHHHHHHHHhHH---------cCCcEEEeccCCCchHHHHHH
Q 028887           94 TDIQREALPVLF---------SSRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus        94 t~~Q~~~i~~i~---------~g~~~l~~a~TGsGKT~~~l~  126 (202)
                      ++.|+.++..+.         .|+.+++.||+|+|||...-.
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~   57 (180)
T 3ec2_A           16 NVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVA   57 (180)
T ss_dssp             SHHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHH
Confidence            456777665542         468899999999999976543

>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*

Probab=95.04  E-value=0.12  Score=46.63  Aligned_cols=73  Identities=16%  Similarity=0.151  Sum_probs=58.3

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCC
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKP  165 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~  165 (202)
                      .+++.|...+..+...+.+++..+-|+|||.+...-++..+... .+..++++.|+++.|..+.+.++.+....
T Consensus       163 ~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~-~~~~i~~va~t~~qA~~~~~~i~~~i~~~  235 (592)
T 3cpe_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN-KDKAVGILAHKGSMSAEVLDRTKQAIELL  235 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTS-SSCEEEEEESSHHHHHHHHHHHHHHHTTS
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhC-CCCeEEEEECCHHHHHHHHHHHHHHHHhC
Confidence            58999999998775567899999999999998765555444432 24479999999999999998888887654

>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=94.91  E-value=0.14  Score=43.91  Aligned_cols=72  Identities=17%  Similarity=0.162  Sum_probs=56.6

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .++|.|...+..+...+.+++..+-+.|||.+....++..+.. ..+..+++++|+++.|..+.+.++.+...
T Consensus       163 ~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~-~~g~~v~~vA~t~~qA~~vf~~i~~mi~~  234 (385)
T 2o0j_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCF-NKDKAVGILAHKGSMSAEVLDRTKQAIEL  234 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHS-SSSCEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHh-CCCCeEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            6899999999876555778999999999999877665554332 23447999999999999888888877653

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=93.11  E-value=0.14  Score=39.88  Aligned_cols=52  Identities=17%  Similarity=0.230  Sum_probs=34.0

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      .|.-+++.|++|+|||...+.-+......+.   .++++.-. +-..++.+++..+
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~~~~~~~~~~~---~v~~~~~e-~~~~~~~~~~~~~   73 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQQFLWNGLKMGE---PGIYVALE-EHPVQVRQNMAQF   73 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHHHHTTC---CEEEEESS-SCHHHHHHHHHTT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHhcCC---eEEEEEcc-CCHHHHHHHHHHc
Confidence            4677899999999999876555444444443   57776643 3345666666543

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=92.80  E-value=0.099  Score=37.85  Aligned_cols=21  Identities=14%  Similarity=0.061  Sum_probs=17.4

Q ss_pred             HHcCCcEEEeccCCCchHHHH
Q 028887          104 LFSSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       104 i~~g~~~l~~a~TGsGKT~~~  124 (202)
                      ...+.++++.|++|+|||...
T Consensus        24 ~~~~~~vll~G~~GtGKt~lA   44 (143)
T 3co5_A           24 AKRTSPVFLTGEAGSPFETVA   44 (143)
T ss_dssp             HTCSSCEEEEEETTCCHHHHH
T ss_pred             hCCCCcEEEECCCCccHHHHH
Confidence            345678999999999999764

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=92.52  E-value=0.098  Score=45.73  Aligned_cols=45  Identities=24%  Similarity=0.356  Sum_probs=34.4

Q ss_pred             cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887          109 DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      -.++.|+.|+|||....--+    .. +   ..+|++||++++..+.+.+.+.
T Consensus       163 v~~I~G~aGsGKTt~I~~~~----~~-~---~~lVlTpT~~aa~~l~~kl~~~  207 (446)
T 3vkw_A          163 VVLVDGVPGCGKTKEILSRV----NF-E---EDLILVPGRQAAEMIRRRANAS  207 (446)
T ss_dssp             EEEEEECTTSCHHHHHHHHC----CT-T---TCEEEESCHHHHHHHHHHHTTT
T ss_pred             EEEEEcCCCCCHHHHHHHHh----cc-C---CeEEEeCCHHHHHHHHHHhhhc
Confidence            46899999999998764332    11 2   4699999999999998887543

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=92.38  E-value=0.12  Score=37.45  Aligned_cols=21  Identities=14%  Similarity=0.094  Sum_probs=17.6

Q ss_pred             HcCCcEEEeccCCCchHHHHH
Q 028887          105 FSSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       105 ~~g~~~l~~a~TGsGKT~~~l  125 (202)
                      ..+.++++.|++|+|||...-
T Consensus        22 ~~~~~vll~G~~GtGKt~lA~   42 (145)
T 3n70_A           22 ETDIAVWLYGAPGTGRMTGAR   42 (145)
T ss_dssp             TCCSCEEEESSTTSSHHHHHH
T ss_pred             CCCCCEEEECCCCCCHHHHHH
Confidence            456789999999999997753

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=92.17  E-value=0.2  Score=38.03  Aligned_cols=39  Identities=15%  Similarity=0.197  Sum_probs=28.4

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCH
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTR  148 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr  148 (202)
                      |+-.++.|+.|+|||...+--+......+.   +++++.|..
T Consensus         3 g~i~vi~G~~gsGKTT~ll~~~~~~~~~g~---~v~~~~~~~   41 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELLSFVEIYKLGKK---KVAVFKPKI   41 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHTTC---EEEEEEEC-
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHHHCCC---eEEEEeecc
Confidence            556789999999999887666555554444   678877763

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=91.30  E-value=0.22  Score=38.67  Aligned_cols=51  Identities=20%  Similarity=0.242  Sum_probs=32.4

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHh-cCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNA-QRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~-~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      |.-+++.|++|+|||...+--+.+.... +.   .+++++-+ +-..++.+++..+
T Consensus        30 G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~---~v~~~s~E-~~~~~~~~~~~~~   81 (251)
T 2zts_A           30 GTTVLLTGGTGTGKTTFAAQFIYKGAEEYGE---PGVFVTLE-ERARDLRREMASF   81 (251)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHHHHCC---CEEEEESS-SCHHHHHHHHHTT
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhcCC---Cceeeccc-CCHHHHHHHHHHc
Confidence            4678999999999997766555554433 33   46666544 3345555555544

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=90.98  E-value=0.18  Score=39.86  Aligned_cols=40  Identities=15%  Similarity=0.095  Sum_probs=29.2

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCH
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTR  148 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr  148 (202)
                      .|.-+++.|++|+|||...+-.+......+.   +++++.|..
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~~r~~~~g~---kVli~~~~~   50 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRLHRLEYADV---KYLVFKPKI   50 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHHHHHHHTTC---CEEEEEECC
T ss_pred             CcEEEEEECCCCCcHHHHHHHHHHHHHhcCC---EEEEEEecc
Confidence            3556888999999999887766666555554   677776554

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=90.95  E-value=0.23  Score=38.20  Aligned_cols=40  Identities=15%  Similarity=0.064  Sum_probs=29.2

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCH
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTR  148 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr  148 (202)
                      .|+-.++.|+.|+|||...+-.+......+.   +++++-|..
T Consensus         7 ~g~i~v~~G~mgsGKTT~ll~~a~r~~~~g~---kV~v~k~~~   46 (191)
T 1xx6_A            7 HGWVEVIVGPMYSGKSEELIRRIRRAKIAKQ---KIQVFKPEI   46 (191)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHTTC---CEEEEEEC-
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHCCC---EEEEEEecc
Confidence            3556788999999999887766666555555   788887764

>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=90.58  E-value=0.34  Score=41.53  Aligned_cols=44  Identities=23%  Similarity=0.346  Sum_probs=30.9

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHH
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGM  152 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~  152 (202)
                      ...++++.|+||+|||...-.-+.+.+..+.   .++|+=|..|+..
T Consensus        52 ~~~h~~i~G~tGsGKs~~~~~li~~~~~~g~---~viv~Dpkge~~~   95 (437)
T 1e9r_A           52 EPRHLLVNGATGTGKSVLLRELAYTGLLRGD---RMVIVDPNGDMLS   95 (437)
T ss_dssp             GGGCEEEEECTTSSHHHHHHHHHHHHHHTTC---EEEEEEETTHHHH
T ss_pred             CcceEEEECCCCCCHHHHHHHHHHHHHHCCC---cEEEEeCCCchhH
Confidence            4578999999999999875223333344343   6788888888764

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=90.45  E-value=0.45  Score=35.91  Aligned_cols=25  Identities=28%  Similarity=0.329  Sum_probs=18.5

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVN  133 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~  133 (202)
                      +.+++.|++|+|||.... .+...+.
T Consensus        55 ~~~~l~G~~GtGKT~la~-~i~~~~~   79 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLA-AIANELA   79 (202)
T ss_dssp             CEEEEECSTTSSHHHHHH-HHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHHH
Confidence            679999999999997643 3444443

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=90.14  E-value=0.57  Score=38.50  Aligned_cols=20  Identities=20%  Similarity=0.265  Sum_probs=16.9

Q ss_pred             CCcEEEeccCCCchHHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~  126 (202)
                      +..+++.|++|+|||.....
T Consensus       152 ~~~lll~G~~GtGKT~La~a  171 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLAA  171 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHH
Confidence            57899999999999976543

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=90.00  E-value=0.85  Score=37.50  Aligned_cols=51  Identities=12%  Similarity=-0.067  Sum_probs=32.8

Q ss_pred             HcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHH
Q 028887          105 FSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVAR  159 (202)
Q Consensus       105 ~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~  159 (202)
                      ..|.-+++.|++|+|||...+--..+....+.   .+++++-+ +-..|+..++.
T Consensus        66 ~~G~l~li~G~pG~GKTtl~l~ia~~~a~~g~---~vl~~slE-~s~~~l~~R~~  116 (315)
T 3bh0_A           66 KRRNFVLIAARPSMGKTAFALKQAKNMSDNDD---VVNLHSLE-MGKKENIKRLI  116 (315)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHHHHHTTTC---EEEEEESS-SCHHHHHHHHH
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCC---eEEEEECC-CCHHHHHHHHH
Confidence            34567999999999999765554444444333   68888755 33445554444

>3u4q_B ATP-dependent helicase/deoxyribonuclease subunit; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_B*

Probab=89.98  E-value=0.42  Score=46.42  Aligned_cols=51  Identities=18%  Similarity=0.190  Sum_probs=38.0

Q ss_pred             EEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          111 ILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       111 l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      +|.|..|||||.+.+--+...+..+..+.++|+|||+. .+.++.+++....
T Consensus         5 lV~agAGSGKT~~l~~ri~~ll~~~~~~~~il~lVP~q-~TFt~~~rl~~~l   55 (1166)
T 3u4q_B            5 FLVGRSGSGKTKLIINSIQDELRRAPFGKPIIFLVPDQ-MTFLMEYELAKTP   55 (1166)
T ss_dssp             EEEECTTSSHHHHHHHHHHHHHHHCTTSSCEEEECCGG-GHHHHHHHHTCCS
T ss_pred             EEEeCCCCChHHHHHHHHHHHHHhCCCCCcEEEEecCc-ccHHHHHHHHHhh
Confidence            68899999999998888887777655556899999975 5555555554433

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=89.95  E-value=0.74  Score=35.06  Aligned_cols=52  Identities=17%  Similarity=0.181  Sum_probs=30.1

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      .|.-+++.|++|+|||.....-+......+.   .++++.... ...++.+++..+
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~---~v~~~~~~~-~~~~~~~~~~~~   73 (235)
T 2w0m_A           22 QGFFIALTGEPGTGKTIFSLHFIAKGLRDGD---PCIYVTTEE-SRDSIIRQAKQF   73 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHHHHHHHTC---CEEEEESSS-CHHHHHHHHHHT
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHCCC---eEEEEEccc-CHHHHHHHHHHh
Confidence            4567899999999999765443333333333   466654322 234445555444

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=88.71  E-value=0.48  Score=39.12  Aligned_cols=55  Identities=18%  Similarity=0.134  Sum_probs=33.0

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHh---cCCccEEEEecCCHHh-HHHHHHHHHHh
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNA---QRSAVQAVIVVPTREL-GMQVTKVARVL  161 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~---~~~~~~~Lil~Ptr~L-a~Q~~~~~~~l  161 (202)
                      |.-+++.|++|+|||...+..+......   +..+..++++.-+..+ ..++.++++.+
T Consensus       107 G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~~~~~~~  165 (324)
T 2z43_A          107 RTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIENMAKAL  165 (324)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHHHHHHh
Confidence            4678999999999997766554443222   1112368888765432 34444444444

>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=88.67  E-value=0.57  Score=35.81  Aligned_cols=20  Identities=20%  Similarity=0.159  Sum_probs=16.7

Q ss_pred             cCCcEEEeccCCCchHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l  125 (202)
                      .+..+++.|++|+|||...-
T Consensus        51 ~~~~~ll~G~~G~GKT~la~   70 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLIH   70 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHH
Confidence            35789999999999997653

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=88.27  E-value=0.49  Score=36.74  Aligned_cols=35  Identities=20%  Similarity=0.065  Sum_probs=28.1

Q ss_pred             CCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHH
Q 028887           91 VLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus        91 ~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l  125 (202)
                      ..-+--|..++..+..|.-+.+.||+|+|||...-
T Consensus         6 ~pk~~g~~~~l~~i~~Ge~~~liG~nGsGKSTLl~   40 (208)
T 3b85_A            6 RPKTLGQKHYVDAIDTNTIVFGLGPAGSGKTYLAM   40 (208)
T ss_dssp             CCCSHHHHHHHHHHHHCSEEEEECCTTSSTTHHHH
T ss_pred             ccCCHhHHHHHHhccCCCEEEEECCCCCCHHHHHH
Confidence            33455677788888889999999999999997753

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=87.34  E-value=0.3  Score=35.74  Aligned_cols=19  Identities=26%  Similarity=0.333  Sum_probs=15.7

Q ss_pred             CCcEEEeccCCCchHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l  125 (202)
                      +..+++.|++|+|||...-
T Consensus        43 ~~~~ll~G~~G~GKT~l~~   61 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAIVE   61 (195)
T ss_dssp             SCEEEEECCTTSCHHHHHH
T ss_pred             CCceEEECCCCCCHHHHHH
Confidence            3679999999999997643

>3hjh_A Transcription-repair-coupling factor; MFD, mutation frequency decline, ATP-binding, DNA DAMA repair, DNA-binding, helicase, hydrolase; 1.95A {Escherichia coli} PDB: 2b2n_A* 4dfc_A

Probab=87.00  E-value=0.81  Score=40.30  Aligned_cols=52  Identities=10%  Similarity=0.142  Sum_probs=39.8

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      .|....+.|.|||||+++..-.+ +.  .++   ..||++|+...|.|+++.++.+.+
T Consensus        13 ~~~~~~l~g~~gs~ka~~~a~l~-~~--~~~---p~lvv~~~~~~A~~l~~~l~~~~~   64 (483)
T 3hjh_A           13 AGEQRLLGELTGAACATLVAEIA-ER--HAG---PVVLIAPDMQNALRLHDEISQFTD   64 (483)
T ss_dssp             TTCEEEEECCCTTHHHHHHHHHH-HH--SSS---CEEEEESSHHHHHHHHHHHHHTCS
T ss_pred             CCCeEEEeCCCchHHHHHHHHHH-HH--hCC---CEEEEeCCHHHHHHHHHHHHhhCC
Confidence            45678899999999997643322 11  122   489999999999999999999865

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=86.95  E-value=0.29  Score=36.61  Aligned_cols=21  Identities=14%  Similarity=0.170  Sum_probs=17.2

Q ss_pred             cCCcEEEeccCCCchHHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~  126 (202)
                      .|+-+++.||+|+|||...-.
T Consensus         4 ~g~~i~i~GpsGsGKSTL~~~   24 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHIKNT   24 (180)
T ss_dssp             CCCEEEEECCTTSSHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            567789999999999976543

>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=86.92  E-value=1.6  Score=34.82  Aligned_cols=20  Identities=25%  Similarity=0.368  Sum_probs=16.6

Q ss_pred             cCCcEEEeccCCCchHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l  125 (202)
                      .+..+++.|++|+|||...-
T Consensus        49 ~~~~vll~G~~GtGKT~la~   68 (310)
T 1ofh_A           49 TPKNILMIGPTGVGKTEIAR   68 (310)
T ss_dssp             CCCCEEEECCTTSSHHHHHH
T ss_pred             CCceEEEECCCCCCHHHHHH
Confidence            35789999999999997653

>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=86.81  E-value=1  Score=36.74  Aligned_cols=19  Identities=21%  Similarity=0.256  Sum_probs=15.8

Q ss_pred             CCcEEEeccCCCchHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l  125 (202)
                      +..+++.||+|+|||...-
T Consensus        37 ~~~lll~G~~GtGKT~la~   55 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLLQ   55 (324)
T ss_dssp             CSSEEEECSSSSSHHHHHH
T ss_pred             CCeEEEECCCCCcHHHHHH
Confidence            3679999999999996643

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=86.80  E-value=0.37  Score=39.55  Aligned_cols=24  Identities=25%  Similarity=0.303  Sum_probs=19.4

Q ss_pred             HHhHHcCCcEEEeccCCCchHHHH
Q 028887          101 LPVLFSSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       101 i~~i~~g~~~l~~a~TGsGKT~~~  124 (202)
                      ...+..+.++++.|++|+|||...
T Consensus        40 ~~~l~~~~~vll~G~pGtGKT~la   63 (331)
T 2r44_A           40 LIGICTGGHILLEGVPGLAKTLSV   63 (331)
T ss_dssp             HHHHHHTCCEEEESCCCHHHHHHH
T ss_pred             HHHHHcCCeEEEECCCCCcHHHHH
Confidence            334566889999999999999764

>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=86.72  E-value=0.56  Score=37.11  Aligned_cols=19  Identities=21%  Similarity=0.436  Sum_probs=16.4

Q ss_pred             cCCcEEEeccCCCchHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~  124 (202)
                      .+..+++.|++|+|||...
T Consensus        28 ~~~~vll~G~~GtGKt~la   46 (265)
T 2bjv_A           28 LDKPVLIIGERGTGKELIA   46 (265)
T ss_dssp             SCSCEEEECCTTSCHHHHH
T ss_pred             CCCCEEEECCCCCcHHHHH
Confidence            4678999999999999764

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=86.27  E-value=0.36  Score=36.81  Aligned_cols=21  Identities=24%  Similarity=0.409  Sum_probs=16.2

Q ss_pred             cCCcEEEeccCCCchHHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~  126 (202)
                      .|+-+.+.||+|+|||...-+
T Consensus         3 ~g~~i~lvGpsGaGKSTLl~~   23 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLLKK   23 (198)
T ss_dssp             --CCEEEECCTTSSHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            577899999999999977543

>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=85.94  E-value=2.6  Score=31.26  Aligned_cols=17  Identities=29%  Similarity=0.442  Sum_probs=14.6

Q ss_pred             CcEEEeccCCCchHHHH
Q 028887          108 RDCILHAQTGSGKTLTY  124 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~  124 (202)
                      ..+++.|++|+|||...
T Consensus        39 ~~~ll~G~~G~GKT~l~   55 (226)
T 2chg_A           39 PHLLFSGPPGTGKTATA   55 (226)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            35999999999999764

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=85.86  E-value=0.31  Score=35.68  Aligned_cols=19  Identities=32%  Similarity=0.340  Sum_probs=15.8

Q ss_pred             CCcEEEeccCCCchHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l  125 (202)
                      +..+++.|++|+|||....
T Consensus        43 ~~~vll~G~~G~GKT~la~   61 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIVE   61 (187)
T ss_dssp             SCEEEEESCGGGCHHHHHH
T ss_pred             CCceEEECCCCCCHHHHHH
Confidence            4679999999999997653

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=85.86  E-value=0.82  Score=33.32  Aligned_cols=21  Identities=14%  Similarity=0.185  Sum_probs=17.5

Q ss_pred             cCCcEEEeccCCCchHHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~  126 (202)
                      .|..+++.|++|+|||...-.
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~~   55 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQA   55 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH
Confidence            678899999999999976443

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=85.75  E-value=0.49  Score=41.84  Aligned_cols=30  Identities=23%  Similarity=0.234  Sum_probs=23.0

Q ss_pred             HHHHHHHHhHHcCCcEEEeccCCCchHHHH
Q 028887           95 DIQREALPVLFSSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus        95 ~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~  124 (202)
                      ..=..++-.+..|.++++.||+|+|||...
T Consensus        29 ~~i~~l~~al~~~~~VLL~GpPGtGKT~LA   58 (500)
T 3nbx_X           29 HAIRLCLLAALSGESVFLLGPPGIAKSLIA   58 (500)
T ss_dssp             HHHHHHHHHHHHTCEEEEECCSSSSHHHHH
T ss_pred             HHHHHHHHHHhcCCeeEeecCchHHHHHHH
Confidence            333445555678899999999999999764

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=85.67  E-value=0.93  Score=37.13  Aligned_cols=54  Identities=19%  Similarity=0.140  Sum_probs=33.0

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhc---------CCc----cEEEEecCCHHh-HHHHHHHHHHh
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQ---------RSA----VQAVIVVPTREL-GMQVTKVARVL  161 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~---------~~~----~~~Lil~Ptr~L-a~Q~~~~~~~l  161 (202)
                      .-+++.|++|+|||...+-.+.+.....         ..+    ..++|+.-+..+ ..++.++++.+
T Consensus        99 ~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~~~~~~  166 (322)
T 2i1q_A           99 SVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEHA  166 (322)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHHHHHHc
Confidence            5689999999999987665544422111         111    478888766543 45555555544

