Psyllid ID: psy7691

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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-----
Protein Sequence
MHNHAKTQERAARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQDLANSNPNSKGG
Secondary Structure (PSIPRED)
ccccccccHHHHcccHHHHHHHHHHcccEEEcccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEEEcccccEEEEEEccccccccHHHHcccccccccccccEEEEEccccHHHHHHHHHHHHHccccccHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
ccccEEccHHHHHccHHHHHHHHHHccEEEEccccccccccHHHccccHHHHHHHHHcccccccHHHHccHHHHHccccEEEEEEcccccccEEEEccccccHHHHEEEEccccccccccEEEEEEcccccHHHHHHHHHHHHHcccccHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
MHNHAKTQERAARLSESEVEAFRQKKEitvkgnnipcptqeltegcfpnavlqhlkgqgfeeptaiqaqgwpialsgrdmvgiaqtgsgktlAVINfdypnssedyihrigrtgrcassgtaytfftpnngKQAKELIAVLTeasqpippqlqdlansnpnskgg
Flexible Loop (DISEMBL)
mhnhaktqeraarlseseveafrqkkeitvkgnniPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASqpippqlqdlansnpnskgg
Low Complexity Region (SEG)
MHNHAKTQERAARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQDLANSNPNSKGG
Disordered region (IsUnstruct)
****************************TVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVL************************
Disordered Region (DISOPRED)
MHNHAKTQERAARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRT**CASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQD***********
Disordered Region (DISEMBL)
*******************EAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQDLAN********
Disordered Region (DISPRO)
*HNHAKTQERAARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQDLANSN******
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MHNHAKTQERAARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQDLANSNPNSKGG
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	165	2.2.26 [Sep-21-2011]
Q4X195	547	ATP-dependent RNA helicas	yes	N/A	0.490	0.148	0.658	7e-25
A1DGZ7	545	ATP-dependent RNA helicas	N/A	N/A	0.490	0.148	0.658	7e-25
Q8SRB2	495	ATP-dependent RNA helicas	yes	N/A	0.521	0.173	0.559	6e-24
A6RGE3	542	ATP-dependent RNA helicas	N/A	N/A	0.472	0.143	0.628	2e-23
A2QC74	565	ATP-dependent RNA helicas	yes	N/A	0.515	0.150	0.561	2e-23
Q2U070	554	ATP-dependent RNA helicas	yes	N/A	0.503	0.149	0.590	2e-23
Q5QMN3	494	DEAD-box ATP-dependent RN	yes	N/A	0.515	0.172	0.552	3e-23
A1C6C4	549	ATP-dependent RNA helicas	N/A	N/A	0.472	0.142	0.615	3e-23
Q5B0J9	563	ATP-dependent RNA helicas	yes	N/A	0.478	0.140	0.607	3e-23
Q4IF76	555	ATP-dependent RNA helicas	yes	N/A	0.472	0.140	0.589	8e-23

>sp|Q4X195|DBP2_ASPFU ATP-dependent RNA helicase dbp2 OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) GN=dbp2 PE=3 SV=2

 Score =  112 bits (281), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 54/82 (65%), Positives = 64/82 (78%), Gaps = 1/82 (1%)

Query: 11  AARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQG 70
           AAR SE EVE FR+K E+TV+G N+P P +   E  FP  VL  +K QGFE PTAIQ+QG
Sbjct: 93  AAR-SEREVEEFRKKHEMTVQGRNVPRPVENFDEAGFPQYVLSEVKAQGFERPTAIQSQG 151

Query: 71  WPIALSGRDMVGIAQTGSGKTL 92
           WP+ALSGRD+VGIA+TGSGKTL
Sbjct: 152 WPMALSGRDVVGIAETGSGKTL 173

ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.
Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (taxid: 330879)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|A1DGZ7|DBP2_NEOFI ATP-dependent RNA helicase dbp2 OS=Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) GN=dbp2 PE=3 SV=1

 Score =  112 bits (281), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 54/82 (65%), Positives = 64/82 (78%), Gaps = 1/82 (1%)

Query: 11  AARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQG 70
           AAR SE EVE FR+K E+TV+G N+P P +   E  FP  VL  +K QGFE PTAIQ+QG
Sbjct: 91  AAR-SEREVEEFRKKHEMTVQGRNVPRPVENFDEAGFPQYVLSEVKAQGFERPTAIQSQG 149

Query: 71  WPIALSGRDMVGIAQTGSGKTL 92
           WP+ALSGRD+VGIA+TGSGKTL
Sbjct: 150 WPMALSGRDVVGIAETGSGKTL 171

ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.

Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) (taxid: 331117)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q8SRB2|DBP2_ENCCU ATP-dependent RNA helicase DBP2 OS=Encephalitozoon cuniculi (strain GB-M1) GN=DBP2 PE=3 SV=1

 Score =  110 bits (274), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 52/93 (55%), Positives = 66/93 (70%)

Query: 3   NHAKTQERAARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEE 62
           N  +  E  +R++ SEV +FR+  E+ VKG N+P P Q+  E  F + V+  L  +GF E
Sbjct: 50  NFYQEAESISRMTPSEVSSFRKTNEMIVKGTNVPHPIQKFEEAGFSSEVVSSLVEKGFSE 109

Query: 63  PTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVI 95
           PTAIQ QGWP+ALSGRDMVGIAQTGSGKTL+ I
Sbjct: 110 PTAIQGQGWPMALSGRDMVGIAQTGSGKTLSFI 142

ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.

Encephalitozoon cuniculi (strain GB-M1) (taxid: 284813)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A6RGE3|DBP2_AJECN ATP-dependent RNA helicase DBP2 OS=Ajellomyces capsulata (strain NAm1 / WU24) GN=DBP2 PE=3 SV=1

 Score =  108 bits (269), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 49/78 (62%), Positives = 60/78 (76%)

Query: 15  SESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIA 74
           S  EV+AFR++ EITV+G N+P P +   E  FP  V+  +K QGF  PTAIQAQGWP+A
Sbjct: 100 STHEVDAFRKEHEITVQGKNVPRPVETFDEAGFPQYVMSEVKAQGFARPTAIQAQGWPMA 159

Query: 75  LSGRDMVGIAQTGSGKTL 92
           LSGRD+VGIA+TGSGKTL
Sbjct: 160 LSGRDVVGIAETGSGKTL 177

ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.

Ajellomyces capsulata (strain NAm1 / WU24) (taxid: 339724)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A2QC74|DBP2_ASPNC ATP-dependent RNA helicase dbp2 OS=Aspergillus niger (strain CBS 513.88 / FGSC A1513) GN=dbp2 PE=3 SV=1

 Score =  108 bits (269), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 50/89 (56%), Positives = 64/89 (71%), Gaps = 4/89 (4%)

Query: 4   HAKTQERAARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEP 63
           HA   ER+ R    +V+ FR+K E+ V+G N+P P +   E  FP  VL  +K QGF+ P
Sbjct: 105 HADVAERSQR----DVDEFRKKHEMAVQGRNVPRPVETFDEAGFPQYVLSEVKAQGFDRP 160

Query: 64  TAIQAQGWPIALSGRDMVGIAQTGSGKTL 92
           TAIQ+QGWP+ALSGRD+VGIA+TGSGKTL
Sbjct: 161 TAIQSQGWPMALSGRDVVGIAETGSGKTL 189

ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.

Aspergillus niger (strain CBS 513.88 / FGSC A1513) (taxid: 425011)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q2U070|DBP2_ASPOR ATP-dependent RNA helicase dbp2 OS=Aspergillus oryzae (strain ATCC 42149 / RIB 40) GN=dbp2 PE=3 SV=1

 Score =  107 bits (268), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 49/83 (59%), Positives = 63/83 (75%)

Query: 11  AARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQG 70
            A  S+ +V+ FR+K E++V+G NIP P +   E  FP  VL  +K QGFE PTAIQ+QG
Sbjct: 101 VANRSQRDVDEFRKKFEMSVQGKNIPRPVETFDEAGFPQYVLSEVKAQGFERPTAIQSQG 160

Query: 71  WPIALSGRDMVGIAQTGSGKTLA 93
           WP+ALSGRD+VGIA+TGSGKTL+
Sbjct: 161 WPMALSGRDVVGIAETGSGKTLS 183

ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.

Aspergillus oryzae (strain ATCC 42149 / RIB 40) (taxid: 510516)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5QMN3|RH20_ORYSJ DEAD-box ATP-dependent RNA helicase 20 OS=Oryza sativa subsp. japonica GN=Os01g0197200 PE=3 SV=2

 Score =  107 bits (268), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 47/85 (55%), Positives = 65/85 (76%)

Query: 11  AARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQG 70
            A ++E EVEA+R+++EITV+G ++P P +E  +  FP  VLQ +   GF EPT IQ+QG
Sbjct: 62  VAGMTEEEVEAYRRRREITVEGRDVPKPVREFRDVGFPEYVLQEITKAGFVEPTPIQSQG 121

Query: 71  WPIALSGRDMVGIAQTGSGKTLAVI 95
           WP+AL GRD++GIA+TGSGKTLA +
Sbjct: 122 WPMALRGRDLIGIAETGSGKTLAYL 146

ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A1C6C4|DBP2_ASPCL ATP-dependent RNA helicase dbp2 OS=Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1) GN=dbp2 PE=3 SV=1

 Score =  107 bits (268), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 48/78 (61%), Positives = 61/78 (78%)

Query: 15  SESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIA 74
           S+ EV+ FRQ+ ++TV+G N+P P +   E  FP  VL  +K QGFE PTAIQ+QGWP+A
Sbjct: 100 SQREVDEFRQEHKMTVQGKNVPRPVETFDEAGFPQYVLSEVKSQGFERPTAIQSQGWPMA 159

Query: 75  LSGRDMVGIAQTGSGKTL 92
           LSGRD+VGIA+TGSGKTL
Sbjct: 160 LSGRDVVGIAETGSGKTL 177

ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5B0J9|DBP2_EMENI ATP-dependent RNA helicase dbp2 OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) GN=dbp2 PE=3 SV=1

 Score =  107 bits (268), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 48/79 (60%), Positives = 63/79 (79%)

Query: 15  SESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIA 74
           S+ EV+ FR+K E+TV+G ++P P +   E  FP  VL  +K QGFE+PTAIQ+QGWP+A
Sbjct: 115 SQREVDEFRKKCEMTVQGRDVPRPVETFDEAGFPQYVLSEVKAQGFEKPTAIQSQGWPMA 174

Query: 75  LSGRDMVGIAQTGSGKTLA 93
           LSGRD+VGIA+TGSGKTL+
Sbjct: 175 LSGRDVVGIAETGSGKTLS 193

ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.

Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (taxid: 227321)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q4IF76|DBP2_GIBZE ATP-dependent RNA helicase DBP2 OS=Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) GN=DBP2 PE=3 SV=1

 Score =  106 bits (264), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 46/78 (58%), Positives = 62/78 (79%)

Query: 15  SESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIA 74
           S+++VEAFR+K ++T+ G+N+P P +   E  FP  V+  +K QGF  PTAIQ+QGWP+A
Sbjct: 109 SDADVEAFRRKHQMTIAGSNVPKPVETFDEAGFPRYVMDEVKAQGFPAPTAIQSQGWPMA 168

Query: 75  LSGRDMVGIAQTGSGKTL 92
           LSGRD+VGIA+TGSGKTL
Sbjct: 169 LSGRDVVGIAETGSGKTL 186

ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.

Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) (taxid: 229533)

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	165
383862185	713	PREDICTED: probable ATP-dependent RNA he	0.6	0.138	0.552	5e-26
380014980	728	PREDICTED: probable ATP-dependent RNA he	0.563	0.127	0.554	2e-25
340717724	713	PREDICTED: probable ATP-dependent RNA he	0.563	0.130	0.554	2e-25
350418218	712	PREDICTED: probable ATP-dependent RNA he	0.563	0.130	0.554	2e-25
328780921	726	PREDICTED: probable ATP-dependent RNA he	0.563	0.128	0.554	2e-25
332025289	706	Putative ATP-dependent RNA helicase DDX1	0.539	0.126	0.621	8e-25
307202009	724	Probable ATP-dependent RNA helicase DDX1	0.6	0.136	0.536	9e-25
307183175	705	Probable ATP-dependent RNA helicase DDX1	0.539	0.126	0.621	1e-24
345493222	710	PREDICTED: probable ATP-dependent RNA he	0.6	0.139	0.528	1e-24
258617566	646	DEAD box ATP-dependent RNA helicase-like	0.533	0.136	0.619	2e-24

>gi|383862185|ref|XP_003706564.1| PREDICTED: probable ATP-dependent RNA helicase DDX17-like [Megachile rotundata]

 Score =  122 bits (306), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 69/125 (55%), Positives = 82/125 (65%), Gaps = 26/125 (20%)

Query: 65  AIQAQGWP-IALSG------RDMVGIAQTGSGKTLA------------------VINFDY 99
           AI+ +GWP I++ G      RD V +++  +GKT+                   VINFDY
Sbjct: 372 AIKREGWPAISIHGDKSQPERDYV-LSEFRNGKTMILVATDVAARGLDVEDVKYVINFDY 430

Query: 100 PNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQDLANSN 159
           PNSSEDYIHRIGRTGRC S+GTAY +FTPNN +QAKELI+VL EA Q I PQL DLANS 
Sbjct: 431 PNSSEDYIHRIGRTGRCQSAGTAYAYFTPNNARQAKELISVLEEAGQVINPQLADLANSI 490

Query: 160 PNSKG 164
            NS G
Sbjct: 491 KNSYG 495

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380014980|ref|XP_003691490.1| PREDICTED: probable ATP-dependent RNA helicase DDX17-like [Apis florea]

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 66/119 (55%), Positives = 79/119 (66%), Gaps = 26/119 (21%)

Query: 65  AIQAQGWP-IALSG------RDMVGIAQTGSGKTLA------------------VINFDY 99
           AI+ +GWP I++ G      RD V +++  +GKT+                   VINFDY
Sbjct: 374 AIKREGWPAISIHGDKSQPERDYV-LSEFRNGKTMILVATDVAARGLDVEDVKYVINFDY 432

Query: 100 PNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQDLANS 158
           PNSSEDYIHRIGRTGRC S+GTAY +FTPNN +QAKELI+VL EA Q I PQL DLANS
Sbjct: 433 PNSSEDYIHRIGRTGRCQSAGTAYAYFTPNNARQAKELISVLEEAGQAINPQLADLANS 491

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340717724|ref|XP_003397328.1| PREDICTED: probable ATP-dependent RNA helicase DDX17-like [Bombus terrestris]

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 66/119 (55%), Positives = 79/119 (66%), Gaps = 26/119 (21%)

Query: 65  AIQAQGWP-IALSG------RDMVGIAQTGSGKTLA------------------VINFDY 99
           AI+ +GWP I++ G      RD V +++  +GKT+                   VINFDY
Sbjct: 373 AIKREGWPAISIHGDKSQPERDYV-LSEFRNGKTMILVATDVAARGLDVEDVKYVINFDY 431

Query: 100 PNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQDLANS 158
           PNSSEDYIHRIGRTGRC S+GTAY +FTPNN +QAKELI+VL EA Q I PQL DLANS
Sbjct: 432 PNSSEDYIHRIGRTGRCQSAGTAYAYFTPNNARQAKELISVLEEAGQTINPQLADLANS 490

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350418218|ref|XP_003491789.1| PREDICTED: probable ATP-dependent RNA helicase DDX17-like [Bombus impatiens]

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 66/119 (55%), Positives = 79/119 (66%), Gaps = 26/119 (21%)

Query: 65  AIQAQGWP-IALSG------RDMVGIAQTGSGKTLA------------------VINFDY 99
           AI+ +GWP I++ G      RD V +++  +GKT+                   VINFDY
Sbjct: 371 AIKREGWPAISIHGDKSQPERDYV-LSEFRNGKTMILVATDVAARGLDVEDVKYVINFDY 429

Query: 100 PNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQDLANS 158
           PNSSEDYIHRIGRTGRC S+GTAY +FTPNN +QAKELI+VL EA Q I PQL DLANS
Sbjct: 430 PNSSEDYIHRIGRTGRCQSAGTAYAYFTPNNARQAKELISVLEEAGQTINPQLADLANS 488

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328780921|ref|XP_394723.3| PREDICTED: probable ATP-dependent RNA helicase DDX17-like [Apis mellifera]

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 66/119 (55%), Positives = 79/119 (66%), Gaps = 26/119 (21%)

Query: 65  AIQAQGWP-IALSG------RDMVGIAQTGSGKTLA------------------VINFDY 99
           AI+ +GWP I++ G      RD V +++  +GKT+                   VINFDY
Sbjct: 372 AIKREGWPAISIHGDKSQPERDYV-LSEFRNGKTMILVATDVAARGLDVEDVKYVINFDY 430

Query: 100 PNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQDLANS 158
           PNSSEDYIHRIGRTGRC S+GTAY +FTPNN +QAKELI+VL EA Q I PQL DLANS
Sbjct: 431 PNSSEDYIHRIGRTGRCQSAGTAYAYFTPNNARQAKELISVLEEAGQAINPQLADLANS 489

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332025289|gb|EGI65460.1| Putative ATP-dependent RNA helicase DDX17 [Acromyrmex echinatior]

 Score =  118 bits (296), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 59/95 (62%), Positives = 69/95 (72%), Gaps = 6/95 (6%)

Query: 76  SGRDMVGIAQTGSGKTL------AVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPN 129
           +G+ M+ +A   + + L       VINFDYPNSSEDYIHRIGRTGRC S+GTAY +FTPN
Sbjct: 402 NGKTMILVATDVAARGLDVEDVKYVINFDYPNSSEDYIHRIGRTGRCQSAGTAYAYFTPN 461

Query: 130 NGKQAKELIAVLTEASQPIPPQLQDLANSNPNSKG 164
           N +QAKELIAVL EA Q I PQL D+ANS  N  G
Sbjct: 462 NARQAKELIAVLEEAGQAINPQLADMANSVRNQYG 496

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307202009|gb|EFN81574.1| Probable ATP-dependent RNA helicase DDX17 [Harpegnathos saltator]

 Score =  118 bits (295), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 67/125 (53%), Positives = 80/125 (64%), Gaps = 26/125 (20%)

Query: 65  AIQAQGWP-IALSG------RDMVGIAQTGSGKTLA------------------VINFDY 99
           AI+ +GW  I++ G      RD V +++  +GKT+                   VINFDY
Sbjct: 374 AIKREGWSAISIHGDKSQPERDYV-LSEFRNGKTMILVATDVAARGLDVEDVKYVINFDY 432

Query: 100 PNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQDLANSN 159
           PNSSEDYIHRIGRTGRC S+GTAY +FTPNN +QAKELIAVL EA Q I PQL D+ANS 
Sbjct: 433 PNSSEDYIHRIGRTGRCQSAGTAYAYFTPNNARQAKELIAVLEEAGQAINPQLADMANSI 492

Query: 160 PNSKG 164
            N  G
Sbjct: 493 RNQYG 497

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307183175|gb|EFN70084.1| Probable ATP-dependent RNA helicase DDX17 [Camponotus floridanus]

 Score =  117 bits (294), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 59/95 (62%), Positives = 69/95 (72%), Gaps = 6/95 (6%)

Query: 76  SGRDMVGIAQTGSGKTL------AVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPN 129
           +G+ M+ +A   + + L       VINFDYPNSSEDYIHRIGRTGRC S+GTAY +FTPN
Sbjct: 404 NGKTMILVATDVAARGLDVEDVKYVINFDYPNSSEDYIHRIGRTGRCQSAGTAYAYFTPN 463

Query: 130 NGKQAKELIAVLTEASQPIPPQLQDLANSNPNSKG 164
           N +QAKELIAVL EA Q I PQL D+ANS  N  G
Sbjct: 464 NARQAKELIAVLEEAGQTINPQLADIANSMRNQYG 498

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345493222|ref|XP_003427025.1| PREDICTED: probable ATP-dependent RNA helicase DDX17-like isoform 2 [Nasonia vitripennis]

 Score =  117 bits (293), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 66/125 (52%), Positives = 79/125 (63%), Gaps = 26/125 (20%)

Query: 65  AIQAQGWP-IALSG------RDMVGIAQTGSGKTLA------------------VINFDY 99
           AI+  GWP IA+ G      RD V +++  +GKT                    V+NFDY
Sbjct: 312 AIKRNGWPAIAIHGDKSQPERDYV-LSEFRNGKTAILVATDVAARGLDVEDVKYVVNFDY 370

Query: 100 PNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQDLANSN 159
           PNSSEDYIHRIGRTGRC S+GTAY +FTPNN +QAKELI+VL EA Q I PQL ++ANS 
Sbjct: 371 PNSSEDYIHRIGRTGRCQSAGTAYAYFTPNNARQAKELISVLEEAGQIINPQLAEMANSQ 430

Query: 160 PNSKG 164
            N  G
Sbjct: 431 RNQYG 435

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|258617566|gb|ACV83780.1| DEAD box ATP-dependent RNA helicase-like protein [Heliconius melpomene]

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 57/92 (61%), Positives = 67/92 (72%), Gaps = 4/92 (4%)

Query: 4   HAKTQERAARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEP 63
           HA  + R    S+ EVE FR  KEITV GN++P P Q   EG FP+ ++  +K QG+EEP
Sbjct: 203 HANVEGR----SDDEVEMFRATKEITVSGNDVPRPNQVFDEGNFPDHIMNTIKEQGWEEP 258

Query: 64  TAIQAQGWPIALSGRDMVGIAQTGSGKTLAVI 95
           T IQAQGWPIALSGRDMVGIA TGSGKTLA +
Sbjct: 259 TGIQAQGWPIALSGRDMVGIASTGSGKTLAYM 290

Source: Heliconius melpomene

Species: Heliconius melpomene

Genus: Heliconius

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	165
FB|FBgn0029979	945	CG10777 [Drosophila melanogast	0.430	0.075	0.690	1.5e-43
ASPGD|ASPL0000006660	563	AN5931 [Emericella nidulans (t	0.478	0.140	0.607	1.4e-42
UNIPROTKB|F1MBQ8	614	DDX5 "Uncharacterized protein"	0.509	0.136	0.583	3.9e-42
UNIPROTKB|J3KTA4	614	DDX5 "Probable ATP-dependent R	0.509	0.136	0.583	3.9e-42
UNIPROTKB|P17844	614	DDX5 "Probable ATP-dependent R	0.509	0.136	0.583	3.9e-42
UNIPROTKB|A5A6J2	614	DDX5 "Probable ATP-dependent R	0.509	0.136	0.583	3.9e-42
UNIPROTKB|Q4R6M5	614	DDX5 "Probable ATP-dependent R	0.509	0.136	0.583	3.9e-42
UNIPROTKB|Q5R4I9	614	DDX5 "Probable ATP-dependent R	0.509	0.136	0.583	3.9e-42
UNIPROTKB|F1PEA6	671	DDX5 "Uncharacterized protein"	0.509	0.125	0.583	5.7e-42
MGI|MGI:105037	614	Ddx5 "DEAD (Asp-Glu-Ala-Asp) b	0.509	0.136	0.571	8.3e-42

FB|FBgn0029979 CG10777 [Drosophila melanogaster (taxid:7227)]

 Score = 253 (94.1 bits), Expect = 1.5e-43, Sum P(2) = 1.5e-43
 Identities = 49/71 (69%), Positives = 56/71 (78%)

Query:    94 VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ 153
             VIN+DYPNSSE+Y+HRIGRTGRC   GTAYTFFTP+N KQA+ELI+VL EA Q     L 
Sbjct:   563 VINYDYPNSSENYVHRIGRTGRCQQLGTAYTFFTPDNAKQARELISVLEEAGQTPSQALL 622

Query:   154 DLANSNPNSKG 164
             DLA S P+S G
Sbjct:   623 DLARSMPSSGG 633

GO:0003724 "RNA helicase activity" evidence=ISS

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

ASPGD|ASPL0000006660 AN5931 [Emericella nidulans (taxid:162425)]

 Score = 258 (95.9 bits), Expect = 1.4e-42, Sum P(2) = 1.4e-42
 Identities = 48/79 (60%), Positives = 63/79 (79%)

Query:    15 SESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIA 74
             S+ EV+ FR+K E+TV+G ++P P +   E  FP  VL  +K QGFE+PTAIQ+QGWP+A
Sbjct:   115 SQREVDEFRKKCEMTVQGRDVPRPVETFDEAGFPQYVLSEVKAQGFEKPTAIQSQGWPMA 174

Query:    75 LSGRDMVGIAQTGSGKTLA 93
             LSGRD+VGIA+TGSGKTL+
Sbjct:   175 LSGRDVVGIAETGSGKTLS 193

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0005730 "nucleolus" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

UNIPROTKB|F1MBQ8 DDX5 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 249 (92.7 bits), Expect = 3.9e-42, Sum P(2) = 3.9e-42
 Identities = 49/84 (58%), Positives = 60/84 (71%)

Query:    12 ARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGW 71
             AR +  EVE +R+ KEITV+G+N P P     E  FP  V+  +  Q F EPTAIQAQGW
Sbjct:    66 ARRTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGW 125

Query:    72 PIALSGRDMVGIAQTGSGKTLAVI 95
             P+ALSG DMVG+AQTGSGKTL+ +
Sbjct:   126 PVALSGLDMVGVAQTGSGKTLSYL 149

GO:0072332 "intrinsic apoptotic signaling pathway by p53 class mediator" evidence=IEA

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

GO:0060765 "regulation of androgen receptor signaling pathway" evidence=IEA

GO:0050681 "androgen receptor binding" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0043517 "positive regulation of DNA damage response, signal transduction by p53 class mediator" evidence=IEA

GO:0036002 "pre-mRNA binding" evidence=IEA

GO:0033148 "positive regulation of intracellular estrogen receptor signaling pathway" evidence=IEA

GO:0030331 "estrogen receptor binding" evidence=IEA

GO:0007623 "circadian rhythm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0001701 "in utero embryonic development" evidence=IEA

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

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003724 "RNA helicase activity" evidence=IEA

UNIPROTKB|J3KTA4 DDX5 "Probable ATP-dependent RNA helicase DDX5" [Homo sapiens (taxid:9606)]

 Score = 249 (92.7 bits), Expect = 3.9e-42, Sum P(2) = 3.9e-42
 Identities = 49/84 (58%), Positives = 60/84 (71%)

Query:    12 ARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGW 71
             AR +  EVE +R+ KEITV+G+N P P     E  FP  V+  +  Q F EPTAIQAQGW
Sbjct:    66 ARRTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGW 125

Query:    72 PIALSGRDMVGIAQTGSGKTLAVI 95
             P+ALSG DMVG+AQTGSGKTL+ +
Sbjct:   126 PVALSGLDMVGVAQTGSGKTLSYL 149

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003712 "transcription cofactor activity" evidence=IEA

GO:0003724 "RNA helicase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|P17844 DDX5 "Probable ATP-dependent RNA helicase DDX5" [Homo sapiens (taxid:9606)]

 Score = 249 (92.7 bits), Expect = 3.9e-42, Sum P(2) = 3.9e-42
 Identities = 49/84 (58%), Positives = 60/84 (71%)

Query:    12 ARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGW 71
             AR +  EVE +R+ KEITV+G+N P P     E  FP  V+  +  Q F EPTAIQAQGW
Sbjct:    66 ARRTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGW 125

Query:    72 PIALSGRDMVGIAQTGSGKTLAVI 95
             P+ALSG DMVG+AQTGSGKTL+ +
Sbjct:   126 PVALSGLDMVGVAQTGSGKTLSYL 149

GO:0005524 "ATP binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0001701 "in utero embryonic development" evidence=IEA

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

GO:0005516 "calmodulin binding" evidence=IEA

GO:0007623 "circadian rhythm" evidence=IEA

GO:0019899 "enzyme binding" evidence=IEA

GO:0045069 "regulation of viral genome replication" evidence=IEA

GO:0048306 "calcium-dependent protein binding" evidence=IEA

GO:0003724 "RNA helicase activity" evidence=IMP;NAS

GO:0016049 "cell growth" evidence=NAS

GO:0005634 "nucleus" evidence=IDA;NAS

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0043517 "positive regulation of DNA damage response, signal transduction by p53 class mediator" evidence=IMP

GO:0072332 "intrinsic apoptotic signaling pathway by p53 class mediator" evidence=IMP

GO:0005730 "nucleolus" evidence=IDA

GO:2001014 "regulation of skeletal muscle cell differentiation" evidence=ISS

GO:0045667 "regulation of osteoblast differentiation" evidence=ISS

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0050681 "androgen receptor binding" evidence=IDA

GO:0060765 "regulation of androgen receptor signaling pathway" evidence=IMP

GO:0033148 "positive regulation of intracellular estrogen receptor signaling pathway" evidence=IDA

GO:0003713 "transcription coactivator activity" evidence=IDA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0030331 "estrogen receptor binding" evidence=IDA

GO:0036002 "pre-mRNA binding" evidence=IDA

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

GO:0030529 "ribonucleoprotein complex" evidence=IDA

UNIPROTKB|A5A6J2 DDX5 "Probable ATP-dependent RNA helicase DDX5" [Pan troglodytes (taxid:9598)]

 Score = 249 (92.7 bits), Expect = 3.9e-42, Sum P(2) = 3.9e-42
 Identities = 49/84 (58%), Positives = 60/84 (71%)

Query:    12 ARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGW 71
             AR +  EVE +R+ KEITV+G+N P P     E  FP  V+  +  Q F EPTAIQAQGW
Sbjct:    66 ARRTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGW 125

Query:    72 PIALSGRDMVGIAQTGSGKTLAVI 95
             P+ALSG DMVG+AQTGSGKTL+ +
Sbjct:   126 PVALSGLDMVGVAQTGSGKTLSYL 149

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISS

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

GO:0003713 "transcription coactivator activity" evidence=ISS

GO:0003724 "RNA helicase activity" evidence=ISS

GO:0005730 "nucleolus" evidence=ISS

GO:0030331 "estrogen receptor binding" evidence=ISS

GO:0043517 "positive regulation of DNA damage response, signal transduction by p53 class mediator" evidence=ISS

GO:0045667 "regulation of osteoblast differentiation" evidence=ISS

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0050681 "androgen receptor binding" evidence=ISS

GO:0060765 "regulation of androgen receptor signaling pathway" evidence=ISS

GO:0072332 "intrinsic apoptotic signaling pathway by p53 class mediator" evidence=ISS

GO:2001014 "regulation of skeletal muscle cell differentiation" evidence=ISS

UNIPROTKB|Q4R6M5 DDX5 "Probable ATP-dependent RNA helicase DDX5" [Macaca fascicularis (taxid:9541)]

 Score = 249 (92.7 bits), Expect = 3.9e-42, Sum P(2) = 3.9e-42
 Identities = 49/84 (58%), Positives = 60/84 (71%)

Query:    12 ARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGW 71
             AR +  EVE +R+ KEITV+G+N P P     E  FP  V+  +  Q F EPTAIQAQGW
Sbjct:    66 ARRTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGW 125

Query:    72 PIALSGRDMVGIAQTGSGKTLAVI 95
             P+ALSG DMVG+AQTGSGKTL+ +
Sbjct:   126 PVALSGLDMVGVAQTGSGKTLSYL 149

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISS

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

GO:0003713 "transcription coactivator activity" evidence=ISS

GO:0003724 "RNA helicase activity" evidence=ISS

GO:0005730 "nucleolus" evidence=ISS

GO:0030331 "estrogen receptor binding" evidence=ISS

GO:0043517 "positive regulation of DNA damage response, signal transduction by p53 class mediator" evidence=ISS

GO:0045667 "regulation of osteoblast differentiation" evidence=ISS

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0050681 "androgen receptor binding" evidence=ISS

GO:0060765 "regulation of androgen receptor signaling pathway" evidence=ISS

GO:0072332 "intrinsic apoptotic signaling pathway by p53 class mediator" evidence=ISS

GO:2001014 "regulation of skeletal muscle cell differentiation" evidence=ISS

UNIPROTKB|Q5R4I9 DDX5 "Probable ATP-dependent RNA helicase DDX5" [Pongo abelii (taxid:9601)]

 Score = 249 (92.7 bits), Expect = 3.9e-42, Sum P(2) = 3.9e-42
 Identities = 49/84 (58%), Positives = 60/84 (71%)

Query:    12 ARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGW 71
             AR +  EVE +R+ KEITV+G+N P P     E  FP  V+  +  Q F EPTAIQAQGW
Sbjct:    66 ARRTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGW 125

Query:    72 PIALSGRDMVGIAQTGSGKTLAVI 95
             P+ALSG DMVG+AQTGSGKTL+ +
Sbjct:   126 PVALSGLDMVGVAQTGSGKTLSYL 149

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISS

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

GO:0003713 "transcription coactivator activity" evidence=ISS

GO:0003724 "RNA helicase activity" evidence=ISS

GO:0005730 "nucleolus" evidence=ISS

GO:0030331 "estrogen receptor binding" evidence=ISS

GO:0043517 "positive regulation of DNA damage response, signal transduction by p53 class mediator" evidence=ISS

GO:0045667 "regulation of osteoblast differentiation" evidence=ISS

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0050681 "androgen receptor binding" evidence=ISS

GO:0060765 "regulation of androgen receptor signaling pathway" evidence=ISS

GO:0072332 "intrinsic apoptotic signaling pathway by p53 class mediator" evidence=ISS

GO:2001014 "regulation of skeletal muscle cell differentiation" evidence=ISS

UNIPROTKB|F1PEA6 DDX5 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 249 (92.7 bits), Expect = 5.7e-42, Sum P(2) = 5.7e-42
 Identities = 49/84 (58%), Positives = 60/84 (71%)

Query:    12 ARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGW 71
             AR +  EVE +R+ KEITV+G+N P P     E  FP  V+  +  Q F EPTAIQAQGW
Sbjct:   123 ARRTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGW 182

Query:    72 PIALSGRDMVGIAQTGSGKTLAVI 95
             P+ALSG DMVG+AQTGSGKTL+ +
Sbjct:   183 PVALSGLDMVGVAQTGSGKTLSYL 206

GO:0005524 "ATP binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0003724 "RNA helicase activity" evidence=IEA

GO:0003712 "transcription cofactor activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

MGI|MGI:105037 Ddx5 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 5" [Mus musculus (taxid:10090)]

 Score = 246 (91.7 bits), Expect = 8.3e-42, Sum P(2) = 8.3e-42
 Identities = 48/84 (57%), Positives = 60/84 (71%)

Query:    12 ARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGW 71
             AR +  EV+ +R+ KEITV+G+N P P     E  FP  V+  +  Q F EPTAIQAQGW
Sbjct:    66 ARRTAQEVDTYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGW 125

Query:    72 PIALSGRDMVGIAQTGSGKTLAVI 95
             P+ALSG DMVG+AQTGSGKTL+ +
Sbjct:   126 PVALSGLDMVGVAQTGSGKTLSYL 149

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0001701 "in utero embryonic development" evidence=IMP

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003712 "transcription cofactor activity" evidence=IDA

GO:0003713 "transcription coactivator activity" evidence=ISO

GO:0003723 "RNA binding" evidence=IEA

GO:0003724 "RNA helicase activity" evidence=ISO

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

GO:0004386 "helicase activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005516 "calmodulin binding" evidence=ISO

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IC

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005730 "nucleolus" evidence=ISO

GO:0006200 "ATP catabolic process" evidence=ISO

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

GO:0006397 "mRNA processing" evidence=IEA

GO:0007623 "circadian rhythm" evidence=IMP

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

GO:0008380 "RNA splicing" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

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

GO:0019899 "enzyme binding" evidence=ISO

GO:0030331 "estrogen receptor binding" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=ISO

GO:0033148 "positive regulation of intracellular estrogen receptor signaling pathway" evidence=ISO

GO:0036002 "pre-mRNA binding" evidence=ISO

GO:0043517 "positive regulation of DNA damage response, signal transduction by p53 class mediator" evidence=ISO

GO:0045069 "regulation of viral genome replication" evidence=ISO

GO:0045667 "regulation of osteoblast differentiation" evidence=IMP

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

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0048306 "calcium-dependent protein binding" evidence=ISO

GO:0050681 "androgen receptor binding" evidence=ISO

GO:0060765 "regulation of androgen receptor signaling pathway" evidence=ISO

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

GO:0072332 "intrinsic apoptotic signaling pathway by p53 class mediator" evidence=ISO