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=85.64  E-value=0.37  Score=38.93  Aligned_cols=19  Identities=26%  Similarity=0.368  Sum_probs=15.9

Q ss_pred             CCcEEEeccCCCchHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l  125 (202)
                      +..+++.||+|+|||...-
T Consensus        67 ~~~vll~G~~GtGKT~la~   85 (309)
T 3syl_A           67 TLHMSFTGNPGTGKTTVAL   85 (309)
T ss_dssp             CCEEEEEECTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            3469999999999997753

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=85.42  E-value=0.71  Score=35.75  Aligned_cols=39  Identities=13%  Similarity=0.096  Sum_probs=31.4

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCC
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPT  147 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Pt  147 (202)
                      .|+=.++.|+.|+|||.-.+-.+-.....+.   +++++.|.
T Consensus        19 ~g~l~fiyG~MgsGKTt~Ll~~i~n~~~~~~---kvl~~kp~   57 (195)
T 1w4r_A           19 RGQIQVILGPMFSGKSTELMRRVRRFQIAQY---KCLVIKYA   57 (195)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHHHHHTTC---CEEEEEET
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHHcCC---eEEEEccc
Confidence            4566899999999999887777766666655   78999887

>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=85.31  E-value=0.85  Score=38.01  Aligned_cols=19  Identities=42%  Similarity=0.534  Sum_probs=16.4

Q ss_pred             cCCcEEEeccCCCchHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~  124 (202)
                      .+..+++.||+|+|||...
T Consensus        50 ~~~~vll~GppGtGKT~la   68 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLA   68 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            3468999999999999875

>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=84.98  E-value=0.42  Score=38.97  Aligned_cols=19  Identities=32%  Similarity=0.490  Sum_probs=16.3

Q ss_pred             cCCcEEEeccCCCchHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~  124 (202)
                      .++.++++||+|+|||...
T Consensus        48 ~~~~vLL~Gp~GtGKT~la   66 (301)
T 3cf0_A           48 PSKGVLFYGPPGCGKTLLA   66 (301)
T ss_dssp             CCSEEEEECSSSSSHHHHH
T ss_pred             CCceEEEECCCCcCHHHHH
Confidence            3567999999999999765

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=84.95  E-value=1.1  Score=35.18  Aligned_cols=40  Identities=15%  Similarity=0.130  Sum_probs=29.9

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHH
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRE  149 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~  149 (202)
                      |+-.++.|+-|+|||...+--+......+.   +++++-|.+.
T Consensus        28 G~l~vitG~MgsGKTT~lL~~a~r~~~~g~---kVli~k~~~d   67 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELIRRVRRTQFAKQ---HAIVFKPCID   67 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHTTC---CEEEEECC--
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHCCC---EEEEEEeccC
Confidence            444667888899999888877777766666   7899888765

>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=84.90  E-value=1.3  Score=37.38  Aligned_cols=43  Identities=23%  Similarity=0.417  Sum_probs=29.4

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhH
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELG  151 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La  151 (202)
                      .+.++++.|+||+|||...-.-+.+....+   .+++++=|..+..
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~~~~~~~~~~---~~~~~~D~~~~~~   76 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKMLLLREYMQG---SRVIIIDPEREYK   76 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHHHTTT---CCEEEEESSCCSH
T ss_pred             ccCceEEEcCCCCCHHHHHHHHHHHHHHCC---CEEEEEeCCcCHH
Confidence            456899999999999976544444433333   3677777876643

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=84.87  E-value=0.47  Score=36.38  Aligned_cols=20  Identities=20%  Similarity=0.169  Sum_probs=16.8

Q ss_pred             cCCcEEEeccCCCchHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l  125 (202)
                      .|+-+++.||+|+|||...-
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~   26 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVRE   26 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHHH
Confidence            46778999999999998754

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=84.72  E-value=0.92  Score=38.23  Aligned_cols=37  Identities=19%  Similarity=0.166  Sum_probs=26.6

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecC
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP  146 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~P  146 (202)
                      |+-+++.|++|+|||...+..+.+....+.   .++++..
T Consensus        63 G~ii~I~G~pGsGKTtLal~la~~~~~~g~---~vlyid~   99 (356)
T 1u94_A           63 GRIVEIYGPESSGKTTLTLQVIAAAQREGK---TCAFIDA   99 (356)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHTTC---CEEEEES
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCC---eEEEEeC
Confidence            467899999999999887666555554443   5666654

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=84.70  E-value=0.49  Score=35.88  Aligned_cols=22  Identities=23%  Similarity=0.096  Sum_probs=17.6

Q ss_pred             HcCCcEEEeccCCCchHHHHHH
Q 028887          105 FSSRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       105 ~~g~~~l~~a~TGsGKT~~~l~  126 (202)
                      ..++.+++.|++|||||...-.
T Consensus        23 ~~~~~i~l~G~~GsGKsTl~~~   44 (199)
T 3vaa_A           23 NAMVRIFLTGYMGAGKTTLGKA   44 (199)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHH
T ss_pred             CCCCEEEEEcCCCCCHHHHHHH
Confidence            3567899999999999987543

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=84.67  E-value=0.44  Score=38.30  Aligned_cols=19  Identities=32%  Similarity=0.485  Sum_probs=16.2

Q ss_pred             CCcEEEeccCCCchHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l  125 (202)
                      ++.+++.||+|+|||...-
T Consensus        54 ~~~vll~Gp~GtGKT~la~   72 (297)
T 3b9p_A           54 AKGLLLFGPPGNGKTLLAR   72 (297)
T ss_dssp             CSEEEEESSSSSCHHHHHH
T ss_pred             CCeEEEECcCCCCHHHHHH
Confidence            5689999999999997653

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=84.66  E-value=0.44  Score=37.99  Aligned_cols=20  Identities=30%  Similarity=0.439  Sum_probs=16.6

Q ss_pred             cCCcEEEeccCCCchHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l  125 (202)
                      .++.++++||+|+|||...-
T Consensus        50 ~~~~~ll~G~~GtGKT~la~   69 (285)
T 3h4m_A           50 PPKGILLYGPPGTGKTLLAK   69 (285)
T ss_dssp             CCSEEEEESSSSSSHHHHHH
T ss_pred             CCCeEEEECCCCCcHHHHHH
Confidence            45679999999999997653

>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=84.66  E-value=0.46  Score=37.23  Aligned_cols=18  Identities=33%  Similarity=0.529  Sum_probs=15.4

Q ss_pred             CCcEEEeccCCCchHHHH
Q 028887          107 SRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~  124 (202)
                      .+.++++||+|+|||...
T Consensus        39 ~~~vll~G~~GtGKT~la   56 (262)
T 2qz4_A           39 PKGALLLGPPGCGKTLLA   56 (262)
T ss_dssp             CCEEEEESCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            467999999999999764

>3nwn_A Kinesin-like protein KIF9; motor domain, ADP, structural genomics, structural consortium, SGC, contractIle protein; HET: ADP; 2.00A {Homo sapiens}

Probab=84.65  E-value=0.7  Score=39.13  Aligned_cols=22  Identities=32%  Similarity=0.400  Sum_probs=17.6

Q ss_pred             hHHcCCc--EEEeccCCCchHHHH
Q 028887          103 VLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       103 ~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      .++.|.+  ++.+|.||||||..-
T Consensus        99 ~~l~G~N~tifAYGQTGSGKTyTM  122 (359)
T 3nwn_A           99 QALDGYNGTIMCYGQTGAGKTYTM  122 (359)
T ss_dssp             HHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHhCCCCEEEEEeCCCCCCccEEe
Confidence            3567865  788999999999764

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=84.62  E-value=0.53  Score=41.73  Aligned_cols=38  Identities=26%  Similarity=0.154  Sum_probs=24.6

Q ss_pred             HHHCCCCCCcHHHHHHHH-hHHcCCcEEEeccCCCchHHHH
Q 028887           85 MEETGYVLPTDIQREALP-VLFSSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus        85 l~~~g~~~~t~~Q~~~i~-~i~~g~~~l~~a~TGsGKT~~~  124 (202)
                      +.+.|.  +++.+..-+. .+..|..+++.|+||||||...
T Consensus       239 l~~~G~--~~~~~l~~l~~~v~~g~~i~I~GptGSGKTTlL  277 (511)
T 2oap_1          239 LIEKGT--VPSGVLAYLWLAIEHKFSAIVVGETASGKTTTL  277 (511)
T ss_dssp             HHHTTS--SCHHHHHHHHHHHHTTCCEEEEESTTSSHHHHH
T ss_pred             HHhcCC--CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH
Confidence            334452  3444333343 3467888999999999999653

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=84.61  E-value=0.56  Score=39.51  Aligned_cols=21  Identities=33%  Similarity=0.400  Sum_probs=18.2

Q ss_pred             HHcCCcEEEeccCCCchHHHH
Q 028887          104 LFSSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       104 i~~g~~~l~~a~TGsGKT~~~  124 (202)
                      +..|..+++.|+||+|||...
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            467899999999999999754

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=84.59  E-value=1.3  Score=33.56  Aligned_cols=35  Identities=17%  Similarity=0.008  Sum_probs=23.9

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecC
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP  146 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~P  146 (202)
                      .|.-+++.|++|+|||.....-+.   ..+.   .++++.-
T Consensus        19 ~G~~~~i~G~~GsGKTtl~~~l~~---~~~~---~v~~i~~   53 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLALQTGL---LSGK---KVAYVDT   53 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHH---HHCS---EEEEEES
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH---HcCC---cEEEEEC
Confidence            356789999999999977654443   3333   5666653

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=84.57  E-value=0.36  Score=40.22  Aligned_cols=26  Identities=8%  Similarity=-0.091  Sum_probs=18.9

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVN  133 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~  133 (202)
                      +.++++.||+|+|||.+.-. ++..+.
T Consensus        45 ~~~lli~GpPGTGKT~~v~~-v~~~L~   70 (318)
T 3te6_A           45 NKLFYITNADDSTKFQLVND-VMDELI   70 (318)
T ss_dssp             CCEEEEECCCSHHHHHHHHH-HHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHH-HHHHHH
Confidence            46799999999999976543 334443

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=84.51  E-value=1.1  Score=37.60  Aligned_cols=40  Identities=15%  Similarity=0.008  Sum_probs=28.2

Q ss_pred             cEEEeccCCCchHHHHHHHHHHHHHh--cCCccEEEEecCCHHhH
Q 028887          109 DCILHAQTGSGKTLTYLLLIFSLVNA--QRSAVQAVIVVPTRELG  151 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~~~l~~l~~--~~~~~~~Lil~Ptr~La  151 (202)
                      -+++.|++|+|||...+-.+.+....  +.   .++++..+..+.
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~---~vlyId~E~s~~   71 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQYPDA---VCLFYDSEFGIT   71 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHHCTTC---EEEEEESSCCCC
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcCCCc---eEEEEeccchhh
Confidence            47899999999998877666655544  33   677776655543

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=84.47  E-value=1.7  Score=34.62  Aligned_cols=57  Identities=12%  Similarity=0.139  Sum_probs=33.4

Q ss_pred             HHcCCcEEEeccCCCchHHHHHHHHHHHHHhcC--------CccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          104 LFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR--------SAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       104 i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~--------~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      +..|.-+++.|++|+|||.....-+. .+..+.        ..-.++++.-.-.+ .++..++..++
T Consensus        27 l~~G~i~~i~G~~GsGKTtl~~~l~~-~~~~g~~~~g~~~~~~~~v~~~~~e~~~-~~~~~r~~~~g   91 (279)
T 1nlf_A           27 MVAGTVGALVSPGGAGKSMLALQLAA-QIAGGPDLLEVGELPTGPVIYLPAEDPP-TAIHHRLHALG   91 (279)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHH-HHHTCCCTTCCCCCCCCCEEEEESSSCH-HHHHHHHHHHH
T ss_pred             ccCCCEEEEEcCCCCCHHHHHHHHHH-HHhcCCCcCCCccCCCccEEEEECCCCH-HHHHHHHHHHH
Confidence            45678899999999999987655443 333330        01246666544332 44444555444

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=84.25  E-value=1.3  Score=34.25  Aligned_cols=34  Identities=21%  Similarity=0.164  Sum_probs=29.4

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEe
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIV  144 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil  144 (202)
                      -.+++.+.+|.|||.+.+-..+..+..+.   +++|+
T Consensus        29 g~i~v~tG~GkGKTTaA~GlalRA~g~G~---rV~~v   62 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAARAVGHGK---NVGVV   62 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHHHTTC---CEEEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHCCC---eEEEE
Confidence            46999999999999999999988888776   67776

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=84.24  E-value=0.41  Score=35.52  Aligned_cols=22  Identities=23%  Similarity=0.170  Sum_probs=17.9

Q ss_pred             HcCCcEEEeccCCCchHHHHHH
Q 028887          105 FSSRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       105 ~~g~~~l~~a~TGsGKT~~~l~  126 (202)
                      ..++.+++.|++|+|||...-.
T Consensus         9 ~~~~~i~i~G~~GsGKst~~~~   30 (180)
T 3iij_A            9 MLLPNILLTGTPGVGKTTLGKE   30 (180)
T ss_dssp             CCCCCEEEECSTTSSHHHHHHH
T ss_pred             ccCCeEEEEeCCCCCHHHHHHH
Confidence            4567899999999999987543

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=84.18  E-value=1  Score=38.11  Aligned_cols=38  Identities=24%  Similarity=0.135  Sum_probs=24.1

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCC
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPT  147 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Pt  147 (202)
                      |.-+++.|++|+|||...+..+......+.   .++++...
T Consensus        61 G~i~~I~GppGsGKSTLal~la~~~~~~gg---~VlyId~E   98 (356)
T 3hr8_A           61 GRIVEIFGQESSGKTTLALHAIAEAQKMGG---VAAFIDAE   98 (356)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHHHHTTC---CEEEEESS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhcCC---eEEEEecc
Confidence            456899999999999765544433333333   45665544

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=84.13  E-value=2.4  Score=36.68  Aligned_cols=39  Identities=13%  Similarity=0.046  Sum_probs=28.4

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCC
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPT  147 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Pt  147 (202)
                      .|.-+++.|++|+|||...+--+.+....+.   .+++++-+
T Consensus       196 ~G~liiIaG~pG~GKTtlal~ia~~~a~~g~---~vl~fSlE  234 (444)
T 3bgw_A          196 RRNFVLIAARPSMGKTAFALKQAKNMSDNDD---VVNLHSLE  234 (444)
T ss_dssp             SSCEEEEEECSSSSHHHHHHHHHHHHHHTTC---EEEEECSS
T ss_pred             CCcEEEEEeCCCCChHHHHHHHHHHHHHcCC---EEEEEECC
Confidence            3466899999999999776665555555443   78888755

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=84.12  E-value=1.6  Score=37.64  Aligned_cols=37  Identities=19%  Similarity=0.214  Sum_probs=23.1

Q ss_pred             HHHHHHHHhHH--cCCcEEEeccCCCchHHHHHHHHHHHH
Q 028887           95 DIQREALPVLF--SSRDCILHAQTGSGKTLTYLLLIFSLV  132 (202)
Q Consensus        95 ~~Q~~~i~~i~--~g~~~l~~a~TGsGKT~~~l~~~l~~l  132 (202)
                      +.+...+..++  .|.-+++.||||||||... -.++..+
T Consensus       153 ~~~~~~L~~l~~~~ggii~I~GpnGSGKTTlL-~allg~l  191 (418)
T 1p9r_A          153 AHNHDNFRRLIKRPHGIILVTGPTGSGKSTTL-YAGLQEL  191 (418)
T ss_dssp             HHHHHHHHHHHTSSSEEEEEECSTTSCHHHHH-HHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHhhc
Confidence            34444554444  3456899999999999653 3344444

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=84.02  E-value=0.49  Score=35.63  Aligned_cols=20  Identities=30%  Similarity=0.340  Sum_probs=16.8

Q ss_pred             cCCcEEEeccCCCchHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l  125 (202)
                      .|.-+.+.||+|+|||...-
T Consensus         6 ~g~ii~l~Gp~GsGKSTl~~   25 (205)
T 3tr0_A            6 KANLFIISAPSGAGKTSLVR   25 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHHH
Confidence            57778999999999998643

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=83.86  E-value=0.46  Score=41.30  Aligned_cols=50  Identities=12%  Similarity=0.157  Sum_probs=28.1

Q ss_pred             HHhCCCCHHHHHHHHHCC---CCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHH
Q 028887           72 LCQGHVPEHVLRRMEETG---YVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus        72 l~~~gl~~~l~~~l~~~g---~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~  124 (202)
                      |...|-.+...+.+.+.=   +.+|...+...+   ...+.++++||+|+|||+..
T Consensus       180 ~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~---~~prGvLLyGPPGTGKTllA  232 (434)
T 4b4t_M          180 YSDVGGLDKQIEELVEAIVLPMKRADKFKDMGI---RAPKGALMYGPPGTGKTLLA  232 (434)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCC---CCCCEEEEESCTTSSHHHHH
T ss_pred             hHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCeeEEECcCCCCHHHHH
Confidence            344466666666665421   112222221111   12367999999999999764

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=83.86  E-value=1.2  Score=37.29  Aligned_cols=36  Identities=22%  Similarity=0.117  Sum_probs=25.4

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEec
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVV  145 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~  145 (202)
                      |.-+++.|++|+|||...+..+......+.   .++++.
T Consensus        61 G~iv~I~G~pGsGKTtLal~la~~~~~~g~---~vlyi~   96 (349)
T 2zr9_A           61 GRVIEIYGPESSGKTTVALHAVANAQAAGG---IAAFID   96 (349)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHTTC---CEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhCCC---eEEEEE
Confidence            467999999999999877666555554433   455554

>1bg2_A Kinesin; motor protein, ATPase, microtubule associated; HET: ADP; 1.80A {Homo sapiens} SCOP: c.37.1.9 PDB: 2p4n_K* 1mkj_A* 2kin_A* 3kin_A*

Probab=83.86  E-value=0.84  Score=38.09  Aligned_cols=22  Identities=32%  Similarity=0.295  Sum_probs=17.8

Q ss_pred             hHHcCCc--EEEeccCCCchHHHH
Q 028887          103 VLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       103 ~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      .++.|.+  ++.+|.||||||..-
T Consensus        72 ~~l~G~n~tifAYGqTGSGKTyTm   95 (325)
T 1bg2_A           72 DVLEGYNGTIFAYGQTSSGKTHTM   95 (325)
T ss_dssp             HHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhCCCeEEEEEECCCCCCCceEe
Confidence            3467865  788999999999875

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=83.84  E-value=2  Score=35.05  Aligned_cols=18  Identities=22%  Similarity=0.252  Sum_probs=15.5

Q ss_pred             CcEEEeccCCCchHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l  125 (202)
                      ..+++.|++|+|||...-
T Consensus        56 ~~vll~G~~GtGKT~la~   73 (338)
T 3pfi_A           56 DHILFSGPAGLGKTTLAN   73 (338)
T ss_dssp             CCEEEECSTTSSHHHHHH
T ss_pred             CeEEEECcCCCCHHHHHH
Confidence            579999999999997653

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=83.57  E-value=0.5  Score=39.13  Aligned_cols=19  Identities=32%  Similarity=0.564  Sum_probs=15.8

Q ss_pred             CCcEEEeccCCCchHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l  125 (202)
                      ++.+++.||+|+|||...-
T Consensus        70 ~~~vLl~GppGtGKT~la~   88 (368)
T 3uk6_A           70 GRAVLIAGQPGTGKTAIAM   88 (368)
T ss_dssp             TCEEEEEESTTSSHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHH
Confidence            3579999999999997643

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=83.42  E-value=0.67  Score=33.88  Aligned_cols=19  Identities=26%  Similarity=0.386  Sum_probs=16.0

Q ss_pred             cCCcEEEeccCCCchHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~  124 (202)
                      .+..+++.|++|||||...
T Consensus         3 ~~~~i~l~G~~GsGKSTl~   21 (173)
T 1kag_A            3 EKRNIFLVGPMGAGKSTIG   21 (173)
T ss_dssp             CCCCEEEECCTTSCHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            3567999999999999764

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=83.34  E-value=0.54  Score=35.37  Aligned_cols=21  Identities=19%  Similarity=0.115  Sum_probs=17.2

Q ss_pred             HcCCcEEEeccCCCchHHHHH
Q 028887          105 FSSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       105 ~~g~~~l~~a~TGsGKT~~~l  125 (202)
                      ..|.-+.+.|++|||||...-
T Consensus         4 ~~g~~i~l~G~~GsGKSTl~~   24 (207)
T 2j41_A            4 EKGLLIVLSGPSGVGKGTVRK   24 (207)
T ss_dssp             CCCCEEEEECSTTSCHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHH
Confidence            357788999999999997653

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=83.34  E-value=0.55  Score=40.47  Aligned_cols=18  Identities=39%  Similarity=0.562  Sum_probs=15.8

Q ss_pred             CCcEEEeccCCCchHHHH
Q 028887          107 SRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~  124 (202)
                      .+.++++||+|+|||+..
T Consensus       182 prGvLL~GPPGTGKTllA  199 (405)
T 4b4t_J          182 PKGVILYGPPGTGKTLLA  199 (405)
T ss_dssp             CCCEEEESCSSSSHHHHH
T ss_pred             CCceEEeCCCCCCHHHHH
Confidence            367999999999999774