GO:2001014 "regulation of skeletal muscle cell differentiation" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q61656	DDX5_MOUSE	3, ., 6, ., 4, ., 1, 3	0.5714	0.5090	0.1368	yes	N/A
A2QC74	DBP2_ASPNC	3, ., 6, ., 4, ., 1, 3	0.5617	0.5151	0.1504	yes	N/A
Q8SRB2	DBP2_ENCCU	3, ., 6, ., 4, ., 1, 3	0.5591	0.5212	0.1737	yes	N/A
Q5B0J9	DBP2_EMENI	3, ., 6, ., 4, ., 1, 3	0.6075	0.4787	0.1403	yes	N/A
Q6BY27	DBP2_DEBHA	3, ., 6, ., 4, ., 1, 3	0.5569	0.4303	0.1324	yes	N/A
A5A6J2	DDX5_PANTR	3, ., 6, ., 4, ., 1, 3	0.5833	0.5090	0.1368	yes	N/A
Q5QMN3	RH20_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.5529	0.5151	0.1720	yes	N/A
A3LQW7	DBP2_PICST	3, ., 6, ., 4, ., 1, 3	0.5662	0.4969	0.1547	yes	N/A
P17844	DDX5_HUMAN	3, ., 6, ., 4, ., 1, 3	0.5833	0.5090	0.1368	yes	N/A
Q6FLF3	DBP2_CANGA	3, ., 6, ., 4, ., 1, 3	0.5696	0.4787	0.1452	yes	N/A
Q5R4I9	DDX5_PONAB	3, ., 6, ., 4, ., 1, 3	0.5833	0.5090	0.1368	yes	N/A
Q4X195	DBP2_ASPFU	3, ., 6, ., 4, ., 1, 3	0.6585	0.4909	0.1480	yes	N/A
Q755N4	DBP2_ASHGO	3, ., 6, ., 4, ., 1, 3	0.5054	0.5333	0.1579	yes	N/A
Q9C718	RH20_ARATH	3, ., 6, ., 4, ., 1, 3	0.5119	0.4909	0.1616	yes	N/A
Q2U070	DBP2_ASPOR	3, ., 6, ., 4, ., 1, 3	0.5903	0.5030	0.1498	yes	N/A
P24783	DBP2_YEAST	3, ., 6, ., 4, ., 1, 3	0.5222	0.5212	0.1575	yes	N/A
P24782	DBP2_SCHPO	3, ., 6, ., 4, ., 1, 3	0.5164	0.5030	0.1509	yes	N/A
Q6C4D4	DBP2_YARLI	3, ., 6, ., 4, ., 1, 3	0.5054	0.5515	0.1648	yes	N/A
Q4IF76	DBP2_GIBZE	3, ., 6, ., 4, ., 1, 3	0.5897	0.4727	0.1405	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	165
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	9e-30
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	4e-27
cd00268	203	cd00268, DEADc, DEAD-box helicases	4e-19
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	6e-17
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	1e-16
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	9e-12
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	1e-11
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	2e-11
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	3e-11
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	1e-10
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	7e-10
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	8e-10
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	2e-09
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	2e-09
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	4e-09
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	1e-08
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	2e-08
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	2e-08
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	3e-08
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	3e-08
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	3e-08
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	5e-08
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	8e-08
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	1e-07
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	1e-06
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	1e-06
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	2e-06
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	2e-05
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	5e-04

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

 Score =  112 bits (283), Expect = 9e-30
 Identities = 50/94 (53%), Positives = 62/94 (65%), Gaps = 1/94 (1%)

Query: 3   NHAKTQERAARLSESEVEAFRQKKEIT-VKGNNIPCPTQELTEGCFPNAVLQHLKGQGFE 61
           N  K     + LS  EV+  R++KEIT + G N+P P        FP+ +L+ LK  GF 
Sbjct: 92  NFYKEHPEVSALSSKEVDEIRKEKEITIIAGENVPKPVVSFEYTSFPDYILKSLKNAGFT 151

Query: 62  EPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVI 95
           EPT IQ QGWPIALSGRDM+GIA+TGSGKTLA +
Sbjct: 152 EPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFL 185

Length = 545

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

 Score =  105 bits (264), Expect = 4e-27
 Identities = 38/68 (55%), Positives = 51/68 (75%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ 153
           VINFD+PN  EDY+HRIGRTGR  + G +YTF TP+  + A++L+ VL EA QP+PP+L+
Sbjct: 449 VINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELE 508

Query: 154 DLANSNPN 161
            L+N   N
Sbjct: 509 KLSNERSN 516

Length = 545

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

 Score = 79.5 bits (197), Expect = 4e-19
 Identities = 25/43 (58%), Positives = 32/43 (74%)

Query: 51 VLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
          +L+ +   GFE+PT IQA+  P  LSGRD++G AQTGSGKT A
Sbjct: 10 LLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAA 52

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 = 76.8 bits (189), Expect = 6e-17
 Identities = 26/43 (60%), Positives = 32/43 (74%)

Query: 51 VLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
          +LQ LK  GFEEPT IQ    P+ L+GRD++G AQTG+GKT A
Sbjct: 40 LLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAA 82

Length = 513

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

 Score = 75.6 bits (186), Expect = 1e-16
 Identities = 36/81 (44%), Positives = 47/81 (58%)

Query: 13  RLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWP 72
            LS S+ E  R+K EI VKG  +P P    +    P  +L +L+  G+E PT IQ Q  P
Sbjct: 94  GLSSSQAELLRRKLEIHVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIP 153

Query: 73  IALSGRDMVGIAQTGSGKTLA 93
            ALSGR ++  A TGSGKT +
Sbjct: 154 AALSGRSLLVSADTGSGKTAS 174

Length = 518

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

 Score = 61.7 bits (150), Expect = 9e-12
 Identities = 31/88 (35%), Positives = 44/88 (50%), Gaps = 11/88 (12%)

Query: 77  GRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKE 136
           G D++ + Q        VI FD PN+ ++YIH+IGR  R    GTA  F    +     E
Sbjct: 431 GVDLLRVRQ--------VIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRNLFPE 482

Query: 137 LIAVLTEASQPIPPQLQDLANSNPNSKG 164
           L+A+L  +   IP   ++LANS     G
Sbjct: 483 LVALLKSSGAAIP---RELANSRYLGSG 507

Length = 518

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

 Score = 61.0 bits (149), Expect = 1e-11
 Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 5/72 (6%)

Query: 93  AVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQL 152
           AVIN++     E ++HRIGRTGR  S G A +   P   ++A  +     E         
Sbjct: 313 AVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAI-----EDYLGRKLNW 367

Query: 153 QDLANSNPNSKG 164
           + L + +P S  
Sbjct: 368 EPLPSLSPLSGV 379

Length = 460

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

 Score = 61.0 bits (148), Expect = 2e-11
 Identities = 24/63 (38%), Positives = 29/63 (46%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ 153
           VIN+D P   EDY+HRIGRTGR    G A +F T     +  + I    E   P    L 
Sbjct: 345 VINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLKRIEKRLERKLPSAVLLP 404

Query: 154 DLA 156
              
Sbjct: 405 LDE 407

Length = 513

>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

 Score = 57.2 bits (139), Expect = 3e-11
 Identities = 16/32 (50%), Positives = 18/32 (56%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTF 125
           VIN+D P S   Y+ RIGR GR    GTA   
Sbjct: 100 VINYDLPWSPSSYLQRIGRAGRAGQKGTAILL 131

Length = 131

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

 Score = 58.1 bits (141), Expect = 1e-10
 Identities = 22/43 (51%), Positives = 31/43 (72%)

Query: 51 VLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
          V++ L+ +GF   T IQA   P+ L+GRD+ G AQTG+GKT+A
Sbjct: 19 VVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMA 61

Length = 423

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

 Score = 56.0 bits (136), Expect = 7e-10
 Identities = 23/46 (50%), Positives = 31/46 (67%)

Query: 48 PNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
          P A+L +L   G+ E T IQAQ  P  L+G+D++  A+TGSGKT A
Sbjct: 12 PPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAA 57

Length = 460

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

 Score = 54.2 bits (131), Expect = 8e-10
 Identities = 19/30 (63%), Positives = 22/30 (73%)

Query: 64 TAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
          T IQAQ  P  LSG+D++  A TGSGKTLA
Sbjct: 1  TPIQAQAIPAILSGKDVLVQAPTGSGKTLA 30

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

 Score = 54.9 bits (133), Expect = 2e-09
 Identities = 23/42 (54%), Positives = 31/42 (73%)

Query: 52 LQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
          L+ L+ +G+  PTAIQA+  P AL GRD++G A TG+GKT A
Sbjct: 13 LEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAA 54

Length = 434

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

 Score = 54.4 bits (131), Expect = 2e-09
 Identities = 24/44 (54%), Positives = 31/44 (70%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL 137
           VIN+D P S E+YIHRIGR+GR    G A  F TP++ +Q KE+
Sbjct: 339 VINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEI 382

Length = 401

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

 Score = 54.1 bits (130), Expect = 4e-09
 Identities = 23/43 (53%), Positives = 33/43 (76%)

Query: 51 VLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
          +L+ L   G+E+P+ IQA+  P  L+GRD++G+AQTGSGKT A
Sbjct: 17 ILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAA 59

Length = 629

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

 Score = 53.0 bits (128), Expect = 1e-08
 Identities = 21/67 (31%), Positives = 29/67 (43%), Gaps = 7/67 (10%)

Query: 49  NAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA----VIN---FDYPN 101
           +  ++    + F   T  Q    P   SG +++ IA TGSGKT A    VIN        
Sbjct: 9   DPRVREWFKRKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKG 68

Query: 102 SSEDYIH 108
             ED I+
Sbjct: 69  KLEDGIY 75

Length = 814

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

 Score = 52.3 bits (126), Expect = 2e-08
 Identities = 17/32 (53%), Positives = 23/32 (71%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTF 125
           V N+D P+  EDY+HRIGRTGR  +SG + + 
Sbjct: 327 VFNYDLPDDCEDYVHRIGRTGRAGASGHSISL 358

Length = 423

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

 Score = 51.0 bits (122), Expect = 2e-08
 Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 1/44 (2%)

Query: 55 LKGQGFEEPTAIQAQGWPIALSG-RDMVGIAQTGSGKTLAVINF 97
          ++  GFE     Q +     LSG RD++  A TGSGKTLA +  
Sbjct: 1  IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLP 44

Length = 201

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

 Score = 51.5 bits (124), Expect = 3e-08
 Identities = 19/29 (65%), Positives = 22/29 (75%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTA 122
           VINFD P S++ Y+HRIGRTGR    GTA
Sbjct: 317 VINFDMPRSADTYLHRIGRTGRAGRKGTA 345

Length = 434

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

 Score = 51.5 bits (123), Expect = 3e-08
 Identities = 24/46 (52%), Positives = 30/46 (65%)

Query: 50 AVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVI 95
          A+L  L+  GF   T IQA   P+AL G D+ G AQTG+GKTLA +
Sbjct: 19 ALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFL 64

Length = 572

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

 Score = 51.3 bits (123), Expect = 3e-08
 Identities = 21/41 (51%), Positives = 28/41 (68%)

Query: 51 VLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKT 91
          +L+ +  QG+ EPT IQ Q  P  L GRD++  AQTG+GKT
Sbjct: 12 ILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKT 52

Length = 456

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

 Score = 51.0 bits (122), Expect = 5e-08
 Identities = 18/29 (62%), Positives = 24/29 (82%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTA 122
           V+N++ PN  EDY+HRIGRTGR A++G A
Sbjct: 317 VVNYELPNVPEDYVHRIGRTGRAAATGEA 345

Length = 456

>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain

 Score = 46.7 bits (112), Expect = 8e-08
 Identities = 13/22 (59%), Positives = 15/22 (68%)

Query: 94  VINFDYPNSSEDYIHRIGRTGR 115
           VIN+D P +   YI RIGR GR
Sbjct: 55  VINYDLPWNPASYIQRIGRAGR 76

The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. Length = 78

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

 Score = 49.9 bits (119), Expect = 1e-07
 Identities = 21/48 (43%), Positives = 30/48 (62%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVL 141
           VINF  P   +DY+HRIGRTGR  +SG + +F   ++  Q  E+  +L
Sbjct: 407 VINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLPEIEELL 454

Length = 475

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

 Score = 46.7 bits (111), Expect = 1e-06
 Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 13/79 (16%)

Query: 33 NNIPCPTQELTEGCFPNAVLQH--LKG---QGFEEPTAIQAQGWPIALSGRDMVGIAQTG 87
            I     E+ +  F    L    L+G    GFE+P+AIQ +G    L G D +G AQ+G
Sbjct: 17 GTIESNYDEIVD-SFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSG 75

Query: 88 SGKT-------LAVINFDY 99
          +GKT       L +I++D 
Sbjct: 76 TGKTATFVIAALQLIDYDL 94

Length = 401

>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain

 Score = 44.1 bits (105), Expect = 1e-06
 Identities = 13/22 (59%), Positives = 14/22 (63%)

Query: 94  VINFDYPNSSEDYIHRIGRTGR 115
           VI +D P S   YI RIGR GR
Sbjct: 59  VIIYDLPWSPASYIQRIGRAGR 80

Length = 82

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

 Score = 46.4 bits (110), Expect = 2e-06
 Identities = 18/32 (56%), Positives = 22/32 (68%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTF 125
           V+N+D P  SE Y+HRIGRTGR   +G A  F
Sbjct: 317 VVNYDIPMDSESYVHRIGRTGRAGRAGRALLF 348

Length = 629

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

 Score = 43.4 bits (102), Expect = 2e-05
 Identities = 17/32 (53%), Positives = 21/32 (65%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTF 125
           V N+D P  +EDY+HRIGRT R    G A +F
Sbjct: 329 VYNYDLPFDAEDYVHRIGRTARLGEEGDAISF 360

Length = 572

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

 Score = 39.1 bits (91), Expect = 5e-04
 Identities = 19/35 (54%), Positives = 22/35 (62%)

Query: 59  GFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
           GF   T IQAQ     L+G D +G AQTG+GKT A
Sbjct: 106 GFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAA 140

Length = 475

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	165
KOG0336|consensus	629		99.93
PTZ00110	545	helicase; Provisional	99.93
KOG0341|consensus	610		99.93
KOG0333|consensus	673		99.88
KOG0339|consensus	731		99.87
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.87
KOG0328|consensus	400		99.84
KOG0334|consensus	997		99.83
KOG0330|consensus	476		99.82
KOG0335|consensus	482		99.82
KOG0331|consensus	519		99.79
KOG0326|consensus	459		99.71
KOG0340|consensus	442		99.68
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.67
KOG0343|consensus	758		99.66
KOG0346|consensus	569		99.64
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.64
KOG0344|consensus	593		99.64
KOG0332|consensus	477		99.62
KOG0338|consensus	691		99.6
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.59
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.59
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.58
KOG0331|consensus	519		99.58
KOG0327|consensus	397		99.57
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.56
KOG0348|consensus	708		99.56
KOG0345|consensus	567		99.56
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.53
KOG0342|consensus	543		99.52
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.5
KOG0347|consensus	731		99.5
PTZ00424	401	helicase 45; Provisional	99.46
KOG4284|consensus	980		99.44
KOG0337|consensus	529		99.39
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.39
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.32
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.32
KOG0340|consensus	442		99.3
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.29
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.27
KOG0344|consensus	593		99.26
KOG0342|consensus	543		99.24
PRK02362	737	ski2-like helicase; Provisional	99.19
PRK13767	876	ATP-dependent helicase; Provisional	99.18
PRK00254	720	ski2-like helicase; Provisional	99.12
KOG0334|consensus	997		99.09
KOG0338|consensus	691		99.08
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.06
KOG0350|consensus	620		99.04
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	98.99
KOG0329|consensus	387		98.99
KOG0348|consensus	708		98.99
KOG0347|consensus	731		98.98
KOG0346|consensus	569		98.97
PRK01172	674	ski2-like helicase; Provisional	98.96
KOG0350|consensus	620		98.94
KOG0345|consensus	567		98.92
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	98.91
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	98.88
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	98.87
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	98.86
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	98.86
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	98.84
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	98.78
KOG0343|consensus	758		98.77
COG1205	851	Distinct helicase family with a unique C-terminal	98.76
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	98.73
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	98.73
PTZ00424	401	helicase 45; Provisional	98.68
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	98.68
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	98.67
KOG0329|consensus	387		98.66
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	98.66
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	98.65
PRK14701	1638	reverse gyrase; Provisional	98.64
PRK09401	1176	reverse gyrase; Reviewed	98.64
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	98.63
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	98.63
KOG0349|consensus	725		98.56
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	98.52
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	98.5
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	98.49
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	98.47
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	98.47
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	98.43
PRK10689	1147	transcription-repair coupling factor; Provisional	98.37
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	98.3
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	98.25
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	98.24
PRK09200	790	preprotein translocase subunit SecA; Reviewed	98.16
PHA02558	501	uvsW UvsW helicase; Provisional	98.01
PRK04914	956	ATP-dependent helicase HepA; Validated	97.96
KOG0337|consensus	529		97.9
smart00487	201	DEXDc DEAD-like helicases superfamily.	97.85
COG1202	830	Superfamily II helicase, archaea-specific [General	97.85
PHA02653	675	RNA helicase NPH-II; Provisional	97.8
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	97.76
PRK05298	652	excinuclease ABC subunit B; Provisional	97.75
PRK09200	790	preprotein translocase subunit SecA; Reviewed	97.71
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	97.7
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	97.69
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	97.69
PRK05580	679	primosome assembly protein PriA; Validated	97.66
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	97.62
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	97.62
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	97.53
COG1204	766	Superfamily II helicase [General function predicti	97.53
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	97.46
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	97.35
KOG0349|consensus	725		97.35
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	97.34
KOG0351|consensus	941		97.32
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	97.28
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	97.28
PRK13767	876	ATP-dependent helicase; Provisional	97.27
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	97.26
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	97.18
PRK13766	773	Hef nuclease; Provisional	97.16
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	97.15
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	97.13
KOG0952|consensus	1230		97.13
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	97.1
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	97.1
PHA02653	675	RNA helicase NPH-II; Provisional	97.09
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	97.07
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	97.02
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	97.02
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	96.99
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	96.92
PRK02362	737	ski2-like helicase; Provisional	96.91
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	96.77
PRK10689	1147	transcription-repair coupling factor; Provisional	96.64
PRK13766	773	Hef nuclease; Provisional	96.64
KOG0351|consensus	941		96.6
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	96.49
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	96.49
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	96.41
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	96.35
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	96.32
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	96.32
PF13245	76	AAA_19: Part of AAA domain	96.18
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	96.13
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	96.04
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	96.03
KOG0352|consensus	641		95.86
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	95.85
PRK12904	830	preprotein translocase subunit SecA; Reviewed	95.74
KOG0354|consensus	746		95.72
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	95.59
KOG0353|consensus	695		95.52
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	95.51
PRK09694	878	helicase Cas3; Provisional	95.42
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	95.41
smart00490	82	HELICc helicase superfamily c-terminal domain.	95.37
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	95.32
KOG0352|consensus	641		95.27
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	95.24
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	95.23
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	95.16
PRK01172	674	ski2-like helicase; Provisional	95.15
PRK00254	720	ski2-like helicase; Provisional	95.14
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	94.9
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	94.81
PHA02558	501	uvsW UvsW helicase; Provisional	94.81
KOG0354|consensus	746		94.8
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	94.58
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	93.82
PRK13107	908	preprotein translocase subunit SecA; Reviewed	93.7
PRK05580	679	primosome assembly protein PriA; Validated	93.68
KOG0951|consensus	1674		93.5
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	93.46
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	93.32
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	92.94
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	92.47
TIGR00595	505	priA primosomal protein N'. All proteins in this f	91.98
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	91.96
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	91.33
COG1198	730	PriA Primosomal protein N' (replication factor Y)	91.32
TIGR00376	637	DNA helicase, putative. The gene product may repre	91.02
TIGR00595	505	priA primosomal protein N'. All proteins in this f	90.83
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	90.74
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	90.46
PRK13897	606	type IV secretion system component VirD4; Provisio	90.39
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	90.36
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	88.65
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	88.62
KOG0353|consensus	695		88.55
PRK09694	878	helicase Cas3; Provisional	87.97
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	87.5
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	87.29
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	87.27
PRK10875	615	recD exonuclease V subunit alpha; Provisional	86.99
PRK11054	684	helD DNA helicase IV; Provisional	86.94
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	86.73
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	86.38
PRK13850	670	type IV secretion system protein VirD4; Provisiona	86.38
PRK13822	641	conjugal transfer coupling protein TraG; Provision	86.16
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	85.72
PRK13889	988	conjugal transfer relaxase TraA; Provisional	85.27
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	85.2
KOG1802|consensus	935		85.03
KOG0947|consensus	1248		84.91
PRK13880	636	conjugal transfer coupling protein TraG; Provision	84.87
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	84.8
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	84.34
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	84.26
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	84.25
PRK13833	323	conjugal transfer protein TrbB; Provisional	83.93
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	83.71
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	83.69
PRK10536	262	hypothetical protein; Provisional	83.64
PF13871	278	Helicase_C_4: Helicase_C-like	83.58
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	83.25
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	83.01
KOG1803|consensus	649		82.91
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	82.78
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	82.59
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	82.56
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	81.65
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	81.31
COG1201	814	Lhr Lhr-like helicases [General function predictio	81.17
PRK13764	602	ATPase; Provisional	80.68
CHL00122	870	secA preprotein translocase subunit SecA; Validate	80.23

>KOG0336|consensus

Probab=99.93  E-value=2.9e-26  Score=191.01  Aligned_cols=92  Identities=36%  Similarity=0.615  Sum_probs=83.8

Q ss_pred             CCCccCChHhhcCCHHHHHHHHhhcCcEEec-------CCCCCCcccccc-CCCcHHHHHHHHhCCCCCCchHHHHHHHH
Q psy7691           2 HNHAKTQERAARLSESEVEAFRQKKEITVKG-------NNIPCPTQELTE-GCFPNAVLQHLKGQGFEEPTAIQAQGWPI   73 (165)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~-------~~~p~~i~~f~~-l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~   73 (165)
                      ++||++....+++|+++++.+|+++......       ..+|.|.-+|++ ...++++.+++++.||.+|||||.+|||.
T Consensus       174 knfYke~~e~s~ls~~q~~~~r~en~~it~dd~K~gekrpIPnP~ctFddAFq~~pevmenIkK~GFqKPtPIqSQaWPI  253 (629)
T KOG0336|consen  174 KNFYKESNETSNLSKEQLQEWRKENFNITCDDLKEGEKRPIPNPVCTFDDAFQCYPEVMENIKKTGFQKPTPIQSQAWPI  253 (629)
T ss_pred             hhhhhcCchhccCCHHHHHHHHHcCCcEEecccccCCcccCCCCcCcHHHHHhhhHHHHHHHHhccCCCCCcchhcccce
Confidence            7899999999999999999999776544332       458999999987 59999999999999999999999999999


Q ss_pred             HHcCCCeeeecccCCcccce
Q psy7691          74 ALSGRDMVGIAQTGSGKTLA   93 (165)
Q Consensus        74 ~l~G~di~~~a~tgsGKt~~   93 (165)
                      ++.|.|++++|+||+|||++
T Consensus       254 ~LQG~DliGVAQTgtgKtL~  273 (629)
T KOG0336|consen  254 LLQGIDLIGVAQTGTGKTLA  273 (629)
T ss_pred             eecCcceEEEEecCCCcCHH
Confidence            99999999999999999996

>PTZ00110 helicase; Provisional

Probab=99.93  E-value=3.3e-25  Score=194.33  Aligned_cols=92  Identities=54%  Similarity=0.897  Sum_probs=88.2

Q ss_pred             CCCccCChHhhcCCHHHHHHHHhhcCcEE-ecCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCe
Q psy7691           2 HNHAKTQERAARLSESEVEAFRQKKEITV-KGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDM   80 (165)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~-~~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di   80 (165)
                      ++||.+++.+..+++++++.++..+.+.+ .|.++|.|+..|+++++++.++++|.++||..||++|.+|||.++.|+|+
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~g~~~p~p~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dv  170 (545)
T PTZ00110         91 KNFYKEHPEVSALSSKEVDEIRKEKEITIIAGENVPKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDM  170 (545)
T ss_pred             hhcccCChhhhcCCHHHHHHHHHhcCcEEecCCCCCcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCE
Confidence            58999999999999999999999999887 68999999999999999999999999999999999999999999999999


Q ss_pred             eeecccCCcccce
Q psy7691          81 VGIAQTGSGKTLA   93 (165)
Q Consensus        81 ~~~a~tgsGKt~~   93 (165)
                      +++|+||||||++
T Consensus       171 I~~ApTGSGKTla  183 (545)
T PTZ00110        171 IGIAETGSGKTLA  183 (545)
T ss_pred             EEEeCCCChHHHH
Confidence            9999999999973

>KOG0341|consensus

Probab=99.93  E-value=1.1e-25  Score=186.66  Aligned_cols=92  Identities=45%  Similarity=0.702  Sum_probs=89.1

Q ss_pred             CCCccCChHhhcCCHHHHHHHHhhcCcEEecCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCee
Q psy7691           2 HNHAKTQERAARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMV   81 (165)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~   81 (165)
                      +-.|+++.-+..+|+++-+..|+...|.+.|.++|+||.+|.++..|..+++.|++.|+..|||||.+.+|.++.|+|.+
T Consensus       132 ~T~WkPP~hir~mS~e~~e~vRk~~~I~veGd~ipPPIksF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmI  211 (610)
T KOG0341|consen  132 KTAWKPPRHIRKMSEEQRELVRKQLHILVEGDDIPPPIKSFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMI  211 (610)
T ss_pred             hhccCCcHHHHHhhHHHHHHHHHhheEEeeCCCCCCchhhhhhccCCHHHHHHHHhcCCCCCCceeecCcceEeecCcee
Confidence            44689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccCCcccce
Q psy7691          82 GIAQTGSGKTLA   93 (165)
Q Consensus        82 ~~a~tgsGKt~~   93 (165)
                      ++|.||||||+.
T Consensus       212 GIAfTGSGKTlv  223 (610)
T KOG0341|consen  212 GIAFTGSGKTLV  223 (610)
T ss_pred             eEEeecCCceEE
Confidence            999999999984

>KOG0333|consensus

Probab=99.88  E-value=7.6e-23  Score=174.40  Aligned_cols=84  Identities=40%  Similarity=0.699  Sum_probs=80.4

Q ss_pred             HhhcCCHHHHHHHHhhcCcEEecCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCc
Q psy7691          10 RAARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSG   89 (165)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~i~~~~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsG   89 (165)
                      .++++++.+|..|+++..+..+|..+|.|+.+|++.++|.++++.+...||..|||||++|||..+.-+|++++|.||||
T Consensus       215 ~l~Em~~rdwri~redynis~kg~~lpnplrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsG  294 (673)
T KOG0333|consen  215 VLAEMTERDWRIFREDYNISIKGGRLPNPLRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSG  294 (673)
T ss_pred             hHHhcCCccceeeecceeeeecCCCCCccccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccCC
Confidence            46677777999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccce
Q psy7691          90 KTLA   93 (165)
Q Consensus        90 Kt~~   93 (165)
                      ||+|
T Consensus       295 ktaa  298 (673)
T KOG0333|consen  295 KTAA  298 (673)
T ss_pred             cccc
Confidence            9976

>KOG0339|consensus

Probab=99.87  E-value=2.4e-22  Score=170.99  Aligned_cols=92  Identities=35%  Similarity=0.570  Sum_probs=90.4

Q ss_pred             CCCccCChHhhcCCHHHHHHHHhhcCcEEecCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCee
Q psy7691           2 HNHAKTQERAARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMV   81 (165)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~   81 (165)
                      ++||-++++|..+++.++-.+|..+.+.+.|...|+|+.+|++.+.++.|..++++..|++||++|-+++|.+++|+|++
T Consensus       185 kdfy~e~esI~gl~~~d~~~~r~~Lnlrv~g~s~~rpvtsfeh~gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvi  264 (731)
T KOG0339|consen  185 KDFYEEHESIEGLTKMDVIDLRLTLNLRVSGSSPPRPVTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVI  264 (731)
T ss_pred             cccccChhhhhccccccchhhHhhhcceeccCCCCCCcchhhhcCchHHHHHHHhhhhcccCCcccccccccccccccch
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccCCcccce
Q psy7691          82 GIAQTGSGKTLA   93 (165)
Q Consensus        82 ~~a~tgsGKt~~   93 (165)
                      ++|.||||||.|
T Consensus       265 gIAktgSgktaA  276 (731)
T KOG0339|consen  265 GIAKTGSGKTAA  276 (731)
T ss_pred             heeeccCcchhH
Confidence            999999999987

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

Probab=99.87  E-value=1.6e-21  Score=170.25  Aligned_cols=138  Identities=30%  Similarity=0.406  Sum_probs=119.5

Q ss_pred             CCCccCChHhhc-CCHHHHHHHHhhcCcEEecCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCe
Q psy7691           2 HNHAKTQERAAR-LSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDM   80 (165)
Q Consensus         2 ~~~~~~~~~~~~-~~~~~~~~~~~~~~i~~~~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di   80 (165)
                      ++||-.+++... +++++++.+|++..+.+.|.+.|.|+..|+++++++.++++|.+.||..||++|.+|||.++.|+|+
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~r~~~~i~~~g~~~p~pi~~f~~~~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dv  161 (518)
T PLN00206         82 ECFYVRDPGSTSGLSSSQAELLRRKLEIHVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSL  161 (518)
T ss_pred             CcCCccCcchhccCCHHHHHHHHHHCCCEecCCCCCchhcCHHhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCE
Confidence            467777777765 9999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeecccCCcccceeeecCCCCChhHHHHhhccCC---CCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCC
Q psy7691          81 VGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTG---RCASSGTAYTFFTPNNGKQAKELIAVLTEASQPI  148 (165)
Q Consensus        81 ~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~---r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~  148 (165)
                      +++|+||||||++|+   +|     .+.++....   -....+..+++++|+ ++++.|+.+.+......+
T Consensus       162 iv~ApTGSGKTlayl---lP-----il~~l~~~~~~~~~~~~~~~aLIL~PT-reLa~Qi~~~~~~l~~~~  223 (518)
T PLN00206        162 LVSADTGSGKTASFL---VP-----IISRCCTIRSGHPSEQRNPLAMVLTPT-RELCVQVEDQAKVLGKGL  223 (518)
T ss_pred             EEEecCCCCccHHHH---HH-----HHHHHHhhccccccccCCceEEEEeCC-HHHHHHHHHHHHHHhCCC
Confidence            999999999999999   99     676653221   112357789999999 999999988877655443

>KOG0328|consensus

Probab=99.84  E-value=2.2e-20  Score=149.89  Aligned_cols=67  Identities=28%  Similarity=0.466  Sum_probs=60.7

Q ss_pred             CcEEecCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccce
Q psy7691          27 EITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA   93 (165)
Q Consensus        27 ~i~~~~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~   93 (165)
                      ....+.++.-.++.+|++++|.+++++.+...||.+|+.+|..|++.+++|+|++++|+.|+|||.+
T Consensus        14 ~~~feTs~~~~v~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~   80 (400)
T KOG0328|consen   14 TVEFETSEKVKVIPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTAT   80 (400)
T ss_pred             ceeEeeccCcccccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEE
Confidence            3444455666789999999999999999999999999999999999999999999999999999985

>KOG0334|consensus

Probab=99.83  E-value=1.7e-20  Score=169.63  Aligned_cols=137  Identities=34%  Similarity=0.528  Sum_probs=123.0

Q ss_pred             CCCccCChHhhcCCHHHHHHHHhhcC-cEEecCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCe
Q psy7691           2 HNHAKTQERAARLSESEVEAFRQKKE-ITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDM   80 (165)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~-i~~~~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di   80 (165)
                      |+||.+.+++..++.++|+.++.... +.+.|.+.|.|+.+|.+.++...++..++++||..|++||.+|||.++.|+|+
T Consensus       326 knfy~e~~di~~ms~~eV~~yr~~l~~i~v~g~~~pkpv~sW~q~gl~~~il~tlkkl~y~k~~~IQ~qAiP~ImsGrdv  405 (997)
T KOG0334|consen  326 KNFYIEVRDIKRMSAAEVDEYRCELDGIKVKGKECPKPVTSWTQCGLSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDV  405 (997)
T ss_pred             hcccccchhHHHHHHHHHHHhhcCccceeeccCCCCcccchHhhCCchHHHHHHHHHhcCCCCcchhhhhcchhccCcce
Confidence            68999999999999999999998887 99999999999999999999999999999999999999999999999999999


Q ss_pred             eeecccCCcccceeeecCCCCChhHHHHhh--ccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCC
Q psy7691          81 VGIAQTGSGKTLAVINFDYPNSSEDYIHRI--GRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPI  148 (165)
Q Consensus        81 ~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~--gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~  148 (165)
                      +++|.||||||++|+   ||     .+..+  -|+.-.|. |+-.+|++|+ ++++.||.+.+..-.+.+
T Consensus       406 IgvakTgSGKT~af~---LP-----mirhi~dQr~~~~gd-GPi~li~aPt-rela~QI~r~~~kf~k~l  465 (997)
T KOG0334|consen  406 IGVAKTGSGKTLAFL---LP-----MIRHIKDQRPLEEGD-GPIALILAPT-RELAMQIHREVRKFLKLL  465 (997)
T ss_pred             EEeeccCCccchhhh---cc-----hhhhhhcCCChhhCC-CceEEEEcCC-HHHHHHHHHHHHHHHhhc
Confidence            999999999999999   89     33222  24444445 9999999999 999999999988765553

>KOG0330|consensus

Probab=99.82  E-value=3.5e-20  Score=153.59  Aligned_cols=56  Identities=38%  Similarity=0.625  Sum_probs=53.9

Q ss_pred             CccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccce
Q psy7691          38 PTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA   93 (165)
Q Consensus        38 ~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~   93 (165)
                      ...+|.+|++.+++.++++..||..||+||.++||.++.|+|+++.|.||||||.+
T Consensus        59 ~~~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~a  114 (476)
T KOG0330|consen   59 SFKSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGA  114 (476)
T ss_pred             hhcchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhh
Confidence            45689999999999999999999999999999999999999999999999999997

>KOG0335|consensus

Probab=99.82  E-value=1.7e-20  Score=159.70  Aligned_cols=68  Identities=35%  Similarity=0.578  Sum_probs=63.6

Q ss_pred             cCcEEecCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccce
Q psy7691          26 KEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA   93 (165)
Q Consensus        26 ~~i~~~~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~   93 (165)
                      ..+.+.|.++|.++..|++..+++.+..+++..||..|||+|+.+||.+..|+|++++|+||||||.|
T Consensus        60 i~v~~~G~~~p~~i~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~a  127 (482)
T KOG0335|consen   60 IPVKVSGRDVPPHIPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAA  127 (482)
T ss_pred             eeeeccCCccCCCcccccccchhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHH
Confidence            34556688999999999999999999999999999999999999999999999999999999999997

>KOG0331|consensus

Probab=99.79  E-value=7.8e-20  Score=157.57  Aligned_cols=138  Identities=42%  Similarity=0.679  Sum_probs=117.0

Q ss_pred             CCCccCChHhhcCCHHHHHHHHhhcCcEEecCC-CCCCccccccCC-----------------------------CcHHH
Q psy7691           2 HNHAKTQERAARLSESEVEAFRQKKEITVKGNN-IPCPTQELTEGC-----------------------------FPNAV   51 (165)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~-~p~~i~~f~~l~-----------------------------l~~~l   51 (165)
                      +++|++++........+.+..+.++.+.+.+.+ +|.|+..|+...                             +++.+
T Consensus        23 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~v~~~~~~p~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~ls~~~  102 (519)
T KOG0331|consen   23 KNFYKEHPSVKKRGSAEVERKRKKNEITVKGGDSVPKPVKSFEESGFPAKVLEEIPKLSRSSGESDSSAAFQELGLSEEL  102 (519)
T ss_pred             ccccccccccccccccccccccCcceeeccCCCCCCCCccchhcccCCccccccccccccccccCCcchhhhcccccHHH
Confidence            578899999999999999999999999999876 888887776543                             44556


Q ss_pred             HHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhcc-CCCCC-CCCceEEEECCC
Q psy7691          52 LQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGR-TGRCA-SSGTAYTFFTPN  129 (165)
Q Consensus        52 ~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr-~~r~~-~~g~~~~~~~p~  129 (165)
                      .++++..||..|||||.++||.++.|+|++++|.||||||++|+   +|     +++++-. .+..+ ..++.+++++|+
T Consensus       103 ~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~---lP-----~i~~l~~~~~~~~~~~~P~vLVL~PT  174 (519)
T KOG0331|consen  103 MKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYL---LP-----AIVHLNNEQGKLSRGDGPIVLVLAPT  174 (519)
T ss_pred             HHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhh---hH-----HHHHHHhccccccCCCCCeEEEEcCc
Confidence            66677999999999999999999999999999999999999999   99     7777754 23333 468899999999


Q ss_pred             cHHHHHHHHHHHHhcCCCC
Q psy7691         130 NGKQAKELIAVLTEASQPI  148 (165)
Q Consensus       130 ~~~~~~~i~~~l~~~~~~~  148 (165)
                       |+++.||.+.+.+....+
T Consensus       175 -RELA~QV~~~~~~~~~~~  192 (519)
T KOG0331|consen  175 -RELAVQVQAEAREFGKSL  192 (519)
T ss_pred             -HHHHHHHHHHHHHHcCCC
Confidence             999999999988865554

>KOG0326|consensus

Probab=99.71  E-value=5.6e-18  Score=138.02  Aligned_cols=60  Identities=37%  Similarity=0.666  Sum_probs=56.6