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=83.33  E-value=0.51  Score=35.91  Aligned_cols=21  Identities=14%  Similarity=0.189  Sum_probs=17.6

Q ss_pred             HHcCCcEEEeccCCCchHHHH
Q 028887          104 LFSSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       104 i~~g~~~l~~a~TGsGKT~~~  124 (202)
                      +..|+-+++.|++|+|||...
T Consensus         9 ~~~~~~i~l~G~sGsGKsTl~   29 (204)
T 2qor_A            9 MARIPPLVVCGPSGVGKGTLI   29 (204)
T ss_dssp             CCCCCCEEEECCTTSCHHHHH
T ss_pred             cccCCEEEEECCCCCCHHHHH
Confidence            346788999999999999764

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=83.01  E-value=0.63  Score=35.58  Aligned_cols=17  Identities=24%  Similarity=0.534  Sum_probs=14.7

Q ss_pred             CcEEEeccCCCchHHHH
Q 028887          108 RDCILHAQTGSGKTLTY  124 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~  124 (202)
                      +-+++.||+|+|||...
T Consensus         2 RpIVi~GPSG~GK~Tl~   18 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLL   18 (186)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            56899999999999764

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=82.96  E-value=0.44  Score=38.30  Aligned_cols=21  Identities=29%  Similarity=0.243  Sum_probs=17.4

Q ss_pred             HHcCCcEEEeccCCCchHHHH
Q 028887          104 LFSSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       104 i~~g~~~l~~a~TGsGKT~~~  124 (202)
                      +..|.-+.+.||||||||...
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            456778999999999999764

>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=82.83  E-value=0.59  Score=38.39  Aligned_cols=17  Identities=24%  Similarity=0.387  Sum_probs=15.1

Q ss_pred             CcEEEeccCCCchHHHH
Q 028887          108 RDCILHAQTGSGKTLTY  124 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~  124 (202)
                      +.++++||+|+|||...
T Consensus        52 ~~vLl~GppGtGKT~la   68 (322)
T 3eie_A           52 SGILLYGPPGTGKSYLA   68 (322)
T ss_dssp             CEEEEECSSSSCHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            56999999999999765

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=82.83  E-value=0.89  Score=37.18  Aligned_cols=19  Identities=32%  Similarity=0.636  Sum_probs=16.3

Q ss_pred             cCCcEEEeccCCCchHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~  124 (202)
                      .+..+++.|++|+|||.+.
T Consensus        24 ~~~~vLi~Ge~GtGKt~lA   42 (304)
T 1ojl_A           24 SDATVLIHGDSGTGKELVA   42 (304)
T ss_dssp             TTSCEEEESCTTSCHHHHH
T ss_pred             CCCcEEEECCCCchHHHHH
Confidence            4578999999999999764

>3dc4_A Kinesin-like protein NOD; catalytic domain, ATPase, microtubule, ADP, nucleotide-binding protein, ATP-binding, coiled coil, motor protein; HET: ADP; 1.90A {Drosophila melanogaster} PDB: 3dcb_A* 3dco_N* 3pxn_A*

Probab=82.80  E-value=0.85  Score=38.39  Aligned_cols=21  Identities=29%  Similarity=0.487  Sum_probs=17.0

Q ss_pred             HHcCCc--EEEeccCCCchHHHH
Q 028887          104 LFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       104 i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      ++.|.+  ++.+|.||||||..-
T Consensus        90 ~l~G~N~tifAYGQTGSGKTyTM  112 (344)
T 3dc4_A           90 LLEGFQCTALAYGQTGTGKSYSM  112 (344)
T ss_dssp             HHHTCCEEEEEESSTTSSHHHHH
T ss_pred             hhCCCceEEEEecCCCCCCCeEE
Confidence            467765  688999999999874

>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=82.79  E-value=0.64  Score=34.17  Aligned_cols=19  Identities=26%  Similarity=0.296  Sum_probs=15.9

Q ss_pred             CCcEEEeccCCCchHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l  125 (202)
                      ++-+++.|++|||||.+.-
T Consensus         3 ~~~i~l~G~~GsGKST~a~   21 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIVR   21 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHH
Confidence            4568999999999998753

>4a14_A Kinesin, kinesin-like protein KIF7; motor protein, motor domain; HET: ADP; 1.60A {Homo sapiens} SCOP: c.37.1.0 PDB: 2xt3_A*

Probab=82.78  E-value=0.98  Score=37.97  Aligned_cols=21  Identities=43%  Similarity=0.561  Sum_probs=17.1

Q ss_pred             HHcCCc--EEEeccCCCchHHHH
Q 028887          104 LFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       104 i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      ++.|.+  ++.+|+||||||..-
T Consensus        79 ~l~G~n~tifAYGqTGSGKTyTm  101 (344)
T 4a14_A           79 FFEGFNATVFAYGQTGSGKTYTM  101 (344)
T ss_dssp             HHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHhhcCeeEEEecccCCCceEee
Confidence            467765  788999999999874

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=82.71  E-value=0.58  Score=36.83  Aligned_cols=17  Identities=29%  Similarity=0.544  Sum_probs=14.9

Q ss_pred             CcEEEeccCCCchHHHH
Q 028887          108 RDCILHAQTGSGKTLTY  124 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~  124 (202)
                      +.+++.|++|+|||...
T Consensus        46 ~~vll~G~~GtGKT~la   62 (257)
T 1lv7_A           46 KGVLMVGPPGTGKTLLA   62 (257)
T ss_dssp             CEEEEECCTTSCHHHHH
T ss_pred             CeEEEECcCCCCHHHHH
Confidence            56999999999999764

>2y65_A Kinesin, kinesin heavy chain; motor protein; HET: ADP; 2.20A {Drosophila melanogaster} PDB: 2y5w_A*

Probab=82.63  E-value=0.99  Score=38.30  Aligned_cols=21  Identities=33%  Similarity=0.370  Sum_probs=17.3

Q ss_pred             HHcCCc--EEEeccCCCchHHHH
Q 028887          104 LFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       104 i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      ++.|.+  ++.+|.||||||..-
T Consensus        80 ~l~G~n~tifAYGqTGSGKTyTm  102 (365)
T 2y65_A           80 VLAGYNGTIFAYGQTSSGKTHTM  102 (365)
T ss_dssp             HHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HhCCCceEEEeecCCCCCCceEE
Confidence            467765  788999999999885

>2vvg_A Kinesin-2; motor protein, nucleotide-binding, microtubule, ATP-binding; HET: ADP; 1.60A {Giardia intestinalis}

Probab=82.59  E-value=1  Score=38.05  Aligned_cols=21  Identities=33%  Similarity=0.433  Sum_probs=17.2

Q ss_pred             HHcCCc--EEEeccCCCchHHHH
Q 028887          104 LFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       104 i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      ++.|.+  ++.+|.||||||..-
T Consensus        85 ~l~G~n~tifAYGqTGSGKTyTm  107 (350)
T 2vvg_A           85 VLEGFNSTIFAYGQTGAGKTWTM  107 (350)
T ss_dssp             HHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HhCCCceeEEeecCCCCCCCEEe
Confidence            467765  788999999999875

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=82.53  E-value=0.73  Score=35.69  Aligned_cols=22  Identities=14%  Similarity=0.155  Sum_probs=17.2

Q ss_pred             HHcCCcEEEeccCCCchHHHHH
Q 028887          104 LFSSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       104 i~~g~~~l~~a~TGsGKT~~~l  125 (202)
                      +..|+-+.+.||+|+|||...-
T Consensus        20 i~~G~~~~lvGpsGsGKSTLl~   41 (218)
T 1z6g_A           20 MNNIYPLVICGPSGVGKGTLIK   41 (218)
T ss_dssp             --CCCCEEEECSTTSSHHHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHHHH
Confidence            3568889999999999997643

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=82.47  E-value=4.3  Score=33.91  Aligned_cols=50  Identities=20%  Similarity=0.197  Sum_probs=31.8

Q ss_pred             HcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHH
Q 028887          105 FSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVA  158 (202)
Q Consensus       105 ~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~  158 (202)
                      ..|.-+++.|++|+|||...+--+......+.   .++|++.+-. ..|+..++
T Consensus        44 ~~G~LiiIaG~pG~GKTt~al~ia~~~a~~g~---~Vl~fSlEms-~~ql~~Rl   93 (338)
T 4a1f_A           44 NKGSLVIIGARPSMGKTSLMMNMVLSALNDDR---GVAVFSLEMS-AEQLALRA   93 (338)
T ss_dssp             CTTCEEEEEECTTSCHHHHHHHHHHHHHHTTC---EEEEEESSSC-HHHHHHHH
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCC---eEEEEeCCCC-HHHHHHHH
Confidence            34566899999999999776555544444333   6788775422 34444444

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=82.44  E-value=0.67  Score=34.36  Aligned_cols=20  Identities=25%  Similarity=0.142  Sum_probs=16.6

Q ss_pred             CCcEEEeccCCCchHHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~  126 (202)
                      ++.+++.|++|||||.+.-.
T Consensus         5 ~~~i~l~G~~GsGKst~a~~   24 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQ   24 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            56789999999999987543

>2h58_A Kinesin-like protein KIFC3 variant; motor domain, ADP, structural genomics, structur Al genomics consortium, SGC; HET: ADP; 1.85A {Homo sapiens}

Probab=82.36  E-value=1  Score=37.60  Aligned_cols=25  Identities=28%  Similarity=0.316  Sum_probs=19.4

Q ss_pred             HHHhHHcCCc--EEEeccCCCchHHHH
Q 028887          100 ALPVLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       100 ~i~~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      .+..++.|.+  ++.+|.||||||...
T Consensus        72 lv~~~l~G~n~tifAYGqTGSGKTyTm   98 (330)
T 2h58_A           72 LVTSCIDGFNVCIFAYGQTGAGKTYTM   98 (330)
T ss_dssp             HHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHHhCCCEEEEEeECCCCCCCcEEE
Confidence            3445678866  788999999999775

>3b6u_A Kinesin-like protein KIF3B; structural genomics consortium, motor domain, ADP, SGC, ATP-binding, coiled coil, microtubule, motor protein; HET: ADP; 1.80A {Homo sapiens} PDB: 3b6v_A*

Probab=82.30  E-value=1  Score=38.39  Aligned_cols=21  Identities=33%  Similarity=0.450  Sum_probs=17.1

Q ss_pred             HHcCCc--EEEeccCCCchHHHH
Q 028887          104 LFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       104 i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      ++.|.+  ++.+|.||||||..-
T Consensus        97 ~l~G~n~tifAYGqTGSGKTyTM  119 (372)
T 3b6u_A           97 VLQGFNGTIFAYGQTGTGKTYTM  119 (372)
T ss_dssp             HHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HhCCCeeeEEeecCCCCCCCEeE
Confidence            467865  788999999999774

>3gbj_A KIF13B protein; kinesin, motor domain, ADP, structural genomics, structural genomics consortium, SGC, ATP-binding, microtubule, motor protein; HET: ADP; 2.10A {Homo sapiens} SCOP: c.37.1.9

Probab=82.30  E-value=1  Score=38.07  Aligned_cols=23  Identities=35%  Similarity=0.426  Sum_probs=18.3

Q ss_pred             HhHHcCCc--EEEeccCCCchHHHH
Q 028887          102 PVLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       102 ~~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      ..++.|.+  ++.+|.||||||...
T Consensus        86 ~~~l~G~n~tifAYGqTGSGKTyTm  110 (354)
T 3gbj_A           86 QNAFDGYNACIFAYGQTGSGKSYTM  110 (354)
T ss_dssp             HHHHTTCCEEEEEEECTTSSHHHHH
T ss_pred             HHHhCCceeEEEeeCCCCCCCceEE
Confidence            34567866  688999999999875

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=82.23  E-value=0.58  Score=37.22  Aligned_cols=18  Identities=28%  Similarity=0.248  Sum_probs=15.4

Q ss_pred             CcEEEeccCCCchHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l  125 (202)
                      ..++++||+|+|||...-
T Consensus        65 ~~vLl~G~~GtGKT~la~   82 (272)
T 1d2n_A           65 VSVLLEGPPHSGKTALAA   82 (272)
T ss_dssp             EEEEEECSTTSSHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHH
Confidence            469999999999998753

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=82.19  E-value=0.7  Score=38.44  Aligned_cols=20  Identities=35%  Similarity=0.474  Sum_probs=17.4

Q ss_pred             HHcCCcEEEeccCCCchHHH
Q 028887          104 LFSSRDCILHAQTGSGKTLT  123 (202)
Q Consensus       104 i~~g~~~l~~a~TGsGKT~~  123 (202)
                      +..|..+.+.|+||||||..
T Consensus       168 i~~g~~v~i~G~~GsGKTTl  187 (330)
T 2pt7_A          168 IAIGKNVIVCGGTGSGKTTY  187 (330)
T ss_dssp             HHHTCCEEEEESTTSCHHHH
T ss_pred             ccCCCEEEEECCCCCCHHHH
Confidence            45788999999999999974

>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=82.17  E-value=0.56  Score=34.95  Aligned_cols=21  Identities=24%  Similarity=0.309  Sum_probs=17.2

Q ss_pred             HcCCcEEEeccCCCchHHHHH
Q 028887          105 FSSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       105 ~~g~~~l~~a~TGsGKT~~~l  125 (202)
                      ..|.-+++.|++|+|||...-
T Consensus         7 ~~g~~i~l~G~~GsGKSTl~~   27 (191)
T 1zp6_A            7 LGGNILLLSGHPGSGKSTIAE   27 (191)
T ss_dssp             CTTEEEEEEECTTSCHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHH
Confidence            456779999999999997643

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=82.17  E-value=0.59  Score=40.66  Aligned_cols=18  Identities=33%  Similarity=0.540  Sum_probs=15.8

Q ss_pred             CCcEEEeccCCCchHHHH
Q 028887          107 SRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~  124 (202)
                      .+.++++||+|+|||+..
T Consensus       215 prGvLL~GPPGtGKTllA  232 (437)
T 4b4t_L          215 PKGVLLYGPPGTGKTLLA  232 (437)
T ss_dssp             CCEEEEESCTTSSHHHHH
T ss_pred             CCeEEEECCCCCcHHHHH
Confidence            367999999999999875

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=82.04  E-value=0.64  Score=38.34  Aligned_cols=18  Identities=28%  Similarity=0.457  Sum_probs=15.5

Q ss_pred             CcEEEeccCCCchHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l  125 (202)
                      +.++++||+|+|||...-
T Consensus        46 ~~iLL~GppGtGKT~la~   63 (322)
T 1xwi_A           46 RGILLFGPPGTGKSYLAK   63 (322)
T ss_dssp             SEEEEESSSSSCHHHHHH
T ss_pred             ceEEEECCCCccHHHHHH
Confidence            679999999999997653

>1goj_A Kinesin, kinesin heavy chain; motor protein, ATPase; HET: ADP; 2.3A {Neurospora crassa} SCOP: c.37.1.9

Probab=82.01  E-value=1  Score=38.12  Aligned_cols=21  Identities=29%  Similarity=0.494  Sum_probs=17.2

Q ss_pred             HHcCCc--EEEeccCCCchHHHH
Q 028887          104 LFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       104 i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      ++.|.+  ++.+|.||||||..-
T Consensus        76 ~l~G~n~tifAYGqTGSGKTyTm   98 (355)
T 1goj_A           76 ILNGYNGTVFAYGQTGAGKSYTM   98 (355)
T ss_dssp             HTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HhCCCcceEEEECCCCCCcceEe
Confidence            467765  788999999999875

>1t5c_A CENP-E protein, centromeric protein E; kinesin motor-domain-ADP complex, stranded beta-sheet core with solvent exposed alpha-helices; HET: ADP PIN; 2.50A {Homo sapiens}

Probab=81.93  E-value=1.1  Score=37.87  Aligned_cols=22  Identities=32%  Similarity=0.294  Sum_probs=17.7

Q ss_pred             hHHcCCc--EEEeccCCCchHHHH
Q 028887          103 VLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       103 ~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      .++.|.+  ++.+|.||||||...
T Consensus        72 ~~l~G~n~tifAYGqTGSGKTyTM   95 (349)
T 1t5c_A           72 SAIQGYNGTIFAYGQTASGKTYTM   95 (349)
T ss_dssp             HHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHcCCccceeeecCCCCCCCeEE
Confidence            3467765  788999999999876

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=81.93  E-value=0.61  Score=40.44  Aligned_cols=18  Identities=33%  Similarity=0.575  Sum_probs=15.6

Q ss_pred             CCcEEEeccCCCchHHHH
Q 028887          107 SRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~  124 (202)
                      .+.++++||+|+|||+..
T Consensus       206 prGiLL~GPPGtGKT~la  223 (428)
T 4b4t_K          206 PRGVLLYGPPGTGKTMLV  223 (428)
T ss_dssp             CCEEEEESCTTTTHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            367999999999999775

>2zfi_A Kinesin-like protein KIF1A, kinesin heavy chain isoform 5C; alpha and beta protein, enzyme, ATPase, P-loop, motor protein, ATP-binding, coiled coil; HET: ADP; 1.55A {Mus musculus} SCOP: c.37.1.9 PDB: 1vfw_A* 1vfx_A* 1vfz_A* 1vfv_A* 2zfj_A* 2zfk_A* 2zfl_A* 2zfm_A* 1i5s_A* 1i6i_A* 2hxf_C* 1ia0_K* 2hxh_C*

Probab=81.89  E-value=1.1  Score=38.03  Aligned_cols=22  Identities=32%  Similarity=0.430  Sum_probs=17.5

Q ss_pred             hHHcCCc--EEEeccCCCchHHHH
Q 028887          103 VLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       103 ~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      .++.|.+  ++.+|.||||||...
T Consensus        84 ~~l~G~N~tifAYGqTGSGKTyTm  107 (366)
T 2zfi_A           84 HAFEGYNVCIFAYGQTGAGKSYTM  107 (366)
T ss_dssp             HHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhcCCeeEEEEeCCCCCCCceEe
Confidence            3467765  788999999999765

>3lre_A Kinesin-like protein KIF18A; motor protein, nucleotide binding, microtubule binding, ATP- cell projection, cytoskeleton, glycoprotein, microtubule; HET: ADP; 2.20A {Homo sapiens} SCOP: c.37.1.0

Probab=81.78  E-value=1  Score=38.03  Aligned_cols=21  Identities=29%  Similarity=0.450  Sum_probs=17.2

Q ss_pred             HHcCCc--EEEeccCCCchHHHH
Q 028887          104 LFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       104 i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      ++.|.+  ++.+|.||||||..-
T Consensus       101 ~l~G~n~tifAYGqTGSGKTyTm  123 (355)
T 3lre_A          101 FLNGYNCTVLAYGATGAGKTHTM  123 (355)
T ss_dssp             HTTTCCEEEEEECCTTSSHHHHH
T ss_pred             HhCCCceEEEEeCCCCCCceeee
Confidence            467765  788999999999875

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=81.74  E-value=0.68  Score=35.79  Aligned_cols=21  Identities=14%  Similarity=0.229  Sum_probs=17.7

Q ss_pred             HcCCcEEEeccCCCchHHHHH
Q 028887          105 FSSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       105 ~~g~~~l~~a~TGsGKT~~~l  125 (202)
                      ..|+-+++.||+|+|||...-
T Consensus        17 ~~g~~ivl~GPSGaGKsTL~~   37 (197)
T 3ney_A           17 QGRKTLVLIGASGVGRSHIKN   37 (197)
T ss_dssp             CSCCEEEEECCTTSSHHHHHH
T ss_pred             CCCCEEEEECcCCCCHHHHHH
Confidence            467889999999999998654

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=81.69  E-value=0.7  Score=33.36  Aligned_cols=17  Identities=24%  Similarity=0.231  Sum_probs=14.2

Q ss_pred             cEEEeccCCCchHHHHH
Q 028887          109 DCILHAQTGSGKTLTYL  125 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l  125 (202)
                      -+++.|++|||||...-
T Consensus         3 ~I~l~G~~GsGKsT~a~   19 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAK   19 (179)
T ss_dssp             EEEEECCTTSCHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999998653

>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=81.66  E-value=3.6  Score=33.30  Aligned_cols=43  Identities=16%  Similarity=0.153  Sum_probs=29.4

Q ss_pred             HHHHHHHHCCCCCCcHHHHHH-HHhHHcCC-----cEEEeccCCCchHHHHH
Q 028887           80 HVLRRMEETGYVLPTDIQREA-LPVLFSSR-----DCILHAQTGSGKTLTYL  125 (202)
Q Consensus        80 ~l~~~l~~~g~~~~t~~Q~~~-i~~i~~g~-----~~l~~a~TGsGKT~~~l  125 (202)
                      .+.+-|+-.||.   +++-.. +...+.|+     .++++||.|+|||..+.
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            566667777764   444332 34455553     49999999999998876

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=81.63  E-value=0.63  Score=37.81  Aligned_cols=17  Identities=18%  Similarity=0.182  Sum_probs=14.6

Q ss_pred             CcEEEeccCCCchHHHH
Q 028887          108 RDCILHAQTGSGKTLTY  124 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~  124 (202)
                      +.++++||+|+|||...
T Consensus        37 ~~lLl~GppGtGKT~la   53 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQC   53 (293)
T ss_dssp             SEEEEEECTTSCHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            46899999999999764

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=81.61  E-value=0.62  Score=34.54  Aligned_cols=20  Identities=25%  Similarity=0.223  Sum_probs=16.9

Q ss_pred             cCCcEEEeccCCCchHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l  125 (202)
                      .|.-+.+.|++|||||..+-
T Consensus         8 ~gei~~l~G~nGsGKSTl~~   27 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFAK   27 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHH
Confidence            46678899999999998765

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=81.60  E-value=1.3  Score=33.38  Aligned_cols=16  Identities=25%  Similarity=0.358  Sum_probs=14.1

Q ss_pred             cEEEeccCCCchHHHH
Q 028887          109 DCILHAQTGSGKTLTY  124 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~  124 (202)
                      .+++.|++|+|||...
T Consensus        47 ~~ll~G~~G~GKT~l~   62 (250)
T 1njg_A           47 AYLFSGTRGVGKTSIA   62 (250)
T ss_dssp             EEEEECSTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5899999999999764

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=81.56  E-value=0.76  Score=35.88  Aligned_cols=23  Identities=22%  Similarity=0.260  Sum_probs=17.8

Q ss_pred             HHcCCcEEEeccCCCchHHHHHH
Q 028887          104 LFSSRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       104 i~~g~~~l~~a~TGsGKT~~~l~  126 (202)
                      +-.|.-+++.||+|+|||...-.
T Consensus        13 ~~~G~ii~l~GpsGsGKSTLlk~   35 (219)
T 1s96_A           13 MAQGTLYIVSAPSGAGKSSLIQA   35 (219)
T ss_dssp             --CCCEEEEECCTTSCHHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHH
Confidence            45688899999999999986543

>1x88_A Kinesin-like protein KIF11; switch II, motor domain, NECK linker, cell cycle; HET: ADP NAT; 1.80A {Homo sapiens} SCOP: c.37.1.9 PDB: 3hqd_A* 3ken_A* 2pg2_A* 1yrs_A* 2fme_A* 2g1q_A* 2gm1_A* 1ii6_A* 2uyi_A* 2uym_A* 2wog_A* 2x2r_A* 2x7c_A* 2x7d_A* 2x7e_A* 2xae_A* 3k3b_A* 3k5e_A* 3l9h_A* 1q0b_A* ...