Q ss_pred             eeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCChHHH
Q psy7691          94 VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ  153 (165)
Q Consensus        94 ~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p~~~~  153 (165)
                      |+|||.|...++|+||+||+||.|..|.++.+++-.++..+.+|++-+....+++|+.++
T Consensus       394 VINFDfpk~aEtYLHRIGRsGRFGhlGlAInLityedrf~L~~IE~eLGtEI~pip~~iD  453 (459)
T KOG0326|consen  394 VINFDFPKNAETYLHRIGRSGRFGHLGLAINLITYEDRFNLYRIEQELGTEIKPIPSNID  453 (459)
T ss_pred             EEecCCCCCHHHHHHHccCCccCCCcceEEEEEehhhhhhHHHHHHHhccccccCCCcCC
Confidence            679999999999999999999999999999999999999999999999999999996543

>KOG0340|consensus

Probab=99.68  E-value=1e-16  Score=131.86  Aligned_cols=98  Identities=28%  Similarity=0.421  Sum_probs=90.6

Q ss_pred             ccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCC
Q psy7691          39 TQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCAS  118 (165)
Q Consensus        39 i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~  118 (165)
                      ...|+.|++++++.+.|+.+|+..|||+|..|||.++.|+|++++|.||||||.+|.   +|     .++|..-.    .
T Consensus         6 ~~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFa---LP-----il~rLsed----P   73 (442)
T KOG0340|consen    6 AKPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFA---LP-----ILNRLSED----P   73 (442)
T ss_pred             cCchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhh---HH-----HHHhhccC----C
Confidence            458999999999999999999999999999999999999999999999999999998   99     99998764    6


Q ss_pred             CCceEEEECCCcHHHHHHHHHHHHhcCCCCC
Q psy7691         119 SGTAYTFFTPNNGKQAKELIAVLTEASQPIP  149 (165)
Q Consensus       119 ~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p  149 (165)
                      .|.-.++++|+ ++++.|+.+.+...++.+.
T Consensus        74 ~giFalvlTPT-rELA~QiaEQF~alGk~l~  103 (442)
T KOG0340|consen   74 YGIFALVLTPT-RELALQIAEQFIALGKLLN  103 (442)
T ss_pred             CcceEEEecch-HHHHHHHHHHHHHhccccc
Confidence            78889999999 9999999999988877753

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

Probab=99.67  E-value=1.2e-16  Score=139.52  Aligned_cols=98  Identities=33%  Similarity=0.511  Sum_probs=86.0

Q ss_pred             cccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCC
Q psy7691          40 QELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASS  119 (165)
Q Consensus        40 ~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~  119 (165)
                      ..|+++++.+.++++|.++||..||+||.++||.++.|+|++++|+||||||+||.   +|     .++++.+...  ..
T Consensus        29 ~~F~~l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~---lP-----~l~~l~~~~~--~~   98 (513)
T COG0513          29 PEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFL---LP-----LLQKILKSVE--RK   98 (513)
T ss_pred             CCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHH---HH-----HHHHHhcccc--cC
Confidence            78999999999999999999999999999999999999999999999999999999   99     8888865311  11


Q ss_pred             CceEEEECCCcHHHHHHHHHHHHhcCCCC
Q psy7691         120 GTAYTFFTPNNGKQAKELIAVLTEASQPI  148 (165)
Q Consensus       120 g~~~~~~~p~~~~~~~~i~~~l~~~~~~~  148 (165)
                      ...+++++|+ |+++.||.+.+.......
T Consensus        99 ~~~aLil~PT-RELA~Qi~~~~~~~~~~~  126 (513)
T COG0513          99 YVSALILAPT-RELAVQIAEELRKLGKNL  126 (513)
T ss_pred             CCceEEECCC-HHHHHHHHHHHHHHHhhc
Confidence            1128899999 899999999998877655

>KOG0343|consensus

Probab=99.66  E-value=1.1e-16  Score=137.79  Aligned_cols=123  Identities=28%  Similarity=0.396  Sum_probs=107.1

Q ss_pred             hhcCCHHHHHHHHhhcCcEEecCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcc
Q psy7691          11 AARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGK   90 (165)
Q Consensus        11 ~~~~~~~~~~~~~~~~~i~~~~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGK   90 (165)
                      +....+++++.+..+.....     ...+..|+++.+....++.|++.+|..+|.+|..+||.++.|.||++.|.|||||
T Consensus        45 ~~~~Eee~i~~l~~ky~ei~-----~~~~~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGK  119 (758)
T KOG0343|consen   45 LRQQEEEEIEELKQKYAEID-----STTIKKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGK  119 (758)
T ss_pred             hhhhhHHHHHHHHHHHHHhh-----hhhhhhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCc
Confidence            34455667777766554222     2347799999999999999999999999999999999999999999999999999


Q ss_pred             cceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCC
Q psy7691          91 TLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQP  147 (165)
Q Consensus        91 t~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~  147 (165)
                      |+||+   +|     .++++-|.++.+..|..+++++|+ |+++.|+...+...+..
T Consensus       120 TLAFl---vP-----vlE~L~r~kWs~~DGlGalIISPT-RELA~QtFevL~kvgk~  167 (758)
T KOG0343|consen  120 TLAFL---VP-----VLEALYRLKWSPTDGLGALIISPT-RELALQTFEVLNKVGKH  167 (758)
T ss_pred             eeeeh---HH-----HHHHHHHcCCCCCCCceeEEecch-HHHHHHHHHHHHHHhhc
Confidence            99999   99     899999998989999999999999 99999999999886543

>KOG0346|consensus

Probab=99.64  E-value=1e-16  Score=134.86  Aligned_cols=104  Identities=28%  Similarity=0.478  Sum_probs=90.3

Q ss_pred             cccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhc---cCCCC
Q psy7691          40 QELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIG---RTGRC  116 (165)
Q Consensus        40 ~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~g---r~~r~  116 (165)
                      ..|++++|++.+++++.+.||..||-+|..|||.++.|.|+++.|.||||||+||+   +|     .++.+-   .++ .
T Consensus        19 ktFe~~gLD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYl---iP-----llqkll~~k~t~-~   89 (569)
T KOG0346|consen   19 KTFEEFGLDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYL---IP-----LLQKLLAEKKTN-D   89 (569)
T ss_pred             ccHHHhCCCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHH---HH-----HHHHHHHhhhcc-c
Confidence            68999999999999999999999999999999999999999999999999999999   99     666542   233 6


Q ss_pred             CCCCceEEEECCCcHHHHHHHHHHHHhcCCCCChHHH
Q psy7691         117 ASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ  153 (165)
Q Consensus       117 ~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p~~~~  153 (165)
                      +..|+..+++.|+ ++++.|+.+.+++...-.+.++.
T Consensus        90 ~e~~~sa~iLvPT-kEL~qQvy~viekL~~~c~k~lr  125 (569)
T KOG0346|consen   90 GEQGPSAVILVPT-KELAQQVYKVIEKLVEYCSKDLR  125 (569)
T ss_pred             ccccceeEEEech-HHHHHHHHHHHHHHHHHHHHhhh
Confidence            7889999999999 99999999888876555544443

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.64  E-value=5.7e-16  Score=131.98  Aligned_cols=98  Identities=28%  Similarity=0.387  Sum_probs=83.2

Q ss_pred             ccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCC---
Q psy7691          39 TQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGR---  115 (165)
Q Consensus        39 i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r---  115 (165)
                      ...|+++++++.++++|.++||..||++|.+|||.++.|.|++++|+||||||++|+   +|     .++++-....   
T Consensus         7 ~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~l---lp-----~l~~l~~~~~~~~   78 (423)
T PRK04837          7 EQKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFL---TA-----TFHYLLSHPAPED   78 (423)
T ss_pred             CCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHH---HH-----HHHHHHhcccccc
Confidence            468999999999999999999999999999999999999999999999999999998   89     6776643211   


Q ss_pred             CCCCCceEEEECCCcHHHHHHHHHHHHhcC
Q psy7691         116 CASSGTAYTFFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus       116 ~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~  145 (165)
                      ....+..+++++|+ ++++.|+.+.+....
T Consensus        79 ~~~~~~~~lil~Pt-reLa~Qi~~~~~~l~  107 (423)
T PRK04837         79 RKVNQPRALIMAPT-RELAVQIHADAEPLA  107 (423)
T ss_pred             cccCCceEEEECCc-HHHHHHHHHHHHHHh
Confidence            11346789999999 999999887766543

>KOG0344|consensus

Probab=99.64  E-value=5.4e-16  Score=133.90  Aligned_cols=128  Identities=27%  Similarity=0.438  Sum_probs=108.8

Q ss_pred             HHHHHhhcCcEEecCCCCCCccccccC----CCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCccccee
Q psy7691          19 VEAFRQKKEITVKGNNIPCPTQELTEG----CFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAV   94 (165)
Q Consensus        19 ~~~~~~~~~i~~~~~~~p~~i~~f~~l----~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~   94 (165)
                      ....|+.+++.+.|.++|.|+..|+.+    .++..+++++...+|..||++|++|+|.++.++|+++|+|||||||++|
T Consensus       111 ~~~~Rk~~k~~v~G~~~~~~l~~f~~lt~~~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf  190 (593)
T KOG0344|consen  111 LLGIRKSNKINVDGFHLPPPLLSFSDLTYDYSMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAF  190 (593)
T ss_pred             cccchhcceeeccCCCCCCccccccccchhhhhcHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhh
Confidence            335567789999999999999999984    7999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCCChhHHHHhhccCC-CCCCCCceEEEECCCcHHHHHHHHHHHHhcC--CCCChHHHHH
Q psy7691          95 INFDYPNSSEDYIHRIGRTG-RCASSGTAYTFFTPNNGKQAKELIAVLTEAS--QPIPPQLQDL  155 (165)
Q Consensus        95 ~~~~lP~~~~~~i~r~gr~~-r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~--~~~p~~~~~~  155 (165)
                      .   +|     .++++--.. +.+..|...+++.|+ ++++.|+.+-+....  ...+.....+
T Consensus       191 ~---~P-----il~~L~~~~~~~~~~gl~a~Il~pt-reLa~Qi~re~~k~~~~~~t~~~a~~~  245 (593)
T KOG0344|consen  191 N---LP-----ILQHLKDLSQEKHKVGLRALILSPT-RELAAQIYREMRKYSIDEGTSLRAAQF  245 (593)
T ss_pred             h---hH-----HHHHHHHhhcccCccceEEEEecch-HHHHHHHHHHHHhcCCCCCCchhhhhc
Confidence            9   99     666663322 566788899999999 999999999998887  4444443333

>KOG0332|consensus

Probab=99.62  E-value=1.3e-15  Score=126.15  Aligned_cols=56  Identities=27%  Similarity=0.489  Sum_probs=53.1

Q ss_pred             CccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcC--CCeeeecccCCcccce
Q psy7691          38 PTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSG--RDMVGIAQTGSGKTLA   93 (165)
Q Consensus        38 ~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G--~di~~~a~tgsGKt~~   93 (165)
                      .+.+|++|+|.+++++.|..++|..|+.||..|+|.++.-  +++++++..|+|||.|
T Consensus        88 S~ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaa  145 (477)
T KOG0332|consen   88 SAKSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAA  145 (477)
T ss_pred             ccccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHH
Confidence            4788999999999999999999999999999999999887  7899999999999986

>KOG0338|consensus

Probab=99.60  E-value=6.1e-16  Score=132.22  Aligned_cols=96  Identities=27%  Similarity=0.435  Sum_probs=83.8

Q ss_pred             ccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhc-cCCCCC
Q psy7691          39 TQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIG-RTGRCA  117 (165)
Q Consensus        39 i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~g-r~~r~~  117 (165)
                      ..+|.+|+|+..+++++..+||..|||||..+||.++.|+||+++|.||||||.||.   +|     .+.|+- |+.+  
T Consensus       180 ~~sF~~mNLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~---lP-----iLERLlYrPk~--  249 (691)
T KOG0338|consen  180 NESFQSMNLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFA---LP-----ILERLLYRPKK--  249 (691)
T ss_pred             hhhHHhcccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhH---HH-----HHHHHhcCccc--
Confidence            458999999999999999999999999999999999999999999999999999999   99     888763 4322  


Q ss_pred             CCCceEEEECCCcHHHHHHHHHHHHhcC
Q psy7691         118 SSGTAYTFFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus       118 ~~g~~~~~~~p~~~~~~~~i~~~l~~~~  145 (165)
                      .....+++++|+ |+++-|+.....+..
T Consensus       250 ~~~TRVLVL~PT-RELaiQv~sV~~qla  276 (691)
T KOG0338|consen  250 VAATRVLVLVPT-RELAIQVHSVTKQLA  276 (691)
T ss_pred             CcceeEEEEecc-HHHHHHHHHHHHHHH
Confidence            345578999999 999988887776643

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.59  E-value=3e-15  Score=128.89  Aligned_cols=96  Identities=27%  Similarity=0.402  Sum_probs=82.2

Q ss_pred             ccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCC--CCC
Q psy7691          41 ELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGR--CAS  118 (165)
Q Consensus        41 ~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r--~~~  118 (165)
                      +|+++++++.++++|.++||..||++|.+|+|.++.|+|++++|+||||||++|+   +|     .++++.....  .+.
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~---lp-----il~~l~~~~~~~~~~   73 (456)
T PRK10590          2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFT---LP-----LLQHLITRQPHAKGR   73 (456)
T ss_pred             CHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHH---HH-----HHHHhhhcccccccC
Confidence            6999999999999999999999999999999999999999999999999999999   99     7777643211  123


Q ss_pred             CCceEEEECCCcHHHHHHHHHHHHhcC
Q psy7691         119 SGTAYTFFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus       119 ~g~~~~~~~p~~~~~~~~i~~~l~~~~  145 (165)
                      .+..+++++|+ ++++.|+.+.+....
T Consensus        74 ~~~~aLil~Pt-reLa~Qi~~~~~~~~   99 (456)
T PRK10590         74 RPVRALILTPT-RELAAQIGENVRDYS   99 (456)
T ss_pred             CCceEEEEeCc-HHHHHHHHHHHHHHh
Confidence            34578999999 999999988877643

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.59  E-value=4.3e-15  Score=131.31  Aligned_cols=99  Identities=27%  Similarity=0.339  Sum_probs=83.4

Q ss_pred             ccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCC---
Q psy7691          39 TQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGR---  115 (165)
Q Consensus        39 i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r---  115 (165)
                      ...|++++|++.++++|.+.||..||++|.++||.++.|.|++++|+||||||++|+   +|     .++++-....   
T Consensus         8 ~~~f~~l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafl---lp-----il~~l~~~~~~~~   79 (572)
T PRK04537          8 DLTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFL---VA-----VMNRLLSRPALAD   79 (572)
T ss_pred             CCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHH---HH-----HHHHHHhcccccc
Confidence            357999999999999999999999999999999999999999999999999999999   89     7777632111   


Q ss_pred             CCCCCceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         116 CASSGTAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       116 ~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      ....+..++|++|+ ++++.|+.+.+.....
T Consensus        80 ~~~~~~raLIl~PT-reLa~Qi~~~~~~l~~  109 (572)
T PRK04537         80 RKPEDPRALILAPT-RELAIQIHKDAVKFGA  109 (572)
T ss_pred             cccCCceEEEEeCc-HHHHHHHHHHHHHHhc
Confidence            11235689999999 9999999887766543

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.58  E-value=4.1e-15  Score=126.98  Aligned_cols=95  Identities=33%  Similarity=0.478  Sum_probs=80.7

Q ss_pred             ccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCC
Q psy7691          41 ELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSG  120 (165)
Q Consensus        41 ~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g  120 (165)
                      .|+++++++.+++.|.++||..||++|.++++.++.|.|++++|+||+|||++|+   +|     .++++-...+....+
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~---lp-----~l~~l~~~~~~~~~~   73 (434)
T PRK11192          2 TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFL---LP-----ALQHLLDFPRRKSGP   73 (434)
T ss_pred             CHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHH---HH-----HHHHHhhccccCCCC
Confidence            6999999999999999999999999999999999999999999999999999998   88     676664322222234


Q ss_pred             ceEEEECCCcHHHHHHHHHHHHhc
Q psy7691         121 TAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus       121 ~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      ..+++++|+ ++++.|+.+.+...
T Consensus        74 ~~~lil~Pt-~eLa~Q~~~~~~~l   96 (434)
T PRK11192         74 PRILILTPT-RELAMQVADQAREL   96 (434)
T ss_pred             ceEEEECCc-HHHHHHHHHHHHHH
Confidence            578999998 89999888776654

>KOG0331|consensus

Probab=99.58  E-value=9.4e-15  Score=126.31  Aligned_cols=116  Identities=38%  Similarity=0.615  Sum_probs=99.4

Q ss_pred             CCCccccc-cCCCcHHHHHHHHhCCCCCC------chHHHH---------------HHHHHHcCCCeeeecccCCcccce
Q psy7691          36 PCPTQELT-EGCFPNAVLQHLKGQGFEEP------TAIQAQ---------------GWPIALSGRDMVGIAQTGSGKTLA   93 (165)
Q Consensus        36 p~~i~~f~-~l~l~~~l~~~l~~~g~~~~------t~~Q~~---------------a~~~~l~G~di~~~a~tgsGKt~~   93 (165)
                      +..++.|. ....++++.+++...||...      +..|+.               |++.+.||.||..+.        +
T Consensus       341 ~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdVAaRGLDi~dV~--------l  412 (519)
T KOG0331|consen  341 EGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDVAARGLDVPDVD--------L  412 (519)
T ss_pred             CCcEEEEecchhhHHHHHHHHHhcCcceeeecccccHHHHHHHHHhcccCCcceEEEcccccccCCCcccc--------E
Confidence            34455665 56899999999999886542      222322               788888999999888        9


Q ss_pred             eeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCChHHHHHhhhC
Q psy7691          94 VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQDLANSN  159 (165)
Q Consensus        94 ~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p~~~~~~~~~~  159 (165)
                      |||||+|.++++|+||+|||||+|.+|.+++++++.+..++..+.+.++..++.+|+.+..++...
T Consensus       413 VInydfP~~vEdYVHRiGRTGRa~~~G~A~tfft~~~~~~a~~l~~~l~e~~q~v~~~l~~~~~~~  478 (519)
T KOG0331|consen  413 VINYDFPNNVEDYVHRIGRTGRAGKKGTAITFFTSDNAKLARELIKVLREAGQTVPPDLLEYARVS  478 (519)
T ss_pred             EEeCCCCCCHHHHHhhcCccccCCCCceEEEEEeHHHHHHHHHHHHHHHHccCCCChHHHHHHhhc
Confidence            999999999999999999999999999999999999999999999999999999999999986654

>KOG0327|consensus

Probab=99.57  E-value=3.4e-15  Score=123.67  Aligned_cols=62  Identities=35%  Similarity=0.701  Sum_probs=57.6

Q ss_pred             eeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCChHHHHH
Q psy7691          94 VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQDL  155 (165)
Q Consensus        94 ~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p~~~~~~  155 (165)
                      ++|||+|...++|+||+||+||.|++|.++.+++-.+...+..+.++..-...++|....++
T Consensus       335 vinydlP~~~~~yihR~gr~gr~grkg~~in~v~~~d~~~lk~ie~~y~~~i~e~p~~~~~l  396 (397)
T KOG0327|consen  335 VVNYDLPARKENYIHRIGRAGRFGRKGVAINFVTEEDVRDLKDIEKFYNTPIEELPSNFADL  396 (397)
T ss_pred             eeeeccccchhhhhhhcccccccCCCceeeeeehHhhHHHHHhHHHhcCCcceecccchhhc
Confidence            57999999999999999999999999999999999999999999999999999999877654

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.56  E-value=7.9e-15  Score=126.18  Aligned_cols=92  Identities=27%  Similarity=0.392  Sum_probs=81.0

Q ss_pred             cccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCC
Q psy7691          40 QELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASS  119 (165)
Q Consensus        40 ~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~  119 (165)
                      .+|+++++++.++++|.+.||..||++|.+|+|.++.|.|++++|+||||||++|.   +|     .++++...    ..
T Consensus         4 ~~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~---lp-----il~~l~~~----~~   71 (460)
T PRK11776          4 TAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFG---LG-----LLQKLDVK----RF   71 (460)
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHH---HH-----HHHHhhhc----cC
Confidence            47999999999999999999999999999999999999999999999999999998   89     78877421    23


Q ss_pred             CceEEEECCCcHHHHHHHHHHHHhc
Q psy7691         120 GTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus       120 g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      +..+++++|+ ++++.|+.+.++..
T Consensus        72 ~~~~lil~Pt-reLa~Q~~~~~~~~   95 (460)
T PRK11776         72 RVQALVLCPT-RELADQVAKEIRRL   95 (460)
T ss_pred             CceEEEEeCC-HHHHHHHHHHHHHH
Confidence            4567889998 89999998877654

>KOG0348|consensus

Probab=99.56  E-value=7.7e-15  Score=126.09  Aligned_cols=103  Identities=26%  Similarity=0.386  Sum_probs=89.5

Q ss_pred             CccccccCCCcHHHHHHHHh-CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccC--C
Q psy7691          38 PTQELTEGCFPNAVLQHLKG-QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRT--G  114 (165)
Q Consensus        38 ~i~~f~~l~l~~~l~~~l~~-~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~--~  114 (165)
                      ....|.+++|++.++..|+. +++..||.+|.+|||.++.|+|+++.++||||||+||+   +|     ++|++-+-  .
T Consensus       134 ts~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYl---lP-----iVq~Lq~m~~k  205 (708)
T KOG0348|consen  134 TSAAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYL---LP-----IVQSLQAMEPK  205 (708)
T ss_pred             ccccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHH---HH-----HHHHHHhcCcc
Confidence            45679999999999999988 79999999999999999999999999999999999999   99     77766431  1


Q ss_pred             CCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCC
Q psy7691         115 RCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIP  149 (165)
Q Consensus       115 r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p  149 (165)
                      -....|+-.+++.|+ |+++.|+...++....+..
T Consensus       206 i~Rs~G~~ALVivPT-REL~~Q~y~~~qKLl~~~h  239 (708)
T KOG0348|consen  206 IQRSDGPYALVIVPT-RELALQIYETVQKLLKPFH  239 (708)
T ss_pred             ccccCCceEEEEech-HHHHHHHHHHHHHHhcCce
Confidence            222578889999999 9999999999999887753

>KOG0345|consensus

Probab=99.56  E-value=9e-15  Score=123.98  Aligned_cols=97  Identities=29%  Similarity=0.400  Sum_probs=79.9

Q ss_pred             cccccCC--CcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCC
Q psy7691          40 QELTEGC--FPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCA  117 (165)
Q Consensus        40 ~~f~~l~--l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~  117 (165)
                      ..|++++  |.+++++++...||..+||+|..|||.++.+.|+++-|+||||||+||+   +|     ++.-+-|..-..
T Consensus         4 ~~~~~l~~~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFl---lP-----~le~i~rr~~~~   75 (567)
T KOG0345|consen    4 KSFSSLAPPLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFL---LP-----MLEIIYRREAKT   75 (567)
T ss_pred             cchhhcCCCccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHH---HH-----HHHHHHhhccCC
Confidence            3678775  4599999999999999999999999999999999999999999999999   99     666663322222


Q ss_pred             CCC-ceEEEECCCcHHHHHHHHHHHHhcC
Q psy7691         118 SSG-TAYTFFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus       118 ~~g-~~~~~~~p~~~~~~~~i~~~l~~~~  145 (165)
                      ..+ ...++++|+ |+++.||.+.+..-.
T Consensus        76 ~~~~vgalIIsPT-RELa~QI~~V~~~F~  103 (567)
T KOG0345|consen   76 PPGQVGALIISPT-RELARQIREVAQPFL  103 (567)
T ss_pred             CccceeEEEecCc-HHHHHHHHHHHHHHH
Confidence            333 568888888 999999998776543

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.53  E-value=1.6e-14  Score=128.87  Aligned_cols=93  Identities=30%  Similarity=0.516  Sum_probs=81.7

Q ss_pred             ccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCC
Q psy7691          39 TQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCAS  118 (165)
Q Consensus        39 i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~  118 (165)
                      ...|++++|++.++++|.++||..||++|.++||.++.|.|++++|+||||||++|.   +|     .++++...    .
T Consensus         5 ~~~f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~---lp-----ll~~l~~~----~   72 (629)
T PRK11634          5 ETTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFS---LP-----LLHNLDPE----L   72 (629)
T ss_pred             cCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHH---HH-----HHHHhhhc----c
Confidence            457999999999999999999999999999999999999999999999999999998   89     77777432    2


Q ss_pred             CCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691         119 SGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus       119 ~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      .+..+++++|+ ++++.|+.+.+...
T Consensus        73 ~~~~~LIL~PT-reLa~Qv~~~l~~~   97 (629)
T PRK11634         73 KAPQILVLAPT-RELAVQVAEAMTDF   97 (629)
T ss_pred             CCCeEEEEeCc-HHHHHHHHHHHHHH
Confidence            44678999999 89999988776654

>KOG0342|consensus

Probab=99.52  E-value=1.7e-14  Score=122.63  Aligned_cols=100  Identities=30%  Similarity=0.443  Sum_probs=85.8

Q ss_pred             CccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCC
Q psy7691          38 PTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCA  117 (165)
Q Consensus        38 ~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~  117 (165)
                      +...|++..|++..+++++++||..+|++|..+++.++.|+|+++.|.||||||+||+   +|     -++-+-...-..
T Consensus        80 ~~~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFL---iP-----aie~l~k~~~~~  151 (543)
T KOG0342|consen   80 TTFRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFL---LP-----AIELLRKLKFKP  151 (543)
T ss_pred             hhhHhhccccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeeh---hH-----HHHHHHhcccCC
Confidence            3567888999999999999999999999999999999999999999999999999999   99     444443333444


Q ss_pred             CCCceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         118 SSGTAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       118 ~~g~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      +.+..+++++|+ |+++.|+...++....
T Consensus       152 r~~~~vlIi~PT-RELA~Q~~~eak~Ll~  179 (543)
T KOG0342|consen  152 RNGTGVLIICPT-RELAMQIFAEAKELLK  179 (543)
T ss_pred             CCCeeEEEeccc-HHHHHHHHHHHHHHHh
Confidence            588899999999 9999999887776543

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.50  E-value=7.8e-14  Score=120.60  Aligned_cols=101  Identities=22%  Similarity=0.256  Sum_probs=84.3

Q ss_pred             CccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCC-
Q psy7691          38 PTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRC-  116 (165)
Q Consensus        38 ~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~-  116 (165)
                      ....|..+++++.++++|.+.||..+|++|.+||+.++.|.|++++++||||||++|+   +|     .++++...... 
T Consensus        85 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~---lp-----il~~l~~~~~~~  156 (475)
T PRK01297         85 GKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFL---IS-----IINQLLQTPPPK  156 (475)
T ss_pred             CCCCHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHH---HH-----HHHHHHhcCccc
Confidence            3568999999999999999999999999999999999999999999999999999998   89     77776442111 


Q ss_pred             --CCCCceEEEECCCcHHHHHHHHHHHHhcCCC
Q psy7691         117 --ASSGTAYTFFTPNNGKQAKELIAVLTEASQP  147 (165)
Q Consensus       117 --~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~  147 (165)
                        ...+..++++.|+ ++++.|+.+.+......
T Consensus       157 ~~~~~~~~aLil~Pt-reLa~Q~~~~~~~l~~~  188 (475)
T PRK01297        157 ERYMGEPRALIIAPT-RELVVQIAKDAAALTKY  188 (475)
T ss_pred             ccccCCceEEEEeCc-HHHHHHHHHHHHHhhcc
Confidence              0124578889998 99999998888765443

>KOG0347|consensus

Probab=99.50  E-value=3.7e-14  Score=122.30  Aligned_cols=102  Identities=28%  Similarity=0.403  Sum_probs=85.3

Q ss_pred             CCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcC-CCeeeecccCCcccceeeecCCCCChhHHHHhhccCC
Q psy7691          36 PCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSG-RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTG  114 (165)
Q Consensus        36 p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G-~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~  114 (165)
                      +.-+..|.++.++.+++++|..+||..||+||..++|++.+| .||++.|.||||||+||-   +|     .++|.--++
T Consensus       177 ~~DvsAW~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFG---IP-----iv~~l~~~s  248 (731)
T KOG0347|consen  177 KVDVSAWKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFG---IP-----IVERLLESS  248 (731)
T ss_pred             ccChHHHhcCCCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeec---ch-----hhhhhhhcc
Confidence            334788999999999999999999999999999999999999 899999999999999999   99     677543332


Q ss_pred             CCC-------CCC--ceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         115 RCA-------SSG--TAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       115 r~~-------~~g--~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      -+.       ..+  +..++++|+ |+++-|+.+.+.....
T Consensus       249 ~~s~e~~~~~~k~~k~~~LV~tPT-RELa~QV~~Hl~ai~~  288 (731)
T KOG0347|consen  249 DDSQELSNTSAKYVKPIALVVTPT-RELAHQVKQHLKAIAE  288 (731)
T ss_pred             chHhhhhhHHhccCcceeEEecCh-HHHHHHHHHHHHHhcc
Confidence            211       122  247888888 9999999999988755

>PTZ00424 helicase 45; Provisional

Probab=99.46  E-value=2.2e-13  Score=114.78  Aligned_cols=95  Identities=24%  Similarity=0.372  Sum_probs=82.1

Q ss_pred             CccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCC
Q psy7691          38 PTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCA  117 (165)
Q Consensus        38 ~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~  117 (165)
                      ....|+++++++.+.++|.+.||..|+++|.+|++.++.|.|++++|+||||||++|+   +|     .++.+..    .
T Consensus        26 ~~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~---l~-----~l~~~~~----~   93 (401)
T PTZ00424         26 IVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFV---IA-----ALQLIDY----D   93 (401)
T ss_pred             ccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHH---HH-----HHHHhcC----C
Confidence            4678999999999999999999999999999999999999999999999999999988   78     5665532    1


Q ss_pred             CCCceEEEECCCcHHHHHHHHHHHHhcC
Q psy7691         118 SSGTAYTFFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus       118 ~~g~~~~~~~p~~~~~~~~i~~~l~~~~  145 (165)
                      ..+..++++.|+ ++++.|+.+.+....
T Consensus        94 ~~~~~~lil~Pt-~~L~~Q~~~~~~~~~  120 (401)
T PTZ00424         94 LNACQALILAPT-RELAQQIQKVVLALG  120 (401)
T ss_pred             CCCceEEEECCC-HHHHHHHHHHHHHHh
Confidence            345578899999 899999988776654

>KOG4284|consensus

Probab=99.44  E-value=3.3e-13  Score=118.34  Aligned_cols=61  Identities=31%  Similarity=0.371  Sum_probs=56.1

Q ss_pred             CCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccce
Q psy7691          33 NNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA   93 (165)
Q Consensus        33 ~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~   93 (165)
                      +..+.-...|+++.+-..++..|+..+|..||++|..|||.++.++|++++|..|+|||+.
T Consensus        18 DV~~~~~~~fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlV   78 (980)
T KOG4284|consen   18 DVQSNCTPGFEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLV   78 (980)
T ss_pred             ccccCCCCCHHHHHHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEE
Confidence            3345557799999999999999999999999999999999999999999999999999984

>KOG0337|consensus

Probab=99.39  E-value=2.8e-13  Score=113.77  Aligned_cols=95  Identities=31%  Similarity=0.535  Sum_probs=86.3

Q ss_pred             cccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCC
Q psy7691          40 QELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASS  119 (165)
Q Consensus        40 ~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~  119 (165)
                      -.|.+++|...+.+++.+.||..|||+|+.+||.++.|+|+++.|.||||||.||+   ||     .++++-..  . ..
T Consensus        21 g~fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~---ip-----m~e~Lk~~--s-~~   89 (529)
T KOG0337|consen   21 GGFQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFL---IP-----MIEKLKSH--S-QT   89 (529)
T ss_pred             CCccccCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHH---HH-----HHHHHhhc--c-cc
Confidence            48999999999999999999999999999999999999999999999999999999   99     88877443  2 67


Q ss_pred             CceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         120 GTAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       120 g~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      |...+++.|+ ++++.|..+.+..-++
T Consensus        90 g~Ralilspt-reLa~qtlkvvkdlgr  115 (529)
T KOG0337|consen   90 GLRALILSPT-RELALQTLKVVKDLGR  115 (529)
T ss_pred             ccceeeccCc-HHHHHHHHHHHHHhcc
Confidence            7889999999 9999999998887665

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

Probab=99.39  E-value=1e-12  Score=119.29  Aligned_cols=96  Identities=22%  Similarity=0.307  Sum_probs=80.7

Q ss_pred             CCCccccccC--CCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccC
Q psy7691          36 PCPTQELTEG--CFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRT  113 (165)
Q Consensus        36 p~~i~~f~~l--~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~  113 (165)
                      |..--.|...  .+++.+.++|++.||..||++|.+|++.++.|+|++++++||||||++|.   +|     .++++.+.
T Consensus         8 p~~~a~~~~~~~~l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~---LP-----iL~~l~~~   79 (742)
T TIGR03817         8 PARAGRTAPWPAWAHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQ---LP-----VLSALADD   79 (742)
T ss_pred             CCCCcccCCCCCcCCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHH---HH-----HHHHHhhC
Confidence            3333344443  58999999999999999999999999999999999999999999999999   99     88887542


Q ss_pred             CCCCCCCceEEEECCCcHHHHHHHHHHHHhcC
Q psy7691         114 GRCASSGTAYTFFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus       114 ~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~  145 (165)
                           .+..+++++|+ ++++.|+.+.+....
T Consensus        80 -----~~~~aL~l~Pt-raLa~q~~~~l~~l~  105 (742)
T TIGR03817        80 -----PRATALYLAPT-KALAADQLRAVRELT  105 (742)
T ss_pred             -----CCcEEEEEcCh-HHHHHHHHHHHHHhc
Confidence                 35678999999 899998888877653

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.

>cd00268 DEADc DEAD-box helicases

Probab=99.32  E-value=6.1e-12  Score=96.49  Aligned_cols=92  Identities=34%  Similarity=0.529  Sum_probs=77.8

Q ss_pred             cccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCc
Q psy7691          42 LTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGT  121 (165)
Q Consensus        42 f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~  121 (165)
                      |+++.+++.+.+.|.+.|+..|++.|.++++.++.|+|++++++||+|||++++   +|     .++++....  ...+.
T Consensus         1 ~~~~~~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~---~~-----~l~~~~~~~--~~~~~   70 (203)
T cd00268           1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFL---IP-----ILEKLDPSP--KKDGP   70 (203)
T ss_pred             CCcCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHH---HH-----HHHHHHhhc--ccCCc
Confidence            788999999999999999999999999999999999999999999999999887   77     666664421  13566


Q ss_pred             eEEEECCCcHHHHHHHHHHHHhc
Q psy7691         122 AYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus       122 ~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      .+++++|+ ++++.|+.+.+...
T Consensus        71 ~viii~p~-~~L~~q~~~~~~~~   92 (203)
T cd00268          71 QALILAPT-RELALQIAEVARKL   92 (203)
T ss_pred             eEEEEcCC-HHHHHHHHHHHHHH
Confidence            78888998 88888877766554

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.

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

Probab=99.32  E-value=2.1e-12  Score=113.03  Aligned_cols=98  Identities=30%  Similarity=0.473  Sum_probs=80.6

Q ss_pred             ccccc-cCCCcHHHHHHHHhCCCCC------CchHHH---------------HHHHHHHcCCCeeeecccCCcccceeee
Q psy7691          39 TQELT-EGCFPNAVLQHLKGQGFEE------PTAIQA---------------QGWPIALSGRDMVGIAQTGSGKTLAVIN   96 (165)
Q Consensus        39 i~~f~-~l~l~~~l~~~l~~~g~~~------~t~~Q~---------------~a~~~~l~G~di~~~a~tgsGKt~~~~~   96 (165)
                      .+.|. +....+.+...|...||..      .+..++               .|++.+.||.|+..+.        +|+|
T Consensus       276 ~IVF~~tk~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTDvaaRGiDi~~v~--------~Vin  347 (513)
T COG0513         276 VIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVS--------HVIN  347 (513)
T ss_pred             EEEEeCcHHHHHHHHHHHHHCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEechhhccCCccccc--------eeEE
Confidence            44554 4678888999999999754      222222               1677778888888887        9999


Q ss_pred             cCCCCChhHHHHhhccCCCCCCCCceEEEECCC-cHHHHHHHHHHHHhc
Q psy7691          97 FDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPN-NGKQAKELIAVLTEA  144 (165)
Q Consensus        97 ~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~-~~~~~~~i~~~l~~~  144 (165)
                      ||+|.+.++|+||+|||||+|+.|.+++|++|. +...+..+.+.+...
T Consensus       348 yD~p~~~e~yvHRiGRTgRaG~~G~ai~fv~~~~e~~~l~~ie~~~~~~  396 (513)
T COG0513         348 YDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLKRIEKRLERK  396 (513)
T ss_pred             ccCCCCHHHheeccCccccCCCCCeEEEEeCcHHHHHHHHHHHHHHhcc
Confidence            999999999999999999999999999999996 788899999998766

>KOG0340|consensus

Probab=99.30  E-value=3.3e-12  Score=105.50  Aligned_cols=105  Identities=22%  Similarity=0.289  Sum_probs=82.9

Q ss_pred             CCccccccCCCcHHHH-HHHHhCCCCCCch----HHHH-----------------HHHHHHcCCCeeeecccCCccccee
Q psy7691          37 CPTQELTEGCFPNAVL-QHLKGQGFEEPTA----IQAQ-----------------GWPIALSGRDMVGIAQTGSGKTLAV   94 (165)
Q Consensus        37 ~~i~~f~~l~l~~~l~-~~l~~~g~~~~t~----~Q~~-----------------a~~~~l~G~di~~~a~tgsGKt~~~   94 (165)
                      ..++.|.+.....+++ --|+..+++...-    .|.+                 |++.+.||.||+.+.        .|
T Consensus       255 ~simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFrs~~~~iliaTDVAsRGLDIP~V~--------LV  326 (442)
T KOG0340|consen  255 GSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFRSNAARILIATDVASRGLDIPTVE--------LV  326 (442)
T ss_pred             ceEEEEeehhHHHHHHHHHHhhhceeeeehhhcchHHHHHHHHHHHhhcCccEEEEechhhcCCCCCcee--------EE
Confidence            3467777654444444 4466677765322    1222                 677888999999888        89


Q ss_pred             eecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCC
Q psy7691          95 INFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIP  149 (165)
Q Consensus        95 ~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p  149 (165)
                      +|||+|.++.+|+||+||++|+|+.|.+++|+++.+.+++..|++-+.....+.+
T Consensus       327 vN~diPr~P~~yiHRvGRtARAGR~G~aiSivt~rDv~l~~aiE~~igkKl~e~~  381 (442)
T KOG0340|consen  327 VNHDIPRDPKDYIHRVGRTARAGRKGMAISIVTQRDVELLQAIEEEIGKKLTEYN  381 (442)
T ss_pred             EecCCCCCHHHHHHhhcchhcccCCcceEEEechhhHHHHHHHHHHHhccccccc
Confidence            9999999999999999999999999999999999999999999998887666554

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

Probab=99.29  E-value=5.6e-12  Score=110.35  Aligned_cols=79  Identities=33%  Similarity=0.558  Sum_probs=70.2

Q ss_pred             HHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCC
Q psy7691          70 GWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIP  149 (165)
Q Consensus        70 a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p  149 (165)
                      |++.+.+|.|+..+.        +|+|||+|.+.++|+||+||+||.|..|.+++|+.+.+...+.++.+.++..++++|
T Consensus       424 aTdvl~rGiDip~v~--------~VI~~d~P~s~~~yihRiGRaGR~g~~G~ai~f~~~~~~~~~~~l~~~l~~~~~~vp  495 (518)
T PLN00206        424 ATGVLGRGVDLLRVR--------QVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRNLFPELVALLKSSGAAIP  495 (518)
T ss_pred             EecHhhccCCcccCC--------EEEEeCCCCCHHHHHHhccccccCCCCeEEEEEEchhHHHHHHHHHHHHHHcCCCCC
Confidence            445555666666665        899999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHh
Q psy7691         150 PQLQDLA  156 (165)
Q Consensus       150 ~~~~~~~  156 (165)
                      .++....
T Consensus       496 ~~l~~~~  502 (518)
T PLN00206        496 RELANSR  502 (518)
T ss_pred             HHHHhCh
Confidence            9998754

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

Probab=99.27  E-value=5.7e-12  Score=114.28  Aligned_cols=90  Identities=27%  Similarity=0.302  Sum_probs=74.3

Q ss_pred             CCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCC-CCCCCCceEE
Q psy7691          46 CFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTG-RCASSGTAYT  124 (165)
Q Consensus        46 ~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~-r~~~~g~~~~  124 (165)
                      -+++.+.+++... |+.||+.|.+|||.+..|.|++++||||||||+|-+   ||     .+.++-.-+ .....|..++
T Consensus         7 ~l~~~v~~~~~~~-~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAf---Lp-----il~~l~~~~~~~~~~~i~~l   77 (814)
T COG1201           7 ILDPRVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAF---LP-----VINELLSLGKGKLEDGIYAL   77 (814)
T ss_pred             hcCHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHH---HH-----HHHHHHhccCCCCCCceEEE
Confidence            3889999999998 999999999999999999999999999999999998   89     677664442 3335688999


Q ss_pred             EECCCcHHHHHHHHHHHHhcC
Q psy7691         125 FFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus       125 ~~~p~~~~~~~~i~~~l~~~~  145 (165)
                      +++|. +.+..++.+.++...
T Consensus        78 YIsPL-kALn~Di~~rL~~~~   97 (814)
T COG1201          78 YISPL-KALNNDIRRRLEEPL   97 (814)
T ss_pred             EeCcH-HHHHHHHHHHHHHHH
Confidence            99999 666666666555443

>KOG0344|consensus

Probab=99.26  E-value=9.2e-12  Score=107.95  Aligned_cols=116  Identities=27%  Similarity=0.450  Sum_probs=94.5

Q ss_pred             CCCCccccc-cCCCcHHHHHHHH-------hCCCCCCchHHHH---------------HHHHHHcCCCeeeecccCCccc
Q psy7691          35 IPCPTQELT-EGCFPNAVLQHLK-------GQGFEEPTAIQAQ---------------GWPIALSGRDMVGIAQTGSGKT   91 (165)
Q Consensus        35 ~p~~i~~f~-~l~l~~~l~~~l~-------~~g~~~~t~~Q~~---------------a~~~~l~G~di~~~a~tgsGKt   91 (165)
                      .++|+..|. ++.-+.+|...|.       ..=+..-+..|..               |++.+.||.|+-++.       
T Consensus       386 ~~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicTdll~RGiDf~gvn-------  458 (593)
T KOG0344|consen  386 FKPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGERSQKQRDETMERFRIGKIWVLICTDLLARGIDFKGVN-------  458 (593)
T ss_pred             CCCCeEEEEecHHHHHHHHHHhhhccCcceeeEecccchhHHHHHHHHHhccCeeEEEehhhhhccccccCcc-------
Confidence            566666665 4577778888773       2223334555543               677778888887776       


Q ss_pred             ceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCChHHHHHhhh
Q psy7691          92 LAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQDLANS  158 (165)
Q Consensus        92 ~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p~~~~~~~~~  158 (165)
                       .|+|||+|.+...|+||+||+||+|+.|.+++|++-.+.....-+...++..+-+||.|.-.+..-
T Consensus       459 -~VInyD~p~s~~syihrIGRtgRag~~g~Aitfytd~d~~~ir~iae~~~~sG~evpe~~m~~~k~  524 (593)
T KOG0344|consen  459 -LVINYDFPQSDLSYIHRIGRTGRAGRSGKAITFYTDQDMPRIRSIAEVMEQSGCEVPEKIMGIKKL  524 (593)
T ss_pred             -eEEecCCCchhHHHHHHhhccCCCCCCcceEEEeccccchhhhhHHHHHHHcCCcchHHHHhhhhh
Confidence             899999999999999999999999999999999999999999999999999999999999888753

>KOG0342|consensus

Probab=99.24  E-value=7.3e-12  Score=106.83  Aligned_cols=61  Identities=31%  Similarity=0.477  Sum_probs=57.4

Q ss_pred             HHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHH
Q psy7691          70 GWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELI  138 (165)
Q Consensus        70 a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~  138 (165)
                      |++.+.||+|++.+.        ++++||.|.+.++||||+|||||.|..|.++++++|.+...+..+.
T Consensus       386 cTDVaARGlD~P~V~--------~VvQ~~~P~d~~~YIHRvGRTaR~gk~G~alL~l~p~El~Flr~LK  446 (543)
T KOG0342|consen  386 CTDVAARGLDIPDVD--------WVVQYDPPSDPEQYIHRVGRTAREGKEGKALLLLAPWELGFLRYLK  446 (543)
T ss_pred             ecchhhccCCCCCce--------EEEEeCCCCCHHHHHHHhccccccCCCceEEEEeChhHHHHHHHHh
Confidence            889999999999999        9999999999999999999999999999999999999877777766

>PRK02362 ski2-like helicase; Provisional

Probab=99.19  E-value=3.6e-11  Score=109.21  Aligned_cols=88  Identities=25%  Similarity=0.362  Sum_probs=76.2

Q ss_pred             ccccCCCcHHHHHHHHhCCCCCCchHHHHHHHH-HHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCC
Q psy7691          41 ELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPI-ALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASS  119 (165)
Q Consensus        41 ~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~-~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~  119 (165)
                      .|+++++++.+.+++.+.||..++|+|.+|++. ++.|.|++++||||||||+++.   +|     .++++.+       
T Consensus         2 ~~~~l~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~---la-----il~~l~~-------   66 (737)
T PRK02362          2 KIAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAE---LA-----MLKAIAR-------   66 (737)
T ss_pred             ChhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHH---HH-----HHHHHhc-------
Confidence            688999999999999999999999999999998 7889999999999999999988   77     6776632       


Q ss_pred             CceEEEECCCcHHHHHHHHHHHHhc
Q psy7691         120 GTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus       120 g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      +..++++.|+ ++++.|..+.+...
T Consensus        67 ~~kal~i~P~-raLa~q~~~~~~~~   90 (737)
T PRK02362         67 GGKALYIVPL-RALASEKFEEFERF   90 (737)
T ss_pred             CCcEEEEeCh-HHHHHHHHHHHHHh
Confidence            3358889999 88888888777653

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.18  E-value=5e-11  Score=110.12  Aligned_cols=87  Identities=24%  Similarity=0.289  Sum_probs=70.7

Q ss_pred             CCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCC--CCCceE
Q psy7691          46 CFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCA--SSGTAY  123 (165)
Q Consensus        46 ~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~--~~g~~~  123 (165)
                      .+++.+.+++.+ +|..||++|.+|||.++.|.|++++||||||||++++   +|     .++++-+.+..+  ..+..+
T Consensus        17 ~l~~~v~~~~~~-~~~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~---Lp-----il~~l~~~~~~~~~~~~~~~   87 (876)
T PRK13767         17 LLRPYVREWFKE-KFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAF---LA-----IIDELFRLGREGELEDKVYC   87 (876)
T ss_pred             hcCHHHHHHHHH-ccCCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHH---HH-----HHHHHHhhccccCCCCCeEE
Confidence            377788888776 7999999999999999999999999999999999999   88     676664322222  356789


Q ss_pred             EEECCCcHHHHHHHHHHHH
Q psy7691         124 TFFTPNNGKQAKELIAVLT  142 (165)
Q Consensus       124 ~~~~p~~~~~~~~i~~~l~  142 (165)
                      ++++|+ ++++.|+.+.+.
T Consensus        88 LyIsPt-raLa~di~~~L~  105 (876)
T PRK13767         88 LYVSPL-RALNNDIHRNLE  105 (876)
T ss_pred             EEEcCH-HHHHHHHHHHHH
Confidence            999998 888888876554

>PRK00254 ski2-like helicase; Provisional

Probab=99.12  E-value=1.3e-10  Score=105.37  Aligned_cols=88  Identities=25%  Similarity=0.309  Sum_probs=74.9

Q ss_pred             ccccCCCcHHHHHHHHhCCCCCCchHHHHHHHH-HHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCC
Q psy7691          41 ELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPI-ALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASS  119 (165)
Q Consensus        41 ~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~-~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~  119 (165)
                      .|+++++++.+.+.|++.||..++++|.+|++. ++.|.|+++++|||||||+++.   +|     .++++-+      .
T Consensus         2 ~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~---l~-----il~~l~~------~   67 (720)
T PRK00254          2 KVDELRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAE---IV-----MVNKLLR------E   67 (720)
T ss_pred             cHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHH---HH-----HHHHHHh------c
Confidence            578899999999999999999999999999986 7999999999999999999987   78     6666533      1


Q ss_pred             CceEEEECCCcHHHHHHHHHHHHh
Q psy7691         120 GTAYTFFTPNNGKQAKELIAVLTE  143 (165)
Q Consensus       120 g~~~~~~~p~~~~~~~~i~~~l~~  143 (165)
                      +..+++++|+ ++++.|..+.+..
T Consensus        68 ~~~~l~l~P~-~aLa~q~~~~~~~   90 (720)
T PRK00254         68 GGKAVYLVPL-KALAEEKYREFKD   90 (720)
T ss_pred             CCeEEEEeCh-HHHHHHHHHHHHH
Confidence            3457788998 8888888776653

>KOG0334|consensus

Probab=99.09  E-value=2.3e-10  Score=104.59  Aligned_cols=135  Identities=29%  Similarity=0.443  Sum_probs=103.5

Q ss_pred             CCHHHHHHHHhhcCcEEecCCCCCCcccccc-CCCcHHHHHHHHhCCCCCCchH----HH-----------------HHH
Q psy7691          14 LSESEVEAFRQKKEITVKGNNIPCPTQELTE-GCFPNAVLQHLKGQGFEEPTAI----QA-----------------QGW   71 (165)
Q Consensus        14 ~~~~~~~~~~~~~~i~~~~~~~p~~i~~f~~-l~l~~~l~~~l~~~g~~~~t~~----Q~-----------------~a~   71 (165)
                      ..++++..+.+..+.-..    ..+++.|++ ..-+..+.+.|.+.||.+.+..    |.                 .|+
T Consensus       595 ~e~eKf~kL~eLl~e~~e----~~~tiiFv~~qe~~d~l~~~L~~ag~~~~slHGgv~q~dR~sti~dfK~~~~~LLvaT  670 (997)
T KOG0334|consen  595 IENEKFLKLLELLGERYE----DGKTIIFVDKQEKADALLRDLQKAGYNCDSLHGGVDQHDRSSTIEDFKNGVVNLLVAT  670 (997)
T ss_pred             CchHHHHHHHHHHHHHhh----cCCEEEEEcCchHHHHHHHHHHhcCcchhhhcCCCchHHHHhHHHHHhccCceEEEeh
Confidence            345566666554443333    334556654 5899999999999999765421    21                 145


Q ss_pred             HHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCChH
Q psy7691          72 PIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQ  151 (165)
Q Consensus        72 ~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p~~  151 (165)
                      ..+.+|.|+.-.-        .++|||.|+-.++|+||+|||||+|++|.+++|+.|.+...+..|.+.+....+++|+.
T Consensus       671 svvarGLdv~~l~--------Lvvnyd~pnh~edyvhR~gRTgragrkg~AvtFi~p~q~~~a~dl~~al~~~~~~~P~~  742 (997)
T KOG0334|consen  671 SVVARGLDVKELI--------LVVNYDFPNHYEDYVHRVGRTGRAGRKGAAVTFITPDQLKYAGDLCKALELSKQPVPKL  742 (997)
T ss_pred             hhhhcccccccce--------EEEEcccchhHHHHHHHhcccccCCccceeEEEeChHHhhhHHHHHHHHHhccCCCchH
Confidence            5566666654443        89999999999999999999999999999999999988899999999999999999999


Q ss_pred             HHHHhhhCC
Q psy7691         152 LQDLANSNP  160 (165)
Q Consensus       152 ~~~~~~~~~  160 (165)
                      +..+++...
T Consensus       743 l~~l~~~f~  751 (997)
T KOG0334|consen  743 LQALSERFK  751 (997)
T ss_pred             HHHHHHHHH
Confidence            988876543

>KOG0338|consensus

Probab=99.08  E-value=1.6e-10  Score=99.46  Aligned_cols=67  Identities=36%  Similarity=0.601  Sum_probs=61.7

Q ss_pred             HHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691          70 GWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus        70 a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      |++.+.||.||.++-        .||||++|.+.+.|+||+|||+|+|+.|.+++++.-.+|.++..|.+.....
T Consensus       482 aTDvAsRGLDI~gV~--------tVINy~mP~t~e~Y~HRVGRTARAGRaGrsVtlvgE~dRkllK~iik~~~~a  548 (691)
T KOG0338|consen  482 ATDVASRGLDIEGVQ--------TVINYAMPKTIEHYLHRVGRTARAGRAGRSVTLVGESDRKLLKEIIKSSTKA  548 (691)
T ss_pred             EechhhccCCcccee--------EEEeccCchhHHHHHHHhhhhhhcccCcceEEEeccccHHHHHHHHhhhhhc
Confidence            778889999999887        8999999999999999999999999999999999999999999998885443

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.06  E-value=1.4e-10  Score=98.93  Aligned_cols=108  Identities=20%  Similarity=0.321  Sum_probs=80.5

Q ss_pred             Cccccc-cCCCcHHHHHHHHhCCCCCC------ch-HHHH--------------HHHHHHcCCCeeeecccCCcccceee
Q psy7691          38 PTQELT-EGCFPNAVLQHLKGQGFEEP------TA-IQAQ--------------GWPIALSGRDMVGIAQTGSGKTLAVI   95 (165)
Q Consensus        38 ~i~~f~-~l~l~~~l~~~l~~~g~~~~------t~-~Q~~--------------a~~~~l~G~di~~~a~tgsGKt~~~~   95 (165)
                      .++.|. ...-++.+.+.|...|+...      +. .+..              |++.+.+|.|+..+.        +|+
T Consensus       257 ~~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTdv~~rGiDip~v~--------~VI  328 (423)
T PRK04837        257 RAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVT--------HVF  328 (423)
T ss_pred             eEEEEECCHHHHHHHHHHHHhCCCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEechhhcCCCccccC--------EEE
Confidence            344454 45678888888988887531      11 1222              344556777777666        899


Q ss_pred             ecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCChHHH
Q psy7691          96 NFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ  153 (165)
Q Consensus        96 ~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p~~~~  153 (165)
                      |||+|.+.++|+||+||+||.|+.|.+++|+++.+......+.+++.......+....
T Consensus       329 ~~d~P~s~~~yiqR~GR~gR~G~~G~ai~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~  386 (423)
T PRK04837        329 NYDLPDDCEDYVHRIGRTGRAGASGHSISLACEEYALNLPAIETYIGHSIPVSKYDSD  386 (423)
T ss_pred             EeCCCCchhheEeccccccCCCCCeeEEEEeCHHHHHHHHHHHHHhCCCCCCccCChh
Confidence            9999999999999999999999999999999999888888888888776544443333

>KOG0350|consensus

Probab=99.04  E-value=4.1e-10  Score=96.62  Aligned_cols=77  Identities=29%  Similarity=0.399  Sum_probs=61.9

Q ss_pred             HHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHh----c
Q psy7691          69 QGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTE----A  144 (165)
Q Consensus        69 ~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~----~  144 (165)
                      .|.+.+.||.|+-.+.        .|||||+|.+..+|+||+|||+|+|+.|.+++++.-.+..+...+.+..+.    .
T Consensus       488 IcSD~laRGiDv~~v~--------~VINYd~P~~~ktyVHR~GRTARAgq~G~a~tll~~~~~r~F~klL~~~~~~d~~~  559 (620)
T KOG0350|consen  488 ICSDALARGIDVNDVD--------NVINYDPPASDKTYVHRAGRTARAGQDGYAITLLDKHEKRLFSKLLKKTNLWDGVE  559 (620)
T ss_pred             EehhhhhcCCcccccc--------eEeecCCCchhhHHHHhhcccccccCCceEEEeeccccchHHHHHHHHhcccCCcc
Confidence            4788899999998877        899999999999999999999999999999999998876665555554444    3


Q ss_pred             CCCCChHHH
Q psy7691         145 SQPIPPQLQ  153 (165)
Q Consensus       145 ~~~~p~~~~  153 (165)
                      .+++|+...
T Consensus       560 i~~~e~~~~  568 (620)
T KOG0350|consen  560 IQPIEYIFI  568 (620)
T ss_pred             eeecCchHH
Confidence            444444433

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=98.99  E-value=9.1e-10  Score=98.57  Aligned_cols=102  Identities=25%  Similarity=0.393  Sum_probs=77.7

Q ss_pred             ccccccCCCcHHHHHHHHhCCCCC------CchHHH-H--------------HHHHHHcCCCeeeecccCCcccceeeec
Q psy7691          39 TQELTEGCFPNAVLQHLKGQGFEE------PTAIQA-Q--------------GWPIALSGRDMVGIAQTGSGKTLAVINF   97 (165)
Q Consensus        39 i~~f~~l~l~~~l~~~l~~~g~~~------~t~~Q~-~--------------a~~~~l~G~di~~~a~tgsGKt~~~~~~   97 (165)
                      ++.+.+..-...+...|...||..      .+..|. +              |++.+.+|.|+..+.        +|+||
T Consensus       249 IVF~~tk~~a~~l~~~L~~~g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATdv~arGIDip~V~--------~VI~~  320 (629)
T PRK11634        249 IIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERIS--------LVVNY  320 (629)
T ss_pred             EEEeccHHHHHHHHHHHHhCCCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcchHhcCCCcccCC--------EEEEe
Confidence            333344567788888898888753      222222 2              445556667766666        89999


Q ss_pred             CCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCC
Q psy7691          98 DYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPI  148 (165)
Q Consensus        98 ~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~  148 (165)
                      |+|.+.++|+||+||+||+|+.|.+++++.+.+...+..|.+.+.....++
T Consensus       321 d~P~~~e~yvqRiGRtGRaGr~G~ai~~v~~~e~~~l~~ie~~~~~~i~~~  371 (629)
T PRK11634        321 DIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNIERTMKLTIPEV  371 (629)
T ss_pred             CCCCCHHHHHHHhccccCCCCcceEEEEechHHHHHHHHHHHHhCCCccee
Confidence            999999999999999999999999999999988888888888776665444

>KOG0329|consensus

Probab=98.99  E-value=1.4e-09  Score=87.12  Aligned_cols=97  Identities=21%  Similarity=0.326  Sum_probs=79.9

Q ss_pred             cccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCC
Q psy7691          40 QELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASS  119 (165)
Q Consensus        40 ~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~  119 (165)
                      .-|.+.-|-+++++++.+.||..|+.+|.+|||.+.-|+|++++|..|.|||..|+   +.     -+|++.-     -.
T Consensus        42 sgfrdfllkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfv---l~-----tlqqiep-----v~  108 (387)
T KOG0329|consen   42 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFV---LA-----TLQQIEP-----VD  108 (387)
T ss_pred             cchhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeee---hh-----hhhhcCC-----CC
Confidence            34556678999999999999999999999999999999999999999999999888   66     5666632     23


Q ss_pred             C-ceEEEECCCcHHHHHHHHHHHHhcCCCCCh
Q psy7691         120 G-TAYTFFTPNNGKQAKELIAVLTEASQPIPP  150 (165)
Q Consensus       120 g-~~~~~~~p~~~~~~~~i~~~l~~~~~~~p~  150 (165)
                      | ..+++++.+ |+++.||.+-.++-.+-+|.
T Consensus       109 g~vsvlvmcht-relafqi~~ey~rfskymP~  139 (387)
T KOG0329|consen  109 GQVSVLVMCHT-RELAFQISKEYERFSKYMPS  139 (387)
T ss_pred             CeEEEEEEecc-HHHHHHHHHHHHHHHhhCCC
Confidence            3 456667776 99999999888776665554

>KOG0348|consensus

Probab=98.99  E-value=5.1e-10  Score=96.78  Aligned_cols=67  Identities=30%  Similarity=0.482  Sum_probs=59.4

Q ss_pred             HHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHH
Q psy7691          67 QAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVL  141 (165)
Q Consensus        67 Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l  141 (165)
                      -.-|++.+.||.|++.+.        +++.||.|....+|+||+|||+|+|.+|.+++|+.|.+.+..+.+....
T Consensus       500 VLLcTDVAaRGLDlP~V~--------~vVQYd~P~s~adylHRvGRTARaG~kG~alLfL~P~Eaey~~~l~~~~  566 (708)
T KOG0348|consen  500 VLLCTDVAARGLDLPHVG--------LVVQYDPPFSTADYLHRVGRTARAGEKGEALLFLLPSEAEYVNYLKKHH  566 (708)
T ss_pred             EEEehhhhhccCCCCCcC--------eEEEeCCCCCHHHHHHHhhhhhhccCCCceEEEecccHHHHHHHHHhhc
Confidence            345899999999999998        9999999999999999999999999999999999999877665555443

>KOG0347|consensus

Probab=98.98  E-value=4.9e-10  Score=97.15  Aligned_cols=101  Identities=29%  Similarity=0.393  Sum_probs=81.6

Q ss_pred             CCCCcccccc-CCCcHHHHHHHHhCCCCCCch-----HHHH-----------------HHHHHHcCCCeeeecccCCccc
Q psy7691          35 IPCPTQELTE-GCFPNAVLQHLKGQGFEEPTA-----IQAQ-----------------GWPIALSGRDMVGIAQTGSGKT   91 (165)
Q Consensus        35 ~p~~i~~f~~-l~l~~~l~~~l~~~g~~~~t~-----~Q~~-----------------a~~~~l~G~di~~~a~tgsGKt   91 (165)
                      .|+..+.|.+ ...-..+.-.|+..++. |.+     +|.+                 |++.+.||.||+.+.       
T Consensus       462 yPGrTlVF~NsId~vKRLt~~L~~L~i~-p~~LHA~M~QKqRLknLEkF~~~~~~VLiaTDVAARGLDIp~V~-------  533 (731)
T KOG0347|consen  462 YPGRTLVFCNSIDCVKRLTVLLNNLDIP-PLPLHASMIQKQRLKNLEKFKQSPSGVLIATDVAARGLDIPGVQ-------  533 (731)
T ss_pred             cCCceEEEechHHHHHHHHHHHhhcCCC-CchhhHHHHHHHHHHhHHHHhcCCCeEEEeehhhhccCCCCCcc-------
Confidence            6777667765 34555666666666765 444     2332                 788999999999998       


Q ss_pred             ceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691          92 LAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus        92 ~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                       +||||.+|...+-|+||.|||+|++..|..+.++.|.+...+..|.+-+...
T Consensus       534 -HVIHYqVPrtseiYVHRSGRTARA~~~Gvsvml~~P~e~~~~~KL~ktL~k~  585 (731)
T KOG0347|consen  534 -HVIHYQVPRTSEIYVHRSGRTARANSEGVSVMLCGPQEVGPLKKLCKTLKKK  585 (731)
T ss_pred             -eEEEeecCCccceeEecccccccccCCCeEEEEeChHHhHHHHHHHHHHhhc
Confidence             9999999999999999999999999999999999999988888888777654

>KOG0346|consensus

Probab=98.97  E-value=8.5e-10  Score=93.56  Aligned_cols=62  Identities=35%  Similarity=0.685  Sum_probs=54.0

Q ss_pred             HHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHh
Q psy7691          74 ALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTE  143 (165)
Q Consensus        74 ~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~  143 (165)
                      +.||.|+=.++        +|+|||+|.+++.||||+|||+|+++.|.+++|+.|.++.-...|+..+..
T Consensus       363 VsRGIDF~~V~--------~VlNFD~P~t~~sYIHRvGRTaRg~n~GtalSfv~P~e~~g~~~le~~~~d  424 (569)
T KOG0346|consen  363 VSRGIDFHHVS--------NVLNFDFPETVTSYIHRVGRTARGNNKGTALSFVSPKEEFGKESLESILKD  424 (569)
T ss_pred             hhccccchhee--------eeeecCCCCchHHHHHhccccccCCCCCceEEEecchHHhhhhHHHHHHhh
Confidence            57888887777        999999999999999999999999999999999999987755566655544

>PRK01172 ski2-like helicase; Provisional

Probab=98.96  E-value=1.1e-09  Score=98.51  Aligned_cols=86  Identities=19%  Similarity=0.219  Sum_probs=71.1

Q ss_pred             ccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCC
Q psy7691          41 ELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSG  120 (165)
Q Consensus        41 ~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g  120 (165)
                      .|+++++++.+.+.+.+.+|. ++++|.+|++.+..|.|+++++|||||||+++.   ++     .++.+.+       +
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~---la-----il~~l~~-------~   65 (674)
T PRK01172          2 KISDLGYDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAY---SA-----IYETFLA-------G   65 (674)
T ss_pred             cHhhcCCCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHH---HH-----HHHHHHh-------C
Confidence            588899999999999999997 999999999999999999999999999999876   55     4444422       2


Q ss_pred             ceEEEECCCcHHHHHHHHHHHHh
Q psy7691         121 TAYTFFTPNNGKQAKELIAVLTE  143 (165)
Q Consensus       121 ~~~~~~~p~~~~~~~~i~~~l~~  143 (165)
                      ..+++++|+ ++++.|..+.+..
T Consensus        66 ~k~v~i~P~-raLa~q~~~~~~~   87 (674)
T PRK01172         66 LKSIYIVPL-RSLAMEKYEELSR   87 (674)
T ss_pred             CcEEEEech-HHHHHHHHHHHHH
Confidence            346677788 8888887776653

>KOG0350|consensus

Probab=98.94  E-value=2.3e-09  Score=92.12  Aligned_cols=99  Identities=20%  Similarity=0.163  Sum_probs=78.4

Q ss_pred             CccccccCCCcHHHHHH----------HHhCCCCCCchHHHHHHHHHH---------cCCCeeeecccCCcccceeeecC
Q psy7691          38 PTQELTEGCFPNAVLQH----------LKGQGFEEPTAIQAQGWPIAL---------SGRDMVGIAQTGSGKTLAVINFD   98 (165)
Q Consensus        38 ~i~~f~~l~l~~~l~~~----------l~~~g~~~~t~~Q~~a~~~~l---------~G~di~~~a~tgsGKt~~~~~~~   98 (165)
                      ....|+.+++.+.+...          +.++++....|+|...+|.++         +++||.+.|+||||||++|.   
T Consensus       125 slq~~s~l~~se~k~~~d~lea~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~---  201 (620)
T KOG0350|consen  125 SLQIFSVLGKSEMKNLEDTLEATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYV---  201 (620)
T ss_pred             ceeeeeccchhHHHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeeh---
Confidence            46677888777665554          899999999999988887663         57999999999999999999   


Q ss_pred             CCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCC
Q psy7691          99 YPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPI  148 (165)
Q Consensus        99 lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~  148 (165)
                      +|     +++-++.  |. -+-...+++.|+ ++++.|+.+.+.+.+...
T Consensus       202 iP-----IVQ~L~~--R~-v~~LRavVivPt-r~L~~QV~~~f~~~~~~t  242 (620)
T KOG0350|consen  202 IP-----IVQLLSS--RP-VKRLRAVVIVPT-RELALQVYDTFKRLNSGT  242 (620)
T ss_pred             hH-----HHHHHcc--CC-ccceEEEEEeeH-HHHHHHHHHHHHHhccCC
Confidence            99     7876642  21 122567888888 999999999998876654

>KOG0345|consensus

Probab=98.92  E-value=1.3e-09  Score=93.05  Aligned_cols=54  Identities=35%  Similarity=0.648  Sum_probs=51.1

Q ss_pred             HHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCc
Q psy7691          69 QGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN  130 (165)
Q Consensus        69 ~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~  130 (165)
                      -|++.+.||.||.++.        +|++||.|.+.+.++||+|||+|+|+.|.+++++.|.+
T Consensus       312 ~~TDVaARGlDip~iD--------~VvQ~DpP~~~~~FvHR~GRTaR~gr~G~Aivfl~p~E  365 (567)
T KOG0345|consen  312 FCTDVAARGLDIPGID--------LVVQFDPPKDPSSFVHRCGRTARAGREGNAIVFLNPRE  365 (567)
T ss_pred             EeehhhhccCCCCCce--------EEEecCCCCChhHHHhhcchhhhccCccceEEEecccH
Confidence            3788999999999999        99999999999999999999999999999999999964

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=98.91  E-value=2.1e-09  Score=92.61  Aligned_cols=102  Identities=26%  Similarity=0.330  Sum_probs=74.2

Q ss_pred             CCcccccc-CCCcHHHHHHHHhCCCCC------Cch-HHHHHHHHH--------------HcCCCeeeecccCCccccee
Q psy7691          37 CPTQELTE-GCFPNAVLQHLKGQGFEE------PTA-IQAQGWPIA--------------LSGRDMVGIAQTGSGKTLAV   94 (165)
Q Consensus        37 ~~i~~f~~-l~l~~~l~~~l~~~g~~~------~t~-~Q~~a~~~~--------------l~G~di~~~a~tgsGKt~~~   94 (165)
                      ..++.|.. ..-.+.+.+.|...|+..      .+. .+.+++..+              .+|.|+..+.        ++
T Consensus       243 ~~~lVF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTdv~~rGiDi~~v~--------~V  314 (460)
T PRK11776        243 ESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALE--------AV  314 (460)
T ss_pred             CceEEEECCHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEecccccccchhcCC--------eE
Confidence            34455544 467778888888877643      122 233333333              4445544444        89


Q ss_pred             eecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691          95 INFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus        95 ~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      +|||+|.+.++|+||+||+||+|..|.+++++.+.+...+..+.+.+.....
T Consensus       315 I~~d~p~~~~~yiqR~GRtGR~g~~G~ai~l~~~~e~~~~~~i~~~~~~~~~  366 (460)
T PRK11776        315 INYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAIEDYLGRKLN  366 (460)
T ss_pred             EEecCCCCHhHhhhhcccccCCCCcceEEEEEchhHHHHHHHHHHHhCCCCc
Confidence            9999999999999999999999999999999999988888888888766443

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=98.88  E-value=3.5e-09  Score=93.89  Aligned_cols=99  Identities=26%  Similarity=0.429  Sum_probs=74.2

Q ss_pred             Cccccc-cCCCcHHHHHHHHhCCCCCC------chH-HHH--------------HHHHHHcCCCeeeecccCCcccceee
Q psy7691          38 PTQELT-EGCFPNAVLQHLKGQGFEEP------TAI-QAQ--------------GWPIALSGRDMVGIAQTGSGKTLAVI   95 (165)
Q Consensus        38 ~i~~f~-~l~l~~~l~~~l~~~g~~~~------t~~-Q~~--------------a~~~~l~G~di~~~a~tgsGKt~~~~   95 (165)
                      .++.|. .....+.+.+.|.+.|+...      +.. +..              |++.+.+|.|+..+.        +|+
T Consensus       259 k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv~arGIDip~V~--------~VI  330 (572)
T PRK04537        259 RTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVK--------YVY  330 (572)
T ss_pred             cEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehhhhcCCCccCCC--------EEE
Confidence            344554 45678888888988887531      222 222              344455566665555        899


Q ss_pred             ecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691          96 NFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus        96 ~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      |||+|.+.++|+||+||+||.|..|.+++|+++.+...+.++.+.+...
T Consensus       331 nyd~P~s~~~yvqRiGRaGR~G~~G~ai~~~~~~~~~~l~~i~~~~~~~  379 (572)
T PRK04537        331 NYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYAMSLPDIEAYIEQK  379 (572)
T ss_pred             EcCCCCCHHHHhhhhcccccCCCCceEEEEecHHHHHHHHHHHHHHcCC
Confidence            9999999999999999999999999999999998777788888877654

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=98.87  E-value=2.3e-09  Score=92.44  Aligned_cols=100  Identities=28%  Similarity=0.474  Sum_probs=76.2

Q ss_pred             Cccccc-cCCCcHHHHHHHHhCCCCCC------chH-HHH--------------HHHHHHcCCCeeeecccCCcccceee
Q psy7691          38 PTQELT-EGCFPNAVLQHLKGQGFEEP------TAI-QAQ--------------GWPIALSGRDMVGIAQTGSGKTLAVI   95 (165)
Q Consensus        38 ~i~~f~-~l~l~~~l~~~l~~~g~~~~------t~~-Q~~--------------a~~~~l~G~di~~~a~tgsGKt~~~~   95 (165)
                      .++.|. +..-.+.+.+.|...|+...      +.. ..+              |++.+.+|.|+..+.        +|+
T Consensus       247 ~~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTdv~~rGiDip~v~--------~VI  318 (456)
T PRK10590        247 QVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELP--------HVV  318 (456)
T ss_pred             cEEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEccHHhcCCCcccCC--------EEE
Confidence            344454 34567778888888777432      111 112              455566777776666        899


Q ss_pred             ecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcC
Q psy7691          96 NFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus        96 ~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~  145 (165)
                      |||+|.+.++|+||+||+||+|..|.+++++++.+..++..+++.+....
T Consensus       319 ~~~~P~~~~~yvqR~GRaGR~g~~G~ai~l~~~~d~~~~~~ie~~l~~~~  368 (456)
T PRK10590        319 NYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDIEKLLKKEI  368 (456)
T ss_pred             EeCCCCCHHHhhhhccccccCCCCeeEEEEecHHHHHHHHHHHHHhcCCC
Confidence            99999999999999999999999999999999998889999998877654

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=98.86  E-value=4e-09  Score=90.14  Aligned_cols=107  Identities=24%  Similarity=0.354  Sum_probs=72.9

Q ss_pred             Ccccc-ccCCCcHHHHHHHHhCCCCCC------c-hHHHHHHHHHHcCC-Ceeeec-ccCCcc----cceeeecCCCCCh
Q psy7691          38 PTQEL-TEGCFPNAVLQHLKGQGFEEP------T-AIQAQGWPIALSGR-DMVGIA-QTGSGK----TLAVINFDYPNSS  103 (165)
Q Consensus        38 ~i~~f-~~l~l~~~l~~~l~~~g~~~~------t-~~Q~~a~~~~l~G~-di~~~a-~tgsGK----t~~~~~~~lP~~~  103 (165)
                      .++.| .+..-.+.+.+.|...|+...      + ..+..++..+..|. +++++. .-+.|-    .-+|+|||+|.+.
T Consensus       247 ~~lVF~~s~~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd~~~~GiDip~v~~VI~~d~p~s~  326 (434)
T PRK11192        247 RSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSA  326 (434)
T ss_pred             eEEEEeCChHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEccccccCccCCCCCEEEEECCCCCH
Confidence            34444 445677788888888877531      2 22333444444442 222211 111221    1279999999999