Probab=81.47  E-value=1  Score=38.08  Aligned_cols=22  Identities=32%  Similarity=0.413  Sum_probs=17.4

Q ss_pred             hHHcCCc--EEEeccCCCchHHHH
Q 028887          103 VLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       103 ~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      .++.|.+  ++.+|.||||||..-
T Consensus        83 ~~l~G~n~tifAYGqTGSGKTyTM  106 (359)
T 1x88_A           83 EVIMGYNCTIFAYGQTGTGKTFTM  106 (359)
T ss_dssp             HHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             HHhCCCceEEEEeCCCCCCCceEE
Confidence            3467765  788999999999764

>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=81.46  E-value=2.5  Score=41.18  Aligned_cols=56  Identities=20%  Similarity=0.241  Sum_probs=43.2

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhc---------CCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQ---------RSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~---------~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      .|.. +|.|.-|||||.+-..-++..+...         -..-+.|+++=|+.=|..+.+++++..
T Consensus        16 ~g~~-lV~AsAGSGKT~~L~~r~lrLll~~g~~~~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~~L   80 (1180)
T 1w36_B           16 QGER-LIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSNI   80 (1180)
T ss_dssp             SSCE-EEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHHH
T ss_pred             CCCE-EEEECCCCCHHHHHHHHHHHHHhcCCcccccCCCCCHHHEEEEeccHHHHHHHHHHHHHHH
Confidence            3444 9999999999999888888887532         123479999999998888888876543

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=81.44  E-value=0.78  Score=35.00  Aligned_cols=23  Identities=17%  Similarity=0.159  Sum_probs=17.5

Q ss_pred             hHHcCCcEEEeccCCCchHHHHH
Q 028887          103 VLFSSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       103 ~i~~g~~~l~~a~TGsGKT~~~l  125 (202)
                      .+..|.-+.+.||+|+|||...-
T Consensus        16 ~i~~Gei~~l~GpnGsGKSTLl~   38 (207)
T 1znw_A           16 PAAVGRVVVLSGPSAVGKSTVVR   38 (207)
T ss_dssp             ---CCCEEEEECSTTSSHHHHHH
T ss_pred             CCCCCCEEEEECCCCCCHHHHHH
Confidence            56778889999999999997653

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=81.39  E-value=1  Score=38.73  Aligned_cols=25  Identities=32%  Similarity=0.377  Sum_probs=19.5

Q ss_pred             HHHhHHcCCc--EEEeccCCCchHHHH
Q 028887          100 ALPVLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       100 ~i~~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      .+..++.|.+  ++.+|.||||||..-
T Consensus       132 lv~~~l~G~N~tifAYGqTGSGKTyTM  158 (403)
T 4etp_A          132 LVQSSLDGYNVAIFAYGQTGSGKTFTM  158 (403)
T ss_dssp             HHHHHHTTCCEEEEEESCTTSSHHHHH
T ss_pred             HHHHHhCCcceEEEEECCCCCCCceEe
Confidence            3445578876  688999999999875

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=81.13  E-value=1.5  Score=36.40  Aligned_cols=55  Identities=9%  Similarity=0.001  Sum_probs=31.8

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhc---CCccEEEEecCCHHh-HHHHHHHHHHh
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQ---RSAVQAVIVVPTREL-GMQVTKVARVL  161 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~---~~~~~~Lil~Ptr~L-a~Q~~~~~~~l  161 (202)
                      |.-+++.|++|+|||...+..+.......   ..+-.++++.-+..+ ..++.+++..+
T Consensus       122 G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~~~~~~~  180 (343)
T 1v5w_A          122 MAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDIADRF  180 (343)
T ss_dssp             SEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHHHHHHc
Confidence            35689999999999987655444322210   123367888765432 33444444443

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=81.10  E-value=4.5  Score=41.69  Aligned_cols=47  Identities=19%  Similarity=0.217  Sum_probs=35.2

Q ss_pred             HHhHHc------CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHh
Q 028887          101 LPVLFS------SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTREL  150 (202)
Q Consensus       101 i~~i~~------g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~L  150 (202)
                      +..++.      |+.++++||+|+|||...+..+.+....+.   +++++...-.+
T Consensus      1415 LD~lLG~GGi~~g~~vll~GppGtGKT~LA~ala~ea~~~G~---~v~Fi~~e~~~ 1467 (2050)
T 3cmu_A         1415 LDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGK---TCAFIDAEHAL 1467 (2050)
T ss_dssp             HHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHHHTTTC---CEEEECTTSCC
T ss_pred             HHHhcCCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCC---cEEEEEccccc
Confidence            556666      588999999999999988777666665554   68887766433

>3t0q_A AGR253WP; kinesin, alpha and beta proteins, P-loop containing nucleosi triphosphate hydrolases, microtubule motor protein; HET: ADP; 2.35A {Ashbya gossypii}

Probab=81.05  E-value=1  Score=37.90  Aligned_cols=25  Identities=32%  Similarity=0.351  Sum_probs=19.5

Q ss_pred             HHHhHHcCCc--EEEeccCCCchHHHH
Q 028887          100 ALPVLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       100 ~i~~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      .+..++.|.+  ++.+|.||||||..-
T Consensus        77 lv~~~l~G~n~tifAYGqTGSGKTyTm  103 (349)
T 3t0q_A           77 LVQSSLDGYNVCIFAYGQTGSGKTYTM  103 (349)
T ss_dssp             HHHGGGTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHHCCcceeEEEeCCCCCCCceEe
Confidence            4455677866  688999999999875

>1v8k_A Kinesin-like protein KIF2C; microtubule destabilizer, structural P; HET: ANP; 2.25A {Mus musculus} SCOP: c.37.1.9 PDB: 1v8j_A* 2gry_A*

Probab=81.00  E-value=1.1  Score=38.70  Aligned_cols=21  Identities=48%  Similarity=0.733  Sum_probs=17.1

Q ss_pred             HHcCCc--EEEeccCCCchHHHH
Q 028887          104 LFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       104 i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      ++.|.+  ++.+|.||||||..-
T Consensus       150 ~l~G~N~tifAYGQTGSGKTyTM  172 (410)
T 1v8k_A          150 IFEGGKATCFAYGQTGSGKTHTM  172 (410)
T ss_dssp             HHTTCEEEEEEEESTTSSHHHHH
T ss_pred             HhcCCceeEEeecCCCCCCCeEe
Confidence            467765  788999999999875

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=80.99  E-value=1.9  Score=36.45  Aligned_cols=37  Identities=16%  Similarity=0.132  Sum_probs=24.7

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecC
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP  146 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~P  146 (202)
                      |.-+++.|++|+|||...+-.+.+....+.   .++++..
T Consensus        74 G~li~I~G~pGsGKTtlal~la~~~~~~g~---~vlyi~~  110 (366)
T 1xp8_A           74 GRITEIYGPESGGKTTLALAIVAQAQKAGG---TCAFIDA  110 (366)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHTTC---CEEEEES
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHHHHCCC---eEEEEEC
Confidence            466899999999999766555544444333   4555543

>3u06_A Protein claret segregational; motor domain, stalk rotation, power stroke, kinesin-14, MICR binding, NCD, transport, molecular motor; HET: ADP GOL; 2.35A {Drosophila melanogaster} PDB: 2ncd_A* 1n6m_A* 1cz7_A* 3l1c_A*

Probab=80.94  E-value=1.1  Score=38.73  Aligned_cols=25  Identities=32%  Similarity=0.376  Sum_probs=19.4

Q ss_pred             HHHhHHcCCc--EEEeccCCCchHHHH
Q 028887          100 ALPVLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       100 ~i~~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      .+..++.|.+  ++.+|.||||||...
T Consensus       130 lv~~~l~G~n~tifAYGqTGSGKTyTM  156 (412)
T 3u06_A          130 LIQSALDGYNICIFAYGQTGSGKTYTM  156 (412)
T ss_dssp             HHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHHHCCCceEEEEecCCCCCCeeEe
Confidence            3445678866  788899999999875

>2wbe_C Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mitosis, GTP-binding, motor protein, cell division, cell cycle, microtubule, ATP-binding; HET: GTP ANP GDP TA1; 9.40A {Drosophila melanogaster}

Probab=80.71  E-value=1.1  Score=38.10  Aligned_cols=21  Identities=33%  Similarity=0.471  Sum_probs=17.0

Q ss_pred             HHcCCc--EEEeccCCCchHHHH
Q 028887          104 LFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       104 i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      ++.|.+  ++.+|.||||||..-
T Consensus        96 ~l~G~n~tifAYGqTGSGKTyTm  118 (373)
T 2wbe_C           96 VLNGYNCTVFAYGQTGTGKTHTM  118 (373)
T ss_dssp             HHHTCCEEEEEECSTTSSHHHHH
T ss_pred             HhCCceEEEEeecCCCCCcceec
Confidence            467765  788999999999774

>3cob_A Kinesin heavy chain-like protein; motor, switch II, loop L11, conformation, nucleotide, ATP-binding, microtubule, motor protein; HET: ADP; 2.20A {Solanum tuberosum} SCOP: c.37.1.9 PDB: 3cnz_A* 1sdm_A* 3h4s_A*

Probab=80.69  E-value=1  Score=38.34  Aligned_cols=24  Identities=33%  Similarity=0.389  Sum_probs=18.7

Q ss_pred             HHhHHcCCc--EEEeccCCCchHHHH
Q 028887          101 LPVLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       101 i~~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      +..++.|.+  ++.+|.||||||..-
T Consensus        72 v~~~l~G~n~tifAYGqTGSGKTyTM   97 (369)
T 3cob_A           72 VQSAVDGYNVCIFAYGQTGSGKTFTI   97 (369)
T ss_dssp             HHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             hHhhhcCCceEEEEECCCCCCCeEee
Confidence            344577865  678999999999875

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=80.66  E-value=0.79  Score=33.88  Aligned_cols=18  Identities=17%  Similarity=0.326  Sum_probs=15.5

Q ss_pred             CCcEEEeccCCCchHHHH
Q 028887          107 SRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~  124 (202)
                      +..+++.|++|||||...
T Consensus         3 ~~~I~i~G~~GsGKsT~~   20 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSS   20 (192)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            567899999999999764

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=80.58  E-value=5.4  Score=42.28  Aligned_cols=46  Identities=17%  Similarity=0.231  Sum_probs=29.3

Q ss_pred             HHHHHHHHCCCCCCcHHHH-HHH---HhHHcCCcEEEeccCCCchHHHHHH
Q 028887           80 HVLRRMEETGYVLPTDIQR-EAL---PVLFSSRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus        80 ~l~~~l~~~g~~~~t~~Q~-~~i---~~i~~g~~~l~~a~TGsGKT~~~l~  126 (202)
                      .+.+.+.+.|+. +++.+. .++   ..+.....+++.||||+|||.++-.
T Consensus       893 ~i~~~~~~~~l~-~~~~~~~K~~ql~e~~~~r~gvmlvGptgsGKTt~~~~  942 (2695)
T 4akg_A          893 CLKDAGQRSGFS-MSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATWKT  942 (2695)
T ss_dssp             HHHHHHHHHTCC-CCHHHHHHHHHHHHHHHHCSEEEEECSTTSSHHHHHHH
T ss_pred             HHHHHHHHcCCc-ccHHHHHHHHHHHHHHHhcceEEEECCCCCCHHHHHHH
Confidence            344555566764 455442 222   2334567799999999999998644

>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=80.40  E-value=0.87  Score=38.08  Aligned_cols=17  Identities=24%  Similarity=0.387  Sum_probs=15.1

Q ss_pred             CcEEEeccCCCchHHHH
Q 028887          108 RDCILHAQTGSGKTLTY  124 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~  124 (202)
                      +.++++||+|+|||...
T Consensus        85 ~~iLL~GppGtGKT~la  101 (355)
T 2qp9_X           85 SGILLYGPPGTGKSYLA  101 (355)
T ss_dssp             CCEEEECSTTSCHHHHH
T ss_pred             ceEEEECCCCCcHHHHH
Confidence            56999999999999875

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=80.38  E-value=0.9  Score=37.99  Aligned_cols=19  Identities=42%  Similarity=0.511  Sum_probs=16.1

Q ss_pred             CCcEEEeccCCCchHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l  125 (202)
                      ...+++.|++|+|||...-
T Consensus        72 ~~~ill~Gp~GtGKT~la~   90 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMAQ   90 (376)
T ss_dssp             CCCEEEECCTTSSHHHHHH
T ss_pred             CCCEEEECCCCCCHHHHHH
Confidence            4679999999999997653

>2heh_A KIF2C protein; kinesin, motor domain, ADP, structural genomics, structural genomics consortium, SGC, structural protein; HET: ADP; 2.15A {Homo sapiens} PDB: 3edl_D*

Probab=80.34  E-value=1.2  Score=38.06  Aligned_cols=21  Identities=48%  Similarity=0.733  Sum_probs=17.2

Q ss_pred             HHcCCc--EEEeccCCCchHHHH
Q 028887          104 LFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       104 i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      ++.|.+  ++.+|.||||||..-
T Consensus       130 ~l~G~N~tifAYGQTGSGKTyTM  152 (387)
T 2heh_A          130 IFEGGKATCFAYGQTGSGKTHTM  152 (387)
T ss_dssp             HHTTCEEEEEEESCTTSSHHHHH
T ss_pred             HhcCCceEEEEecCCCCCCCeEe
Confidence            467765  788999999999875

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=80.28  E-value=2.2  Score=32.69  Aligned_cols=24  Identities=17%  Similarity=0.108  Sum_probs=18.9

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIF  129 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l  129 (202)
                      .|.-+.+.|++|+|||.....-+.
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~l~~   46 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHTLAV   46 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHH
Confidence            457789999999999987655443

>1f9v_A Kinesin-like protein KAR3; kinesin-related protein, motor protein, microtubinding proteinbule, contractIle protein; HET: ADP; 1.30A {Saccharomyces cerevisiae} SCOP: c.37.1.9 PDB: 1f9t_A* 1f9w_A* 1f9u_A* 3kar_A*

Probab=80.23  E-value=1.4  Score=37.15  Aligned_cols=25  Identities=32%  Similarity=0.377  Sum_probs=19.2

Q ss_pred             HHHhHHcCCc--EEEeccCCCchHHHH
Q 028887          100 ALPVLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       100 ~i~~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      .+..++.|.+  ++.+|.||||||..-
T Consensus        76 lv~~~l~G~n~tifAYGqTGSGKTyTM  102 (347)
T 1f9v_A           76 LVQSSLDGYNVCIFAYGQTGSGKTFTM  102 (347)
T ss_dssp             HHGGGGGTCCEEEEEECCTTSSHHHHH
T ss_pred             HHHHhcCCceeEEEEECCCCCCCcEec
Confidence            3445577866  788999999999865

>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=80.23  E-value=0.79  Score=39.68  Aligned_cols=19  Identities=37%  Similarity=0.543  Sum_probs=16.2

Q ss_pred             CCcEEEeccCCCchHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l  125 (202)
                      ++.++++||+|+|||....
T Consensus        63 ~~~iLl~GppGtGKT~la~   81 (456)
T 2c9o_A           63 GRAVLLAGPPGTGKTALAL   81 (456)
T ss_dssp             TCEEEEECCTTSSHHHHHH
T ss_pred             CCeEEEECCCcCCHHHHHH
Confidence            3679999999999997754

---

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	202
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	2e-12
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	3e-12
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	5e-11
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	5e-11
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	9e-11
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	6e-10
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	1e-09
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	4e-09
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	8e-08
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	9e-08
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	5e-07
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	3e-06
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	5e-06
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	4e-04

>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 = 61.5 bits (148), Expect = 2e-12
 Identities = 20/93 (21%), Positives = 42/93 (45%), Gaps = 4/93 (4%)

Query: 67  LTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLL 126
           + + EL +  +  + +  ++E G       Q EA+  +FS ++ +L   T +GKTL   +
Sbjct: 1   MKVEELAES-ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEM 59

Query: 127 LIFSLVNAQRSAVQAVIVVPTRELGMQVTKVAR 159
            +           +++ VVP R L  +  +  +
Sbjct: 60  AMVREAIKGG---KSLYVVPLRALAGEKYESFK 89

>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 = 61.0 bits (147), Expect = 3e-12
 Identities = 29/81 (35%), Positives = 45/81 (55%)

Query: 77  VPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR 136
           + E +LR +   G+  P+ IQ+ A+       D I  AQ+G+GKT T+ + I   +    
Sbjct: 19  LSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDL 78

Query: 137 SAVQAVIVVPTRELGMQVTKV 157
            A QA+++ PTREL  Q+ KV
Sbjct: 79  KATQALVLAPTRELAQQIQKV 99

>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 = 57.5 bits (138), Expect = 5e-11
 Identities = 26/80 (32%), Positives = 47/80 (58%)

Query: 77  VPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR 136
           + E++LR +   G+  P+ IQ+ A+  +    D +  AQ+G+GKT T+ +     ++   
Sbjct: 17  LDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSV 76

Query: 137 SAVQAVIVVPTRELGMQVTK 156
            A QA+++ PTREL +Q+ K
Sbjct: 77  KAPQALMLAPTRELALQIQK 96

>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 = 57.6 bits (138), Expect = 5e-11
 Identities = 18/83 (21%), Positives = 27/83 (32%), Gaps = 3/83 (3%)

Query: 82  LRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQA 141
                      P  IQ+     +         A TG GKT   L +   L    +   + 
Sbjct: 33  FVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKGK---RC 89

Query: 142 VIVVPTRELGMQVTKVARVLAAK 164
            ++ PT  L +Q  +  R  A K
Sbjct: 90  YVIFPTSLLVIQAAETIRKYAEK 112

>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 = 56.8 bits (136), Expect = 9e-11
 Identities = 29/86 (33%), Positives = 49/86 (56%)

Query: 77  VPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR 136
           + E +LR +   G+  P+ IQ+ A+  +   RD I  +Q+G+GKT T+ + +   ++ Q 
Sbjct: 24  LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV 83

Query: 137 SAVQAVIVVPTRELGMQVTKVARVLA 162
              QA+I+ PTREL +Q+ K    L 
Sbjct: 84  RETQALILAPTRELAVQIQKGLLALG 109

>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 = 55.3 bits (132), Expect = 6e-10
 Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 2/52 (3%)

Query: 108 RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVAR 159
           R  I+    G+GKT  YL  I  +  A +  ++ +I+ PTR +  ++ +  R
Sbjct: 10  RLTIMDLHPGAGKTKRYLPAI--VREAIKRGLRTLILAPTRVVAAEMEEALR 59

>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 = 53.8 bits (128), Expect = 1e-09
 Identities = 29/117 (24%), Positives = 59/117 (50%)

Query: 77  VPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR 136
           +   +L  + E G+  P+ IQ E++P+  S RD +  A+ G+GK+  YL+ +   ++ ++
Sbjct: 10  LKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKK 69

Query: 137 SAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWL 193
             +QA+++VPTREL +QV+++   ++       +           D   L      +
Sbjct: 70  DNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVV 126

>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 = 51.8 bits (123), Expect = 4e-09
 Identities = 21/87 (24%), Positives = 42/87 (48%)

Query: 77  VPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR 136
           +   +LR + + G+  P+++Q E +P      D +  A++G GKT  ++L     +    
Sbjct: 8   LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVT 67

Query: 137 SAVQAVIVVPTRELGMQVTKVARVLAA 163
             V  +++  TREL  Q++K     + 
Sbjct: 68  GQVSVLVMCHTRELAFQISKEYERFSK 94

>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 = 48.4 bits (114), Expect = 8e-08
 Identities = 23/71 (32%), Positives = 42/71 (59%)