Q ss_pred             hHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691         104 EDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus       104 ~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      +.|+||+||+||+|..|.+++++...+...+..+.+++...
T Consensus       327 ~~yiqr~GR~gR~g~~g~ai~l~~~~d~~~~~~i~~~~~~~  367 (434)
T PRK11192        327 DTYLHRIGRTGRAGRKGTAISLVEAHDHLLLGKIERYIEEP  367 (434)
T ss_pred             HHHhhcccccccCCCCceEEEEecHHHHHHHHHHHHHHhcc
Confidence            99999999999999999999999998888888888877654

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=98.86  E-value=3.3e-09  Score=91.87  Aligned_cols=69  Identities=20%  Similarity=0.249  Sum_probs=56.6

Q ss_pred             CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHH
Q psy7691          58 QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL  137 (165)
Q Consensus        58 ~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i  137 (165)
                      .||..++|+|.++++.++.|+|+++++|||+|||++|.   +|     .+..          +...++++|+ ++++.+.
T Consensus         7 ~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~---lp-----~l~~----------~~~~lVi~P~-~~L~~dq   67 (470)
T TIGR00614         7 FGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQ---LP-----ALCS----------DGITLVISPL-ISLMEDQ   67 (470)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHH---HH-----HHHc----------CCcEEEEecH-HHHHHHH
Confidence            69999999999999999999999999999999999988   88     3321          1235778888 8887777


Q ss_pred             HHHHHhcC
Q psy7691         138 IAVLTEAS  145 (165)
Q Consensus       138 ~~~l~~~~  145 (165)
                      .+.+...+
T Consensus        68 ~~~l~~~g   75 (470)
T TIGR00614        68 VLQLKASG   75 (470)
T ss_pred             HHHHHHcC
Confidence            66666544

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

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=98.84  E-value=4.7e-09  Score=96.34  Aligned_cols=118  Identities=19%  Similarity=0.202  Sum_probs=85.9

Q ss_pred             hHhhcCCHHHHHH----HHhhcCcEEecCCCCCCccccccCCCcHHHHHHHH-----hCCCCCC---chHHHHHHHHHHc
Q psy7691           9 ERAARLSESEVEA----FRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLK-----GQGFEEP---TAIQAQGWPIALS   76 (165)
Q Consensus         9 ~~~~~~~~~~~~~----~~~~~~i~~~~~~~p~~i~~f~~l~l~~~l~~~l~-----~~g~~~~---t~~Q~~a~~~~l~   76 (165)
                      +.+..+|++++..    |+....   .|..+..  .--+.+.+..++.+.+.     .+||..|   +|+|.+++|.++.
T Consensus        32 ~~~~~lsd~eL~~kt~~~k~~l~---~~~~ld~--~l~eafal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l  106 (970)
T PRK12899         32 EKFSSLSDDELRNKTAELKQRYQ---DGESLDK--LLPEAYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAM  106 (970)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHH---cCCchHH--HHHHHhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhc
Confidence            3566777766543    443322   2222111  12355788888888877     6899999   9999999999999


Q ss_pred             CCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCC
Q psy7691          77 GRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQP  147 (165)
Q Consensus        77 G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~  147 (165)
                      +.|+++.++||+|||++|+   +|     .++++-. ++      .+.+++|+ ++++.|+.+.+......
T Consensus       107 ~~gvIAeaqTGeGKTLAf~---LP-----~l~~aL~-g~------~v~IVTpT-rELA~Qdae~m~~L~k~  161 (970)
T PRK12899        107 HKGFITEMQTGEGKTLTAV---MP-----LYLNALT-GK------PVHLVTVN-DYLAQRDCEWVGSVLRW  161 (970)
T ss_pred             CCCeEEEeCCCCChHHHHH---HH-----HHHHHhh-cC------CeEEEeCC-HHHHHHHHHHHHHHHhh
Confidence            9999999999999999999   99     5655532 11      26788997 88999999998876443

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=98.78  E-value=1.4e-08  Score=90.71  Aligned_cols=75  Identities=25%  Similarity=0.260  Sum_probs=58.9

Q ss_pred             HHHHHh-CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCc
Q psy7691          52 LQHLKG-QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN  130 (165)
Q Consensus        52 ~~~l~~-~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~  130 (165)
                      .+.|++ .||..++++|.++++.++.|.|+++++|||+|||++|.   +|     .+.+-|          .+++++|+ 
T Consensus        14 ~~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~---lp-----al~~~g----------~tlVisPl-   74 (607)
T PRK11057         14 KQVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQ---IP-----ALVLDG----------LTLVVSPL-   74 (607)
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHH---HH-----HHHcCC----------CEEEEecH-
Confidence            334444 59999999999999999999999999999999999988   88     443321          35777887 


Q ss_pred             HHHHHHHHHHHHhcC
Q psy7691         131 GKQAKELIAVLTEAS  145 (165)
Q Consensus       131 ~~~~~~i~~~l~~~~  145 (165)
                      .+++.+..+.+...+
T Consensus        75 ~sL~~dqv~~l~~~g   89 (607)
T PRK11057         75 ISLMKDQVDQLLANG   89 (607)
T ss_pred             HHHHHHHHHHHHHcC
Confidence            788777766666543

>KOG0343|consensus

Probab=98.77  E-value=7.3e-09  Score=90.09  Aligned_cols=62  Identities=32%  Similarity=0.535  Sum_probs=54.9

Q ss_pred             HHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHH-HHHHHHH
Q psy7691          70 GWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGK-QAKELIA  139 (165)
Q Consensus        70 a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~-~~~~i~~  139 (165)
                      |++.+.||.|+.++.        +|++||-|.++++||||+||++|.+..|.++++++|.+.+ +...|.+
T Consensus       371 ~TDv~aRGLDFpaVd--------wViQ~DCPedv~tYIHRvGRtAR~~~~G~sll~L~psEeE~~l~~Lq~  433 (758)
T KOG0343|consen  371 CTDVAARGLDFPAVD--------WVIQVDCPEDVDTYIHRVGRTARYKERGESLLMLTPSEEEAMLKKLQK  433 (758)
T ss_pred             eehhhhccCCCcccc--------eEEEecCchhHHHHHHHhhhhhcccCCCceEEEEcchhHHHHHHHHHH
Confidence            778889999999998        9999999999999999999999999999999999999844 4444443

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

Probab=98.76  E-value=1.6e-08  Score=93.13  Aligned_cols=87  Identities=23%  Similarity=0.326  Sum_probs=73.8

Q ss_pred             CcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEE
Q psy7691          47 FPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFF  126 (165)
Q Consensus        47 l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~  126 (165)
                      ....+..+|.+.|...++++|.+|+..+..|+|++++++||||||++|.   +|     .++.+.+...+     .++++
T Consensus        55 ~~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~Fl---lP-----Ild~~l~~~~a-----~AL~l  121 (851)
T COG1205          55 RDESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFL---LP-----ILDHLLRDPSA-----RALLL  121 (851)
T ss_pred             hhhHHHHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHH---HH-----HHHHHhhCcCc-----cEEEE
Confidence            4455688899999999999999999999999999999999999999999   99     99988775333     78999


Q ss_pred             CCCc---HHHHHHHHHHHHhcCC
Q psy7691         127 TPNN---GKQAKELIAVLTEASQ  146 (165)
Q Consensus       127 ~p~~---~~~~~~i~~~l~~~~~  146 (165)
                      .|++   ++++..+.+++.....
T Consensus       122 YPtnALa~DQ~~rl~~~~~~~~~  144 (851)
T COG1205         122 YPTNALANDQAERLRELISDLPG  144 (851)
T ss_pred             echhhhHhhHHHHHHHHHHhCCC
Confidence            9997   5677777777776654

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

Probab=98.73  E-value=2e-08  Score=91.93  Aligned_cols=83  Identities=13%  Similarity=0.128  Sum_probs=60.9

Q ss_pred             HHHHHh-CCCCCCchHHHHHHHHHHcCC-CeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCC
Q psy7691          52 LQHLKG-QGFEEPTAIQAQGWPIALSGR-DMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPN  129 (165)
Q Consensus        52 ~~~l~~-~g~~~~t~~Q~~a~~~~l~G~-di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~  129 (165)
                      .++++. .||. ||++|.+++|.++.|+ +++++++||||||.+|..|.+|.         ..   ......++++++|+
T Consensus         5 ~~ff~~~~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~---------~~---~~~~~~rLv~~vPt   71 (844)
T TIGR02621         5 DEWYQGLHGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAV---------EI---GAKVPRRLVYVVNR   71 (844)
T ss_pred             HHHHHHHhCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccc---------cc---cccccceEEEeCch
Confidence            445555 5998 9999999999999998 57778999999999665344551         11   11122355556677


Q ss_pred             cHHHHHHHHHHHHhcCCCC
Q psy7691         130 NGKQAKELIAVLTEASQPI  148 (165)
Q Consensus       130 ~~~~~~~i~~~l~~~~~~~  148 (165)
                       |+++.|+.+.++...+.+
T Consensus        72 -ReLa~Qi~~~~~~~~k~l   89 (844)
T TIGR02621        72 -RTVVDQVTEEAEKIGERL   89 (844)
T ss_pred             -HHHHHHHHHHHHHHHHHh
Confidence             999999999988877655

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.

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=98.73  E-value=1.4e-08  Score=88.00  Aligned_cols=99  Identities=27%  Similarity=0.412  Sum_probs=72.5

Q ss_pred             ccccc-cCCCcHHHHHHHHhCCCCC-------CchHHHHHHHHH--------------HcCCCeeeecccCCcccceeee
Q psy7691          39 TQELT-EGCFPNAVLQHLKGQGFEE-------PTAIQAQGWPIA--------------LSGRDMVGIAQTGSGKTLAVIN   96 (165)
Q Consensus        39 i~~f~-~l~l~~~l~~~l~~~g~~~-------~t~~Q~~a~~~~--------------l~G~di~~~a~tgsGKt~~~~~   96 (165)
                      ++.|. ...-.+.+.+.|...|+..       +...+.+....+              .+|.|+..+.        ++++
T Consensus       338 ~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~~l~~GIDi~~v~--------~VI~  409 (475)
T PRK01297        338 VMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGIS--------HVIN  409 (475)
T ss_pred             EEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEccccccCCcccCCC--------EEEE
Confidence            44444 4456677777888777643       112222333333              3444444444        7999


Q ss_pred             cCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcC
Q psy7691          97 FDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus        97 ~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~  145 (165)
                      ||+|.+..+|+||+||+||.|..|.+++|+...+...+..+.+++....
T Consensus       410 ~~~P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~~d~~~~~~~~~~~~~~~  458 (475)
T PRK01297        410 FTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLPEIEELLGRKI  458 (475)
T ss_pred             eCCCCCHHHHHHhhCccCCCCCCceEEEEecHHHHHHHHHHHHHhCCCC
Confidence            9999999999999999999999999999999888888889988887764

>PTZ00424 helicase 45; Provisional

Probab=98.68  E-value=1e-08  Score=86.40  Aligned_cols=113  Identities=26%  Similarity=0.347  Sum_probs=77.2

Q ss_pred             ccccccCCCcHHHHHHHHhCCCCC------C-chHHHHHHHHHHcC-CCeeeeccc-CCc----ccceeeecCCCCChhH
Q psy7691          39 TQELTEGCFPNAVLQHLKGQGFEE------P-TAIQAQGWPIALSG-RDMVGIAQT-GSG----KTLAVINFDYPNSSED  105 (165)
Q Consensus        39 i~~f~~l~l~~~l~~~l~~~g~~~------~-t~~Q~~a~~~~l~G-~di~~~a~t-gsG----Kt~~~~~~~lP~~~~~  105 (165)
                      ++.+.+..-.+.+.+.|...|+..      . ...+...+..+..| .+++++... +.|    ...++++||+|.+..+
T Consensus       271 ivF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~~l~~GiDip~v~~VI~~~~p~s~~~  350 (401)
T PTZ00424        271 IIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPEN  350 (401)
T ss_pred             EEEecCcHHHHHHHHHHHHCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcccccCCcCcccCCEEEEECCCCCHHH
Confidence            333344456677777787776632      1 22233334444444 233322211 112    1227999999999999


Q ss_pred             HHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCChH
Q psy7691         106 YIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQ  151 (165)
Q Consensus       106 ~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p~~  151 (165)
                      |+||+||+||.|+.|.+++++.+.+.+.+..+.+.+.....+.+..
T Consensus       351 y~qr~GRagR~g~~G~~i~l~~~~~~~~~~~~e~~~~~~~~~~~~~  396 (401)
T PTZ00424        351 YIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIERHYNTQIEEMPME  396 (401)
T ss_pred             EeecccccccCCCCceEEEEEcHHHHHHHHHHHHHHCCcccccCcc
Confidence            9999999999999999999999999999999999988877776543

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=98.68  E-value=3.1e-08  Score=88.08  Aligned_cols=75  Identities=25%  Similarity=0.313  Sum_probs=58.3

Q ss_pred             HHHh-CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHH
Q psy7691          54 HLKG-QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGK  132 (165)
Q Consensus        54 ~l~~-~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~  132 (165)
                      .|++ .||..++++|.++++.++.|.|+++++|||+|||++|.   +|     .+.+         .| ..++++|+ ..
T Consensus         4 ~l~~~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~---lp-----al~~---------~g-~~lVisPl-~s   64 (591)
T TIGR01389         4 VLKRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQ---VP-----ALLL---------KG-LTVVISPL-IS   64 (591)
T ss_pred             HHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHH---HH-----HHHc---------CC-cEEEEcCC-HH
Confidence            3444 69999999999999999999999999999999999988   88     3422         12 35677888 77


Q ss_pred             HHHHHHHHHHhcCCC
Q psy7691         133 QAKELIAVLTEASQP  147 (165)
Q Consensus       133 ~~~~i~~~l~~~~~~  147 (165)
                      ++.+..+.+...+.+
T Consensus        65 L~~dq~~~l~~~gi~   79 (591)
T TIGR01389        65 LMKDQVDQLRAAGVA   79 (591)
T ss_pred             HHHHHHHHHHHcCCc
Confidence            777666666665443

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.

>TIGR01054 rgy reverse gyrase

Probab=98.67  E-value=4.3e-08  Score=93.01  Aligned_cols=84  Identities=19%  Similarity=0.135  Sum_probs=63.6

Q ss_pred             CcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEE
Q psy7691          47 FPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFF  126 (165)
Q Consensus        47 l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~  126 (165)
                      .-.++.+.+.+.....|+++|..++|.++.|+|++++|+||+|||. |.   +|     ..+.+..      .|..++++
T Consensus        63 ~~~~f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~---l~-----~~~~l~~------~g~~vLIL  127 (1171)
T TIGR01054        63 ELKEFEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FG---LA-----MSLFLAK------KGKRCYII  127 (1171)
T ss_pred             HHHHHHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HH---HH-----HHHHHHh------cCCeEEEE
Confidence            3445666676643446999999999999999999999999999996 54   56     3333321      25678999


Q ss_pred             CCCcHHHHHHHHHHHHhcCC
Q psy7691         127 TPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       127 ~p~~~~~~~~i~~~l~~~~~  146 (165)
                      +|+ ++++.|+.+.+.....
T Consensus       128 ~PT-reLa~Qi~~~l~~l~~  146 (1171)
T TIGR01054       128 LPT-TLLVIQVAEKISSLAE  146 (1171)
T ss_pred             eCH-HHHHHHHHHHHHHHHH
Confidence            999 9999998887776543

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.

>KOG0329|consensus

Probab=98.66  E-value=1.8e-08  Score=80.72  Aligned_cols=76  Identities=26%  Similarity=0.484  Sum_probs=64.1

Q ss_pred             HHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCc-HHHHHHHHHHHHhcCCC
Q psy7691          69 QGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN-GKQAKELIAVLTEASQP  147 (165)
Q Consensus        69 ~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~-~~~~~~i~~~l~~~~~~  147 (165)
                      .|++.+-+|+|+=-+.        .++|||+|.+.++|+||++|+||.|.+|.++.+++..+ ...+..+..-++....+
T Consensus       303 vat~lfgrgmdiervN--------i~~NYdmp~~~DtYlHrv~rAgrfGtkglaitfvs~e~da~iLn~vqdRf~v~i~e  374 (387)
T KOG0329|consen  303 VATDLFGRGMDIERVN--------IVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNPVQDRFEVNIKE  374 (387)
T ss_pred             HHhhhhccccCcccce--------eeeccCCCCCchHHHHHhhhhhccccccceeehhcchhhHHHhchhhHhhhccHhh
Confidence            3566677888875554        89999999999999999999999999999999998764 45677888888888888


Q ss_pred             CChHH
Q psy7691         148 IPPQL  152 (165)
Q Consensus       148 ~p~~~  152 (165)
                      +|..+
T Consensus       375 Lpdei  379 (387)
T KOG0329|consen  375 LPDEI  379 (387)
T ss_pred             cCccc
Confidence            88873

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

Probab=98.66  E-value=3.4e-08  Score=73.06  Aligned_cols=70  Identities=27%  Similarity=0.368  Sum_probs=55.7

Q ss_pred             chHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHh
Q psy7691          64 TAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTE  143 (165)
Q Consensus        64 t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~  143 (165)
                      |+.|.++++.+..|.|+++.++||+|||.++.   +|     .++.+.+.     ....++++.|+ ++++.++.+.+..
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~---~~-----~l~~~~~~-----~~~~~lii~P~-~~l~~q~~~~~~~   66 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYI---LP-----ALNRLQEG-----KDARVLIIVPT-RALAEQQFERLRK   66 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHH---HH-----HHHHHHTT-----SSSEEEEEESS-HHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHH---HH-----HHhhhccC-----CCceEEEEeec-ccccccccccccc
Confidence            78999999999999999999999999999988   66     66655442     22378889998 7888888877776


Q ss_pred             cCCC
Q psy7691         144 ASQP  147 (165)
Q Consensus       144 ~~~~  147 (165)
                      ....
T Consensus        67 ~~~~   70 (169)
T PF00270_consen   67 FFSN   70 (169)
T ss_dssp             HTTT
T ss_pred             cccc
Confidence            6554

Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....

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

Probab=98.65  E-value=5.1e-08  Score=91.27  Aligned_cols=87  Identities=17%  Similarity=0.162  Sum_probs=62.2

Q ss_pred             ccccccCCCcHHHHHHHHhCCCCCC------chHHH-H--------------HHHHHHcCCCeeeecccCCcccceeeec
Q psy7691          39 TQELTEGCFPNAVLQHLKGQGFEEP------TAIQA-Q--------------GWPIALSGRDMVGIAQTGSGKTLAVINF   97 (165)
Q Consensus        39 i~~f~~l~l~~~l~~~l~~~g~~~~------t~~Q~-~--------------a~~~~l~G~di~~~a~tgsGKt~~~~~~   97 (165)
                      |+.+..-.-++.+...|...|+...      ++.++ .              |+.++.+|.|+..+.        .||||
T Consensus       684 IIYC~SRke~E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~F~~Gei~VLVATdAFGMGIDkPDVR--------~VIHy  755 (1195)
T PLN03137        684 IIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVR--------FVIHH  755 (1195)
T ss_pred             eeEeCchhHHHHHHHHHHHCCCCeeeeeCCCCHHHHHHHHHHHhcCCCcEEEEechhhcCCCccCCc--------EEEEc
Confidence            3333444677888888988888652      22222 2              233334444444444        79999


Q ss_pred             CCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHH
Q psy7691          98 DYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQ  133 (165)
Q Consensus        98 ~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~  133 (165)
                      ++|.+.+.|+||+||+||+|..+.+++++.+.+...
T Consensus       756 dlPkSiEsYyQriGRAGRDG~~g~cILlys~~D~~~  791 (1195)
T PLN03137        756 SLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSDYIR  791 (1195)
T ss_pred             CCCCCHHHHHhhhcccCCCCCCceEEEEecHHHHHH
Confidence            999999999999999999999999999998765443

>PRK14701 reverse gyrase; Provisional

Probab=98.64  E-value=4.9e-08  Score=94.88  Aligned_cols=82  Identities=18%  Similarity=0.165  Sum_probs=63.2

Q ss_pred             CcHHHHHHHHh-CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEE
Q psy7691          47 FPNAVLQHLKG-QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTF  125 (165)
Q Consensus        47 l~~~l~~~l~~-~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~  125 (165)
                      --.++.+.|++ .|| .|+++|..+++.++.|+|++++||||+|||+++.   ++     .+...       ..|..+++
T Consensus        64 ~~~~~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~---~~-----al~~~-------~~g~~aLV  127 (1638)
T PRK14701         64 EVEEFEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGA---FI-----ALFLA-------LKGKKCYI  127 (1638)
T ss_pred             HHHHHHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHH---HH-----HHHHH-------hcCCeEEE
Confidence            34455666776 799 5999999999999999999999999999998433   23     11111       13557889


Q ss_pred             ECCCcHHHHHHHHHHHHhcC
Q psy7691         126 FTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus       126 ~~p~~~~~~~~i~~~l~~~~  145 (165)
                      ++|+ ++++.|+.+.+....
T Consensus       128 l~PT-reLa~Qi~~~l~~l~  146 (1638)
T PRK14701        128 ILPT-TLLVKQTVEKIESFC  146 (1638)
T ss_pred             EECH-HHHHHHHHHHHHHHH
Confidence            9999 999999988887744

>PRK09401 reverse gyrase; Reviewed

Probab=98.64  E-value=6e-08  Score=92.02  Aligned_cols=81  Identities=20%  Similarity=0.207  Sum_probs=62.5

Q ss_pred             HHHHHHHhC-CCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECC
Q psy7691          50 AVLQHLKGQ-GFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTP  128 (165)
Q Consensus        50 ~l~~~l~~~-g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p  128 (165)
                      +..+.+++. |+ .||++|..++|.++.|.|++++|+||+|||. |.   +|     ....+.+      .|..+++++|
T Consensus        68 ~~~~~f~~~~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~-f~---l~-----~~~~l~~------~g~~alIL~P  131 (1176)
T PRK09401         68 EFEKFFKKKTGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FG---LV-----MSLYLAK------KGKKSYIIFP  131 (1176)
T ss_pred             HHHHHHHHhcCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHH-HH---HH-----HHHHHHh------cCCeEEEEec
Confidence            444456554 78 6999999999999999999999999999996 44   44     2333322      3567899999


Q ss_pred             CcHHHHHHHHHHHHhcCCC
Q psy7691         129 NNGKQAKELIAVLTEASQP  147 (165)
Q Consensus       129 ~~~~~~~~i~~~l~~~~~~  147 (165)
                      + ++++.|+.+.++.....
T Consensus       132 T-reLa~Qi~~~l~~l~~~  149 (1176)
T PRK09401        132 T-RLLVEQVVEKLEKFGEK  149 (1176)
T ss_pred             c-HHHHHHHHHHHHHHhhh
Confidence            9 99999999888876543

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=98.63  E-value=5.7e-08  Score=84.19  Aligned_cols=92  Identities=18%  Similarity=0.250  Sum_probs=65.1

Q ss_pred             ccccccCCCcHHHHHHHHhCCCCCC------ch-HHHHHHH--------------HHHcCCCeeeecccCCcccceeeec
Q psy7691          39 TQELTEGCFPNAVLQHLKGQGFEEP------TA-IQAQGWP--------------IALSGRDMVGIAQTGSGKTLAVINF   97 (165)
Q Consensus        39 i~~f~~l~l~~~l~~~l~~~g~~~~------t~-~Q~~a~~--------------~~l~G~di~~~a~tgsGKt~~~~~~   97 (165)
                      |+.+.+...++.+...|...|+...      ++ ...+...              .+.+|.|+..+.        .|+||
T Consensus       230 IIF~~s~~~~e~la~~L~~~g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~GID~p~V~--------~VI~~  301 (470)
T TIGR00614       230 IIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVR--------FVIHY  301 (470)
T ss_pred             EEEECcHHHHHHHHHHHHhcCCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhccCCcccce--------EEEEe
Confidence            3334455778888888888877531      22 2222333              334445554444        89999


Q ss_pred             CCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHH
Q psy7691          98 DYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELI  138 (165)
Q Consensus        98 ~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~  138 (165)
                      ++|.+.+.|+||+||+||.|..|.+++++.+.+......+.
T Consensus       302 ~~P~s~~~y~Qr~GRaGR~G~~~~~~~~~~~~d~~~~~~~~  342 (470)
T TIGR00614       302 SLPKSMESYYQESGRAGRDGLPSECHLFYAPADINRLRRLL  342 (470)
T ss_pred             CCCCCHHHHHhhhcCcCCCCCCceEEEEechhHHHHHHHHH
Confidence            99999999999999999999999999999998765444443

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

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

Probab=98.63  E-value=6.8e-08  Score=90.44  Aligned_cols=75  Identities=19%  Similarity=0.173  Sum_probs=58.7

Q ss_pred             HHHHHHHHh-CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEEC
Q psy7691          49 NAVLQHLKG-QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFT  127 (165)
Q Consensus        49 ~~l~~~l~~-~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~  127 (165)
                      ..+...++. .||..++++|.++|+.++.|+|+++++|||+|||++|.   +|     .+.+.          ..+++++
T Consensus       446 ~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQ---LP-----AL~~~----------GiTLVIS  507 (1195)
T PLN03137        446 KKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQ---LP-----ALICP----------GITLVIS  507 (1195)
T ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHH---HH-----HHHcC----------CcEEEEe
Confidence            344445554 69999999999999999999999999999999999998   88     45432          2468888


Q ss_pred             CCcHHHHH-HHHHHHH
Q psy7691         128 PNNGKQAK-ELIAVLT  142 (165)
Q Consensus       128 p~~~~~~~-~i~~~l~  142 (165)
                      |+ ++++. |+.++..
T Consensus       508 PL-iSLmqDQV~~L~~  522 (1195)
T PLN03137        508 PL-VSLIQDQIMNLLQ  522 (1195)
T ss_pred             CH-HHHHHHHHHHHHh
Confidence            88 77765 5555543

>KOG0349|consensus

Probab=98.56  E-value=1.4e-08  Score=86.35  Aligned_cols=58  Identities=31%  Similarity=0.361  Sum_probs=56.0

Q ss_pred             cccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCC
Q psy7691          40 QELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYP  100 (165)
Q Consensus        40 ~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP  100 (165)
                      ..|+++++-+++..+..++.|.-||.+|.++||.++.|-|++..|.||||||.||+   +|
T Consensus         2 ~af~e~gv~pel~~a~~e~dw~lptdvqaeaiplilgggdvlmaaetgsgktgaf~---lp   59 (725)
T KOG0349|consen    2 TAFEEFGVLPELGMATDELDWTLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFC---LP   59 (725)
T ss_pred             cchHhhCcchHhhhhhhhhccccccccccccccEEecCCcEEEEeccCCCCcccee---hh
Confidence            46899999999999999999999999999999999999999999999999999999   99

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=98.52  E-value=1.3e-07  Score=84.42  Aligned_cols=97  Identities=20%  Similarity=0.282  Sum_probs=63.9

Q ss_pred             ccccccCCCcHHHHHHHHhCCCCC------Cch-HHHHHHHHHHcCC-Cee-eecccCCccc----ceeeecCCCCChhH
Q psy7691          39 TQELTEGCFPNAVLQHLKGQGFEE------PTA-IQAQGWPIALSGR-DMV-GIAQTGSGKT----LAVINFDYPNSSED  105 (165)
Q Consensus        39 i~~f~~l~l~~~l~~~l~~~g~~~------~t~-~Q~~a~~~~l~G~-di~-~~a~tgsGKt----~~~~~~~lP~~~~~  105 (165)
                      |+.+.+-.-++.+.+.|.+.|+..      .++ ...+....+..|. +++ ++..-|.|=.    -.|+|||+|.+.++
T Consensus       240 IIFc~tr~~~e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GIDip~V~~VI~~d~P~s~~~  319 (607)
T PRK11057        240 IIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIES  319 (607)
T ss_pred             EEEECcHHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccCCCCCcCEEEEeCCCCCHHH
Confidence            333344467778888888877643      122 2233334444443 322 2222234421    27999999999999


Q ss_pred             HHHhhccCCCCCCCCceEEEECCCcHHHHH
Q psy7691         106 YIHRIGRTGRCASSGTAYTFFTPNNGKQAK  135 (165)
Q Consensus       106 ~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~  135 (165)
                      |+||+||+||.|..|.+++++.|.+.....
T Consensus       320 y~Qr~GRaGR~G~~~~~ill~~~~d~~~~~  349 (607)
T PRK11057        320 YYQETGRAGRDGLPAEAMLFYDPADMAWLR  349 (607)
T ss_pred             HHHHhhhccCCCCCceEEEEeCHHHHHHHH
Confidence            999999999999999999999998654433

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=98.50  E-value=2.4e-07  Score=86.21  Aligned_cols=85  Identities=16%  Similarity=0.109  Sum_probs=66.1

Q ss_pred             CcHHHHHHHHh-CCCCCCchHHHHHHHHHHcC------CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCC
Q psy7691          47 FPNAVLQHLKG-QGFEEPTAIQAQGWPIALSG------RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASS  119 (165)
Q Consensus        47 l~~~l~~~l~~-~g~~~~t~~Q~~a~~~~l~G------~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~  119 (165)
                      .+..+.+.+.+ .+|. ||++|..||+.++.+      +|.+++++||+|||.+++   +|     .++.+.       .
T Consensus       436 ~~~~~~~~~~~~~~f~-~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val---~a-----~l~al~-------~  499 (926)
T TIGR00580       436 PDLEWQQEFEDSFPFE-ETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAM---RA-----AFKAVL-------D  499 (926)
T ss_pred             CCHHHHHHHHHhCCCC-CCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHH---HH-----HHHHHH-------h
Confidence            34555555555 6995 999999999999875      799999999999999887   66     444442       2


Q ss_pred             CceEEEECCCcHHHHHHHHHHHHhcCCCC
Q psy7691         120 GTAYTFFTPNNGKQAKELIAVLTEASQPI  148 (165)
Q Consensus       120 g~~~~~~~p~~~~~~~~i~~~l~~~~~~~  148 (165)
                      |..+++++|+ +.++.|..+.+......+
T Consensus       500 g~qvlvLvPT-~~LA~Q~~~~f~~~~~~~  527 (926)
T TIGR00580       500 GKQVAVLVPT-TLLAQQHFETFKERFANF  527 (926)
T ss_pred             CCeEEEEeCc-HHHHHHHHHHHHHHhccC
Confidence            3578999999 899999988887755443

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.

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

Probab=98.49  E-value=1.2e-07  Score=86.40  Aligned_cols=69  Identities=17%  Similarity=0.237  Sum_probs=54.4

Q ss_pred             HHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEEC--CCcHHHHHHHHHHHHhcCC
Q psy7691          70 GWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFT--PNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus        70 a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~--p~~~~~~~~i~~~l~~~~~  146 (165)
                      |++.+.+|.|+..+.        +|+||++|.+.++|+||+||+||.|+.|.+++++.  |.+...+..+.+.++....
T Consensus       335 aTd~lerGIDI~~vd--------~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~~~~d~~~~~~~~~~~~~~~e  405 (742)
T TIGR03817       335 TTNALELGVDISGLD--------AVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARDDPLDTYLVHHPEALFDRPVE  405 (742)
T ss_pred             ECchHhccCCccccc--------EEEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCCChHHHHHHhCHHHHhcCCCc
Confidence            555666777777666        89999999999999999999999999999998886  4455556666666665433

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.

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=98.47  E-value=2.8e-07  Score=82.70  Aligned_cols=81  Identities=20%  Similarity=0.199  Sum_probs=63.8

Q ss_pred             HHHHHHHHhCCCCCCchHHHHHHHHHHcC------CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCce
Q psy7691          49 NAVLQHLKGQGFEEPTAIQAQGWPIALSG------RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTA  122 (165)
Q Consensus        49 ~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G------~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~  122 (165)
                      ..+.+.+...+| .+|+.|.+|++.++.+      ++.+++++||||||++++   +|     .++.+.       .|..
T Consensus       223 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~---l~-----il~~~~-------~g~q  286 (630)
T TIGR00643       223 ELLTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAA---LA-----MLAAIE-------AGYQ  286 (630)
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHH---HH-----HHHHHH-------cCCc
Confidence            344556777899 5999999999999877      367999999999999887   67     555442       3557


Q ss_pred             EEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         123 YTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       123 ~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      +++++|+ +.++.|+.+.+.....
T Consensus       287 vlilaPT-~~LA~Q~~~~~~~l~~  309 (630)
T TIGR00643       287 VALMAPT-EILAEQHYNSLRNLLA  309 (630)
T ss_pred             EEEECCH-HHHHHHHHHHHHHHhc
Confidence            8999999 8899998888776544

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=98.47  E-value=2.9e-07  Score=83.33  Aligned_cols=79  Identities=22%  Similarity=0.233  Sum_probs=62.9

Q ss_pred             HHHHHhCCCCCCchHHHHHHHHHHcC------CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEE
Q psy7691          52 LQHLKGQGFEEPTAIQAQGWPIALSG------RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTF  125 (165)
Q Consensus        52 ~~~l~~~g~~~~t~~Q~~a~~~~l~G------~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~  125 (165)
                      .+.+...+|. +|++|.+|++.+..+      +|.+++++||||||++++   +|     .++.+.       .|..+++
T Consensus       252 ~~~~~~l~f~-lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~---~~-----il~~~~-------~g~q~li  315 (681)
T PRK10917        252 KKFLASLPFE-LTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAA---LA-----ALAAIE-------AGYQAAL  315 (681)
T ss_pred             HHHHHhCCCC-CCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHH---HH-----HHHHHH-------cCCeEEE
Confidence            3345557895 999999999999887      489999999999999988   77     555552       3567899


Q ss_pred             ECCCcHHHHHHHHHHHHhcCCC
Q psy7691         126 FTPNNGKQAKELIAVLTEASQP  147 (165)
Q Consensus       126 ~~p~~~~~~~~i~~~l~~~~~~  147 (165)
                      ++|+ +.++.|+.+.+......
T Consensus       316 laPT-~~LA~Q~~~~l~~l~~~  336 (681)
T PRK10917        316 MAPT-EILAEQHYENLKKLLEP  336 (681)
T ss_pred             Eecc-HHHHHHHHHHHHHHHhh
Confidence            9999 88999888887765433

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

Probab=98.43  E-value=3.1e-07  Score=81.28  Aligned_cols=103  Identities=22%  Similarity=0.293  Sum_probs=72.7

Q ss_pred             CCC-ccccccCCCcHHHHHHHHhCCCCCCc------hHHHHHHH-HHHcCC-C-eeeecccCCc--ccc--eeeecCCCC
Q psy7691          36 PCP-TQELTEGCFPNAVLQHLKGQGFEEPT------AIQAQGWP-IALSGR-D-MVGIAQTGSG--KTL--AVINFDYPN  101 (165)
Q Consensus        36 p~~-i~~f~~l~l~~~l~~~l~~~g~~~~t------~~Q~~a~~-~~l~G~-d-i~~~a~tgsG--Kt~--~~~~~~lP~  101 (165)
                      ..+ |+.+.+-.-.+++.++|...|+....      ...++... .++.+. . ++++-..|.|  |..  .|+|||+|.
T Consensus       230 ~~~GIIYc~sRk~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfViH~~lP~  309 (590)
T COG0514         230 SKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPG  309 (590)
T ss_pred             CCCeEEEEeeHHhHHHHHHHHHHCCCceEEecCCCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCceEEEEecCCC
Confidence            344 66666778999999999999887632      22222222 244443 2 2233444555  332  489999999


Q ss_pred             ChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHH
Q psy7691         102 SSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELI  138 (165)
Q Consensus       102 ~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~  138 (165)
                      ++++|.|.+||+||+|....+++++.|.+......+.
T Consensus       310 s~EsYyQE~GRAGRDG~~a~aill~~~~D~~~~~~~i  346 (590)
T COG0514         310 SIESYYQETGRAGRDGLPAEAILLYSPEDIRWQRYLI  346 (590)
T ss_pred             CHHHHHHHHhhccCCCCcceEEEeeccccHHHHHHHH
Confidence            9999999999999999999999999999855444443

>PRK10689 transcription-repair coupling factor; Provisional

Probab=98.37  E-value=7.4e-07  Score=84.57  Aligned_cols=81  Identities=19%  Similarity=0.135  Sum_probs=62.4

Q ss_pred             HHHHHHHHhCCCCCCchHHHHHHHHHHcC------CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCce
Q psy7691          49 NAVLQHLKGQGFEEPTAIQAQGWPIALSG------RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTA  122 (165)
Q Consensus        49 ~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G------~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~  122 (165)
                      +...+...+..| .||++|.+||+.++.+      +|++++++||+|||..++   .+     ....+       ..|..
T Consensus       588 ~~~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val---~a-----a~~~~-------~~g~q  651 (1147)
T PRK10689        588 EQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAM---RA-----AFLAV-------ENHKQ  651 (1147)
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHH---HH-----HHHHH-------HcCCe
Confidence            344555677899 5999999999999887      899999999999998655   33     11112       13567