Query: 76  HVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ 135
           ++   +L  + E G+  P+ IQ EA+PV  + RD +  A+ G+GKT  +++     V  +
Sbjct: 7   YLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPK 66

Query: 136 RSAVQAVIVVP 146
            + +QA+I+VP
Sbjct: 67  LNKIQALIMVP 77

>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 = 48.1 bits (113), Expect = 9e-08
 Identities = 29/122 (23%), Positives = 49/122 (40%)

Query: 77  VPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQR 136
               ++  ++   +  PT+IQ   +P        +  +QTG+GKT  YLL I   +  +R
Sbjct: 8   FQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPER 67

Query: 137 SAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKVL 196
           + VQAVI  PTREL  Q+      +        +    C +        L +      ++
Sbjct: 68  AEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIV 127

Query: 197 YS 198
             
Sbjct: 128 IG 129

>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 = 46.4 bits (109), Expect = 5e-07
 Identities = 26/90 (28%), Positives = 45/90 (50%), Gaps = 9/90 (10%)

Query: 77  VPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLV---- 132
           +   +   +    Y  PT IQ+ A+P +   RD +  AQTGSGKT  +L+ I + +    
Sbjct: 28  LDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQD 87

Query: 133 -----NAQRSAVQAVIVVPTRELGMQVTKV 157
                 ++ +  + +I+ PTREL +Q+   
Sbjct: 88  LNQQRYSKTAYPKCLILAPTRELAIQILSE 117

>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 = 43.9 bits (102), Expect = 3e-06
 Identities = 21/80 (26%), Positives = 30/80 (37%), Gaps = 8/80 (10%)

Query: 80  HVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAV 139
            VL+     GY      Q E +  + S RDC++   TG GK+L Y +    L        
Sbjct: 15  QVLQET--FGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLNG------ 66

Query: 140 QAVIVVPTRELGMQVTKVAR 159
             V+V P   L        +
Sbjct: 67  LTVVVSPLISLMKDQVDQLQ 86

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 43.2 bits (100), Expect = 5e-06
 Identities = 15/66 (22%), Positives = 25/66 (37%), Gaps = 7/66 (10%)

Query: 81  VLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQ 140
           VLRR      + P   Q           +C++   TG GKTL  +++    +      V 
Sbjct: 2   VLRR----DLIQPRIYQEVIYAKCKE-TNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVL 56

Query: 141 AVIVVP 146
             ++ P
Sbjct: 57  --MLAP 60

>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 = 37.7 bits (87), Expect = 4e-04
 Identities = 15/50 (30%), Positives = 30/50 (60%), Gaps = 1/50 (2%)

Query: 77  VPEHVLRRMEETGYVLPTDIQREALPVLFSSR-DCILHAQTGSGKTLTYL 125
           + +++L  +   G+  PTDIQ + +P+  +   + +  A+TGSGKT ++ 
Sbjct: 11  LSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFA 60

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	202
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.94
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.93
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.92
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.92
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.91
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.91
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.88
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.87
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.83
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.75
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.7
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.65
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.44
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.44
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.43
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.06
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.06
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.0
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.66
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	98.61
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	98.12
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.94
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	97.66
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	97.4
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	97.37
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	97.02
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	96.78
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	96.03
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	95.11
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	95.08
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	94.79
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	94.63
d1ls1a2	207	GTPase domain of the signal sequence recognition p	93.82
d1okkd2	207	GTPase domain of the signal recognition particle r	93.68
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	93.48
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	93.46
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	93.08
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	92.48
d1vmaa2	213	GTPase domain of the signal recognition particle r	92.29
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	92.23
d2qy9a2	211	GTPase domain of the signal recognition particle r	91.78
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	91.47
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	90.76
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	90.6
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	90.56
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	90.33
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	90.22
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	90.18
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	89.49
d1j8yf2	211	GTPase domain of the signal sequence recognition p	89.42
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	89.15
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	88.73
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	88.39
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	88.16
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	88.07
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	88.0
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	87.97
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	87.79
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	87.31
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	87.28
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	87.09
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	86.66
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	86.27
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	85.67
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	85.6
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	85.4
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	85.35
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	85.26
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	84.95
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	84.85
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	84.81
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	84.76
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	84.57
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	84.44
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	84.32
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	84.24
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	83.95
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	83.95
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	83.82
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	83.75
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	83.56
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	83.47
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	83.4
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	83.39
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	82.73
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	82.48
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	82.47
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	82.37
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	82.13
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	82.09
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	82.09
d2zfia1	349	Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090	82.06
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	82.01
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	82.01
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	81.66
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	81.35
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	81.24
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	81.17
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	81.16
d2ncda_	368	Kinesin motor Ncd (non-claret disjunctional) {Frui	81.05
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	80.68
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	80.62
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	80.1
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	80.04

>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=99.94  E-value=3.6e-27  Score=188.70  Aligned_cols=117  Identities=27%  Similarity=0.376  Sum_probs=108.1

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHh
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTREL  150 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~L  150 (202)
                      +|++.||++.++++|.++||..||++|.++||.+++|+|++++|+||||||++|++|+++.+......++++|++|||||
T Consensus        18 sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~~~~~~lil~PtreL   97 (222)
T d2j0sa1          18 TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTREL   97 (222)
T ss_dssp             SGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHH
T ss_pred             CHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhcccccccccccccCceeEEecchHHH
Confidence            45555999999999999999999999999999999999999999999999999999999999888888999999999999


Q ss_pred             HHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHHH
Q 028887          151 GMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLKV  195 (202)
Q Consensus       151 a~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~  195 (202)
                      +.|++++++.++...        .+++..++||.....+..+++.
T Consensus        98 a~Qi~~~~~~l~~~~--------~i~~~~~~g~~~~~~~~~~l~~  134 (222)
T d2j0sa1          98 AVQIQKGLLALGDYM--------NVQCHACIGGTNVGEDIRKLDY  134 (222)
T ss_dssp             HHHHHHHHHHHTTTT--------TCCEEEECTTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCcc--------ceeEEEEeecccchhhHHHhcc
Confidence            999999999999876        5888889999988888877764

>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=99.93  E-value=6e-26  Score=179.54  Aligned_cols=117  Identities=21%  Similarity=0.367  Sum_probs=103.8

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHh
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTREL  150 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~L  150 (202)
                      .|++.||++++++++.++||++|||+|+++||.+++|+|++++|+||||||++|++|+++.+......++++|++|||||
T Consensus         2 ~F~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~lil~PtreL   81 (207)
T d1t6na_           2 GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTREL   81 (207)
T ss_dssp             CSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHH
T ss_pred             CccccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeecccCCCceEEEEeccchh
Confidence            35677999999999999999999999999999999999999999999999999999999999888888999999999999


Q ss_pred             HHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          151 GMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       151 a~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      +.|+.+.++.++....       .+++..++||.....+...+.
T Consensus        82 ~~qi~~~~~~~~~~~~-------~~~~~~~~g~~~~~~~~~~l~  118 (207)
T d1t6na_          82 AFQISKEYERFSKYMP-------NVKVAVFFGGLSIKKDEEVLK  118 (207)
T ss_dssp             HHHHHHHHHHHTTTST-------TCCEEEESCCSCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhhCC-------CceeEEEeccccHHHHHHHHH
Confidence            9999999999998753       355666677777776666554

>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=99.92  E-value=2.3e-25  Score=175.99  Aligned_cols=116  Identities=30%  Similarity=0.479  Sum_probs=100.6

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHh
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTREL  150 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~L  150 (202)
                      +|++.||++++++++.++||+.||++|+++||.+++|+|++++|+||||||++|++|+++++...+.++++||++||+||
T Consensus         4 ~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~~~~~~~lil~pt~el   83 (206)
T d1veca_           4 EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTREL   83 (206)
T ss_dssp             SGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHHH
T ss_pred             ChhccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhcccccccCcceEEEeecchh
Confidence            46677999999999999999999999999999999999999999999999999999999999888888999999999999


Q ss_pred             HHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHH
Q 028887          151 GMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWL  193 (202)
Q Consensus       151 a~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l  193 (202)
                      +.|+++.+..+.....       .+.+...+|+.....+...+
T Consensus        84 ~~q~~~~~~~~~~~~~-------~~~~~~~~g~~~~~~~~~~l  119 (206)
T d1veca_          84 ALQVSQICIQVSKHMG-------GAKVMATTGGTNLRDDIMRL  119 (206)
T ss_dssp             HHHHHHHHHHHTTTSS-------SCCEEEECSSSCHHHHHHHT
T ss_pred             hHHHHHHHHHHhhccc-------CcccccccCCccHHHHHHHH
Confidence            9999999998876542       34555555555555554443

>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=99.92  E-value=2.1e-25  Score=177.88  Aligned_cols=114  Identities=29%  Similarity=0.402  Sum_probs=99.9

Q ss_pred             chHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecC
Q 028887           67 LTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP  146 (202)
Q Consensus        67 ~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~P  146 (202)
                      ..+.+|++.|+++.+++++.++||.+||++|+++||.++.|+|++++|+||||||++|++|+++.+......+++||++|
T Consensus         9 e~i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~~~~~~alil~P   88 (218)
T d2g9na1           9 EIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAP   88 (218)
T ss_dssp             CCCCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECS
T ss_pred             CccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheecccccCccEEEEcc
Confidence            34566777799999999999999999999999999999999999999999999999999999999988888899999999


Q ss_pred             CHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHH
Q 028887          147 TRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRR  188 (202)
Q Consensus       147 tr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~  188 (202)
                      |+||+.|+++.++.+....        .+....++++.....
T Consensus        89 t~eL~~Q~~~~~~~~~~~~--------~~~~~~~~~~~~~~~  122 (218)
T d2g9na1          89 TRELAQQIQKVVMALGDYM--------GASCHACIGGTNVRA  122 (218)
T ss_dssp             SHHHHHHHHHHHHHHHTTT--------TCCEEEECC--CCCS
T ss_pred             cchhhhhHHHHHhhhcccc--------ceeEEeeecccchhH
Confidence            9999999999999999876        355555666554443

>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=99.91  E-value=3.9e-25  Score=175.51  Aligned_cols=117  Identities=28%  Similarity=0.387  Sum_probs=97.4

Q ss_pred             HHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCH
Q 028887           69 LRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTR  148 (202)
Q Consensus        69 ~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr  148 (202)
                      +.+|++.||++.+++++.++||++||++|+++||.++.|+|++++++||||||++|++|+++++.....+++++|++||+
T Consensus         9 ~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~lil~pt~   88 (212)
T d1qdea_           9 VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTR   88 (212)
T ss_dssp             CCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSH
T ss_pred             ccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhccCCCcceEEEcccH
Confidence            44555569999999999999999999999999999999999999999999999999999999998888899999999999


Q ss_pred             HhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHH
Q 028887          149 ELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWL  193 (202)
Q Consensus       149 ~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l  193 (202)
                      +|+.|+++++..+....        .+.+..++++.....+..++
T Consensus        89 el~~q~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~  125 (212)
T d1qdea_          89 ELALQIQKVVMALAFHM--------DIKVHACIGGTSFVEDAEGL  125 (212)
T ss_dssp             HHHHHHHHHHHHHTTTS--------CCCEEEECC----------C
T ss_pred             HHhhhhhhhhccccccc--------ccceeeEeeccchhHHHHHh
Confidence            99999999999988765        46667777777666665544

>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=99.91  E-value=4.1e-25  Score=178.29  Aligned_cols=119  Identities=24%  Similarity=0.354  Sum_probs=104.7

Q ss_pred             chHHHHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhc---------CC
Q 028887           67 LTLRELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ---------RS  137 (202)
Q Consensus        67 ~~~~~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~---------~~  137 (202)
                      .++.+|++.||+++++++|.++||.+||++|..+||.+++|+|++++|+||||||++|++|+++.+...         ..
T Consensus        18 ~~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~~~~   97 (238)
T d1wrba1          18 NVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTA   97 (238)
T ss_dssp             SCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCB
T ss_pred             CccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccccccccCCC
Confidence            345666777999999999999999999999999999999999999999999999999999999998543         24


Q ss_pred             ccEEEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHH
Q 028887          138 AVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWL  193 (202)
Q Consensus       138 ~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l  193 (202)
                      ++++|||+||+||+.|++++++.++...        .+++..++|+.....+.+.+
T Consensus        98 ~~~alil~pt~el~~q~~~~~~~~~~~~--------~~~~~~~~g~~~~~~~~~~~  145 (238)
T d1wrba1          98 YPKCLILAPTRELAIQILSESQKFSLNT--------PLRSCVVYGGADTHSQIREV  145 (238)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHTTS--------SCCEEEECSSSCSHHHHHHH
T ss_pred             CceEEEeccchhhhcchheeeeecccCC--------CcEEEEEeccchhhHHHhhc
Confidence            6789999999999999999999998875        57888888888777776554

>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=99.88  E-value=1.7e-22  Score=159.41  Aligned_cols=114  Identities=26%  Similarity=0.501  Sum_probs=97.9

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCC-cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHH
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSR-DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRE  149 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~-~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~  149 (202)
                      +|++.|+++++++++.++||..|||+|.++||.++.|+ |++++++||+|||++|++|+++.... ..++++||++||++
T Consensus         5 sf~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~-~~~~~~lil~pt~~   83 (208)
T d1hv8a1           5 NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE-NNGIEAIILTPTRE   83 (208)
T ss_dssp             CGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCS-SSSCCEEEECSCHH
T ss_pred             CHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeeccccccccc-ccCcceEEEeeccc
Confidence            45566999999999999999999999999999999885 99999999999999999999987653 45779999999999


Q ss_pred             hHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHH
Q 028887          150 LGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWL  193 (202)
Q Consensus       150 La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l  193 (202)
                      |+.|++++++.++...        +.++...+|+.....|.+.+
T Consensus        84 l~~q~~~~~~~~~~~~--------~~~v~~~~g~~~~~~~~~~l  119 (208)
T d1hv8a1          84 LAIQVADEIESLKGNK--------NLKIAKIYGGKAIYPQIKAL  119 (208)
T ss_dssp             HHHHHHHHHHHHHCSS--------CCCEEEECTTSCHHHHHHHH
T ss_pred             cchhhhhhhhhhcccC--------CeEEEEeeCCCChHHHHHhc
Confidence            9999999999999876        45666666666666665443

>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=99.87  E-value=2.9e-22  Score=157.77  Aligned_cols=116  Identities=31%  Similarity=0.461  Sum_probs=105.5

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHh
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTREL  150 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~L  150 (202)
                      +|++.||++.+++++.++||..||++|+++||.++.|+|+++.|+||||||++|++|+++.+.......++++++|++++
T Consensus         2 sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~~~~~~~~~~~~~~~~   81 (206)
T d1s2ma1           2 TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTREL   81 (206)
T ss_dssp             CGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHH
T ss_pred             ChHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccccccccceeeccchhh
Confidence            45666999999999999999999999999999999999999999999999999999999998887788899999999999


Q ss_pred             HHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHHHH
Q 028887          151 GMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSWLK  194 (202)
Q Consensus       151 a~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~l~  194 (202)
                      +.|...++..+....        ++++..++|+.....+..+++
T Consensus        82 ~~~~~~~~~~~~~~~--------~~~~~~~~g~~~~~~~~~~l~  117 (206)
T d1s2ma1          82 ALQTSQVVRTLGKHC--------GISCMVTTGGTNLRDDILRLN  117 (206)
T ss_dssp             HHHHHHHHHHHTTTT--------TCCEEEECSSSCHHHHHHHTT
T ss_pred             hhhhhhhhhhccccc--------CeeEEeecCccchhhHHHHhc
Confidence            999999999988776        678888888888887776654

>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=99.83  E-value=1.9e-20  Score=147.04  Aligned_cols=95  Identities=28%  Similarity=0.431  Sum_probs=88.1

Q ss_pred             HHHhCCCCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHh
Q 028887           71 ELCQGHVPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTREL  150 (202)
Q Consensus        71 ~l~~~gl~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~L  150 (202)
                      +|++.|+++.+++++++.||++||++|++|||.+++|+|++++||||||||++|++|+++.+......+..++++|++++
T Consensus         2 ~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~~~~~~~~~~~~~~~~   81 (209)
T d1q0ua_           2 QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTREL   81 (209)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHH
T ss_pred             ccccCCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeeccccccccccccccccccccch
Confidence            46777999999999999999999999999999999999999999999999999999999999887778889999999999


Q ss_pred             HHHHHHHHHHhhcCC
Q 028887          151 GMQVTKVARVLAAKP  165 (202)
Q Consensus       151 a~Q~~~~~~~l~~~~  165 (202)
                      +.+..+.+.......
T Consensus        82 ~~~~~~~~~~~~~~~   96 (209)
T d1q0ua_          82 ATQIYHETLKITKFC   96 (209)
T ss_dssp             HHHHHHHHHHHHTTS
T ss_pred             hHHHHHHHHhhhccc
Confidence            999999888776653

>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=99.75  E-value=6.8e-18  Score=134.68  Aligned_cols=80  Identities=23%  Similarity=0.197  Sum_probs=73.0

Q ss_pred             HHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhh
Q 028887           83 RRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLA  162 (202)
Q Consensus        83 ~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~  162 (202)
                      ..+.+.++.+|+++|+.+++.++.|+|+++.||||+|||++++++++....+++   ++||++||++|+.|+++++++++
T Consensus        34 ~~~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~~~---rvliv~Pt~~La~Q~~~~l~~~~  110 (237)
T d1gkub1          34 VEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKGK---RCYVIFPTSLLVIQAAETIRKYA  110 (237)
T ss_dssp             HHHHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTTSC---CEEEEESCHHHHHHHHHHHHHHH
T ss_pred             HHHHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHhcC---eEEEEeccHHHHHHHHHHHHHHH
Confidence            455667888999999999999999999999999999999999999988877665   89999999999999999999998


Q ss_pred             cCC
Q 028887          163 AKP  165 (202)
Q Consensus       163 ~~~  165 (202)
                      ...
T Consensus       111 ~~~  113 (237)
T d1gkub1         111 EKA  113 (237)
T ss_dssp             TTT
T ss_pred             HHc
Confidence            764

>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=99.70  E-value=4.6e-18  Score=132.56  Aligned_cols=85  Identities=21%  Similarity=0.217  Sum_probs=75.8

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHH
Q 028887           77 VPEHVLRRMEETGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTK  156 (202)
Q Consensus        77 l~~~l~~~l~~~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~  156 (202)
                      +++.+...|++.||.+|+|+|.++++.+++|+++++++|||+|||.+++++++..+..++   ++|+++|+++|+.|+.+
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~~~---~vl~l~P~~~L~~q~~~   86 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGG---KSLYVVPLRALAGEKYE   86 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTTC---CEEEEESSHHHHHHHHH
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhccC---cceeecccHHHHHHHHH
Confidence            667788899999999999999999999999999999999999999999999998887665   89999999999999999


Q ss_pred             HHHHhhcC
Q 028887          157 VARVLAAK  164 (202)
Q Consensus       157 ~~~~l~~~  164 (202)
                      +++++.+.
T Consensus        87 ~~~~~~~~   94 (202)
T d2p6ra3          87 SFKKWEKI   94 (202)
T ss_dssp             HHTTTTTT
T ss_pred             HHHHHhhc
Confidence            99988764

>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=99.65  E-value=2.2e-16  Score=123.05  Aligned_cols=85  Identities=24%  Similarity=0.309  Sum_probs=74.8

Q ss_pred             hCCCCHHHHHHHHHC-CCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHH
Q 028887           74 QGHVPEHVLRRMEET-GYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGM  152 (202)
Q Consensus        74 ~~gl~~~l~~~l~~~-g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~  152 (202)
                      ..+|.+...+.+++. ||+.++|.|.++|+.++.|+|+++++|||+|||++|.+|++.   ..+   ++++++|+++|+.
T Consensus         6 ~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~---~~~---~~~~v~P~~~L~~   79 (206)
T d1oywa2           6 VLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALL---LNG---LTVVVSPLISLMK   79 (206)
T ss_dssp             CSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHH---SSS---EEEEECSCHHHHH
T ss_pred             hCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhh---ccC---ceEEeccchhhhh
Confidence            346777777778776 999999999999999999999999999999999999999864   233   7999999999999


Q ss_pred             HHHHHHHHhhcC
Q 028887          153 QVTKVARVLAAK  164 (202)
Q Consensus       153 Q~~~~~~~l~~~  164 (202)
                      |+.+.++.++..
T Consensus        80 q~~~~l~~~~~~   91 (206)
T d1oywa2          80 DQVDQLQANGVA   91 (206)
T ss_dssp             HHHHHHHHTTCC
T ss_pred             hHHHHHHhhccc
Confidence            999999888754

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=99.44  E-value=8.8e-13  Score=104.87  Aligned_cols=99  Identities=19%  Similarity=0.172  Sum_probs=78.6

Q ss_pred             CHHHHHHH-HHCCCCCCcHHHHHHHHhHHc----C--CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHh
Q 028887           78 PEHVLRRM-EETGYVLPTDIQREALPVLFS----S--RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTREL  150 (202)
Q Consensus        78 ~~~l~~~l-~~~g~~~~t~~Q~~~i~~i~~----g--~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~L  150 (202)
                      ++...+.+ ....| .+|+.|..++..+..    +  .+.+++|.||||||++|+.++...+..++   ++++|+||..|
T Consensus        41 ~~~~~~~~~~~lP~-~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~---qv~~l~Pt~~L  116 (233)
T d2eyqa3          41 DREQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHK---QVAVLVPTTLL  116 (233)
T ss_dssp             CHHHHHHHHHTCCS-CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTTC---EEEEECSSHHH
T ss_pred             CHHHHHhhhhcccc-ccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHcCC---ceEEEccHHHh
Confidence            34444554 34455 689999999988743    3  47899999999999999999999998888   99999999999