Q ss_pred             EEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         123 YTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       123 ~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      +++++|+ +.++.|+.+.+.....
T Consensus       652 vlvLvPT-~eLA~Q~~~~f~~~~~  674 (1147)
T PRK10689        652 VAVLVPT-TLLAQQHYDNFRDRFA  674 (1147)
T ss_pred             EEEEeCc-HHHHHHHHHHHHHhhc
Confidence            9999999 9999999888876443

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=98.30  E-value=8.8e-07  Score=78.81  Aligned_cols=97  Identities=21%  Similarity=0.274  Sum_probs=64.6

Q ss_pred             ccccccCCCcHHHHHHHHhCCCCC------Cch-HHHHHHHHHHcCC-Ceeee-cccCCccc----ceeeecCCCCChhH
Q psy7691          39 TQELTEGCFPNAVLQHLKGQGFEE------PTA-IQAQGWPIALSGR-DMVGI-AQTGSGKT----LAVINFDYPNSSED  105 (165)
Q Consensus        39 i~~f~~l~l~~~l~~~l~~~g~~~------~t~-~Q~~a~~~~l~G~-di~~~-a~tgsGKt----~~~~~~~lP~~~~~  105 (165)
                      |+.+.+...++.+.+.|...|+..      .+. ........+..|. +++++ ..-|.|-.    -.|+||++|.+.++
T Consensus       228 IIf~~sr~~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~a~~~GID~p~v~~VI~~~~p~s~~~  307 (591)
T TIGR01389       228 IIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLES  307 (591)
T ss_pred             EEEECcHHHHHHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEechhhccCcCCCCCEEEEcCCCCCHHH
Confidence            333344567888888888877643      222 2233334455553 43332 22234422    26899999999999


Q ss_pred             HHHhhccCCCCCCCCceEEEECCCcHHHHH
Q psy7691         106 YIHRIGRTGRCASSGTAYTFFTPNNGKQAK  135 (165)
Q Consensus       106 ~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~  135 (165)
                      |+|++||+||.|..+.+++++.+.+.....
T Consensus       308 y~Q~~GRaGR~G~~~~~il~~~~~d~~~~~  337 (591)
T TIGR01389       308 YYQEAGRAGRDGLPAEAILLYSPADIALLK  337 (591)
T ss_pred             HhhhhccccCCCCCceEEEecCHHHHHHHH
Confidence            999999999999999999998887654433

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=98.25  E-value=1.7e-06  Score=77.63  Aligned_cols=69  Identities=28%  Similarity=0.245  Sum_probs=57.3

Q ss_pred             CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHH
Q psy7691          58 QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL  137 (165)
Q Consensus        58 ~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i  137 (165)
                      .|.. |+++|..+++.++.|+  ++.+.||+|||+++.   +|     .+...       ..|..+.+++|+ +.++.|.
T Consensus       100 lg~~-p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~---lp-----~~~~a-------l~G~~v~VvTpt-reLA~qd  160 (656)
T PRK12898        100 LGQR-HFDVQLMGGLALLSGR--LAEMQTGEGKTLTAT---LP-----AGTAA-------LAGLPVHVITVN-DYLAERD  160 (656)
T ss_pred             hCCC-CChHHHHHHHHHhCCC--eeeeeCCCCcHHHHH---HH-----HHHHh-------hcCCeEEEEcCc-HHHHHHH
Confidence            4775 8999999999999998  899999999999999   88     34332       245689999999 8999888


Q ss_pred             HHHHHhcC
Q psy7691         138 IAVLTEAS  145 (165)
Q Consensus       138 ~~~l~~~~  145 (165)
                      .+.+....
T Consensus       161 ae~~~~l~  168 (656)
T PRK12898        161 AELMRPLY  168 (656)
T ss_pred             HHHHHHHH
Confidence            88887643

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=98.24  E-value=1.1e-06  Score=78.96  Aligned_cols=91  Identities=21%  Similarity=0.225  Sum_probs=64.1

Q ss_pred             CCccccc-cCCCcHHHHHHHHhCCCCCCc----hHHHH---------------HHHHHHcCCCee---eecccCCcccce
Q psy7691          37 CPTQELT-EGCFPNAVLQHLKGQGFEEPT----AIQAQ---------------GWPIALSGRDMV---GIAQTGSGKTLA   93 (165)
Q Consensus        37 ~~i~~f~-~l~l~~~l~~~l~~~g~~~~t----~~Q~~---------------a~~~~l~G~di~---~~a~tgsGKt~~   93 (165)
                      .|+..|. +..-++.+.+.|...|+....    -.|.+               |++.+.||.||.   .+..-|   -++
T Consensus       474 ~pvLIft~t~~~se~L~~~L~~~gi~~~~Lhg~~~~rE~~ii~~ag~~g~VlVATdmAgRGtDI~l~~~V~~~G---GLh  550 (656)
T PRK12898        474 RPVLVGTRSVAASERLSALLREAGLPHQVLNAKQDAEEAAIVARAGQRGRITVATNMAGRGTDIKLEPGVAARG---GLH  550 (656)
T ss_pred             CCEEEEeCcHHHHHHHHHHHHHCCCCEEEeeCCcHHHHHHHHHHcCCCCcEEEEccchhcccCcCCccchhhcC---CCE
Confidence            4555554 457788888889988886522    11222               344445555554   111101   148


Q ss_pred             eeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCc
Q psy7691          94 VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN  130 (165)
Q Consensus        94 ~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~  130 (165)
                      |+|||+|.+...|+||+||+||.|..|.++.|+++.+
T Consensus       551 VI~~d~P~s~r~y~hr~GRTGRqG~~G~s~~~is~eD  587 (656)
T PRK12898        551 VILTERHDSARIDRQLAGRCGRQGDPGSYEAILSLED  587 (656)
T ss_pred             EEEcCCCCCHHHHHHhcccccCCCCCeEEEEEechhH
Confidence            9999999999999999999999999999999999875

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=98.16  E-value=2.2e-06  Score=78.42  Aligned_cols=92  Identities=22%  Similarity=0.231  Sum_probs=64.5

Q ss_pred             CCCcccccc-CCCcHHHHHHHHhCCCCCCch----HHHH---------------HHHHHHcCCCee---eecccCCcccc
Q psy7691          36 PCPTQELTE-GCFPNAVLQHLKGQGFEEPTA----IQAQ---------------GWPIALSGRDMV---GIAQTGSGKTL   92 (165)
Q Consensus        36 p~~i~~f~~-l~l~~~l~~~l~~~g~~~~t~----~Q~~---------------a~~~~l~G~di~---~~a~tgsGKt~   92 (165)
                      ..|+..|.. ...++.+.+.|.+.|+..-.-    .|.+               |++.+.||.|+.   .+..-|   -+
T Consensus       428 ~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L~~~~~~~e~~~i~~ag~~g~VlIATdmAgRG~DI~l~~~V~~~G---GL  504 (790)
T PRK09200        428 GRPVLIGTGSIEQSETFSKLLDEAGIPHNLLNAKNAAKEAQIIAEAGQKGAVTVATNMAGRGTDIKLGEGVHELG---GL  504 (790)
T ss_pred             CCCEEEEeCcHHHHHHHHHHHHHCCCCEEEecCCccHHHHHHHHHcCCCCeEEEEccchhcCcCCCccccccccc---Cc
Confidence            445556654 567788888898888854210    1222               344455666652   111111   14


Q ss_pred             eeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCc
Q psy7691          93 AVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN  130 (165)
Q Consensus        93 ~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~  130 (165)
                      +|+|||+|.+...|+||+||+||.|..|.+..++++.+
T Consensus       505 ~VI~~d~p~s~r~y~qr~GRtGR~G~~G~s~~~is~eD  542 (790)
T PRK09200        505 AVIGTERMESRRVDLQLRGRSGRQGDPGSSQFFISLED  542 (790)
T ss_pred             EEEeccCCCCHHHHHHhhccccCCCCCeeEEEEEcchH
Confidence            89999999999999999999999999999999999874

>PHA02558 uvsW UvsW helicase; Provisional

Probab=98.01  E-value=2.8e-05  Score=68.14  Aligned_cols=70  Identities=16%  Similarity=0.081  Sum_probs=52.3

Q ss_pred             CCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHH
Q psy7691          60 FEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIA  139 (165)
Q Consensus        60 ~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~  139 (165)
                      ...|++.|.+|++.++.+.+.+++++||+|||+...          .+.+.-...    ....+++++|+ ++++.|..+
T Consensus       112 ~~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~----------~l~~~~~~~----~~~~vLilvpt-~eL~~Q~~~  176 (501)
T PHA02558        112 KIEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQY----------LLSRYYLEN----YEGKVLIIVPT-TSLVTQMID  176 (501)
T ss_pred             cCCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHH----------HHHHHHHhc----CCCeEEEEECc-HHHHHHHHH
Confidence            346999999999999999999999999999998543          121110111    12268888898 899999988


Q ss_pred             HHHhc
Q psy7691         140 VLTEA  144 (165)
Q Consensus       140 ~l~~~  144 (165)
                      .+..-
T Consensus       177 ~l~~~  181 (501)
T PHA02558        177 DFVDY  181 (501)
T ss_pred             HHHHh
Confidence            88764

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=97.96  E-value=1.2e-05  Score=75.07  Aligned_cols=108  Identities=17%  Similarity=0.231  Sum_probs=70.4

Q ss_pred             CCCcccccc-CCCcHHHHHHHH-hCCCCC------CchHHH-HHHHHHHc---CCCeeeecccC-Ccccc----eeeecC
Q psy7691          36 PCPTQELTE-GCFPNAVLQHLK-GQGFEE------PTAIQA-QGWPIALS---GRDMVGIAQTG-SGKTL----AVINFD   98 (165)
Q Consensus        36 p~~i~~f~~-l~l~~~l~~~l~-~~g~~~------~t~~Q~-~a~~~~l~---G~di~~~a~tg-sGKt~----~~~~~~   98 (165)
                      ++.++.|.+ ......+.+.|. ..||..      .+..++ +++..+..   +..+++++.-| .|-.+    +++|||
T Consensus       493 ~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~~~F~~~~~~~~VLIsTdvgseGlNlq~a~~VInfD  572 (956)
T PRK04914        493 SEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLLCSEIGSEGRNFQFASHLVLFD  572 (956)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHHHHHhcCCCCccEEEechhhccCCCcccccEEEEec
Confidence            334555554 578888888884 557754      223333 34445544   23455444333 34322    789999


Q ss_pred             CCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHh
Q psy7691          99 YPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTE  143 (165)
Q Consensus        99 lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~  143 (165)
                      +|.+++.|.||+||++|.|.++.+.+++...+...-..+.+++..
T Consensus       573 lP~nP~~~eQRIGR~~RiGQ~~~V~i~~~~~~~t~~e~i~~~~~~  617 (956)
T PRK04914        573 LPFNPDLLEQRIGRLDRIGQKHDIQIHVPYLEGTAQERLFRWYHE  617 (956)
T ss_pred             CCCCHHHHHHHhcccccCCCCceEEEEEccCCCCHHHHHHHHHhh
Confidence            999999999999999999999887666665554445556655555

>KOG0337|consensus

Probab=97.90  E-value=3.7e-06  Score=71.45  Aligned_cols=102  Identities=24%  Similarity=0.310  Sum_probs=71.9

Q ss_pred             CCccccccC-CCcHHHHHHHHhCCCCCCc----hHHHH-----------------HHHHHHcCCCeeeecccCCccccee
Q psy7691          37 CPTQELTEG-CFPNAVLQHLKGQGFEEPT----AIQAQ-----------------GWPIALSGRDMVGIAQTGSGKTLAV   94 (165)
Q Consensus        37 ~~i~~f~~l-~l~~~l~~~l~~~g~~~~t----~~Q~~-----------------a~~~~l~G~di~~~a~tgsGKt~~~   94 (165)
                      +....|... .=.+.+..-+...|+..-.    --|..                 .++.+.+|.|++.-+        .+
T Consensus       262 ~~t~vf~~tk~hve~~~~ll~~~g~~~s~iysslD~~aRk~~~~~F~~~k~~~lvvTdvaaRG~diplld--------nv  333 (529)
T KOG0337|consen  262 KQTIVFVATKHHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRDFRGRKTSILVVTDVAARGLDIPLLD--------NV  333 (529)
T ss_pred             cceeEEecccchHHHHHHHHHhcCCCccccccccChHhhhhccccccCCccceEEEehhhhccCCCcccc--------cc
Confidence            344455544 4444555557777776421    01111                 244556677766666        79


Q ss_pred             eecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691          95 INFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus        95 ~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      +|||+|.+..-|+||+||..|+|+.|.++.++++++..-+.+|.-.+.....
T Consensus       334 inyd~p~~~klFvhRVgr~aragrtg~aYs~V~~~~~~yl~DL~lflgr~~~  385 (529)
T KOG0337|consen  334 INYDFPPDDKLFVHRVGRVARAGRTGRAYSLVASTDDPYLLDLQLFLGRPLI  385 (529)
T ss_pred             ccccCCCCCceEEEEecchhhccccceEEEEEecccchhhhhhhhhcCCcee
Confidence            9999999999999999999999999999999999987777777776665433

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=97.85  E-value=4.2e-05  Score=56.65  Aligned_cols=75  Identities=32%  Similarity=0.443  Sum_probs=53.7

Q ss_pred             hCCCCCCchHHHHHHHHHHcC-CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHH
Q psy7691          57 GQGFEEPTAIQAQGWPIALSG-RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAK  135 (165)
Q Consensus        57 ~~g~~~~t~~Q~~a~~~~l~G-~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~  135 (165)
                      ..++..+++.|.++++.++.+ ..++..+++|+|||..+.   .+     ..+...+.     ....+++++|+ ..++.
T Consensus         3 ~~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~---~~-----~~~~~~~~-----~~~~~l~~~p~-~~~~~   68 (201)
T smart00487        3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAAL---LP-----ALEALKRG-----KGKRVLVLVPT-RELAE   68 (201)
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHH---HH-----HHHHhccc-----CCCcEEEEeCC-HHHHH
Confidence            346778999999999999998 999999999999999665   33     23322221     13468888887 66666


Q ss_pred             HHHHHHHhcC
Q psy7691         136 ELIAVLTEAS  145 (165)
Q Consensus       136 ~i~~~l~~~~  145 (165)
                      ++.+.+....
T Consensus        69 ~~~~~~~~~~   78 (201)
T smart00487       69 QWAEELKKLG   78 (201)
T ss_pred             HHHHHHHHHh
Confidence            6666555443

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

Probab=97.85  E-value=5.2e-05  Score=67.00  Aligned_cols=89  Identities=27%  Similarity=0.317  Sum_probs=69.1

Q ss_pred             cccccCCCcHHHHHHHHhCCCCCCchHHHHHHHH-HHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCC
Q psy7691          40 QELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPI-ALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCAS  118 (165)
Q Consensus        40 ~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~-~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~  118 (165)
                      ...+++.+|+.+.+-|+..|+....|+|..|+.. ++.|.|.+++++|+||||+.-=...+|        +.      -.
T Consensus       194 ~~vdeLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~--------~~------l~  259 (830)
T COG1202         194 VPVDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIP--------RL------LS  259 (830)
T ss_pred             ccccccCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcH--------HH------Hh
Confidence            4667899999999999999999999999999887 479999999999999999832211122        22      23


Q ss_pred             CCceEEEECCCcHHHHHHHHHHHHh
Q psy7691         119 SGTAYTFFTPNNGKQAKELIAVLTE  143 (165)
Q Consensus       119 ~g~~~~~~~p~~~~~~~~i~~~l~~  143 (165)
                      .|.-.+++.|. ..+++|-.+-+..
T Consensus       260 ~g~KmlfLvPL-VALANQKy~dF~~  283 (830)
T COG1202         260 GGKKMLFLVPL-VALANQKYEDFKE  283 (830)
T ss_pred             CCCeEEEEehh-HHhhcchHHHHHH
Confidence            45578999998 8888776554443

>PHA02653 RNA helicase NPH-II; Provisional

Probab=97.80  E-value=5.9e-05  Score=68.33  Aligned_cols=72  Identities=17%  Similarity=0.123  Sum_probs=50.6

Q ss_pred             hHHHHHHHHHHcCCCeeeecccCCcccceee------ecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHH
Q psy7691          65 AIQAQGWPIALSGRDMVGIAQTGSGKTLAVI------NFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELI  138 (165)
Q Consensus        65 ~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~------~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~  138 (165)
                      .+|.+.++.++.|+|++++|+||||||.++-      +|-+|     .++.+.+-. ....+..++++.|+ ++++.|+.
T Consensus       167 ~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~-----~l~~l~~~~-~~~~~~~ilvt~Pr-reLa~qi~  239 (675)
T PHA02653        167 DVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFG-----GFDNLDKID-PNFIERPIVLSLPR-VALVRLHS  239 (675)
T ss_pred             HHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccc-----hhhhhhhcc-cccCCcEEEEECcH-HHHHHHHH
Confidence            3899999999999999999999999999731      12234     233322110 01234478888888 99999988


Q ss_pred             HHHHh
Q psy7691         139 AVLTE  143 (165)
Q Consensus       139 ~~l~~  143 (165)
                      ..+.+
T Consensus       240 ~~i~~  244 (675)
T PHA02653        240 ITLLK  244 (675)
T ss_pred             HHHHH
Confidence            77754

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=97.76  E-value=6.5e-05  Score=68.36  Aligned_cols=94  Identities=21%  Similarity=0.155  Sum_probs=64.4

Q ss_pred             CCCcccccc-CCCcHHHHHHHHhCCCCCCc--hHHH--H---------------HHHHHHcCCCeeeecccCCcccceee
Q psy7691          36 PCPTQELTE-GCFPNAVLQHLKGQGFEEPT--AIQA--Q---------------GWPIALSGRDMVGIAQTGSGKTLAVI   95 (165)
Q Consensus        36 p~~i~~f~~-l~l~~~l~~~l~~~g~~~~t--~~Q~--~---------------a~~~~l~G~di~~~a~tgsGKt~~~~   95 (165)
                      ..|+..|.. ..-.+.+.+.|.+.|+..-.  .-|.  +               |++.+.||.||..-.-...| -++|+
T Consensus       405 grpvLV~t~si~~se~ls~~L~~~gi~~~~Lna~q~~rEa~ii~~ag~~g~VtIATnmAgRGtDI~l~~V~~~G-Gl~VI  483 (745)
T TIGR00963       405 GQPVLVGTTSVEKSELLSNLLKERGIPHNVLNAKNHEREAEIIAQAGRKGAVTIATNMAGRGTDIKLEEVKELG-GLYVI  483 (745)
T ss_pred             CCCEEEEeCcHHHHHHHHHHHHHcCCCeEEeeCChHHHHHHHHHhcCCCceEEEEeccccCCcCCCccchhhcC-CcEEE
Confidence            456666654 46677888888888875521  1122  1               33444455555430000000 24899


Q ss_pred             ecCCCCChhHHHHhhccCCCCCCCCceEEEECCCc
Q psy7691          96 NFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN  130 (165)
Q Consensus        96 ~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~  130 (165)
                      +|++|.+...|.|+.||+||.|..|.+..+++..+
T Consensus       484 ~t~~p~s~ri~~q~~GRtGRqG~~G~s~~~ls~eD  518 (745)
T TIGR00963       484 GTERHESRRIDNQLRGRSGRQGDPGSSRFFLSLED  518 (745)
T ss_pred             ecCCCCcHHHHHHHhccccCCCCCcceEEEEeccH
Confidence            99999999999999999999999999999999885

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.

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=97.75  E-value=6.5e-05  Score=67.90  Aligned_cols=101  Identities=17%  Similarity=0.212  Sum_probs=66.5

Q ss_pred             ccCCCcHHHHHHHHhCCCCC------Cch-HHHHHHH--------------HHHcCCCeeeecccCCcccceeeecCC--
Q psy7691          43 TEGCFPNAVLQHLKGQGFEE------PTA-IQAQGWP--------------IALSGRDMVGIAQTGSGKTLAVINFDY--   99 (165)
Q Consensus        43 ~~l~l~~~l~~~l~~~g~~~------~t~-~Q~~a~~--------------~~l~G~di~~~a~tgsGKt~~~~~~~l--   99 (165)
                      .+....+.+.+.|.+.|+..      ... ....++.              .+.+|.|+..+.        .++++|.  
T Consensus       454 ~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~rGfdlp~v~--------lVii~d~ei  525 (652)
T PRK05298        454 LTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVS--------LVAILDADK  525 (652)
T ss_pred             CCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHhCCccccCCc--------EEEEeCCcc
Confidence            34567778888888887732      111 1122222              333444444443        5777775  


Q ss_pred             ---CCChhHHHHhhccCCCCCCCCceEEEECCC---------cHHHHHHHHHHHHhcCCCCChHH
Q psy7691         100 ---PNSSEDYIHRIGRTGRCASSGTAYTFFTPN---------NGKQAKELIAVLTEASQPIPPQL  152 (165)
Q Consensus       100 ---P~~~~~~i~r~gr~~r~~~~g~~~~~~~p~---------~~~~~~~i~~~l~~~~~~~p~~~  152 (165)
                         |.+..+|+||+||+||. ..|.+++++...         +.....++...++....-+|...
T Consensus       526 fG~~~~~~~yiqr~GR~gR~-~~G~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~  589 (652)
T PRK05298        526 EGFLRSERSLIQTIGRAARN-VNGKVILYADKITDSMQKAIDETERRREIQIAYNEEHGITPKTI  589 (652)
T ss_pred             cccCCCHHHHHHHhccccCC-CCCEEEEEecCCCHHHHHHHHHHHHHHHHHHHhhhccCCCChhH
Confidence               77899999999999996 789999999843         34556677777777777777554

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=97.71  E-value=5.1e-05  Score=69.66  Aligned_cols=68  Identities=28%  Similarity=0.406  Sum_probs=54.7

Q ss_pred             CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHH
Q psy7691          58 QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL  137 (165)
Q Consensus        58 ~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i  137 (165)
                      .|.. |+++|..+.+.++.|.  ++.+.||+|||+++.   +|.    |++..        .|..+.+++|+ +.+|.|.
T Consensus        75 ~g~~-p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~---lp~----~l~al--------~G~~v~VvTpt-~~LA~qd  135 (790)
T PRK09200         75 LGMR-PYDVQLIGALVLHEGN--IAEMQTGEGKTLTAT---MPL----YLNAL--------EGKGVHLITVN-DYLAKRD  135 (790)
T ss_pred             hCCC-CchHHHHhHHHHcCCc--eeeecCCCcchHHHH---HHH----HHHHH--------cCCCeEEEeCC-HHHHHHH
Confidence            4774 9999999999999987  899999999999998   882    33333        35578999999 8888887


Q ss_pred             HHHHHhc
Q psy7691         138 IAVLTEA  144 (165)
Q Consensus       138 ~~~l~~~  144 (165)
                      .+.+...
T Consensus       136 ~e~~~~l  142 (790)
T PRK09200        136 AEEMGQV  142 (790)
T ss_pred             HHHHHHH
Confidence            7776654

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

Probab=97.70  E-value=8.2e-05  Score=69.07  Aligned_cols=75  Identities=17%  Similarity=0.131  Sum_probs=55.5

Q ss_pred             CcHHHHHHHHhCCCCCCchHHHHHHH----HHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCce
Q psy7691          47 FPNAVLQHLKGQGFEEPTAIQAQGWP----IALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTA  122 (165)
Q Consensus        47 l~~~l~~~l~~~g~~~~t~~Q~~a~~----~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~  122 (165)
                      +.+...+.+...||. +.+.|.+.+.    .+..|.++++.|+||+|||++|+   +|     .+...-       .+..
T Consensus       231 ~~~~~~~~~~~~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayL---lp-----~~~~~~-------~~~~  294 (850)
T TIGR01407       231 LSSLFSKNIDRLGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYL---LP-----ALYYAI-------TEKP  294 (850)
T ss_pred             ccHHHHHhhhhcCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHH---HH-----HHHHhc-------CCCe
Confidence            344677778888997 7899997555    45678899999999999999999   88     444331       1236


Q ss_pred             EEEECCCcHHHHHHHH
Q psy7691         123 YTFFTPNNGKQAKELI  138 (165)
Q Consensus       123 ~~~~~p~~~~~~~~i~  138 (165)
                      +++.+|+ +.+..|+.
T Consensus       295 vvi~t~t-~~Lq~Ql~  309 (850)
T TIGR01407       295 VVISTNT-KVLQSQLL  309 (850)
T ss_pred             EEEEeCc-HHHHHHHH
Confidence            8888888 66666653

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.

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=97.69  E-value=7.5e-05  Score=69.54  Aligned_cols=108  Identities=17%  Similarity=0.190  Sum_probs=71.5

Q ss_pred             CCCcccccc-CCCcHHHHHHHHhCCCCCC--chHH--HH---------------HHHHHHcCCCeee---ecccCCcccc
Q psy7691          36 PCPTQELTE-GCFPNAVLQHLKGQGFEEP--TAIQ--AQ---------------GWPIALSGRDMVG---IAQTGSGKTL   92 (165)
Q Consensus        36 p~~i~~f~~-l~l~~~l~~~l~~~g~~~~--t~~Q--~~---------------a~~~~l~G~di~~---~a~tgsGKt~   92 (165)
                      ..|+..|.. ...++.+.+.|...|+..-  ..-|  .+               |++.+.||.||..   +..-|   -+
T Consensus       598 grpVLIft~Sve~sE~Ls~~L~~~gI~h~vLnakq~~REa~Iia~AG~~g~VtIATNMAGRGtDIkl~~~V~~vG---GL  674 (1025)
T PRK12900        598 GQPVLVGTASVEVSETLSRMLRAKRIAHNVLNAKQHDREAEIVAEAGQKGAVTIATNMAGRGTDIKLGEGVRELG---GL  674 (1025)
T ss_pred             CCCEEEEeCcHHHHHHHHHHHHHcCCCceeecCCHHHhHHHHHHhcCCCCeEEEeccCcCCCCCcCCccchhhhC---Cc
Confidence            456666654 4677888888888887642  1112  22               3444455666541   11000   24


Q ss_pred             eeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHH----HHHHHHHHHhcCC
Q psy7691          93 AVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQ----AKELIAVLTEASQ  146 (165)
Q Consensus        93 ~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~----~~~i~~~l~~~~~  146 (165)
                      ++++++.|.+...|.|+.||+||.|..|.+..|++..+.-+    ...+.+++...+.
T Consensus       675 ~VIgterhes~Rid~Ql~GRtGRqGdpGsS~ffvSleD~Lmr~f~~~~i~~~~~~~~~  732 (1025)
T PRK12900        675 FILGSERHESRRIDRQLRGRAGRQGDPGESVFYVSLEDELMRLFGSDRVISVMDRLGH  732 (1025)
T ss_pred             eeeCCCCCchHHHHHHHhhhhhcCCCCcceEEEechhHHHHHhhCcHHHHHHHHHcCC
Confidence            78999999999999999999999999999999999885322    1256666665544

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=97.69  E-value=5e-05  Score=69.34  Aligned_cols=107  Identities=18%  Similarity=0.162  Sum_probs=68.6

Q ss_pred             CCCcccccc-CCCcHHHHHHHHhCCCCCCc----hHHHH---------------HHHHHHcCCCee-eecccCCccccee
Q psy7691          36 PCPTQELTE-GCFPNAVLQHLKGQGFEEPT----AIQAQ---------------GWPIALSGRDMV-GIAQTGSGKTLAV   94 (165)
Q Consensus        36 p~~i~~f~~-l~l~~~l~~~l~~~g~~~~t----~~Q~~---------------a~~~~l~G~di~-~~a~tgsGKt~~~   94 (165)
                      ..|+..|.. ....+.+.+.|.+.|+..-.    -.|.+               |++.+.||.|+. +-.-...|---.+
T Consensus       424 ~~pvLIft~s~~~se~ls~~L~~~gi~~~~L~a~~~~~E~~ii~~ag~~g~VlIATdmAgRGtDI~l~~~v~~~GGL~vI  503 (762)
T TIGR03714       424 GQPVLLITGSVEMSEIYSELLLREGIPHNLLNAQNAAKEAQIIAEAGQKGAVTVATSMAGRGTDIKLGKGVAELGGLAVI  503 (762)
T ss_pred             CCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCChHHHHHHHHHcCCCCeEEEEccccccccCCCCCccccccCCeEEE
Confidence            345555544 46777788888888875421    12322               344555666664 1111112233368


Q ss_pred             eecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHH-----HHHHHHHHhc
Q psy7691          95 INFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQA-----KELIAVLTEA  144 (165)
Q Consensus        95 ~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~-----~~i~~~l~~~  144 (165)
                      ++|++|...++ +||.||+||.|..|.+..++++.+ .++     ..+.+++...
T Consensus       504 it~~~ps~rid-~qr~GRtGRqG~~G~s~~~is~eD-~l~~~~~~~~~~~~~~~~  556 (762)
T TIGR03714       504 GTERMENSRVD-LQLRGRSGRQGDPGSSQFFVSLED-DLIKRWSPSWLKKYYKKY  556 (762)
T ss_pred             EecCCCCcHHH-HHhhhcccCCCCceeEEEEEccch-hhhhhcchHHHHHHHHHc
Confidence            89999988777 999999999999999999999875 332     3555555543

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.

>PRK05580 primosome assembly protein PriA; Validated

Probab=97.66  E-value=0.00014  Score=66.10  Aligned_cols=67  Identities=16%  Similarity=0.135  Sum_probs=51.3

Q ss_pred             CCchHHHHHHHHHHcC---CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALSG---RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELI  138 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G---~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~  138 (165)
                      .+|+.|.++++.+..+   .+++..++||||||.+++   .+     ..+.+.       .|..++++.|+ .+++.|+.
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l---~~-----i~~~l~-------~g~~vLvLvPt-~~L~~Q~~  207 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYL---QA-----IAEVLA-------QGKQALVLVPE-IALTPQML  207 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHH---HH-----HHHHHH-------cCCeEEEEeCc-HHHHHHHH
Confidence            3789999999999874   789999999999999876   33     222221       23468889998 88888888


Q ss_pred             HHHHhc
Q psy7691         139 AVLTEA  144 (165)
Q Consensus       139 ~~l~~~  144 (165)
                      +.+...
T Consensus       208 ~~l~~~  213 (679)
T PRK05580        208 ARFRAR  213 (679)
T ss_pred             HHHHHH
Confidence            887653

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=97.62  E-value=0.00017  Score=70.03  Aligned_cols=55  Identities=27%  Similarity=0.356  Sum_probs=44.0

Q ss_pred             HHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHH
Q psy7691          69 QGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGK  132 (165)
Q Consensus        69 ~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~  132 (165)
                      .|++.+..|.|+-.+.        .||||+.|.++.+|+||+||+||. ..+.+..++.|.++.
T Consensus       332 VATssLELGIDIg~VD--------lVIq~gsP~sVas~LQRiGRAGR~-~gg~s~gli~p~~r~  386 (1490)
T PRK09751        332 VATSSLELGIDMGAVD--------LVIQVATPLSVASGLQRIGRAGHQ-VGGVSKGLFFPRTRR  386 (1490)
T ss_pred             EeCcHHHccCCcccCC--------EEEEeCCCCCHHHHHHHhCCCCCC-CCCccEEEEEeCcHH
Confidence            3666677788877666        899999999999999999999997 456666667777654

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=97.62  E-value=7e-05  Score=68.14  Aligned_cols=72  Identities=24%  Similarity=0.343  Sum_probs=57.4

Q ss_pred             CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHH
Q psy7691          58 QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL  137 (165)
Q Consensus        58 ~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i  137 (165)
                      .|.. |+++|..+.+.++.|.  ++.++||+|||+++.   +|.    |++.+.        |..+.+++|+ +.+|.|.
T Consensus        53 lg~~-p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~---lpa----~l~aL~--------G~~V~VvTpt-~~LA~qd  113 (745)
T TIGR00963        53 LGMR-PFDVQLIGGIALHKGK--IAEMKTGEGKTLTAT---LPA----YLNALT--------GKGVHVVTVN-DYLAQRD  113 (745)
T ss_pred             hCCC-ccchHHhhhhhhcCCc--eeeecCCCccHHHHH---HHH----HHHHHh--------CCCEEEEcCC-HHHHHHH
Confidence            4775 8999999998888886  899999999999988   883    455552        2247899999 8899988


Q ss_pred             HHHHHhcCCCC
Q psy7691         138 IAVLTEASQPI  148 (165)
Q Consensus       138 ~~~l~~~~~~~  148 (165)
                      .+.+......+
T Consensus       114 ae~~~~l~~~L  124 (745)
T TIGR00963       114 AEWMGQVYRFL  124 (745)
T ss_pred             HHHHHHHhccC
Confidence            88887765543

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.

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=97.53  E-value=0.00019  Score=64.87  Aligned_cols=86  Identities=17%  Similarity=0.251  Sum_probs=56.4

Q ss_pred             ccCCCcHHHHHHHHhCCCCCCc------hH-HHHHHH--------------HHHcCCCeeeecccCCcccceeeecC---
Q psy7691          43 TEGCFPNAVLQHLKGQGFEEPT------AI-QAQGWP--------------IALSGRDMVGIAQTGSGKTLAVINFD---   98 (165)
Q Consensus        43 ~~l~l~~~l~~~l~~~g~~~~t------~~-Q~~a~~--------------~~l~G~di~~~a~tgsGKt~~~~~~~---   98 (165)
                      .+....+.+.+.|.+.|+....      .. ....+.              .+.+|.|+..+.        +++++|   
T Consensus       450 ~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~L~rGfDiP~v~--------lVvi~Dadi  521 (655)
T TIGR00631       450 LTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVS--------LVAILDADK  521 (655)
T ss_pred             CCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcChhcCCeeeCCCc--------EEEEeCccc
Confidence            3456778888888888874311      11 112222              233444444333        677888   


Q ss_pred             --CCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHH
Q psy7691          99 --YPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL  137 (165)
Q Consensus        99 --lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i  137 (165)
                        .|.+..+|+||+||+||. ..|.+++++...+..+...|
T Consensus       522 fG~p~~~~~~iqriGRagR~-~~G~vi~~~~~~~~~~~~ai  561 (655)
T TIGR00631       522 EGFLRSERSLIQTIGRAARN-VNGKVIMYADKITDSMQKAI  561 (655)
T ss_pred             ccCCCCHHHHHHHhcCCCCC-CCCEEEEEEcCCCHHHHHHH
Confidence              799999999999999998 68999988887664444333

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

>COG1204 Superfamily II helicase [General function prediction only]

Probab=97.53  E-value=0.00011  Score=67.52  Aligned_cols=83  Identities=27%  Similarity=0.323  Sum_probs=64.0

Q ss_pred             CCCcHHHHHHHHhCCCCCCchHHHHHHHHH-HcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceE
Q psy7691          45 GCFPNAVLQHLKGQGFEEPTAIQAQGWPIA-LSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAY  123 (165)
Q Consensus        45 l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~-l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~  123 (165)
                      +.+++.+...+...|+....+-|+.++... ..|.|+++++|||||||+...   |-     .++.+.+.      +..+
T Consensus        14 ~~~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~---la-----i~~~l~~~------~~k~   79 (766)
T COG1204          14 VKLDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIAL---LA-----ILSTLLEG------GGKV   79 (766)
T ss_pred             ccccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHH---HH-----HHHHHHhc------CCcE
Confidence            357888888888889988888887777665 455999999999999999655   33     45555442      4568


Q ss_pred             EEECCCcHHHHHHHHHHHH
Q psy7691         124 TFFTPNNGKQAKELIAVLT  142 (165)
Q Consensus       124 ~~~~p~~~~~~~~i~~~l~  142 (165)
                      ++++|. +.++.+..+-+.
T Consensus        80 vYivPl-kALa~Ek~~~~~   97 (766)
T COG1204          80 VYIVPL-KALAEEKYEEFS   97 (766)
T ss_pred             EEEeCh-HHHHHHHHHHhh
Confidence            899999 888888887776

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=97.46  E-value=0.00015  Score=60.98  Aligned_cols=55  Identities=24%  Similarity=0.296  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHcCCC--eeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHH
Q psy7691          66 IQAQGWPIALSGRD--MVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIA  139 (165)
Q Consensus        66 ~Q~~a~~~~l~G~d--i~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~  139 (165)
                      .|.++++.+..+.+  ++++|+||||||.+++   +|     .++.          +...+++.|+ +.++.+..+
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~---~~-----~l~~----------~~~~~~~~P~-~aL~~~~~~   57 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWL---TP-----LLHG----------ENDTIALYPT-NALIEDQTE   57 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHH---HH-----HHHc----------CCCEEEEeCh-HHHHHHHHH
Confidence            48999999999975  6789999999999988   77     4431          1135788888 555554333

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.

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=97.35  E-value=0.00017  Score=60.04  Aligned_cols=52  Identities=23%  Similarity=0.173  Sum_probs=39.5

Q ss_pred             CeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691          79 DMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus        79 di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      |++++++||||||++++   +|     .++.+.+     ..+..++++.|+ +.++.|+.+.+...
T Consensus         1 ~vvi~apTGsGKT~~~~---~~-----~l~~~~~-----~~~~~ii~v~P~-~~L~~q~~~~l~~~   52 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAAL---LW-----ALHSIKS-----QKADRVIIALPT-RATINAMYRRAKEL   52 (358)
T ss_pred             CEEEEeCCCCCHHHHHH---HH-----HHHHHhh-----CCCCeEEEEeeh-HHHHHHHHHHHHHH
Confidence            68899999999999988   66     5555432     233467888898 88888888777665

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.