Q ss_pred             HHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHH
Q 028887          151 GMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRH  189 (202)
Q Consensus       151 a~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~  189 (202)
                      +.|.++.|+++++..+        + .+.+++|.....+
T Consensus       117 a~Q~~~~~~~~~~~~~--------~-~v~~l~~~~~~~~  146 (233)
T d2eyqa3         117 AQQHYDNFRDRFANWP--------V-RIEMISRFRSAKE  146 (233)
T ss_dssp             HHHHHHHHHHHSTTTT--------C-CEEEESTTSCHHH
T ss_pred             HHHHHHHHHHHHhhCC--------C-EEEeccCcccchh
Confidence            9999999999887652        2 3666777555443

>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=99.44  E-value=5.1e-13  Score=102.68  Aligned_cols=71  Identities=23%  Similarity=0.282  Sum_probs=61.3

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCC
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKP  165 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~  165 (202)
                      +|++.|.+++..+. ++++++++|||+|||+++++++...+...+  .++++++|+++|+.|+.+.+++++...
T Consensus         9 ~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~~~--~~il~i~P~~~L~~q~~~~~~~~~~~~   79 (200)
T d1wp9a1           9 QPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKYG--GKVLMLAPTKPLVLQHAESFRRLFNLP   79 (200)
T ss_dssp             CCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHHSC--SCEEEECSSHHHHHHHHHHHHHHBCSC
T ss_pred             CCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHhcC--CcEEEEcCchHHHHHHHHHHHHhhccc
Confidence            79999999998875 567999999999999999988877765432  379999999999999999999998764

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.43  E-value=7e-13  Score=107.31  Aligned_cols=95  Identities=25%  Similarity=0.234  Sum_probs=79.0

Q ss_pred             HHHHHCCCCCCcHHHHHHHHhHHc----C--CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHH
Q 028887           83 RRMEETGYVLPTDIQREALPVLFS----S--RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTK  156 (202)
Q Consensus        83 ~~l~~~g~~~~t~~Q~~~i~~i~~----g--~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~  156 (202)
                      ..+....| .+|+.|..|+..+..    +  .+.+++|.||||||++|+.++...+..+.   ++++|+||..||.|.++
T Consensus        75 ~f~~~LPF-eLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~---q~~~m~Pt~~La~Qh~~  150 (264)
T d1gm5a3          75 EFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGF---QTAFMVPTSILAIQHYR  150 (264)
T ss_dssp             HHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTS---CEEEECSCHHHHHHHHH
T ss_pred             HHHhhccc-cCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhccc---ceeEEeehHhhhHHHHH
Confidence            33466777 699999999998753    2  46899999999999999999999999988   99999999999999999


Q ss_pred             HHHHhhcCCCCcccccccceEEEEEeCCccHHHH
Q 028887          157 VARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHK  190 (202)
Q Consensus       157 ~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~  190 (202)
                      .++++++..+        +. +.+++|+....++
T Consensus       151 ~~~~~f~~~~--------~~-v~~l~~~~~~~~r  175 (264)
T d1gm5a3         151 RTVESFSKFN--------IH-VALLIGATTPSEK  175 (264)
T ss_dssp             HHHHHHTCSS--------CC-EEECCSSSCHHHH
T ss_pred             HHHHhhhhcc--------cc-ceeeccccchHHH
Confidence            9999997652        33 6677776665553

>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=99.06  E-value=1.7e-11  Score=99.28  Aligned_cols=57  Identities=26%  Similarity=0.350  Sum_probs=48.4

Q ss_pred             HHcCCcEEEeccCCCchHHHHHHHHHHHHH-hcCCccEEEEecCCHHhHHHHHHHHHHhhc
Q 028887          104 LFSSRDCILHAQTGSGKTLTYLLLIFSLVN-AQRSAVQAVIVVPTRELGMQVTKVARVLAA  163 (202)
Q Consensus       104 i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~-~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~  163 (202)
                      +..|+++++.||||||||++|+.+++.... ++.   ++||++||++|+.|+.+++++++.
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~~~---~~lvi~Ptr~La~q~~~~l~~~~~   63 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIKRGL---RTLILAPTRVVAAEMEEALRGLPI   63 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHHHTC---CEEEEESSHHHHHHHHHHTTTSCC
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHhcCC---EEEEEccHHHHHHHHHHHHhcCCc
Confidence            457899999999999999999888887543 333   899999999999999998887654

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.06  E-value=1.7e-10  Score=89.47  Aligned_cols=67  Identities=27%  Similarity=0.272  Sum_probs=56.5

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .+.+.|.+++..+++++..++.++||+|||++.+..+. .+  ++   ++||+||+++|+.|+.+.++.++..
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~~~-~~--~~---~~Liv~p~~~L~~q~~~~~~~~~~~  136 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAIN-EL--ST---PTLIVVPTLALAEQWKERLGIFGEE  136 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHH-HS--CS---CEEEEESSHHHHHHHHHHHGGGCGG
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhHHH-Hh--cC---ceeEEEcccchHHHHHHHHHhhccc
Confidence            68999999999999988899999999999988765442 22  22   6999999999999999999887653

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=99.00  E-value=9e-10  Score=89.47  Aligned_cols=71  Identities=24%  Similarity=0.203  Sum_probs=59.0

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .|.+.|.+++..++..+..++.+|||+|||+.....+.......  ..++||+||+++|+.|+.+.+.+++..
T Consensus       113 ~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i~~~~~~~~--~~k~Liivp~~~Lv~Q~~~~f~~~~~~  183 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY--EGKILIIVPTTALTTQMADDFVDYRLF  183 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHC--SSEEEEECSSHHHHHHHHHHHHHHTSC
T ss_pred             ccchHHHHHHHHHHhcCCceeEEEcccCccHHHHHHHHHhhhcc--cceEEEEEcCchhHHHHHHHHHHhhcc
Confidence            68999999999999888899999999999998665544433332  237999999999999999999988754

>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=98.66  E-value=8e-09  Score=73.37  Aligned_cols=55  Identities=20%  Similarity=0.316  Sum_probs=45.2

Q ss_pred             HcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHh
Q 028887          105 FSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVL  161 (202)
Q Consensus       105 ~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l  161 (202)
                      ..|++++++++||+|||.+++..++......  +.++++++|+++++.|+.+.+...
T Consensus         5 ~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~--~~~vli~~p~~~l~~q~~~~~~~~   59 (140)
T d1yksa1           5 KKGMTTVLDFHPGAGKTRRFLPQILAECARR--RLRTLVLAPTRVVLSEMKEAFHGL   59 (140)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTTTS
T ss_pred             HcCCcEEEEcCCCCChhHHHHHHHHHHhhhc--CceeeeeecchhHHHHHHHHhhhh
Confidence            4689999999999999999887777666443  347999999999999998877544

>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=98.61  E-value=3.1e-08  Score=70.93  Aligned_cols=52  Identities=17%  Similarity=0.146  Sum_probs=41.1

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .+..++.+|||+|||..+...+   ...+.   +++|++|+++|+.|+.+.+.+....
T Consensus         8 ~~~~ll~apTGsGKT~~~~~~~---~~~~~---~vli~~P~~~l~~q~~~~~~~~~~~   59 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPAAY---AAQGY---KVLVLNPSVAATLGFGAYMSKAHGV   59 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHHHH---HTTTC---CEEEEESCHHHHHHHHHHHHHHHSC
T ss_pred             CCEEEEEeCCCCCHHHHHHHHH---HHcCC---cEEEEcChHHHHHHHHHHHHHHhhc
Confidence            3567999999999997654333   22333   7999999999999999999888764

>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=98.12  E-value=4e-06  Score=66.73  Aligned_cols=71  Identities=20%  Similarity=0.166  Sum_probs=55.7

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhc-CCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQ-RSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~-~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      +++|.|++++..  ....++|.|+.|||||.+.+.-+...+... ...-++|++++|+.++..+.+++.++...
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn~a~~~i~~~~~~~~~~   72 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLGR   72 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSCT
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcHHHHHHHHHHHHHhcCc
Confidence            478999999964  235589999999999998776666655542 23347999999999999999998887654

>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=97.94  E-value=1.7e-05  Score=63.56  Aligned_cols=71  Identities=18%  Similarity=0.163  Sum_probs=57.3

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCC-ccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRS-AVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~-~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .+++.|.+++..  .+..++|.|+.|||||.+.+--+.+.+..+.. .-++|++++++..+..+..++......
T Consensus        11 ~L~~eQ~~~v~~--~~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~aa~~~~~~~~~~~~~   82 (318)
T d1pjra1          11 HLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLGG   82 (318)
T ss_dssp             TSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHHGG
T ss_pred             hCCHHHHHHHhC--CCCCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHHHHHHHHHHHHhhccc
Confidence            589999999975  24569999999999999988877776665432 237999999999999999998776554

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=97.66  E-value=0.00016  Score=57.67  Aligned_cols=72  Identities=25%  Similarity=0.381  Sum_probs=52.5

Q ss_pred             CCcHHHHHHHHhHH---------cCCcEEEeccCCCchHHHHHHHHHHHHHhcC----CccEEEEecCCHHhHHHHHHHH
Q 028887           92 LPTDIQREALPVLF---------SSRDCILHAQTGSGKTLTYLLLIFSLVNAQR----SAVQAVIVVPTRELGMQVTKVA  158 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~---------~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~----~~~~~Lil~Ptr~La~Q~~~~~  158 (202)
                      .+.|+|.+++.-+.         .+..+++.-..|.|||+..+..+...+....    ....+||+||. .|..||.+++
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qaia~l~~l~~~~~~~~~~~~~~LIV~P~-sl~~qW~~Ei  133 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNEV  133 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHHHHHHHHHHhcccccCCCCcEEEEccc-hhhHHHHHHH
Confidence            68999999997652         2456888889999999865544433333322    12358999997 5899999999


Q ss_pred             HHhhcC
Q 028887          159 RVLAAK  164 (202)
Q Consensus       159 ~~l~~~  164 (202)
                      .++++.
T Consensus       134 ~k~~~~  139 (298)
T d1z3ix2         134 GKWLGG  139 (298)
T ss_dssp             HHHHGG
T ss_pred             HhhcCC
Confidence            998875

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=97.37  E-value=0.00036  Score=53.36  Aligned_cols=71  Identities=13%  Similarity=0.091  Sum_probs=53.3

Q ss_pred             CCcHHHHHHHHhHH----cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLF----SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~----~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .+.++|.+++..+.    .+..+++.-..|.|||...+..+...... .....+||++| ..+..|+.+++.+++..
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~~~~~~~~~-~~~~~~LIv~p-~~l~~~W~~e~~~~~~~   86 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKE-NELTPSLVICP-LSVLKNWEEELSKFAPH   86 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHHHT-TCCSSEEEEEC-STTHHHHHHHHHHHCTT
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHHhhhhhhhc-ccccccceecc-hhhhhHHHHHHHhhccc
Confidence            58899999997542    35668999999999999875554444433 33336899998 78889999999888764

>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=97.02  E-value=0.00072  Score=56.69  Aligned_cols=67  Identities=21%  Similarity=0.302  Sum_probs=51.5

Q ss_pred             CCcHHHHHHHHhHHc----C-CcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVLFS----S-RDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~----g-~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .|+..|-++|..+..    | ++.++.|.||||||++.. .++...  ++   .+|||+|+..+|.|+++.++.+++.
T Consensus        11 ~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA-~l~~~~--~r---p~LVVt~n~~~A~qL~~dL~~~l~~   82 (413)
T d1t5la1          11 EPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTIS-NVIAQV--NK---PTLVIAHNKTLAGQLYSELKEFFPH   82 (413)
T ss_dssp             CCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHHH-HHHHHH--TC---CEEEECSSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHHH-HHHHHh--CC---CEEEEeCCHHHHHHHHHHHHHHcCC
Confidence            578888888876644    4 568999999999995543 333332  23   5899999999999999999999864

>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=96.78  E-value=0.005  Score=50.39  Aligned_cols=69  Identities=20%  Similarity=0.264  Sum_probs=50.1

Q ss_pred             CCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHh-cCCccEEEEecCCHHhHHHHHHHHHH
Q 028887           92 LPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNA-QRSAVQAVIVVPTRELGMQVTKVARV  160 (202)
Q Consensus        92 ~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~-~~~~~~~Lil~Ptr~La~Q~~~~~~~  160 (202)
                      ..++.|..|+..++.++-+++.|+.|||||.....-+...... ...+.++++.+||..=+..+.+....
T Consensus       148 ~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~~~  217 (359)
T d1w36d1         148 DEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGK  217 (359)
T ss_dssp             TSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHTH
T ss_pred             ccccHHHHHHHHHHcCCeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHHHHHHHHHHHHH
Confidence            4567899999999999999999999999998753322221211 23345799999998777777666543

>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=96.03  E-value=0.026  Score=44.18  Aligned_cols=72  Identities=22%  Similarity=0.208  Sum_probs=54.8

Q ss_pred             CCCCCCcHHHHHHHHhHHcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCC
Q 028887           88 TGYVLPTDIQREALPVLFSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKP  165 (202)
Q Consensus        88 ~g~~~~t~~Q~~~i~~i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~  165 (202)
                      .|. +|+++|-..--.+..|+  +..-.||-|||++..+|+.-....++   .+=|++..--||..=.+++..+....
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--IAEMKTGEGKTLTSTLPVYLNALTGK---GVHVVTVNEYLASRDAEQMGKIFEFL  148 (273)
T ss_dssp             HSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTTSS---CEEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred             hce-EEehhHHHHHHHHHhhh--heeecCCCcchhHHHHHHHHHHhcCC---CceEEecCccccchhhhHHhHHHHHc
Confidence            465 68999988877777774  78999999999999888866655565   67788888889886566655555544

>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=95.11  E-value=0.024  Score=46.95  Aligned_cols=67  Identities=27%  Similarity=0.331  Sum_probs=48.3

Q ss_pred             CCcHHHHHHHHhH----HcCC-cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcC
Q 028887           92 LPTDIQREALPVL----FSSR-DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAK  164 (202)
Q Consensus        92 ~~t~~Q~~~i~~i----~~g~-~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~  164 (202)
                      .|+.-|-++|..+    ..|. ...+.|.+||+|+++.. .+++..  ++   .+||++|+.+.|.++++.++.+.+.
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~A-~l~~~~--~r---p~LvVt~~~~~A~~l~~dL~~~l~~   79 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMA-KVIEAL--GR---PALVLAPNKILAAQLAAEFRELFPE   79 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH-HHHHHH--TC---CEEEEESSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHHHH-HHHHHh--CC---CEEEEeCCHHHHHHHHHHHHHhcCc
Confidence            5566776677664    3454 47899999999995432 222222  22   4899999999999999999998764

>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=94.79  E-value=0.014  Score=41.28  Aligned_cols=28  Identities=21%  Similarity=0.322  Sum_probs=20.9

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHHhcC
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVNAQR  136 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~~~~  136 (202)
                      +++++.|++|+|||. .+..++..+....
T Consensus         2 k~v~ItG~~GtGKTt-l~~~i~~~l~~~~   29 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTT-LIHKASEVLKSSG   29 (189)
T ss_dssp             CCEEEESCCSSCHHH-HHHHHHHHHHHTT
T ss_pred             cEEEEECCCCCcHHH-HHHHHHHHHHHCC
Confidence            679999999999998 4445556665443

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=94.63  E-value=0.0055  Score=49.39  Aligned_cols=38  Identities=24%  Similarity=0.327  Sum_probs=26.5

Q ss_pred             HHHHHHHHh-HHcCCcEEEeccCCCchHHHHHHHHHHHHH
Q 028887           95 DIQREALPV-LFSSRDCILHAQTGSGKTLTYLLLIFSLVN  133 (202)
Q Consensus        95 ~~Q~~~i~~-i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~  133 (202)
                      +.+...+.. +..+++++++|+||||||.. +-+++..+.
T Consensus       153 ~~~~~~l~~~v~~~~nili~G~tgSGKTT~-l~al~~~i~  191 (323)
T d1g6oa_         153 EQAISAIKDGIAIGKNVIVCGGTGSGKTTY-IKSIMEFIP  191 (323)
T ss_dssp             HHHHHHHHHHHHHTCCEEEEESTTSSHHHH-HHHHGGGSC
T ss_pred             HHHHHHHHHHHHhCCCEEEEeeccccchHH-HHHHhhhcc
Confidence            444444443 56789999999999999965 455555553

>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=93.82  E-value=0.034  Score=41.71  Aligned_cols=52  Identities=21%  Similarity=0.185  Sum_probs=32.9

Q ss_pred             cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEec--CCHHhHHHHHHHHHHhhc
Q 028887          109 DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVV--PTRELGMQVTKVARVLAA  163 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~--Ptr~La~Q~~~~~~~l~~  163 (202)
                      -+++.||||+|||....-.......+++   ++.+++  ..|.=|.++.+.+.+..+
T Consensus        12 vi~lvGp~GvGKTTTiaKLA~~~~~~g~---kV~lit~Dt~R~gA~eQL~~~a~~l~   65 (207)
T d1ls1a2          12 LWFLVGLQGSGKTTTAAKLALYYKGKGR---RPLLVAADTQRPAAREQLRLLGEKVG   65 (207)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHHHHHTTC---CEEEEECCSSCHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCC---cEEEEecccccchHHHHHHHHHHhcC
Confidence            3577999999999887655444444333   444444  357777666666655544

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=93.68  E-value=0.075  Score=39.76  Aligned_cols=54  Identities=19%  Similarity=0.078  Sum_probs=32.7

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEec--CCHHhHHHHHHHHHHhhc
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVV--PTRELGMQVTKVARVLAA  163 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~--Ptr~La~Q~~~~~~~l~~  163 (202)
                      ++-+++.||||+|||....-........++   ++.+++  ..|.=+.++.+.+-+..+
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA~~~~~~g~---kV~lit~Dt~R~gA~eQL~~~a~~l~   61 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLGRYYQNLGK---KVMFCAGDTFRAAGGTQLSEWGKRLS   61 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHHHTTTC---CEEEECCCCSSTTHHHHHHHHHHHHT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCC---cEEEEEeccccccchhhHhhcccccC
Confidence            345788999999999987665433332322   344443  346666665655555443

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=93.48  E-value=0.047  Score=44.53  Aligned_cols=45  Identities=22%  Similarity=0.321  Sum_probs=32.2

Q ss_pred             HcCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHH
Q 028887          105 FSSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGM  152 (202)
Q Consensus       105 ~~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~  152 (202)
                      ...+++++.|+||+|||......+.+.+..+.   .++|+=|.-++..
T Consensus        48 ~~~~H~~I~G~tGsGKT~~l~~li~~~~~~g~---~~iiiD~kge~~~   92 (433)
T d1e9ra_          48 AEPRHLLVNGATGTGKSVLLRELAYTGLLRGD---RMVIVDPNGDMLS   92 (433)
T ss_dssp             GGGGCEEEEECTTSSHHHHHHHHHHHHHHTTC---EEEEEEETTHHHH
T ss_pred             cccceEEEEeCCCCcHHHHHHHHHHHHHhCCC---CEEEEeCChhHHH
Confidence            44578999999999999775444555555444   6788888877643

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=93.46  E-value=0.022  Score=45.15  Aligned_cols=20  Identities=25%  Similarity=0.368  Sum_probs=17.1

Q ss_pred             cCCcEEEeccCCCchHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l  125 (202)
                      ..+.++++||||+|||+..-
T Consensus        48 ~~~~iLl~GPpG~GKT~lAk   67 (309)
T d1ofha_          48 TPKNILMIGPTGVGKTEIAR   67 (309)
T ss_dssp             CCCCEEEECCTTSSHHHHHH
T ss_pred             CCceEEEECCCCCCHHHHHH
Confidence            35789999999999998864

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=93.08  E-value=0.081  Score=43.40  Aligned_cols=39  Identities=23%  Similarity=0.255  Sum_probs=26.7

Q ss_pred             cHHHHHHHHhHHcCC--cEEEeccCCCchHHHHHHHHHHHHH
Q 028887           94 TDIQREALPVLFSSR--DCILHAQTGSGKTLTYLLLIFSLVN  133 (202)
Q Consensus        94 t~~Q~~~i~~i~~g~--~~l~~a~TGsGKT~~~l~~~l~~l~  133 (202)
                      .+.|.+.+..+....  -+++.||||||||...- .++..+.
T Consensus       143 ~~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl~-~~l~~~~  183 (401)
T d1p9ra_         143 TAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTLY-AGLQELN  183 (401)
T ss_dssp             CHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHHH-HHHHHHC
T ss_pred             cHHHHHHHHHHHhhhhceEEEEcCCCCCccHHHH-HHhhhhc
Confidence            466666666665543  38899999999997654 3455553

>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=92.48  E-value=0.026  Score=47.28  Aligned_cols=20  Identities=25%  Similarity=0.368  Sum_probs=17.0

Q ss_pred             cCCcEEEeccCCCchHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l  125 (202)
                      ..+++|+.||||+|||+..-
T Consensus        48 ~ksNILliGPTGvGKTlLAr   67 (443)
T d1g41a_          48 TPKNILMIGPTGVGKTEIAR   67 (443)
T ss_dssp             CCCCEEEECCTTSSHHHHHH
T ss_pred             ccccEEEECCCCCCHHHHHH
Confidence            45799999999999998753