>KOG0349|consensus

Probab=97.35  E-value=9.8e-05  Score=63.43  Aligned_cols=103  Identities=17%  Similarity=0.273  Sum_probs=67.2

Q ss_pred             HHHHHHhhcCcEEecCCCCCCcccc-ccCCCcHHHHHHHHhCCCCC---------CchHHH---------------HHHH
Q psy7691          18 EVEAFRQKKEITVKGNNIPCPTQEL-TEGCFPNAVLQHLKGQGFEE---------PTAIQA---------------QGWP   72 (165)
Q Consensus        18 ~~~~~~~~~~i~~~~~~~p~~i~~f-~~l~l~~~l~~~l~~~g~~~---------~t~~Q~---------------~a~~   72 (165)
                      .+..++....+.-.....-..-+.| .+..-|+.+-+.+.+.|-..         ..|..+               .|++
T Consensus       487 a~kilkgEy~v~ai~~h~mdkaiifcrtk~dcDnLer~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~dvkflictd  566 (725)
T KOG0349|consen  487 ATKILKGEYGVVAIRRHAMDKAIIFCRTKQDCDNLERMMNQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTD  566 (725)
T ss_pred             hhHHhcCchhhhhhhhhccCceEEEEeccccchHHHHHHHHcCCccceeEEEecCCChhHHHHHHHhhhhcCeEEEEEeh
Confidence            3444444444333332222233344 44566777878777765422         112111               2677


Q ss_pred             HHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECC
Q psy7691          73 IALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTP  128 (165)
Q Consensus        73 ~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p  128 (165)
                      .+.+|.||-+.-        .+||.-||.+..+|+|||||-||+.+-|.+++++..
T Consensus       567 vaargldi~g~p--------~~invtlpd~k~nyvhrigrvgraermglaislvat  614 (725)
T KOG0349|consen  567 VAARGLDITGLP--------FMINVTLPDDKTNYVHRIGRVGRAERMGLAISLVAT  614 (725)
T ss_pred             hhhccccccCCc--------eEEEEecCcccchhhhhhhccchhhhcceeEEEeec
Confidence            778888876655        789999999999999999999999999999988763

>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=97.34  E-value=0.00035  Score=51.77  Aligned_cols=61  Identities=21%  Similarity=0.253  Sum_probs=47.6

Q ss_pred             CchHHHHHHHHHHc-------CCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHH
Q psy7691          63 PTAIQAQGWPIALS-------GRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAK  135 (165)
Q Consensus        63 ~t~~Q~~a~~~~l~-------G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~  135 (165)
                      +.+.|.+|+..+..       ...++..++||+|||...+.         ++.++.+         .+++++|+ ..++.
T Consensus         4 lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~---------~~~~l~~---------~~l~~~p~-~~l~~   64 (184)
T PF04851_consen    4 LRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALA---------LILELAR---------KVLIVAPN-ISLLE   64 (184)
T ss_dssp             E-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHH---------HHHHHHC---------EEEEEESS-HHHHH
T ss_pred             CCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhh---------hhhcccc---------ceeEecCH-HHHHH
Confidence            67889999988873       68899999999999997651         4555654         67888888 78888


Q ss_pred             HHHHHHH
Q psy7691         136 ELIAVLT  142 (165)
Q Consensus       136 ~i~~~l~  142 (165)
                      |..+.+.
T Consensus        65 Q~~~~~~   71 (184)
T PF04851_consen   65 QWYDEFD   71 (184)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8888773

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 ....

>KOG0351|consensus

Probab=97.32  E-value=0.0009  Score=62.63  Aligned_cols=94  Identities=19%  Similarity=0.150  Sum_probs=64.8

Q ss_pred             ccccccCCCcHHHHHHHHhCCCCC------CchHHHHHHHH-HHcCCCeeeec--ccCCcc----cceeeecCCCCChhH
Q psy7691          39 TQELTEGCFPNAVLQHLKGQGFEE------PTAIQAQGWPI-ALSGRDMVGIA--QTGSGK----TLAVINFDYPNSSED  105 (165)
Q Consensus        39 i~~f~~l~l~~~l~~~l~~~g~~~------~t~~Q~~a~~~-~l~G~di~~~a--~tgsGK----t~~~~~~~lP~~~~~  105 (165)
                      |+..-....++.+...|.+.|...      +.+-+++.+.. ++++.=-+++|  ..|.|-    +-+|+||.+|.+.+.
T Consensus       489 IIYC~sr~~ce~vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~~w~~~~~~VivATVAFGMGIdK~DVR~ViH~~lPks~E~  568 (941)
T KOG0351|consen  489 IIYCLSRKECEQVSAVLRSLGKSAAFYHAGLPPKERETVQKAWMSDKIRVIVATVAFGMGIDKPDVRFVIHYSLPKSFEG  568 (941)
T ss_pred             EEEeCCcchHHHHHHHHHHhchhhHhhhcCCCHHHHHHHHHHHhcCCCeEEEEEeeccCCCCCCceeEEEECCCchhHHH
Confidence            445556688999999998888543      33444443332 33443212222  233331    227899999999999


Q ss_pred             HHHhhccCCCCCCCCceEEEECCCcHH
Q psy7691         106 YIHRIGRTGRCASSGTAYTFFTPNNGK  132 (165)
Q Consensus       106 ~i~r~gr~~r~~~~g~~~~~~~p~~~~  132 (165)
                      |.|.+||+||+|....+++++.+.+..
T Consensus       569 YYQE~GRAGRDG~~s~C~l~y~~~D~~  595 (941)
T KOG0351|consen  569 YYQEAGRAGRDGLPSSCVLLYGYADIS  595 (941)
T ss_pred             HHHhccccCcCCCcceeEEecchhHHH
Confidence            999999999999999999999988543

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=97.28  E-value=0.00048  Score=56.38  Aligned_cols=72  Identities=15%  Similarity=0.191  Sum_probs=46.0

Q ss_pred             CchHHHH----HHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHH
Q psy7691          63 PTAIQAQ----GWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELI  138 (165)
Q Consensus        63 ~t~~Q~~----a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~  138 (165)
                      |.+.|.+    ....+..|.++++.||||+|||++++   +|.  ..|....+..    ..+..+.+.+++ ..+..+..
T Consensus         9 ~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L---~~a--l~~~~~~~~~----~~~~kvi~~t~T-~~~~~q~i   78 (289)
T smart00488        9 PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLL---CLT--LTWLRSFPER----IQKIKLIYLSRT-VSEIEKRL   78 (289)
T ss_pred             CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHH---HHH--HHHHHhCccc----ccccceeEEecc-HHHHHHHH
Confidence            5888887    45556788999999999999999999   772  1133222211    123467777776 44555554


Q ss_pred             HHHHhc
Q psy7691         139 AVLTEA  144 (165)
Q Consensus       139 ~~l~~~  144 (165)
                      ..++..
T Consensus        79 ~~l~~~   84 (289)
T smart00488       79 EELRKL   84 (289)
T ss_pred             HHHHhc
Confidence            444443

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=97.28  E-value=0.00048  Score=56.38  Aligned_cols=72  Identities=15%  Similarity=0.191  Sum_probs=46.0

Q ss_pred             CchHHHH----HHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHH
Q psy7691          63 PTAIQAQ----GWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELI  138 (165)
Q Consensus        63 ~t~~Q~~----a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~  138 (165)
                      |.+.|.+    ....+..|.++++.||||+|||++++   +|.  ..|....+..    ..+..+.+.+++ ..+..+..
T Consensus         9 ~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L---~~a--l~~~~~~~~~----~~~~kvi~~t~T-~~~~~q~i   78 (289)
T smart00489        9 PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLL---CLT--LTWLRSFPER----IQKIKLIYLSRT-VSEIEKRL   78 (289)
T ss_pred             CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHH---HHH--HHHHHhCccc----ccccceeEEecc-HHHHHHHH
Confidence            5888887    45556788999999999999999999   772  1133222211    123467777776 44555554


Q ss_pred             HHHHhc
Q psy7691         139 AVLTEA  144 (165)
Q Consensus       139 ~~l~~~  144 (165)
                      ..++..
T Consensus        79 ~~l~~~   84 (289)
T smart00489       79 EELRKL   84 (289)
T ss_pred             HHHHhc
Confidence            444443

>PRK13767 ATP-dependent helicase; Provisional

Probab=97.27  E-value=0.00055  Score=63.90  Aligned_cols=48  Identities=23%  Similarity=0.276  Sum_probs=33.8

Q ss_pred             HHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCC-CCceEEEEC
Q psy7691          72 PIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCAS-SGTAYTFFT  127 (165)
Q Consensus        72 ~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~-~g~~~~~~~  127 (165)
                      +.+.+|.|+..+.        .|++|+.|.+..+|+||+||+||.+. .+...++..
T Consensus       348 s~Le~GIDip~Vd--------~VI~~~~P~sv~~ylQRiGRaGR~~g~~~~g~ii~~  396 (876)
T PRK13767        348 TSLELGIDIGYID--------LVVLLGSPKSVSRLLQRIGRAGHRLGEVSKGRIIVV  396 (876)
T ss_pred             ChHHhcCCCCCCc--------EEEEeCCCCCHHHHHHhcccCCCCCCCCCcEEEEEc
Confidence            3344455554444        89999999999999999999998743 344444443

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=97.26  E-value=0.00036  Score=63.87  Aligned_cols=68  Identities=28%  Similarity=0.372  Sum_probs=51.0

Q ss_pred             CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHH
Q psy7691          58 QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL  137 (165)
Q Consensus        58 ~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i  137 (165)
                      .|. .|+++|..+...+..|  .++..+||+|||+++.   +|.    |++-.  +      |..+.+++|+ +.++.|.
T Consensus        67 lgl-rpydVQlig~l~l~~G--~Iaem~TGeGKTLta~---Lpa----~l~aL--~------g~~V~VVTpn-~yLA~Rd  127 (762)
T TIGR03714        67 LGM-FPYDVQVLGAIVLHQG--NIAEMKTGEGKTLTAT---MPL----YLNAL--T------GKGAMLVTTN-DYLAKRD  127 (762)
T ss_pred             cCC-CccHHHHHHHHHhcCC--ceeEecCCcchHHHHH---HHH----HHHhh--c------CCceEEeCCC-HHHHHHH
Confidence            466 4888888887777777  5889999999999999   882    44433  2      2348899999 8888888


Q ss_pred             HHHHHhc
Q psy7691         138 IAVLTEA  144 (165)
Q Consensus       138 ~~~l~~~  144 (165)
                      .+.+...
T Consensus       128 ae~m~~l  134 (762)
T TIGR03714       128 AEEMGPV  134 (762)
T ss_pred             HHHHHHH
Confidence            7777443

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.

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=97.18  E-value=0.0023  Score=58.98  Aligned_cols=105  Identities=20%  Similarity=0.207  Sum_probs=68.3

Q ss_pred             CCCcccccc-CCCcHHHHHHHHhCCCCCCc----hHHHH---------------HHHHHHcCCCee---eecccCCcccc
Q psy7691          36 PCPTQELTE-GCFPNAVLQHLKGQGFEEPT----AIQAQ---------------GWPIALSGRDMV---GIAQTGSGKTL   92 (165)
Q Consensus        36 p~~i~~f~~-l~l~~~l~~~l~~~g~~~~t----~~Q~~---------------a~~~~l~G~di~---~~a~tgsGKt~   92 (165)
                      ..|+..|.. ..-.+.+.+.|.+.|+..-.    -.|.+               |+..+-||.||.   .+..-|   -+
T Consensus       440 g~pvLI~t~si~~se~ls~~L~~~gi~~~~Lna~~~~~Ea~ii~~ag~~g~VtIATnmAGRGtDI~l~~~V~~~G---GL  516 (796)
T PRK12906        440 GQPVLVGTVAIESSERLSHLLDEAGIPHAVLNAKNHAKEAEIIMNAGQRGAVTIATNMAGRGTDIKLGPGVKELG---GL  516 (796)
T ss_pred             CCCEEEEeCcHHHHHHHHHHHHHCCCCeeEecCCcHHHHHHHHHhcCCCceEEEEeccccCCCCCCCCcchhhhC---Cc
Confidence            456556654 46677888888888875421    12333               233334555542   111111   24


Q ss_pred             eeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHH----HHHHHHHHHh
Q psy7691          93 AVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQ----AKELIAVLTE  143 (165)
Q Consensus        93 ~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~----~~~i~~~l~~  143 (165)
                      +|+++++|.+...|.|+.||+||.|..|.+..+++..+.-+    ...+.+++..
T Consensus       517 hVI~te~pes~ri~~Ql~GRtGRqG~~G~s~~~~sleD~l~~~f~~~~~~~~~~~  571 (796)
T PRK12906        517 AVIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSLEDDLMRRFGSDRVKAFLDR  571 (796)
T ss_pred             EEEeeecCCcHHHHHHHhhhhccCCCCcceEEEEeccchHHHhhCcHHHHHHHHH
Confidence            89999999999999999999999999999999999885222    1245555544

>PRK13766 Hef nuclease; Provisional

Probab=97.16  E-value=0.0011  Score=60.92  Aligned_cols=93  Identities=18%  Similarity=0.180  Sum_probs=61.7

Q ss_pred             CCccccccC-CCcHHHHHHHHhCCCCC--------------Cc-hHHHHHHHHHHcC-CCeeeecccCC-c----cccee
Q psy7691          37 CPTQELTEG-CFPNAVLQHLKGQGFEE--------------PT-AIQAQGWPIALSG-RDMVGIAQTGS-G----KTLAV   94 (165)
Q Consensus        37 ~~i~~f~~l-~l~~~l~~~l~~~g~~~--------------~t-~~Q~~a~~~~l~G-~di~~~a~tgs-G----Kt~~~   94 (165)
                      ..++.|.+. ..+..+.+.|...|+..              .+ ..|..++..+..| .++++....++ |    ..-.+
T Consensus       366 ~kvlIF~~~~~t~~~L~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~g~~~vLvaT~~~~eGldi~~~~~V  445 (773)
T PRK13766        366 SRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLV  445 (773)
T ss_pred             CeEEEEeCcHHHHHHHHHHHHhCCCceEEEEccccccccCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccCCEE
Confidence            456677654 68888888888777642              12 2344455555555 34443333222 3    22379


Q ss_pred             eecCCCCChhHHHHhhccCCCCCCCCceEEEECCCc
Q psy7691          95 INFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN  130 (165)
Q Consensus        95 ~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~  130 (165)
                      ++||.|.+...|+||+||+||.+. |.++.+++..+
T Consensus       446 I~yd~~~s~~r~iQR~GR~gR~~~-~~v~~l~~~~t  480 (773)
T PRK13766        446 IFYEPVPSEIRSIQRKGRTGRQEE-GRVVVLIAKGT  480 (773)
T ss_pred             EEeCCCCCHHHHHHHhcccCcCCC-CEEEEEEeCCC
Confidence            999999999999999999999866 66777776555

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=97.15  E-value=0.00057  Score=61.54  Aligned_cols=45  Identities=18%  Similarity=0.226  Sum_probs=33.7

Q ss_pred             eeeecCCCCC-hhHHHHhhccCCCCCCCCceEEEE-CCCcHHHHHHH
Q psy7691          93 AVINFDYPNS-SEDYIHRIGRTGRCASSGTAYTFF-TPNNGKQAKEL  137 (165)
Q Consensus        93 ~~~~~~lP~~-~~~~i~r~gr~~r~~~~g~~~~~~-~p~~~~~~~~i  137 (165)
                      .+++|+.|.. ...|.|+.||+||.|..|.|+++. .|.......++
T Consensus       529 ~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~il~~~~~~~~~~~~rl  575 (630)
T TIGR00643       529 VMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKNPKSESAKKRL  575 (630)
T ss_pred             EEEEeCCCcCCHHHHHHHhhhcccCCCCcEEEEEECCCCCHHHHHHH
Confidence            6888999864 566777999999999999999998 44433333333

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=97.13  E-value=0.00017  Score=70.12  Aligned_cols=53  Identities=28%  Similarity=0.325  Sum_probs=41.0

Q ss_pred             eecccCCcccceeeecCCCCChhHHHHhhccCCC------CCCCCceEEEECCCcHHHHHHHHHHHHh
Q psy7691          82 GIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGR------CASSGTAYTFFTPNNGKQAKELIAVLTE  143 (165)
Q Consensus        82 ~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r------~~~~g~~~~~~~p~~~~~~~~i~~~l~~  143 (165)
                      ++|+||||||++++   ||     .++++-+...      ....+..+++++|+ ++++.|+.+.++.
T Consensus         1 V~APTGSGKTLAA~---Lp-----aL~~Ll~~~~~~~~~~~~~~~~raLYISPL-KALa~Dv~~~L~~   59 (1490)
T PRK09751          1 VIAPTGSGKTLAAF---LY-----ALDRLFREGGEDTREAHKRKTSRILYISPI-KALGTDVQRNLQI   59 (1490)
T ss_pred             CcCCCCcHHHHHHH---HH-----HHHHHHhcccccccccccCCCCEEEEEeCh-HHHHHHHHHHHHH
Confidence            47999999999999   89     7777644321      11346789999999 9999999988765

>KOG0952|consensus

Probab=97.13  E-value=0.00053  Score=64.04  Aligned_cols=81  Identities=27%  Similarity=0.389  Sum_probs=60.5

Q ss_pred             CCCCCCchHHHHHHHHHHcC-CCeeeecccCCcccceeeecCCCCChhHHHHhhcc---CCCCCCCCceEEEECCCcHHH
Q psy7691          58 QGFEEPTAIQAQGWPIALSG-RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGR---TGRCASSGTAYTFFTPNNGKQ  133 (165)
Q Consensus        58 ~g~~~~t~~Q~~a~~~~l~G-~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr---~~r~~~~g~~~~~~~p~~~~~  133 (165)
                      .+|+....+|.+++|.+... .+.++|||||+|||..+.   |-     +++-+.-   .+--.+.+.-+.+++|. +.+
T Consensus       106 f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~---L~-----ILr~ik~~~~~~~i~k~~fKiVYIaPm-KAL  176 (1230)
T KOG0952|consen  106 FSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAE---LC-----ILRTIKEHEEQGDIAKDDFKIVYIAPM-KAL  176 (1230)
T ss_pred             ccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHH---HH-----HHHHHHhhccccccccCCceEEEEech-HHH
Confidence            37888889999999998765 689999999999999776   44     4544421   12223566789999999 888


Q ss_pred             HHHHHHHHHhcCCC
Q psy7691         134 AKELIAVLTEASQP  147 (165)
Q Consensus       134 ~~~i~~~l~~~~~~  147 (165)
                      +..+.+...+...+
T Consensus       177 a~Em~~~~~kkl~~  190 (1230)
T KOG0952|consen  177 AAEMVDKFSKKLAP  190 (1230)
T ss_pred             HHHHHHHHhhhccc
Confidence            88888777665543

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=97.10  E-value=0.0011  Score=60.34  Aligned_cols=35  Identities=14%  Similarity=0.158  Sum_probs=30.0

Q ss_pred             eeeecCCCCC-hhHHHHhhccCCCCCCCCceEEEEC
Q psy7691          93 AVINFDYPNS-SEDYIHRIGRTGRCASSGTAYTFFT  127 (165)
Q Consensus        93 ~~~~~~lP~~-~~~~i~r~gr~~r~~~~g~~~~~~~  127 (165)
                      .+++|+.|.. ...|.|+.||+||.|..|.|+++..
T Consensus       552 ~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~ill~~  587 (681)
T PRK10917        552 VMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYK  587 (681)
T ss_pred             EEEEeCCCCCCHHHHHHHhhcccCCCCceEEEEEEC
Confidence            6889999974 5566669999999999999999995

>PF00271 Helicase_C: Helicase conserved C-terminal domain; InterPro: IPR001650 The domain, which defines this group of proteins is found in a wide variety of helicases and helicase related proteins

Probab=97.10  E-value=0.00017  Score=46.85  Aligned_cols=25  Identities=56%  Similarity=0.898  Sum_probs=23.5

Q ss_pred             eeeecCCCCChhHHHHhhccCCCCC
Q psy7691          93 AVINFDYPNSSEDYIHRIGRTGRCA  117 (165)
Q Consensus        93 ~~~~~~lP~~~~~~i~r~gr~~r~~  117 (165)
                      .++.|++|.+..+|.|++||.+|.|
T Consensus        54 ~vi~~~~~~~~~~~~Q~~GR~~R~g   78 (78)
T PF00271_consen   54 HVIFYDPPWSPEEYIQRIGRAGRIG   78 (78)
T ss_dssp             EEEESSSESSHHHHHHHHTTSSTTT
T ss_pred             cccccccCCCHHHHHHHhhcCCCCC
Confidence            7899999999999999999999976

It may be that this is not an autonomously folding unit, but an integral part of the helicase. The eukaryotic translation initiation factor 4A (eIF4A) is a member of the DEA(D/H)-box RNA helicase family This is a diverse group of proteins that couples an ATPase activity to RNA binding and unwinding. The structure of the carboxyl-terminal domain of eIF4A has been determined to 1.75 A resolution; it has a parallel alpha-beta topology that superimposes, with minor variations, on the structures and conserved motifs of the equivalent domain in other, distantly related helicases [].; GO: 0003676 nucleic acid binding, 0004386 helicase activity, 0005524 ATP binding; PDB: 2Z83_A 2JGN_C 2I4I_A 2BMF_A 2BHR_B 1WP9_E 2WAX_C 2WAY_C 3JUX_A 3DIN_B ....

>PHA02653 RNA helicase NPH-II; Provisional

Probab=97.09  E-value=0.00051  Score=62.37  Aligned_cols=49  Identities=27%  Similarity=0.308  Sum_probs=37.8

Q ss_pred             HHHcCCCeeeecccCCcccceeeecC---CCC---------ChhHHHHhhccCCCCCCCCceEEEECCCc
Q psy7691          73 IALSGRDMVGIAQTGSGKTLAVINFD---YPN---------SSEDYIHRIGRTGRCASSGTAYTFFTPNN  130 (165)
Q Consensus        73 ~~l~G~di~~~a~tgsGKt~~~~~~~---lP~---------~~~~~i~r~gr~~r~~~~g~~~~~~~p~~  130 (165)
                      .+.+|.|+..+.        +|++++   .|.         +..+|+||.||+||. +.|.++.++++.+
T Consensus       455 IAERGIDIp~V~--------~VID~G~~k~p~~~~g~~~~iSkasa~QRaGRAGR~-~~G~c~rLyt~~~  515 (675)
T PHA02653        455 YLESSVTIRNAT--------HVYDTGRVYVPEPFGGKEMFISKSMRTQRKGRVGRV-SPGTYVYFYDLDL  515 (675)
T ss_pred             hhhccccccCee--------EEEECCCccCCCcccCcccccCHHHHHHhccCcCCC-CCCeEEEEECHHH
Confidence            334455555444        789998   665         677999999999999 7899999998664

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

Probab=97.07  E-value=0.00083  Score=62.29  Aligned_cols=70  Identities=19%  Similarity=0.136  Sum_probs=50.1

Q ss_pred             HhCCCCCCchHHHHHHH----HHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcH
Q psy7691          56 KGQGFEEPTAIQAQGWP----IALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNG  131 (165)
Q Consensus        56 ~~~g~~~~t~~Q~~a~~----~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~  131 (165)
                      ..-||. +.+.|.+-..    .+..|.++++.|+||+|||++|+   +|     ++...        .+..+++.+|+ +
T Consensus       240 ~~~~~e-~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayl---lp-----~l~~~--------~~~~vvI~t~T-~  301 (820)
T PRK07246        240 ALLGLE-ERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYL---LP-----LLAQS--------DQRQIIVSVPT-K  301 (820)
T ss_pred             ccCCCc-cCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHH---HH-----HHHhc--------CCCcEEEEeCc-H
Confidence            334675 6777876333    23566889999999999999999   99     66643        23568888998 8


Q ss_pred             HHHHHHH-HHHHh
Q psy7691         132 KQAKELI-AVLTE  143 (165)
Q Consensus       132 ~~~~~i~-~~l~~  143 (165)
                      ++..|+. +-+..
T Consensus       302 ~Lq~Ql~~~~i~~  314 (820)
T PRK07246        302 ILQDQIMAEEVKA  314 (820)
T ss_pred             HHHHHHHHHHHHH
Confidence            8888883 43433

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

Probab=97.02  E-value=0.004  Score=54.36  Aligned_cols=97  Identities=22%  Similarity=0.197  Sum_probs=72.0

Q ss_pred             CCccccccC-CCcHHHHHHHHhCCCCCC----------------chHHHHHHHHHHcCC-CeeeecccC-----Ccccce
Q psy7691          37 CPTQELTEG-CFPNAVLQHLKGQGFEEP----------------TAIQAQGWPIALSGR-DMVGIAQTG-----SGKTLA   93 (165)
Q Consensus        37 ~~i~~f~~l-~l~~~l~~~l~~~g~~~~----------------t~~Q~~a~~~~l~G~-di~~~a~tg-----sGKt~~   93 (165)
                      ..++.|.+. .-.+.+.+.|.+.|....                ...|.+.|..+-+|. +++++..-|     -|-|-.
T Consensus       367 ~RvIVFT~yRdTae~i~~~L~~~~~~~~~rFiGQa~r~~~~GMsQkeQ~eiI~~Fr~Ge~nVLVaTSVgEEGLDIp~vDl  446 (542)
T COG1111         367 SRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDL  446 (542)
T ss_pred             ceEEEEehhHhHHHHHHHHHHhcCCcceeEEeeccccccccccCHHHHHHHHHHHhcCCceEEEEcccccccCCCCcccE
Confidence            468899988 566788888887766542                136888999998873 555444333     234557


Q ss_pred             eeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHH
Q psy7691          94 VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQA  134 (165)
Q Consensus        94 ~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~  134 (165)
                      ++-|+.-.+..-++||.|||||. +.|.++.+++..+++.+
T Consensus       447 VifYEpvpSeIR~IQR~GRTGR~-r~Grv~vLvt~gtrdea  486 (542)
T COG1111         447 VIFYEPVPSEIRSIQRKGRTGRK-RKGRVVVLVTEGTRDEA  486 (542)
T ss_pred             EEEecCCcHHHHHHHhhCccccC-CCCeEEEEEecCchHHH
Confidence            88899777788999999999998 88999999998865544

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

Probab=97.02  E-value=0.0019  Score=57.60  Aligned_cols=72  Identities=26%  Similarity=0.310  Sum_probs=53.6

Q ss_pred             HHh-CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHH
Q psy7691          55 LKG-QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQ  133 (165)
Q Consensus        55 l~~-~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~  133 (165)
                      |+. .||...-+-|.+.|..++.|.|.+++=|||.||+++|-   +|.    ++    +      .| ..++++|. -.+
T Consensus         9 L~~~fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQ---iPA----ll----~------~G-~TLVVSPL-iSL   69 (590)
T COG0514           9 LKQVFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQ---IPA----LL----L------EG-LTLVVSPL-ISL   69 (590)
T ss_pred             HHHHhCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhh---hHH----Hh----c------CC-CEEEECch-HHH
Confidence            444 48999999999999999999999999999999999998   883    11    1      22 56677777 555


Q ss_pred             HHHHHHHHHhcC
Q psy7691         134 AKELIAVLTEAS  145 (165)
Q Consensus       134 ~~~i~~~l~~~~  145 (165)
                      +.+=.+.++..+
T Consensus        70 M~DQV~~l~~~G   81 (590)
T COG0514          70 MKDQVDQLEAAG   81 (590)
T ss_pred             HHHHHHHHHHcC
Confidence            554444444444

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=96.99  E-value=0.0015  Score=61.27  Aligned_cols=51  Identities=20%  Similarity=0.249  Sum_probs=38.2

Q ss_pred             HHHHHcCCCeeeecccCCcccceeeecCCCC-ChhHHHHhhccCCCCCCCCceEEEECCC
Q psy7691          71 WPIALSGRDMVGIAQTGSGKTLAVINFDYPN-SSEDYIHRIGRTGRCASSGTAYTFFTPN  129 (165)
Q Consensus        71 ~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~-~~~~~i~r~gr~~r~~~~g~~~~~~~p~  129 (165)
                      +..+.+|.|+..+.        .+++++.|. ...+|.||+||+||.|+.|.|++++.+.
T Consensus       719 T~iie~GIDIp~v~--------~VIi~~a~~~gls~l~Qr~GRvGR~g~~g~aill~~~~  770 (926)
T TIGR00580       719 TTIIETGIDIPNAN--------TIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQ  770 (926)
T ss_pred             CChhhcccccccCC--------EEEEecCCCCCHHHHHHHhcCCCCCCCCeEEEEEECCc
Confidence            33444555555444        678888764 4668999999999999999999998764

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.

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

Probab=96.92  E-value=0.0012  Score=59.46  Aligned_cols=59  Identities=22%  Similarity=0.159  Sum_probs=43.9

Q ss_pred             HHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcC
Q psy7691          73 IALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus        73 ~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~  145 (165)
                      .+..+..+++.|+||+|||++|+   +|     .+..+..     ..+..+++.+|+ +++..|+.+-+....
T Consensus        12 al~~~~~lliEA~TGtGKTlAYL---lp-----al~~~~~-----~~~~rvlIstpT-~~Lq~Ql~~~l~~l~   70 (636)
T TIGR03117        12 SLRQKRIGMLEASTGVGKTLAMI---MA-----ALTMLKE-----RPDQKIAIAVPT-LALMGQLWSELERLT   70 (636)
T ss_pred             HHhcCCeEEEEcCCCCcHHHHHH---HH-----HHHHHHh-----ccCceEEEECCc-HHHHHHHHHHHHHHH
Confidence            44667889999999999999999   88     5554321     123578889998 888888887665544

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.

>PRK02362 ski2-like helicase; Provisional

Probab=96.91  E-value=0.0019  Score=59.22  Aligned_cols=43  Identities=19%  Similarity=0.201  Sum_probs=29.7

Q ss_pred             CCCChhHHHHhhccCCCCCCC--CceEEEECCCcHHHHHHHHHHHH
Q psy7691          99 YPNSSEDYIHRIGRTGRCASS--GTAYTFFTPNNGKQAKELIAVLT  142 (165)
Q Consensus        99 lP~~~~~~i~r~gr~~r~~~~--g~~~~~~~p~~~~~~~~i~~~l~  142 (165)
                      .|.+..+|+|++||+||.|..  |.++++..+. .+......+++.
T Consensus       365 ~~~s~~~y~Qm~GRAGR~g~d~~G~~ii~~~~~-~~~~~~~~~~l~  409 (737)
T PRK02362        365 QPIPVLEYHQMAGRAGRPGLDPYGEAVLLAKSY-DELDELFERYIW  409 (737)
T ss_pred             eeCCHHHHHHHhhcCCCCCCCCCceEEEEecCc-hhHHHHHHHHHh
Confidence            588899999999999999965  7677766544 222223344554

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=96.77  E-value=0.0022  Score=53.26  Aligned_cols=26  Identities=27%  Similarity=0.404  Sum_probs=20.7

Q ss_pred             eeeecCCCCChhHHHHhhccCCCCCCCC
Q psy7691          93 AVINFDYPNSSEDYIHRIGRTGRCASSG  120 (165)
Q Consensus        93 ~~~~~~lP~~~~~~i~r~gr~~r~~~~g  120 (165)
                      .+++|+.|  .++|+||+||+||.|+..
T Consensus       298 ~vi~~~~~--~~~~iqr~GR~gR~g~~~  323 (358)
T TIGR01587       298 VMITELAP--IDSLIQRLGRLHRYGRKN  323 (358)
T ss_pred             EEEEcCCC--HHHHHHHhccccCCCCCC
Confidence            45666666  788999999999998654

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.

>PRK10689 transcription-repair coupling factor; Provisional

Probab=96.64  E-value=0.0024  Score=61.19  Aligned_cols=47  Identities=21%  Similarity=0.293  Sum_probs=33.4

Q ss_pred             HHHHHcCCCeeeecccCCcccceee-----ecCCCCChhHHHHhhccCCCCCCCCceEEEECCC
Q psy7691          71 WPIALSGRDMVGIAQTGSGKTLAVI-----NFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPN  129 (165)
Q Consensus        71 ~~~~l~G~di~~~a~tgsGKt~~~~-----~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~  129 (165)
                      +..+.+|.|+..+.        +++     ||++|    +|+||+||+||.|+.|.++++..+.
T Consensus       868 TdIierGIDIP~v~--------~VIi~~ad~fgla----q~~Qr~GRvGR~g~~g~a~ll~~~~  919 (1147)
T PRK10689        868 TTIIETGIDIPTAN--------TIIIERADHFGLA----QLHQLRGRVGRSHHQAYAWLLTPHP  919 (1147)
T ss_pred             CchhhcccccccCC--------EEEEecCCCCCHH----HHHHHhhccCCCCCceEEEEEeCCC
Confidence            34444555555444        555     66665    5999999999999999999877543

>PRK13766 Hef nuclease; Provisional

Probab=96.64  E-value=0.0032  Score=57.78  Aligned_cols=67  Identities=18%  Similarity=0.198  Sum_probs=49.5

Q ss_pred             CCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVL  141 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l  141 (165)
                      .+.+.|.+....++.+ |++++++||+|||..++   ++     ..+++ +     ..+..+++++|+ ..++.|..+.+
T Consensus        15 ~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~---~~-----i~~~l-~-----~~~~~vLvl~Pt-~~L~~Q~~~~~   78 (773)
T PRK13766         15 EARLYQQLLAATALKK-NTLVVLPTGLGKTAIAL---LV-----IAERL-H-----KKGGKVLILAPT-KPLVEQHAEFF   78 (773)
T ss_pred             CccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHH---HH-----HHHHH-H-----hCCCeEEEEeCc-HHHHHHHHHHH
Confidence            5678898888777777 99999999999998766   44     44444 1     133468899998 77777777666


Q ss_pred             Hhc
Q psy7691         142 TEA  144 (165)
Q Consensus       142 ~~~  144 (165)
                      ...
T Consensus        79 ~~~   81 (773)
T PRK13766         79 RKF   81 (773)
T ss_pred             HHH
Confidence            653

>KOG0351|consensus

Probab=96.60  E-value=0.01  Score=55.70  Aligned_cols=69  Identities=22%  Similarity=0.249  Sum_probs=52.4

Q ss_pred             HHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHH
Q psy7691          54 HLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQ  133 (165)
Q Consensus        54 ~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~  133 (165)
                      .....|+....+.|.++|-..+.|+|.++.-+||.||.++|-   ||.-    +           .+...++|+|. ..|
T Consensus       256 l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQ---lPA~----l-----------~~gitvVISPL-~SL  316 (941)
T KOG0351|consen  256 LKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQ---LPAL----L-----------LGGVTVVISPL-ISL  316 (941)
T ss_pred             HHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEee---cccc----c-----------cCCceEEeccH-HHH
Confidence            344469999999999999999999999999999999999998   8831    1           11266777777 555


Q ss_pred             HHHHHHHH
Q psy7691         134 AKELIAVL  141 (165)
Q Consensus       134 ~~~i~~~l  141 (165)
                      +.+-...+
T Consensus       317 m~DQv~~L  324 (941)
T KOG0351|consen  317 MQDQVTHL  324 (941)
T ss_pred             HHHHHHhh
Confidence            55444444

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=96.49  E-value=0.003  Score=58.62  Aligned_cols=55  Identities=18%  Similarity=0.246  Sum_probs=41.0

Q ss_pred             HHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHH
Q psy7691          72 PIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLT  142 (165)
Q Consensus        72 ~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~  142 (165)
                      ..+..+.|++++|+||||||.+|.   +|     .+++...      .+ .++++.|+ +.++.++.+.+.
T Consensus        15 ~~l~~~~~vvv~A~TGSGKTt~~p---l~-----lL~~~~~------~~-~ilvlqPr-R~aA~qia~rva   69 (812)
T PRK11664         15 TALKTAPQVLLKAPTGAGKSTWLP---LQ-----LLQHGGI------NG-KIIMLEPR-RLAARNVAQRLA   69 (812)
T ss_pred             HHHHhCCCEEEEcCCCCCHHHHHH---HH-----HHHcCCc------CC-eEEEECCh-HHHHHHHHHHHH
Confidence            345677899999999999999987   55     5544311      22 57788888 888888888774

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

Probab=96.49  E-value=0.0026  Score=58.98  Aligned_cols=34  Identities=18%  Similarity=0.152  Sum_probs=26.8

Q ss_pred             eeeecCCCCChhHHHHhhccCCCCCCCC-ceEEEECC
Q psy7691          93 AVINFDYPNSSEDYIHRIGRTGRCASSG-TAYTFFTP  128 (165)
Q Consensus        93 ~~~~~~lP~~~~~~i~r~gr~~r~~~~g-~~~~~~~p  128 (165)
                      .+++++.|  .++|+||+||++|.|+.+ ..+.++.+
T Consensus       356 ~VI~d~aP--~esyIQRiGRtgR~G~~~~~~i~vv~~  390 (844)
T TIGR02621       356 HLVCDLAP--FESMQQRFGRVNRFGELQACQIAVVHL  390 (844)
T ss_pred             eEEECCCC--HHHHHHHhcccCCCCCCCCceEEEEee
Confidence            57777776  689999999999999864 45666655

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.