>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=92.29  E-value=0.17  Score=37.85  Aligned_cols=51  Identities=16%  Similarity=0.154  Sum_probs=30.1

Q ss_pred             EEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecC-CHHhHHHHHHHHHHhh
Q 028887          110 CILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP-TRELGMQVTKVARVLA  162 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~P-tr~La~Q~~~~~~~l~  162 (202)
                      +++.||||+|||....--......+++ . -+||-+- .|.=|.++.+.+-+..
T Consensus        14 i~lvGptGvGKTTTiAKLAa~~~~~~~-k-V~lit~Dt~R~gA~eQL~~~a~~l   65 (213)
T d1vmaa2          14 IMVVGVNGTGKTTSCGKLAKMFVDEGK-S-VVLAAADTFRAAAIEQLKIWGERV   65 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHHTTC-C-EEEEEECTTCHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCC-c-eEEEeecccccchhHHHHHHhhhc
Confidence            677999999999987655444443332 2 3344443 4665655555544443

>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=92.23  E-value=0.21  Score=37.05  Aligned_cols=25  Identities=28%  Similarity=0.449  Sum_probs=18.6

Q ss_pred             CcEEEeccCCCchHHHHHHHHHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLLLIFSLVN  133 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~~~l~~l~  133 (202)
                      ..+++.||+|+|||.+. -.+.+.+.
T Consensus        44 ~~lll~GppGtGKT~l~-~~l~~~l~   68 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTL-RKLWELYK   68 (276)
T ss_dssp             CEEEEECCTTSSHHHHH-HHHHHHHT
T ss_pred             CceEEECCCCCCHHHHH-HHHHHHHh
Confidence            57999999999999665 33445553

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=91.78  E-value=0.2  Score=37.40  Aligned_cols=50  Identities=18%  Similarity=0.161  Sum_probs=29.1

Q ss_pred             EEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEec-CC-HHhHHHHHHHHHHhh
Q 028887          110 CILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVV-PT-RELGMQVTKVARVLA  162 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~-Pt-r~La~Q~~~~~~~l~  162 (202)
                      +++.||||+|||....-........++   ++.+++ =| |.=|.++.+.+-+..
T Consensus        12 i~lvGptGvGKTTTiAKLA~~~~~~g~---kV~lit~Dt~R~gA~eQL~~~a~~l   63 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLARQFEQQGK---SVMLAAGDTFRAAAVEQLQVWGQRN   63 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTTTC---CEEEECCCTTCHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCC---cEEEEecccccccchhhhhhhhhhc
Confidence            667999999999987765433332222   344444 33 555555554444443

>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=91.47  E-value=0.043  Score=41.08  Aligned_cols=19  Identities=26%  Similarity=0.342  Sum_probs=16.0

Q ss_pred             CcEEEeccCCCchHHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~  126 (202)
                      .+++++||+|+|||.+.-+
T Consensus        36 ~~~L~~GPpGtGKT~lA~~   54 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLAHI   54 (238)
T ss_dssp             CCEEEESSTTSSHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHH
Confidence            4699999999999987643

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=90.76  E-value=0.073  Score=43.22  Aligned_cols=17  Identities=47%  Similarity=0.601  Sum_probs=15.5

Q ss_pred             CcEEEeccCCCchHHHH
Q 028887          108 RDCILHAQTGSGKTLTY  124 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~  124 (202)
                      .+++..||||+|||+..
T Consensus        69 ~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             cceeeeCCCCccHHHHH
Confidence            57999999999999886

>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=90.60  E-value=0.058  Score=40.37  Aligned_cols=18  Identities=28%  Similarity=0.307  Sum_probs=15.5

Q ss_pred             CcEEEeccCCCchHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l  125 (202)
                      .+++++||+|+|||...-
T Consensus        36 ~~~Ll~GPpG~GKTtla~   53 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLAH   53 (239)
T ss_dssp             CCEEEECCTTSCHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            479999999999997754

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=90.56  E-value=0.13  Score=38.23  Aligned_cols=38  Identities=18%  Similarity=0.232  Sum_probs=27.6

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCC
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPT  147 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Pt  147 (202)
                      |.-+++.|++|+|||...+--+.+.+..+.   .+++++-+
T Consensus        26 gsl~li~G~pGsGKT~l~~qia~~~~~~~~---~~~~is~e   63 (242)
T d1tf7a2          26 DSIILATGATGTGKTLLVSRFVENACANKE---RAILFAYE   63 (242)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHHTTTC---CEEEEESS
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhcc---ccceeecc
Confidence            467999999999999887766666555444   56666543

>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=90.33  E-value=0.067  Score=36.60  Aligned_cols=20  Identities=25%  Similarity=0.300  Sum_probs=16.6

Q ss_pred             CCcEEEeccCCCchHHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~  126 (202)
                      .+++++.|++|+|||.+.-.
T Consensus         2 ~k~I~l~G~~GsGKSTvak~   21 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGRQ   21 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHH
Confidence            36799999999999987643

>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=90.22  E-value=0.085  Score=39.69  Aligned_cols=16  Identities=44%  Similarity=0.490  Sum_probs=14.2

Q ss_pred             cEEEeccCCCchHHHH
Q 028887          109 DCILHAQTGSGKTLTY  124 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~  124 (202)
                      .+++.||+|+|||...
T Consensus        34 ~ilL~GpPGtGKT~la   49 (273)
T d1gvnb_          34 AFLLGGQPGSGKTSLR   49 (273)
T ss_dssp             EEEEECCTTSCTHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4899999999999865

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=90.18  E-value=0.048  Score=38.25  Aligned_cols=19  Identities=26%  Similarity=0.356  Sum_probs=16.5

Q ss_pred             cCCcEEEeccCCCchHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~  124 (202)
                      .|+-+++.|++|||||.+.
T Consensus         3 ~g~iI~l~G~~GsGKSTia   21 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIA   21 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            5777899999999999864

>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=89.49  E-value=0.084  Score=36.90  Aligned_cols=20  Identities=20%  Similarity=0.343  Sum_probs=16.6

Q ss_pred             CCcEEEeccCCCchHHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~  126 (202)
                      +.++++.|++|+|||.+.-.
T Consensus         5 ~~~I~i~G~~GsGKTT~~~~   24 (174)
T d1y63a_           5 GINILITGTPGTGKTSMAEM   24 (174)
T ss_dssp             SCEEEEECSTTSSHHHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHHHH
Confidence            45799999999999987543

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=89.42  E-value=0.4  Score=35.65  Aligned_cols=52  Identities=13%  Similarity=0.071  Sum_probs=25.1

Q ss_pred             EEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecC-CHHhHHHHHHHHHHhhc
Q 028887          110 CILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVP-TRELGMQVTKVARVLAA  163 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~P-tr~La~Q~~~~~~~l~~  163 (202)
                      +++.||||+|||....-.......+++ . -++|-+= .|.=+..+.+.+-+..+
T Consensus        15 i~lvGptGvGKTTTiAKLA~~~~~~g~-k-V~lit~Dt~R~ga~eQL~~~a~~l~   67 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLAYFYKKKGF-K-VGLVGADVYRPAALEQLQQLGQQIG   67 (211)
T ss_dssp             EEEECSCCC----HHHHHHHHHHHTTC-C-EEEEECCCSSHHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCC-c-eEEEEeeccccchhHHHHHhccccC
Confidence            566899999999887655433333322 2 2444443 35555544444444433

>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=89.15  E-value=0.41  Score=38.65  Aligned_cols=52  Identities=21%  Similarity=0.290  Sum_probs=38.0

Q ss_pred             cEEEeccCCCchHHHHHHHHHHHHHhcC---------CccEEEEecCCHHhHHHHHHHHHH
Q 028887          109 DCILHAQTGSGKTLTYLLLIFSLVNAQR---------SAVQAVIVVPTRELGMQVTKVARV  160 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~~~l~~l~~~~---------~~~~~Lil~Ptr~La~Q~~~~~~~  160 (202)
                      .++|.|.-|||||.+..-=++..+..+.         ..-.+|+|+=|+.=|..+.+++.+
T Consensus        18 ~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~   78 (485)
T d1w36b1          18 ERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRS   78 (485)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHH
T ss_pred             CeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHH
Confidence            4889999999999888777777664322         112588999998777777666543

>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=88.73  E-value=0.095  Score=35.91  Aligned_cols=16  Identities=25%  Similarity=0.121  Sum_probs=13.5

Q ss_pred             cEEEeccCCCchHHHH
Q 028887          109 DCILHAQTGSGKTLTY  124 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~  124 (202)
                      -+++.|++|||||...
T Consensus         4 lIii~G~pGsGKTTla   19 (152)
T d1ly1a_           4 IILTIGCPGSGKSTWA   19 (152)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3788999999999864

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=88.39  E-value=0.1  Score=36.10  Aligned_cols=16  Identities=31%  Similarity=0.428  Sum_probs=14.0

Q ss_pred             cEEEeccCCCchHHHH
Q 028887          109 DCILHAQTGSGKTLTY  124 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~  124 (202)
                      -+++.|++|||||.+.
T Consensus         4 lI~i~G~~GsGKTTva   19 (176)
T d2bdta1           4 LYIITGPAGVGKSTTC   19 (176)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3789999999999875

>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=88.16  E-value=0.084  Score=36.90  Aligned_cols=18  Identities=17%  Similarity=0.233  Sum_probs=15.4

Q ss_pred             CcEEEeccCCCchHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l  125 (202)
                      +.+++.|++|+|||...-
T Consensus         8 K~I~i~G~~GsGKTTla~   25 (192)
T d1lw7a2           8 KTVAILGGESSGKSVLVN   25 (192)
T ss_dssp             EEEEEECCTTSHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            579999999999997653

>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=88.07  E-value=0.12  Score=35.83  Aligned_cols=18  Identities=28%  Similarity=0.307  Sum_probs=15.0

Q ss_pred             CcEEEeccCCCchHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l  125 (202)
                      ..+++.|++|||||...-
T Consensus         5 ~~I~i~G~pGsGKTTia~   22 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGK   22 (173)
T ss_dssp             CCEEEECSTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            468899999999997653

>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=88.00  E-value=0.46  Score=35.84  Aligned_cols=41  Identities=7%  Similarity=0.037  Sum_probs=27.7

Q ss_pred             HHcCCcEEEeccCCCchHHHHHHHHHHHHH-hcCCccEEEEecCC
Q 028887          104 LFSSRDCILHAQTGSGKTLTYLLLIFSLVN-AQRSAVQAVIVVPT  147 (202)
Q Consensus       104 i~~g~~~l~~a~TGsGKT~~~l~~~l~~l~-~~~~~~~~Lil~Pt  147 (202)
                      +..|.-+++.|+||+|||...+-.+.+... .+.   .+++++.+
T Consensus        32 ~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~---~v~~~s~E   73 (277)
T d1cr2a_          32 ARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGK---KVGLAMLE   73 (277)
T ss_dssp             BCTTCEEEEECSTTSSHHHHHHHHHHHHHHTSCC---CEEEEESS
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHHHHHhhhhhccc---ceeEeeec
Confidence            345677999999999999665554444332 233   68888765

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=87.97  E-value=0.21  Score=36.26  Aligned_cols=40  Identities=20%  Similarity=0.330  Sum_probs=25.7

Q ss_pred             cCCcEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCC
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPT  147 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Pt  147 (202)
                      .|.-+++.|++|+|||...+--+.+....+..  .++++...
T Consensus        25 ~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~--~~~~~s~e   64 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDE--PGVFVTFE   64 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHHCC--CEEEEESS
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCC--Cccccccc
Confidence            34679999999999997765444443333321  46666543

>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=87.79  E-value=0.11  Score=38.88  Aligned_cols=18  Identities=33%  Similarity=0.407  Sum_probs=15.2

Q ss_pred             CcEEEeccCCCchHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l  125 (202)
                      +.++++||+|+|||.+.-
T Consensus        53 ~~lll~GPpG~GKTt~a~   70 (253)
T d1sxja2          53 RAAMLYGPPGIGKTTAAH   70 (253)
T ss_dssp             SEEEEECSTTSSHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            469999999999997653

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=87.31  E-value=1.1  Score=32.52  Aligned_cols=64  Identities=17%  Similarity=0.111  Sum_probs=39.1

Q ss_pred             HHHHHHhHHc---CCcEEEeccCCCchHHHHHHHHHHHHHh-cCCccEEEEecCCHH--hHHHHHHHHHHh
Q 028887           97 QREALPVLFS---SRDCILHAQTGSGKTLTYLLLIFSLVNA-QRSAVQAVIVVPTRE--LGMQVTKVARVL  161 (202)
Q Consensus        97 Q~~~i~~i~~---g~~~l~~a~TGsGKT~~~l~~~l~~l~~-~~~~~~~Lil~Ptr~--La~Q~~~~~~~l  161 (202)
                      |.+.+..+.+   +..++++|+.|+|||....... ..+.. ....+-.+++.|...  -..|+.+..+.+
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~-~~i~~~~~~h~D~~~i~~~~~~I~Id~IR~i~~~~   71 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSLELP-EYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFL   71 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHH-HHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHH-HHHhccccCCCCEEEEeCCcCCCCHHHHHHHHHHH
Confidence            4445555433   3579999999999998876554 33322 233456888888632  255665544433

>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=87.28  E-value=0.13  Score=38.16  Aligned_cols=18  Identities=28%  Similarity=0.397  Sum_probs=15.2

Q ss_pred             CcEEEeccCCCchHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l  125 (202)
                      .+++++||+|+|||...-
T Consensus        46 ~~lll~Gp~G~GKTtla~   63 (231)
T d1iqpa2          46 PHLLFAGPPGVGKTTAAL   63 (231)
T ss_dssp             CEEEEESCTTSSHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHH
Confidence            469999999999997754

>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=87.09  E-value=0.13  Score=39.21  Aligned_cols=18  Identities=28%  Similarity=0.248  Sum_probs=15.2

Q ss_pred             CcEEEeccCCCchHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l  125 (202)
                      +.++++||+|+|||...-
T Consensus        41 ~~vLL~GppGtGKT~la~   58 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALAA   58 (246)
T ss_dssp             EEEEEECSTTSSHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHH
Confidence            359999999999997753

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=86.66  E-value=0.11  Score=36.23  Aligned_cols=20  Identities=20%  Similarity=0.092  Sum_probs=17.0

Q ss_pred             HcCCcEEEeccCCCchHHHH
Q 028887          105 FSSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       105 ~~g~~~l~~a~TGsGKT~~~  124 (202)
                      ..|..+++.|.+|||||.+.
T Consensus         4 ~~g~~I~l~G~~GsGKTTia   23 (183)
T d1m8pa3           4 TQGFTIFLTGYMNSGKDAIA   23 (183)
T ss_dssp             TCCEEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHH
Confidence            45677889999999999875

>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=86.27  E-value=0.16  Score=35.21  Aligned_cols=20  Identities=25%  Similarity=0.306  Sum_probs=15.9

Q ss_pred             cCCcEEEeccCCCchHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l  125 (202)
                      ..+-+++.|++|||||.+.-
T Consensus         2 ~~kiI~l~G~~GsGKsTva~   21 (178)
T d1qhxa_           2 TTRMIILNGGSSAGKSGIVR   21 (178)
T ss_dssp             CCCEEEEECCTTSSHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHH
Confidence            34568899999999997753

>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=85.67  E-value=0.57  Score=34.24  Aligned_cols=19  Identities=32%  Similarity=0.396  Sum_probs=15.7

Q ss_pred             cEEEeccCCCchHHHHHHH
Q 028887          109 DCILHAQTGSGKTLTYLLL  127 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~~  127 (202)
                      +++++||+|+|||.+.-+-
T Consensus        38 ~~ll~Gp~G~GKTt~a~~l   56 (224)
T d1sxjb2          38 HMIISGMPGIGKTTSVHCL   56 (224)
T ss_dssp             CEEEECSTTSSHHHHHHHH
T ss_pred             eEEEECCCCCCchhhHHHH
Confidence            5899999999999875443

>d1bg2a_ c.37.1.9 (A:) Kinesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.60  E-value=0.29  Score=38.53  Aligned_cols=25  Identities=28%  Similarity=0.239  Sum_probs=19.5

Q ss_pred             HHhHHcCCc--EEEeccCCCchHHHHH
Q 028887          101 LPVLFSSRD--CILHAQTGSGKTLTYL  125 (202)
Q Consensus       101 i~~i~~g~~--~l~~a~TGsGKT~~~l  125 (202)
                      ++.+++|.+  ++..|+||||||....
T Consensus        68 v~~~l~G~n~~i~aYGqtgSGKTyT~~   94 (323)
T d1bg2a_          68 VKDVLEGYNGTIFAYGQTSSGKTHTME   94 (323)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHHHT
T ss_pred             HHHHHcCCCcceeeecccCCCCceecc
Confidence            344578875  7889999999998853

>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=85.40  E-value=0.18  Score=37.08  Aligned_cols=19  Identities=32%  Similarity=0.431  Sum_probs=15.1

Q ss_pred             CcEEEeccCCCchHHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~  126 (202)
                      .+++++||+|+|||...-.
T Consensus        34 ~~lll~Gp~G~GKTtl~~~   52 (237)
T d1sxjd2          34 PHMLFYGPPGTGKTSTILA   52 (237)
T ss_dssp             CCEEEECSTTSSHHHHHHH
T ss_pred             CeEEEECCCCCChHHHHHH
Confidence            3589999999999976433

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=85.35  E-value=0.19  Score=35.21  Aligned_cols=18  Identities=22%  Similarity=0.318  Sum_probs=15.2

Q ss_pred             CcEEEeccCCCchHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l  125 (202)
                      +++++.|+.|+|||.+.-
T Consensus         1 k~I~liG~~GsGKsTi~k   18 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTLAR   18 (161)
T ss_dssp             CCEEEECCTTSCHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHH
Confidence            578999999999997753

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=85.26  E-value=2.2  Score=30.41  Aligned_cols=54  Identities=11%  Similarity=0.087  Sum_probs=38.3

Q ss_pred             HHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHH-HHHHHhc
Q 028887          128 IFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHK-SWLKVLY  197 (202)
Q Consensus       128 ~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~-~~l~~l~  197 (202)
                      +.+.+..+.   ++||.|+++..+..+.+.+++.+-.             ...+||...+.++ +.++.++
T Consensus        24 i~~~~~~g~---r~lvfc~t~~~~~~l~~~L~~~Gi~-------------a~~~Hg~~~~~eR~~~l~~F~   78 (174)
T d1c4oa2          24 IRERAARGE---RTLVTVLTVRMAEELTSFLVEHGIR-------------ARYLHHELDAFKRQALIRDLR   78 (174)
T ss_dssp             HHHHHHTTC---EEEEECSSHHHHHHHHHHHHHTTCC-------------EEEECTTCCHHHHHHHHHHHH
T ss_pred             HHHHHhcCC---cEEEEEcchhHHHHHHHHHHhcCCc-------------eEEEecccchHHHHHHHHHHH
Confidence            334445555   8999999999999999999876533             6678887776664 3444443

>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=84.95  E-value=0.2  Score=35.99  Aligned_cols=18  Identities=22%  Similarity=0.466  Sum_probs=15.1

Q ss_pred             CcEEEeccCCCchHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l  125 (202)
                      +.+++.||+|+|||...-
T Consensus         2 rpIvl~GpsG~GK~tl~~   19 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLK   19 (186)
T ss_dssp             CCEEEECCTTSSHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            568999999999998643

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=84.85  E-value=0.29  Score=35.98  Aligned_cols=35  Identities=20%  Similarity=0.174  Sum_probs=24.6

Q ss_pred             CcHHHHHHHHhH----HcCC---cEEEeccCCCchHHHHHHH
Q 028887           93 PTDIQREALPVL----FSSR---DCILHAQTGSGKTLTYLLL  127 (202)
Q Consensus        93 ~t~~Q~~~i~~i----~~g~---~~l~~a~TGsGKT~~~l~~  127 (202)
                      .+|.|..++..+    ..++   .++++||.|+|||.....-
T Consensus         3 ~yPw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~   44 (207)
T d1a5ta2           3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYAL   44 (207)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHH
T ss_pred             CCcccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHH
Confidence            356777766654    3443   3899999999999876543

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=84.81  E-value=0.79  Score=33.71  Aligned_cols=40  Identities=10%  Similarity=0.125  Sum_probs=23.2

Q ss_pred             cEEEeccCCCchHHHHHHHHHHHHHhcCCccEEEEecCCHHhHH
Q 028887          109 DCILHAQTGSGKTLTYLLLIFSLVNAQRSAVQAVIVVPTRELGM  152 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~~~l~~l~~~~~~~~~Lil~Ptr~La~  152 (202)
                      .++++|++|+|||-.. .++.+......  ..++++ +..++..
T Consensus        38 ~l~l~G~~G~GKTHLl-~A~~~~~~~~~--~~~~~~-~~~~~~~   77 (213)
T d1l8qa2          38 PIFIYGSVGTGKTHLL-QAAGNEAKKRG--YRVIYS-SADDFAQ   77 (213)
T ss_dssp             SEEEECSSSSSHHHHH-HHHHHHHHHTT--CCEEEE-EHHHHHH
T ss_pred             cEEEECCCCCcHHHHH-HHHHHHhccCc--cceEEe-chHHHHH
Confidence            4899999999999544 34444443322  244444 4444443

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=84.76  E-value=0.21  Score=34.64  Aligned_cols=19  Identities=26%  Similarity=0.254  Sum_probs=15.3

Q ss_pred             CcEEEeccCCCchHHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~  126 (202)
                      +-+++.|++|||||...-.
T Consensus         7 ~iivl~G~~GsGKsT~a~~   25 (171)
T d1knqa_           7 HIYVLMGVSGSGKSAVASE   25 (171)
T ss_dssp             EEEEEECSTTSCHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            3478899999999987644

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=84.57  E-value=1.1  Score=33.25  Aligned_cols=52  Identities=15%  Similarity=0.055  Sum_probs=41.3

Q ss_pred             HHHHHHHhcCCccEEEEecCCHHhHHHHHHHHHHhhcCCCCcccccccceEEEEEeCCccHHHHHH
Q 028887          127 LIFSLVNAQRSAVQAVIVVPTRELGMQVTKVARVLAAKPLDTDLEHKLCTVMALLDGGMLRRHKSW  192 (202)
Q Consensus       127 ~~l~~l~~~~~~~~~Lil~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~  192 (202)
                      .+...+.++.   |+.+++|..+-...+.+.++++++..           .+++.||....+++++
T Consensus        23 ~I~~El~rGg---Qvy~V~p~I~~~e~~~~~l~~~~p~~-----------~i~~lHGkm~~~eke~   74 (211)
T d2eyqa5          23 AILREILRGG---QVYYLYNDVENIQKAAERLAELVPEA-----------RIAIGHGQMRERELER   74 (211)
T ss_dssp             HHHHHHTTTC---EEEEECCCSSCHHHHHHHHHHHCTTS-----------CEEECCSSCCHHHHHH
T ss_pred             HHHHHHHcCC---eEEEEEcCccchhhHHHHHHHhCCce-----------EEEEEEeccCHHHHHH
Confidence            4555666666   99999999999999999999988763           3888999888877543

>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=84.44  E-value=0.34  Score=34.20  Aligned_cols=24  Identities=17%  Similarity=0.108  Sum_probs=18.7

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFS  130 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~  130 (202)
                      |+-+++.|++|+|||...+--+.+
T Consensus        23 G~v~~i~G~~GsGKT~l~l~la~~   46 (242)
T d1n0wa_          23 GSITEMFGEFRTGKTQICHTLAVT   46 (242)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHH
Confidence            467999999999999776554444

>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=84.32  E-value=0.13  Score=38.62  Aligned_cols=17  Identities=24%  Similarity=0.098  Sum_probs=13.3

Q ss_pred             EEEeccCCCchHHHHHH
Q 028887          110 CILHAQTGSGKTLTYLL  126 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~l~  126 (202)
                      ++++||+|+|||...-.
T Consensus        49 l~l~GppGtGKT~l~~~   65 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLAKF   65 (287)
T ss_dssp             EECTTCCSSSHHHHHHH
T ss_pred             EEeECCCCCCHHHHHHH
Confidence            45689999999987533

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.24  E-value=0.22  Score=38.02  Aligned_cols=17  Identities=41%  Similarity=0.595  Sum_probs=14.8

Q ss_pred             CcEEEeccCCCchHHHH
Q 028887          108 RDCILHAQTGSGKTLTY  124 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~  124 (202)
                      +.++++||+|+|||...
T Consensus        39 ~giLL~GppGtGKT~l~   55 (258)
T d1e32a2          39 RGILLYGPPGTGKTLIA   55 (258)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             ceeEEecCCCCCchHHH
Confidence            56999999999999763

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=83.95  E-value=0.25  Score=35.17  Aligned_cols=18  Identities=22%  Similarity=0.359  Sum_probs=15.8

Q ss_pred             CCcEEEeccCCCchHHHH
Q 028887          107 SRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~  124 (202)
                      |+-+++.||+|+||+...
T Consensus         2 G~iivl~GpsG~GK~tl~   19 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTVV   19 (182)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            667899999999999874

>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=83.95  E-value=0.23  Score=38.07  Aligned_cols=18  Identities=28%  Similarity=0.521  Sum_probs=15.6

Q ss_pred             CCcEEEeccCCCchHHHH
Q 028887          107 SRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~  124 (202)
                      .+.++++||+|+|||...
T Consensus        45 ~~~iLL~GppGtGKT~la   62 (256)
T d1lv7a_          45 PKGVLMVGPPGTGKTLLA   62 (256)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CCeEEeeCCCCCCccHHH
Confidence            367999999999999874

>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=83.82  E-value=0.23  Score=37.81  Aligned_cols=17  Identities=29%  Similarity=0.403  Sum_probs=15.0

Q ss_pred             CcEEEeccCCCchHHHH
Q 028887          108 RDCILHAQTGSGKTLTY  124 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~  124 (202)
                      +.++++||+|+|||...
T Consensus        43 ~giLl~GppGtGKT~la   59 (247)
T d1ixza_          43 KGVLLVGPPGVGKTHLA   59 (247)
T ss_dssp             SEEEEECCTTSSHHHHH
T ss_pred             ceEEEecCCCCChhHHH
Confidence            46999999999999875

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=83.75  E-value=0.26  Score=36.28  Aligned_cols=20  Identities=25%  Similarity=0.310  Sum_probs=16.9

Q ss_pred             cCCcEEEeccCCCchHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYL  125 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l  125 (202)
                      +|+-+++.||+|+||+...-
T Consensus         1 ~G~livi~GPSG~GK~tl~~   20 (205)
T d1s96a_           1 QGTLYIVSAPSGAGKSSLIQ   20 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHH
Confidence            46778999999999998753

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.56  E-value=0.27  Score=35.49  Aligned_cols=17  Identities=29%  Similarity=0.571  Sum_probs=14.6

Q ss_pred             CcEEEeccCCCchHHHH
Q 028887          108 RDCILHAQTGSGKTLTY  124 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~  124 (202)
                      +.+++.||+|+|||...
T Consensus         1 rpIvl~GPsGsGK~tl~   17 (190)
T d1lvga_           1 RPVVLSGPSGAGKSTLL   17 (190)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            45899999999999864

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=83.47  E-value=0.53  Score=33.68  Aligned_cols=34  Identities=18%  Similarity=0.139  Sum_probs=22.0

Q ss_pred             CcEEEecc-CCCchHHHHHHHHHHHHHhcCCccEEEEe
Q 028887          108 RDCILHAQ-TGSGKTLTYLLLIFSLVNAQRSAVQAVIV  144 (202)
Q Consensus       108 ~~~l~~a~-TGsGKT~~~l~~~l~~l~~~~~~~~~Lil  144 (202)
                      |.++|+|. ||.|||.+-+.-....-.++.   +++++
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~G~---rVl~i   36 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAAGY---RTAGY   36 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHTTC---CEEEE
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHCCC---eEEEE
Confidence            34667776 699999887665544444444   56554

>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=83.40  E-value=0.25  Score=36.62  Aligned_cols=17  Identities=24%  Similarity=0.454  Sum_probs=14.8

Q ss_pred             cEEEeccCCCchHHHHH
Q 028887          109 DCILHAQTGSGKTLTYL  125 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l  125 (202)
                      .+++.||.|+|||....
T Consensus        35 ~lll~Gp~G~GKTt~~~   51 (252)
T d1sxje2          35 HLLLYGPNGTGKKTRCM   51 (252)
T ss_dssp             CEEEECSTTSSHHHHHH
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            58999999999997754

>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=83.39  E-value=0.34  Score=35.49  Aligned_cols=18  Identities=28%  Similarity=0.420  Sum_probs=14.8

Q ss_pred             cEEEeccCCCchHHHHHH
Q 028887          109 DCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~  126 (202)
                      +++++||+|+|||...-.
T Consensus        37 ~lLl~Gp~G~GKttl~~~   54 (227)
T d1sxjc2          37 HLLFYGPPGTGKTSTIVA   54 (227)
T ss_dssp             CEEEECSSSSSHHHHHHH
T ss_pred             eEEEECCCCCChhHHHHH
Confidence            589999999999966443

>d1goja_ c.37.1.9 (A:) Kinesin {Neurospora crassa [TaxId: 5141]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Neurospora crassa [TaxId: 5141]

Probab=82.73  E-value=0.42  Score=38.11  Aligned_cols=23  Identities=26%  Similarity=0.400  Sum_probs=18.1

Q ss_pred             HhHHcCCc--EEEeccCCCchHHHH
Q 028887          102 PVLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       102 ~~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      ..++.|.+  ++.+|+||||||...
T Consensus        73 ~~~l~G~n~ti~aYG~tgSGKT~Tm   97 (354)
T d1goja_          73 DDILNGYNGTVFAYGQTGAGKSYTM   97 (354)
T ss_dssp             HHHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhhccCceeEEecccCCCCcceee
Confidence            34567876  788899999999774

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=82.48  E-value=0.83  Score=31.11  Aligned_cols=24  Identities=25%  Similarity=0.267  Sum_probs=16.6

Q ss_pred             EEEeccCCCchHHHHHHHHHHHHHh
Q 028887          110 CILHAQTGSGKTLTYLLLIFSLVNA  134 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~l~~~l~~l~~  134 (202)
                      +.+.|+.|||||... --++..+..
T Consensus         5 i~itG~~GSGKTTL~-~~L~~~l~~   28 (170)
T d1np6a_           5 LAFAAWSGTGKTTLL-KKLIPALCA   28 (170)
T ss_dssp             EEEECCTTSCHHHHH-HHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHH-HHHHHHHHH
Confidence            678999999999554 444444443

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=82.47  E-value=0.58  Score=37.56  Aligned_cols=37  Identities=16%  Similarity=0.091  Sum_probs=23.2

Q ss_pred             CCCCCcHHHHHHHHhHHcC----CcEEEeccCCCchHHHHH
Q 028887           89 GYVLPTDIQREALPVLFSS----RDCILHAQTGSGKTLTYL  125 (202)
Q Consensus        89 g~~~~t~~Q~~~i~~i~~g----~~~l~~a~TGsGKT~~~l  125 (202)
                      |+......-..++..++.|    +.++++||+|+|||....
T Consensus       132 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~~g~~~~gk~~~~~  172 (362)
T d1svma_         132 LLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAA  172 (362)
T ss_dssp             TSTTHHHHHHHHHHHHHHCCTTCCEEEEECSTTSSHHHHHH
T ss_pred             cccchHHHHHHHHHHHHhCCCCcCeEEEECCCCCCHHHHHH
Confidence            3444333333444444444    569999999999997653

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=82.37  E-value=0.66  Score=35.53  Aligned_cols=37  Identities=22%  Similarity=0.225  Sum_probs=27.2

Q ss_pred             HHHhHHc-C-----CcEEEeccCCCchHHHHHHHHHHHHHhcC
Q 028887          100 ALPVLFS-S-----RDCILHAQTGSGKTLTYLLLIFSLVNAQR  136 (202)
Q Consensus       100 ~i~~i~~-g-----~~~l~~a~TGsGKT~~~l~~~l~~l~~~~  136 (202)
                      .+..++. |     +-+.+.|++|+|||...+..+.....++.
T Consensus        41 ~lD~~Lg~GGi~~g~itei~G~~gsGKTtl~l~~~~~~q~~g~   83 (263)
T d1u94a1          41 SLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGK   83 (263)
T ss_dssp             HHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHhcCCCccCceEEEEecCCCcHHHHHHHHHHHHHHcCCC
Confidence            4555553 3     56899999999999998777777665543

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.13  E-value=0.29  Score=37.49  Aligned_cols=18  Identities=33%  Similarity=0.510  Sum_probs=15.4

Q ss_pred             CCcEEEeccCCCchHHHH
Q 028887          107 SRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~  124 (202)
                      .+.++++||+|+|||...
T Consensus        41 ~~giLL~Gp~GtGKT~l~   58 (265)
T d1r7ra3          41 SKGVLFYGPPGCGKTLLA   58 (265)
T ss_dssp             CCEEEEBCCTTSSHHHHH
T ss_pred             CCeEEEECCCCCcchhHH
Confidence            356999999999999764

>d1v8ka_ c.37.1.9 (A:) Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif2c [TaxId: 10090]

Probab=82.09  E-value=0.5  Score=37.86  Aligned_cols=22  Identities=45%  Similarity=0.700  Sum_probs=17.4

Q ss_pred             hHHcCCc--EEEeccCCCchHHHH
Q 028887          103 VLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       103 ~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      .++.|.+  ++.+|.||||||...
T Consensus       108 ~~l~G~n~tifaYGqTGSGKTyTm  131 (362)
T d1v8ka_         108 TIFEGGKATCFAYGQTGSGKTHTM  131 (362)
T ss_dssp             HHHTTCEEEEEEEESTTSSHHHHH
T ss_pred             HHHhccCceEEeeccCCCCCceee
Confidence            3467865  678899999999775

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.09  E-value=0.31  Score=34.74  Aligned_cols=16  Identities=19%  Similarity=0.206  Sum_probs=13.7

Q ss_pred             cEEEeccCCCchHHHH
Q 028887          109 DCILHAQTGSGKTLTY  124 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~  124 (202)
                      -++++|++|||||...
T Consensus        16 liil~G~pGsGKST~a   31 (172)
T d1yj5a2          16 VVVAVGFPGAGKSTFI   31 (172)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4899999999999754

>d2zfia1 c.37.1.9 (A:4-352) Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif1a [TaxId: 10090]

Probab=82.06  E-value=0.5  Score=37.55  Aligned_cols=23  Identities=30%  Similarity=0.408  Sum_probs=18.4

Q ss_pred             HhHHcCCc--EEEeccCCCchHHHH
Q 028887          102 PVLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       102 ~~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      +.++.|.+  ++.+|.||||||...
T Consensus        80 ~~~l~G~n~ti~aYGqTgSGKT~Tm  104 (349)
T d2zfia1          80 QHAFEGYNVCIFAYGQTGAGKSYTM  104 (349)
T ss_dssp             HHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhccCceeeeeccCCCCCceee
Confidence            34577865  788999999999885

>d1sdma_ c.37.1.9 (A:) Kinesin heavy chain-like protein {Potato (Solanum tuberosum) [TaxId: 4113]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin heavy chain-like protein
species: Potato (Solanum tuberosum) [TaxId: 4113]

Probab=82.01  E-value=0.41  Score=38.43  Aligned_cols=24  Identities=33%  Similarity=0.389  Sum_probs=19.2

Q ss_pred             HHhHHcCCc--EEEeccCCCchHHHH
Q 028887          101 LPVLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       101 i~~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      +..++.|.+  ++..|+||||||...
T Consensus        67 v~~~l~G~n~~i~aYGqTGSGKTyTm   92 (364)
T d1sdma_          67 VQSAVDGYNVCIFAYGQTGSGKTFTI   92 (364)
T ss_dssp             HHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHhcCCceeeeccccCCCCccccc
Confidence            455677865  788999999999885

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.01  E-value=0.16  Score=36.04  Aligned_cols=20  Identities=25%  Similarity=0.317  Sum_probs=15.9

Q ss_pred             CCcEEEeccCCCchHHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~  126 (202)
                      |..+++.|++|||||...-.
T Consensus        19 g~vI~L~G~pGSGKTTiAk~   38 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSMA   38 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            45677999999999987543

>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=81.66  E-value=0.35  Score=35.23  Aligned_cols=23  Identities=17%  Similarity=0.104  Sum_probs=17.9

Q ss_pred             cCCcEEEeccCCCchHHHHHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTYLLLI  128 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~l~~~  128 (202)
                      .|+-+++.|++|+|||...+--+
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq~~   55 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHTLA   55 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHT
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHH
Confidence            34679999999999997655443

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=81.35  E-value=0.38  Score=34.28  Aligned_cols=20  Identities=20%  Similarity=0.214  Sum_probs=16.3

Q ss_pred             CCcEEEeccCCCchHHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~  126 (202)
                      |..+++.||+|||||...-.
T Consensus         3 ~~riil~G~pGSGKsT~a~~   22 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQAPK   22 (190)
T ss_dssp             CCEEEEECCTTSSHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHH
Confidence            55688899999999987543

>d1x88a1 c.37.1.9 (A:18-362) Kinesin {Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]

Probab=81.24  E-value=0.5  Score=37.48  Aligned_cols=24  Identities=33%  Similarity=0.425  Sum_probs=18.6

Q ss_pred             HHhHHcCCc--EEEeccCCCchHHHH
Q 028887          101 LPVLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       101 i~~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      +..++.|.+  ++..|+||||||...
T Consensus        73 v~~~l~G~n~~i~aYGqtgSGKTyTm   98 (345)
T d1x88a1          73 LDEVIMGYNCTIFAYGQTGTGKTFTM   98 (345)
T ss_dssp             HHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             HHHHhccCCceEEeeeeccccceEEe
Confidence            344577865  788999999999763

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=81.17  E-value=0.3  Score=38.33  Aligned_cols=19  Identities=16%  Similarity=0.370  Sum_probs=16.4

Q ss_pred             cCCcEEEeccCCCchHHHH
Q 028887          106 SSRDCILHAQTGSGKTLTY  124 (202)
Q Consensus       106 ~g~~~l~~a~TGsGKT~~~  124 (202)
                      .+.++++.|++|+|||...
T Consensus        27 ~~h~vLl~G~pG~GKT~la   45 (333)
T d1g8pa_          27 GIGGVLVFGDRGTGKSTAV   45 (333)
T ss_dssp             GGCCEEEECCGGGCTTHHH
T ss_pred             CCCeEEEECCCCccHHHHH
Confidence            4568999999999999874

>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=81.16  E-value=0.43  Score=35.07  Aligned_cols=24  Identities=25%  Similarity=0.127  Sum_probs=18.7

Q ss_pred             CCcEEEeccCCCchHHHHHHHHHH
Q 028887          107 SRDCILHAQTGSGKTLTYLLLIFS  130 (202)
Q Consensus       107 g~~~l~~a~TGsGKT~~~l~~~l~  130 (202)
                      |+-+++.|++|+|||...+--+.+
T Consensus        36 G~~~li~G~pGsGKT~~~lq~~~~   59 (254)
T d1pzna2          36 QAITEVFGEFGSGKTQLAHTLAVM   59 (254)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHH
Confidence            467999999999999876554444

>d2ncda_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=81.05  E-value=0.46  Score=38.16  Aligned_cols=25  Identities=32%  Similarity=0.376  Sum_probs=19.6

Q ss_pred             HHHhHHcCCc--EEEeccCCCchHHHH
Q 028887          100 ALPVLFSSRD--CILHAQTGSGKTLTY  124 (202)
Q Consensus       100 ~i~~i~~g~~--~l~~a~TGsGKT~~~  124 (202)
                      .++.++.|.+  ++..|+||||||...
T Consensus       116 lv~~vl~G~n~ti~aYGqtGSGKT~Tm  142 (368)
T d2ncda_         116 LIQSALDGYNICIFAYGQTGSGKTYTM  142 (368)
T ss_dssp             HHHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHhcccceeEEeeccCCCccceEe
Confidence            3455678865  788999999999774

>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=80.68  E-value=0.37  Score=33.54  Aligned_cols=23  Identities=26%  Similarity=0.364  Sum_probs=16.8

Q ss_pred             cEEEeccCCCchHHHHHHHHHHHH
Q 028887          109 DCILHAQTGSGKTLTYLLLIFSLV  132 (202)
Q Consensus       109 ~~l~~a~TGsGKT~~~l~~~l~~l  132 (202)
                      .+++.||+|+|||.. +-.++..+
T Consensus         2 ki~I~G~~G~GKSTL-l~~i~~~l   24 (178)
T d1ye8a1           2 KIIITGEPGVGKTTL-VKKIVERL   24 (178)
T ss_dssp             EEEEECCTTSSHHHH-HHHHHHHH
T ss_pred             EEEEECCCCcHHHHH-HHHHHhcC
Confidence            478999999999975 33444444

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=80.62  E-value=0.37  Score=33.40  Aligned_cols=17  Identities=18%  Similarity=0.327  Sum_probs=14.3

Q ss_pred             CcEEEeccCCCchHHHH
Q 028887          108 RDCILHAQTGSGKTLTY  124 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~  124 (202)
                      +-+++.|++|||||...
T Consensus         2 kiI~i~G~~GsGKsT~~   18 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSS   18 (190)
T ss_dssp             CEEEEECCTTSCHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            45789999999999764

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=80.10  E-value=1.2  Score=30.75  Aligned_cols=24  Identities=17%  Similarity=-0.043  Sum_probs=16.0

Q ss_pred             EEEeccCCCchHHHHHHHHHHHHHh
Q 028887          110 CILHAQTGSGKTLTYLLLIFSLVNA  134 (202)
Q Consensus       110 ~l~~a~TGsGKT~~~l~~~l~~l~~  134 (202)
                      +-+.|..|||||... --++..+..
T Consensus         4 i~I~G~~gSGKTTli-~~l~~~L~~   27 (165)
T d1xjca_           4 WQVVGYKHSGKTTLM-EKWVAAAVR   27 (165)
T ss_dssp             EEEECCTTSSHHHHH-HHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHH-HHHHHHHHh
Confidence            358999999999653 344444443

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=80.04  E-value=0.44  Score=33.35  Aligned_cols=19  Identities=16%  Similarity=0.083  Sum_probs=15.6

Q ss_pred             CcEEEeccCCCchHHHHHH
Q 028887          108 RDCILHAQTGSGKTLTYLL  126 (202)
Q Consensus       108 ~~~l~~a~TGsGKT~~~l~  126 (202)
                      +.+++.|+.|+|||.+.-.
T Consensus         3 ~~Iil~G~~GsGKSTia~~   21 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRE   21 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHH
Confidence            5688999999999987544