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

Probab=96.41  E-value=0.003  Score=59.48  Aligned_cols=78  Identities=22%  Similarity=0.231  Sum_probs=53.7

Q ss_pred             HHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCc
Q psy7691          51 VLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN  130 (165)
Q Consensus        51 l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~  130 (165)
                      +.......+|. +-++|++|+..+.+|..++++|+||+|||. |-.|-        +++..|      .|..+.+.+|. 
T Consensus       109 ~~~~~~~~~F~-LD~fQ~~a~~~Ler~esVlV~ApTssGKTv-VaeyA--------i~~al~------~~qrviYTsPI-  171 (1041)
T COG4581         109 LAPPAREYPFE-LDPFQQEAIAILERGESVLVCAPTSSGKTV-VAEYA--------IALALR------DGQRVIYTSPI-  171 (1041)
T ss_pred             cCcHHHhCCCC-cCHHHHHHHHHHhCCCcEEEEccCCCCcch-HHHHH--------HHHHHH------cCCceEeccch-
Confidence            34455667896 789999999999999999999999999997 33222        333333      22236666666 


Q ss_pred             HHHHHHHHHHHHhcC
Q psy7691         131 GKQAKELIAVLTEAS  145 (165)
Q Consensus       131 ~~~~~~i~~~l~~~~  145 (165)
                      ..+.+|..+-+...-
T Consensus       172 KALsNQKyrdl~~~f  186 (1041)
T COG4581         172 KALSNQKYRDLLAKF  186 (1041)
T ss_pred             hhhhhhHHHHHHHHh
Confidence            666666655554433

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

Probab=96.35  E-value=0.01  Score=55.79  Aligned_cols=78  Identities=22%  Similarity=0.296  Sum_probs=53.5

Q ss_pred             HHHHHHHHhC-CCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEEC
Q psy7691          49 NAVLQHLKGQ-GFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFT  127 (165)
Q Consensus        49 ~~l~~~l~~~-g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~  127 (165)
                      +++.+.+.++ || .|+..|.-..-.+.+|..+-++||||.|||..-..+      .-|+-.         +|....++.
T Consensus        69 e~~~~fF~k~~G~-~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~------sl~~a~---------kgkr~yii~  132 (1187)
T COG1110          69 EEFEEFFKKATGF-RPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLM------SLYLAK---------KGKRVYIIV  132 (1187)
T ss_pred             HHHHHHHHHhhCC-CchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHH------HHHHHh---------cCCeEEEEe
Confidence            3444455665 66 699999999999999999999999999999733211      114432         334677888


Q ss_pred             CCcHHHHHHHHHHHHh
Q psy7691         128 PNNGKQAKELIAVLTE  143 (165)
Q Consensus       128 p~~~~~~~~i~~~l~~  143 (165)
                      || ..++.|..+-++.
T Consensus       133 PT-~~Lv~Q~~~kl~~  147 (1187)
T COG1110         133 PT-TTLVRQVYERLKK  147 (1187)
T ss_pred             cC-HHHHHHHHHHHHH
Confidence            88 5565555555544

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

Probab=96.32  E-value=0.0087  Score=51.81  Aligned_cols=61  Identities=21%  Similarity=0.255  Sum_probs=46.3

Q ss_pred             CCchHHHHHHHHHHc----CCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALS----GRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL  137 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~----G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i  137 (165)
                      .+.+.|.+|+..+..    ++..+++.|||+|||....    -     .+.++++.         +++++|+ .+++.|-
T Consensus        36 ~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~----~-----~~~~~~~~---------~Lvlv~~-~~L~~Qw   96 (442)
T COG1061          36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAA----E-----AIAELKRS---------TLVLVPT-KELLDQW   96 (442)
T ss_pred             CCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHH----H-----HHHHhcCC---------EEEEECc-HHHHHHH
Confidence            478899999999988    8999999999999998543    1     44444331         8888888 7887777


Q ss_pred             HHHH
Q psy7691         138 IAVL  141 (165)
Q Consensus       138 ~~~l  141 (165)
                      .+.+
T Consensus        97 ~~~~  100 (442)
T COG1061          97 AEAL  100 (442)
T ss_pred             HHHH
Confidence            5433

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=96.32  E-value=0.006  Score=56.81  Aligned_cols=72  Identities=25%  Similarity=0.325  Sum_probs=52.3

Q ss_pred             CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHH
Q psy7691          58 QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL  137 (165)
Q Consensus        58 ~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i  137 (165)
                      .|.. |+++|..+--.+..|.  ++.++||+|||+++.   +|.    |++-.  +      |..+.+++|+ +.|+.|.
T Consensus        79 lg~~-~ydvQliGg~~Lh~G~--Iaem~TGeGKTL~a~---Lpa----~~~al--~------G~~V~VvTpn-~yLA~qd  139 (896)
T PRK13104         79 LGLR-HFDVQLIGGMVLHEGN--IAEMRTGEGKTLVAT---LPA----YLNAI--S------GRGVHIVTVN-DYLAKRD  139 (896)
T ss_pred             cCCC-cchHHHhhhhhhccCc--cccccCCCCchHHHH---HHH----HHHHh--c------CCCEEEEcCC-HHHHHHH
Confidence            4665 7889987655556664  579999999999998   883    33322  2      2347799999 8999999


Q ss_pred             HHHHHhcCCCC
Q psy7691         138 IAVLTEASQPI  148 (165)
Q Consensus       138 ~~~l~~~~~~~  148 (165)
                      .+.+......+
T Consensus       140 ~e~m~~l~~~l  150 (896)
T PRK13104        140 SQWMKPIYEFL  150 (896)
T ss_pred             HHHHHHHhccc
Confidence            88887754443

>PF13245 AAA_19: Part of AAA domain

Probab=96.18  E-value=0.016  Score=38.01  Aligned_cols=55  Identities=25%  Similarity=0.352  Sum_probs=35.1

Q ss_pred             HcCCCee-eecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHH
Q psy7691          75 LSGRDMV-GIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVL  141 (165)
Q Consensus        75 l~G~di~-~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l  141 (165)
                      +.+..++ +.++.|||||..+.+         .+.+.-+. +... +..+++++|+ +..+..|.+.+
T Consensus         7 l~~~~~~vv~g~pGtGKT~~~~~---------~i~~l~~~-~~~~-~~~vlv~a~t-~~aa~~l~~rl   62 (76)
T PF13245_consen    7 LAGSPLFVVQGPPGTGKTTTLAA---------RIAELLAA-RADP-GKRVLVLAPT-RAAADELRERL   62 (76)
T ss_pred             HhhCCeEEEECCCCCCHHHHHHH---------HHHHHHHH-hcCC-CCeEEEECCC-HHHHHHHHHHH
Confidence            3344544 599999999964431         33333221 2223 6789999999 77777887777

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=96.13  E-value=0.0093  Score=55.44  Aligned_cols=55  Identities=22%  Similarity=0.242  Sum_probs=41.4

Q ss_pred             HHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHH
Q psy7691          72 PIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLT  142 (165)
Q Consensus        72 ~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~  142 (165)
                      ..+..+.+++++|+||||||.+|.   +|     +++...       .+..++++.|+ +.++.++.+.+.
T Consensus        12 ~~l~~~~~vIi~a~TGSGKTT~vp---l~-----lL~~~~-------~~~~ilvlqPr-R~aA~qiA~rva   66 (819)
T TIGR01970        12 DALAAHPQVVLEAPPGAGKSTAVP---LA-----LLDAPG-------IGGKIIMLEPR-RLAARSAAQRLA   66 (819)
T ss_pred             HHHHcCCcEEEECCCCCCHHHHHH---HH-----HHHhhc-------cCCeEEEEeCc-HHHHHHHHHHHH
Confidence            345567899999999999999987   66     555542       12367888888 888888888774

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.

>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

Probab=96.04  E-value=0.0035  Score=43.73  Aligned_cols=87  Identities=23%  Similarity=0.343  Sum_probs=50.7

Q ss_pred             Cccccc-cCCCcHHHHHHHHhCCCC------CCch-HHHHHHHHHHcCC-Ceeeecc-cCCccc----ceeeecCCCCCh
Q psy7691          38 PTQELT-EGCFPNAVLQHLKGQGFE------EPTA-IQAQGWPIALSGR-DMVGIAQ-TGSGKT----LAVINFDYPNSS  103 (165)
Q Consensus        38 ~i~~f~-~l~l~~~l~~~l~~~g~~------~~t~-~Q~~a~~~~l~G~-di~~~a~-tgsGKt----~~~~~~~lP~~~  103 (165)
                      ++..|. .....+.+.+.|.+.++.      ..++ .....+..+..|. .++.+.. -|.|-.    ..++.++.|.+.
T Consensus        30 ~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~~~~~G~d~~~~~~vi~~~~~~~~  109 (131)
T cd00079          30 KVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSP  109 (131)
T ss_pred             cEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcChhhcCcChhhCCEEEEeCCCCCH
Confidence            344444 445667777777764442      1111 1222333344443 3332222 233432    257778899999


Q ss_pred             hHHHHhhccCCCCCCCCceEE
Q psy7691         104 EDYIHRIGRTGRCASSGTAYT  124 (165)
Q Consensus       104 ~~~i~r~gr~~r~~~~g~~~~  124 (165)
                      .+++|++||++|.|..|.+..
T Consensus       110 ~~~~Q~~GR~~R~~~~~~~~~  130 (131)
T cd00079         110 SSYLQRIGRAGRAGQKGTAIL  130 (131)
T ss_pred             HHheecccccccCCCCceEEe
Confidence            999999999999998776554

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=96.03  E-value=0.011  Score=53.91  Aligned_cols=72  Identities=14%  Similarity=0.108  Sum_probs=47.9

Q ss_pred             CCCCchHHHHHH----HHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHH
Q psy7691          60 FEEPTAIQAQGW----PIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAK  135 (165)
Q Consensus        60 ~~~~t~~Q~~a~----~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~  135 (165)
                      |..+.|.|.+..    ..+..|.+++.-+|||+|||++.+   .|  ...|..+-+       ....+.+.+.+ ..++.
T Consensus         8 y~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL---~~--aL~~~~~~~-------~~~kIiy~sRT-hsQl~   74 (705)
T TIGR00604         8 YEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLL---SL--ILAYQQEKP-------EVRKIIYASRT-HSQLE   74 (705)
T ss_pred             CCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHH---HH--HHHHHHhcc-------ccccEEEEccc-chHHH
Confidence            555578887644    345677899999999999999887   45  112433321       12356666666 67777


Q ss_pred             HHHHHHHhc
Q psy7691         136 ELIAVLTEA  144 (165)
Q Consensus       136 ~i~~~l~~~  144 (165)
                      |+.+-+...
T Consensus        75 q~i~Elk~~   83 (705)
T TIGR00604        75 QATEELRKL   83 (705)
T ss_pred             HHHHHHHhh
Confidence            777777664

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).

>KOG0352|consensus

Probab=95.86  E-value=0.034  Score=48.14  Aligned_cols=80  Identities=25%  Similarity=0.296  Sum_probs=54.7

Q ss_pred             HHHHHHHh-CCCCCC-chHHHHHHHHHHcC-CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEE
Q psy7691          50 AVLQHLKG-QGFEEP-TAIQAQGWPIALSG-RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFF  126 (165)
Q Consensus        50 ~l~~~l~~-~g~~~~-t~~Q~~a~~~~l~G-~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~  126 (165)
                      .+..+|++ .||... |+.|..|+..+..+ .||.++=|||+||+++|-   ||.    .++          .| ..+++
T Consensus         6 ~VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQ---LPa----L~~----------~g-ITIV~   67 (641)
T KOG0352|consen    6 KVREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQ---LPA----LVH----------GG-ITIVI   67 (641)
T ss_pred             HHHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhh---chH----HHh----------CC-eEEEe
Confidence            45556666 477664 78999999988766 699999999999999988   882    111          22 33444


Q ss_pred             CCCcHHHHHHHHHHHHhcCCCC
Q psy7691         127 TPNNGKQAKELIAVLTEASQPI  148 (165)
Q Consensus       127 ~p~~~~~~~~i~~~l~~~~~~~  148 (165)
                      +|. -.+..+=...+.....++
T Consensus        68 SPL-iALIkDQiDHL~~LKVp~   88 (641)
T KOG0352|consen   68 SPL-IALIKDQIDHLKRLKVPC   88 (641)
T ss_pred             hHH-HHHHHHHHHHHHhcCCch
Confidence            555 666666566666554443

>TIGR00603 rad25 DNA repair helicase rad25

Probab=95.85  E-value=0.019  Score=52.72  Aligned_cols=42  Identities=19%  Similarity=0.322  Sum_probs=34.3

Q ss_pred             eeeecCCC-CChhHHHHhhccCCCCCCCCce-------EEEECCCcHHHH
Q psy7691          93 AVINFDYP-NSSEDYIHRIGRTGRCASSGTA-------YTFFTPNNGKQA  134 (165)
Q Consensus        93 ~~~~~~lP-~~~~~~i~r~gr~~r~~~~g~~-------~~~~~p~~~~~~  134 (165)
                      .+++++.| .+..+|+||+||.+|.+..|.+       +.++++.+.+..
T Consensus       563 vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~dT~E~~  612 (732)
T TIGR00603       563 VLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQEMY  612 (732)
T ss_pred             EEEEeCCCCCCHHHHHHHhcccccCCCCCccccccceEEEEecCCchHHH
Confidence            68888887 4889999999999999877664       788888876543

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).

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=95.74  E-value=0.01  Score=55.02  Aligned_cols=70  Identities=26%  Similarity=0.343  Sum_probs=51.8

Q ss_pred             CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHH
Q psy7691          58 QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL  137 (165)
Q Consensus        58 ~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i  137 (165)
                      .|.. |+++|..+-=.+..|.  ++..+||+|||+++.   +|.    |++.+  +      |..+-+++|+ +.+|.|.
T Consensus        78 lg~~-~~dvQlig~l~L~~G~--Iaem~TGeGKTLva~---lpa----~l~aL--~------G~~V~IvTpn-~yLA~rd  138 (830)
T PRK12904         78 LGMR-HFDVQLIGGMVLHEGK--IAEMKTGEGKTLVAT---LPA----YLNAL--T------GKGVHVVTVN-DYLAKRD  138 (830)
T ss_pred             hCCC-CCccHHHhhHHhcCCc--hhhhhcCCCcHHHHH---HHH----HHHHH--c------CCCEEEEecC-HHHHHHH
Confidence            5775 8999998766667774  689999999999988   883    56665  1      1235589999 7888877


Q ss_pred             HHHHHhcCC
Q psy7691         138 IAVLTEASQ  146 (165)
Q Consensus       138 ~~~l~~~~~  146 (165)
                      .+.+.....
T Consensus       139 ~e~~~~l~~  147 (830)
T PRK12904        139 AEWMGPLYE  147 (830)
T ss_pred             HHHHHHHHh
Confidence            777766433

>KOG0354|consensus

Probab=95.72  E-value=0.02  Score=52.25  Aligned_cols=71  Identities=24%  Similarity=0.243  Sum_probs=45.4

Q ss_pred             CCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVL  141 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l  141 (165)
                      .+-.-|.+-...+| |.++++++|||+|||..-..     .   ..+.. |. +   ..--++|++|+ +.++.|-...+
T Consensus        62 ~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~-----V---m~nh~-rw-~---p~~KiVF~aP~-~pLv~QQ~a~~  126 (746)
T KOG0354|consen   62 ELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAV-----I---MKNHF-EW-R---PKGKVVFLAPT-RPLVNQQIACF  126 (746)
T ss_pred             cccHHHHHHhHHhh-cCCeEEEeecCCCccchHHH-----H---HHHHH-hc-C---CcceEEEeeCC-chHHHHHHHHH
Confidence            35567888778888 99999999999999984320     0   11111 32 2   22568889999 44444433666


Q ss_pred             HhcCCC
Q psy7691         142 TEASQP  147 (165)
Q Consensus       142 ~~~~~~  147 (165)
                      ...+.+
T Consensus       127 ~~~~~~  132 (746)
T KOG0354|consen  127 SIYLIP  132 (746)
T ss_pred             hhccCc
Confidence            555544

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

Probab=95.59  E-value=0.02  Score=43.69  Aligned_cols=70  Identities=21%  Similarity=0.239  Sum_probs=42.0

Q ss_pred             CchHHHHHHHHHHcCCC-eeeecccCCcccceeeecCCCCChhHHHHhhccC--CCCCCCCceEEEECCCcHHHHHHHHH
Q psy7691          63 PTAIQAQGWPIALSGRD-MVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRT--GRCASSGTAYTFFTPNNGKQAKELIA  139 (165)
Q Consensus        63 ~t~~Q~~a~~~~l~G~d-i~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~--~r~~~~g~~~~~~~p~~~~~~~~i~~  139 (165)
                      ..+.|..|+..++...+ .++.+|+|+|||..+..         .+..+.+.  .+....+..+++++++....-.-+.+
T Consensus         2 ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~~---------~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~   72 (236)
T PF13086_consen    2 LNESQREAIQSALSSNGITLIQGPPGTGKTTTLAS---------IIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILER   72 (236)
T ss_dssp             --HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHHH---------HHHHH-------HCCCSS-EEEEESSHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHHH---------HHHHhccchhhhhhhccccceeecCCchhHHHHHHH
Confidence            45789999999988888 88999999999964331         33333110  12234667899999995443333333


Q ss_pred             HH
Q psy7691         140 VL  141 (165)
Q Consensus       140 ~l  141 (165)
                      +.
T Consensus        73 l~   74 (236)
T PF13086_consen   73 LK   74 (236)
T ss_dssp             HH
T ss_pred             HH
Confidence            33

>KOG0353|consensus

Probab=95.52  E-value=0.016  Score=49.40  Aligned_cols=51  Identities=25%  Similarity=0.349  Sum_probs=41.2

Q ss_pred             CcHHHHHHHHh-CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCC
Q psy7691          47 FPNAVLQHLKG-QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYP  100 (165)
Q Consensus        47 l~~~l~~~l~~-~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP  100 (165)
                      -..+..+.|++ ....+..|.|..+|...+.|.|++.+-+||.||+++|-   ||
T Consensus        78 ws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyq---lp  129 (695)
T KOG0353|consen   78 WSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQ---LP  129 (695)
T ss_pred             CchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhh---hh
Confidence            33455555554 25567788999999999999999999999999999987   77

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=95.51  E-value=0.0096  Score=55.33  Aligned_cols=36  Identities=25%  Similarity=0.502  Sum_probs=30.2

Q ss_pred             eeeecCCCCC------------------hhHHHHhhccCCCCCCCCceEEEECCC
Q psy7691          93 AVINFDYPNS------------------SEDYIHRIGRTGRCASSGTAYTFFTPN  129 (165)
Q Consensus        93 ~~~~~~lP~~------------------~~~~i~r~gr~~r~~~~g~~~~~~~p~  129 (165)
                      .||++++|..                  ..+|+||.||+||. ..|.|+.+++..
T Consensus       283 ~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRAGR~-~~G~cyrL~t~~  336 (819)
T TIGR01970       283 VVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRL-EPGVCYRLWSEE  336 (819)
T ss_pred             EEEEcCcccccccccccCCceeeEEEECHHHHHhhhhhcCCC-CCCEEEEeCCHH
Confidence            7999999853                  23589999999999 899999999755

This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.

>PRK09694 helicase Cas3; Provisional

Probab=95.42  E-value=0.027  Score=52.78  Aligned_cols=64  Identities=27%  Similarity=0.319  Sum_probs=40.6

Q ss_pred             CCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIA  139 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~  139 (165)
                      .|+|.|..+......+.-++..|+||+|||.+.+   +      ..+++...+.    ...+.+..|+ +..++++.+
T Consensus       286 ~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL---~------~A~~l~~~~~----~~gi~~aLPT-~Atan~m~~  349 (878)
T PRK09694        286 QPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAAL---A------YAWRLIDQGL----ADSIIFALPT-QATANAMLS  349 (878)
T ss_pred             CChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHH---H------HHHHHHHhCC----CCeEEEECcH-HHHHHHHHH
Confidence            5899999875443344567889999999999865   2      3444432211    2357788887 544444443

>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=95.41  E-value=0.019  Score=46.09  Aligned_cols=65  Identities=20%  Similarity=0.099  Sum_probs=38.2

Q ss_pred             CchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCC-CCCceEEEECCCcHHHHHHHHHHH
Q psy7691          63 PTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCA-SSGTAYTFFTPNNGKQAKELIAVL  141 (165)
Q Consensus        63 ~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~-~~g~~~~~~~p~~~~~~~~i~~~l  141 (165)
                      +|+.|.+++..  ...++++.|..|||||...            ++|+.+.-..+ -....+++++.+ +..+..+...+
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l------------~~ri~~ll~~~~~~~~~Il~lTft-~~aa~e~~~ri   65 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTL------------LERIAYLLYEGGVPPERILVLTFT-NAAAQEMRERI   65 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHH------------HHHHHHHHHTSSSTGGGEEEEESS-HHHHHHHHHHH
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHH------------HHHHHHhhccccCChHHheecccC-HHHHHHHHHHH
Confidence            36788887755  5568899999999999843            34432211111 334469999998 44444444333


Q ss_pred             H
Q psy7691         142 T  142 (165)
Q Consensus       142 ~  142 (165)
                      .
T Consensus        66 ~   66 (315)
T PF00580_consen   66 R   66 (315)
T ss_dssp             H
T ss_pred             H
Confidence            3

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 ....

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=95.37  E-value=0.011  Score=37.69  Aligned_cols=25  Identities=52%  Similarity=0.882  Sum_probs=22.3

Q ss_pred             eeeecCCCCChhHHHHhhccCCCCC
Q psy7691          93 AVINFDYPNSSEDYIHRIGRTGRCA  117 (165)
Q Consensus        93 ~~~~~~lP~~~~~~i~r~gr~~r~~  117 (165)
                      .++.++.|.+..+|.|++||++|.|
T Consensus        58 ~vi~~~~~~~~~~~~Q~~gR~~R~g   82 (82)
T smart00490       58 LVIIYDLPWSPASYIQRIGRAGRAG   82 (82)
T ss_pred             EEEEeCCCCCHHHHHHhhcccccCC
Confidence            6788899999999999999998865

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

Probab=95.32  E-value=0.033  Score=52.55  Aligned_cols=65  Identities=18%  Similarity=0.141  Sum_probs=44.3

Q ss_pred             CCCCCchHHHHHHH----HHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHH
Q psy7691          59 GFEEPTAIQAQGWP----IALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQA  134 (165)
Q Consensus        59 g~~~~t~~Q~~a~~----~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~  134 (165)
                      ||. +-+-|.+-..    .+..+.++++-|+||+|||++|+   +|     .+... +     ..+..+++.++| ..+-
T Consensus       255 ~~e-~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYL---lp-----a~~~a-~-----~~~~~vvIsT~T-~~LQ  318 (928)
T PRK08074        255 KYE-KREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYL---LP-----AAYFA-K-----KKEEPVVISTYT-IQLQ  318 (928)
T ss_pred             CCc-CCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHH---HH-----HHHHh-h-----ccCCeEEEEcCC-HHHH
Confidence            665 6777776333    34567889999999999999999   89     44322 1     234567777877 6665


Q ss_pred             HHHHH
Q psy7691         135 KELIA  139 (165)
Q Consensus       135 ~~i~~  139 (165)
                      .|+..
T Consensus       319 ~Ql~~  323 (928)
T PRK08074        319 QQLLE  323 (928)
T ss_pred             HHHHH
Confidence            66543

>KOG0352|consensus

Probab=95.27  E-value=0.032  Score=48.32  Aligned_cols=87  Identities=21%  Similarity=0.271  Sum_probs=60.5

Q ss_pred             cCCCcHHHHHHHHhCCCCCC-----------chHHHHHHHHHHcCCCeeeeccc---CCc--c--cceeeecCCCCChhH
Q psy7691          44 EGCFPNAVLQHLKGQGFEEP-----------TAIQAQGWPIALSGRDMVGIAQT---GSG--K--TLAVINFDYPNSSED  105 (165)
Q Consensus        44 ~l~l~~~l~~~l~~~g~~~~-----------t~~Q~~a~~~~l~G~di~~~a~t---gsG--K--t~~~~~~~lP~~~~~  105 (165)
                      +-+-++++.=.|...|+...           |.+|..    .|++ +++++..|   |.|  |  .-.|+||++|.++.-
T Consensus       264 TR~~cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe~----WM~~-~~PvI~AT~SFGMGVDKp~VRFViHW~~~qn~Ag  338 (641)
T KOG0352|consen  264 TRNECEQVAIMLEIAGIPAMAYHAGLKKKERTEVQEK----WMNN-EIPVIAATVSFGMGVDKPDVRFVIHWSPSQNLAG  338 (641)
T ss_pred             cHHHHHHHHHHhhhcCcchHHHhcccccchhHHHHHH----HhcC-CCCEEEEEeccccccCCcceeEEEecCchhhhHH
Confidence            33556666666666666432           445543    4455 44444443   444  2  225899999999999


Q ss_pred             HHHhhccCCCCCCCCceEEEECCCcHHHHH
Q psy7691         106 YIHRIGRTGRCASSGTAYTFFTPNNGKQAK  135 (165)
Q Consensus       106 ~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~  135 (165)
                      |-|..||+||+|..+.+-+++...++....
T Consensus       339 YYQESGRAGRDGk~SyCRLYYsR~D~~~i~  368 (641)
T KOG0352|consen  339 YYQESGRAGRDGKRSYCRLYYSRQDKNALN  368 (641)
T ss_pred             HHHhccccccCCCccceeeeecccchHHHH
Confidence            999999999999999999999988865543

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=95.24  E-value=0.012  Score=56.93  Aligned_cols=86  Identities=20%  Similarity=0.216  Sum_probs=53.5

Q ss_pred             CCCcccccc-CCCcHHHHHHHHhCCCCC---------Cc-hHHHHH------------HHHHHcCCCeeeecccCCcccc
Q psy7691          36 PCPTQELTE-GCFPNAVLQHLKGQGFEE---------PT-AIQAQG------------WPIALSGRDMVGIAQTGSGKTL   92 (165)
Q Consensus        36 p~~i~~f~~-l~l~~~l~~~l~~~g~~~---------~t-~~Q~~a------------~~~~l~G~di~~~a~tgsGKt~   92 (165)
                      +..++.|-. ..-.+.+.+.|.+.++..         .+ ..|..+            ++.+.+|.||..+.        
T Consensus       286 ~GdILVFLpg~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ~~Vf~~~g~rkIIVATNIAEtSITIpgI~--------  357 (1294)
T PRK11131        286 PGDILIFMSGEREIRDTADALNKLNLRHTEILPLYARLSNSEQNRVFQSHSGRRIVLATNVAETSLTVPGIK--------  357 (1294)
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHhcCCCcceEeecccCCCHHHHHHHhcccCCeeEEEeccHHhhccccCcce--------
Confidence            344666644 345566777777766542         12 234333            33333444444443        


Q ss_pred             eeeecC---------------CCC---ChhHHHHhhccCCCCCCCCceEEEECCCc
Q psy7691          93 AVINFD---------------YPN---SSEDYIHRIGRTGRCASSGTAYTFFTPNN  130 (165)
Q Consensus        93 ~~~~~~---------------lP~---~~~~~i~r~gr~~r~~~~g~~~~~~~p~~  130 (165)
                      .||+++               +|.   +..+|.||.||+||. ..|.|+.+++..+
T Consensus       358 yVID~Gl~k~~~Yd~~~~~~~Lp~~~iSkasa~QRaGRAGR~-~~G~c~rLyte~d  412 (1294)
T PRK11131        358 YVIDPGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRV-SEGICIRLYSEDD  412 (1294)
T ss_pred             EEEECCCccccccccccCcccCCeeecCHhhHhhhccccCCC-CCcEEEEeCCHHH
Confidence            788875               453   347899999999999 7899999998653

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=95.23  E-value=0.032  Score=38.44  Aligned_cols=53  Identities=30%  Similarity=0.347  Sum_probs=34.7

Q ss_pred             CeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcC
Q psy7691          79 DMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus        79 di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~  145 (165)
                      .++..++||+|||..++   .      ++.+..+.    .....+++++|. ..+..+..+.+....
T Consensus         2 ~~~i~~~~G~GKT~~~~---~------~~~~~~~~----~~~~~~lv~~p~-~~l~~~~~~~~~~~~   54 (144)
T cd00046           2 DVLLAAPTGSGKTLAAL---L------PILELLDS----LKGGQVLVLAPT-RELANQVAERLKELF   54 (144)
T ss_pred             CEEEECCCCCchhHHHH---H------HHHHHHhc----ccCCCEEEEcCc-HHHHHHHHHHHHHHh
Confidence            57889999999998765   2      34333332    123467888888 677776666655544

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

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=95.16  E-value=0.015  Score=54.08  Aligned_cols=36  Identities=19%  Similarity=0.427  Sum_probs=29.8

Q ss_pred             eeeecCCCCC------------------hhHHHHhhccCCCCCCCCceEEEECCC
Q psy7691          93 AVINFDYPNS------------------SEDYIHRIGRTGRCASSGTAYTFFTPN  129 (165)
Q Consensus        93 ~~~~~~lP~~------------------~~~~i~r~gr~~r~~~~g~~~~~~~p~  129 (165)
                      .||++++|..                  ..+|+||.||+||. ..|.|+.+++..
T Consensus       286 ~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRaGR~-~~G~cyrL~t~~  339 (812)
T PRK11664        286 LVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRL-EPGICLHLYSKE  339 (812)
T ss_pred             EEEECCCcccccccccCCcceeEEEeechhhhhhhccccCCC-CCcEEEEecCHH
Confidence            7899888753                  24799999999998 689999998855

>PRK01172 ski2-like helicase; Provisional

Probab=95.15  E-value=0.03  Score=50.80  Aligned_cols=41  Identities=22%  Similarity=0.251  Sum_probs=26.4

Q ss_pred             CCChhHHHHhhccCCCCCC--CCceEEEECCCcHHHHHHHHHHHH
Q psy7691         100 PNSSEDYIHRIGRTGRCAS--SGTAYTFFTPNNGKQAKELIAVLT  142 (165)
Q Consensus       100 P~~~~~~i~r~gr~~r~~~--~g~~~~~~~p~~~~~~~~i~~~l~  142 (165)
                      |-+..+|.||+||+||.|.  .|.+++++...+  ....+.+++.
T Consensus       347 ~~s~~~~~Qm~GRAGR~g~d~~g~~~i~~~~~~--~~~~~~~~l~  389 (674)
T PRK01172        347 YLSNMEIKQMIGRAGRPGYDQYGIGYIYAASPA--SYDAAKKYLS  389 (674)
T ss_pred             eCCHHHHHHHhhcCCCCCCCCcceEEEEecCcc--cHHHHHHHHc
Confidence            3457789999999999995  455666655432  1233455553

>PRK00254 ski2-like helicase; Provisional

Probab=95.14  E-value=0.031  Score=51.19  Aligned_cols=35  Identities=26%  Similarity=0.421  Sum_probs=25.3

Q ss_pred             ecCCCC-ChhHHHHhhccCCCCC--CCCceEEEECCCc
Q psy7691          96 NFDYPN-SSEDYIHRIGRTGRCA--SSGTAYTFFTPNN  130 (165)
Q Consensus        96 ~~~lP~-~~~~~i~r~gr~~r~~--~~g~~~~~~~p~~  130 (165)
                      +|+.|. ...+|+||+||+||.|  ..|.++++..+.+
T Consensus       352 ~~~~~~~~~~~~~Qm~GRAGR~~~d~~G~~ii~~~~~~  389 (720)
T PRK00254        352 NFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEE  389 (720)
T ss_pred             CCCceeCCHHHHHHhhhccCCCCcCCCceEEEEecCcc
Confidence            355543 3568999999999976  5677887776654

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

Probab=94.90  E-value=0.057  Score=51.95  Aligned_cols=71  Identities=17%  Similarity=0.202  Sum_probs=51.0

Q ss_pred             CCchHHHHHHHHHH----cC-CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHH
Q psy7691          62 EPTAIQAQGWPIAL----SG-RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKE  136 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l----~G-~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~  136 (165)
                      .+.+.|.+|+..+.    .| +.++++.+||||||...+    .     ++.++-+.++    ...++|+++. .++..|
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai----~-----li~~L~~~~~----~~rVLfLvDR-~~L~~Q  478 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAI----A-----LMYRLLKAKR----FRRILFLVDR-SALGEQ  478 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHH----H-----HHHHHHhcCc----cCeEEEEecH-HHHHHH
Confidence            36889999987764    34 578899999999997543    2     5555544432    2367888877 889999


Q ss_pred             HHHHHHhcCC
Q psy7691         137 LIAVLTEASQ  146 (165)
Q Consensus       137 i~~~l~~~~~  146 (165)
                      ..+.+.....
T Consensus       479 a~~~F~~~~~  488 (1123)
T PRK11448        479 AEDAFKDTKI  488 (1123)
T ss_pred             HHHHHHhccc
Confidence            8888877543

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=94.81  E-value=0.068  Score=48.94  Aligned_cols=38  Identities=45%  Similarity=0.474  Sum_probs=27.9

Q ss_pred             CCCCCchHHHHHHHHH---HcC------CCeeeecccCCcccceeeecCCC
Q psy7691          59 GFEEPTAIQAQGWPIA---LSG------RDMVGIAQTGSGKTLAVINFDYP  100 (165)
Q Consensus        59 g~~~~t~~Q~~a~~~~---l~G------~di~~~a~tgsGKt~~~~~~~lP  100 (165)
                      ||. +-+-|.+-...+   +.+      ..+++-|+||+|||++|+   +|
T Consensus        23 ~~e-~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYL---lP   69 (697)
T PRK11747         23 GFI-PRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYL---LA   69 (697)
T ss_pred             CCC-cCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHH---HH
Confidence            675 567777633333   333      568899999999999999   88

>PHA02558 uvsW UvsW helicase; Provisional

Probab=94.81  E-value=0.023  Score=49.86  Aligned_cols=90  Identities=16%  Similarity=0.012  Sum_probs=55.0

Q ss_pred             CCccccccCCCcHHHHHHHHhCCCCC------CchHHHHHHHH-HHcCCC-eeee--cccCCcc----cceeeecCCCCC
Q psy7691          37 CPTQELTEGCFPNAVLQHLKGQGFEE------PTAIQAQGWPI-ALSGRD-MVGI--AQTGSGK----TLAVINFDYPNS  102 (165)
Q Consensus        37 ~~i~~f~~l~l~~~l~~~l~~~g~~~------~t~~Q~~a~~~-~l~G~d-i~~~--a~tgsGK----t~~~~~~~lP~~  102 (165)
                      .+++.|....-.+.+.+.|.+.|+..      .+..++..+-. +..|.. ++++  +--|.|=    .-++++++.|.+
T Consensus       346 ~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLvaT~~~l~eG~Dip~ld~vIl~~p~~s  425 (501)
T PHA02558        346 NTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYGVFSTGISIKNLHHVIFAHPSKS  425 (501)
T ss_pred             CEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHhCCCCeEEEEEcceeccccccccccEEEEecCCcc
Confidence            45666666555677788888877643      23344443322 333443 2222  2334442    225677888888


Q ss_pred             hhHHHHhhccCCCCCCCCceEEEE
Q psy7691         103 SEDYIHRIGRTGRCASSGTAYTFF  126 (165)
Q Consensus       103 ~~~~i~r~gr~~r~~~~g~~~~~~  126 (165)
                      ...|+||+||++|.+..+..+.++
T Consensus       426 ~~~~~QriGR~~R~~~~K~~~~i~  449 (501)
T PHA02558        426 KIIVLQSIGRVLRKHGSKSIATVW  449 (501)
T ss_pred             hhhhhhhhhccccCCCCCceEEEE
Confidence            889999999999998766555544

>KOG0354|consensus

Probab=94.80  E-value=0.064  Score=49.10  Aligned_cols=89  Identities=19%  Similarity=0.195  Sum_probs=60.6

Q ss_pred             CCccccccC-CCcHHHHHHHHh-CCC-----------------CCCchHHHHHHHHHHcCC-CeeeecccC-----Cccc
Q psy7691          37 CPTQELTEG-CFPNAVLQHLKG-QGF-----------------EEPTAIQAQGWPIALSGR-DMVGIAQTG-----SGKT   91 (165)
Q Consensus        37 ~~i~~f~~l-~l~~~l~~~l~~-~g~-----------------~~~t~~Q~~a~~~~l~G~-di~~~a~tg-----sGKt   91 (165)
                      ..++.|.+. .....|.++|.+ ...                 ..-...|.+.+..+..|. ++++...-|     -|-.
T Consensus       414 sR~IIFve~R~sa~~l~~~l~~~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G~~NvLVATSV~EEGLDI~ec  493 (746)
T KOG0354|consen  414 SRTIIFVETRESALALKKWLLQLHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRDGEINVLVATSVAEEGLDIGEC  493 (746)
T ss_pred             ccEEEEEehHHHHHHHHHHHHhhhhcccccceeeeccccccccccCHHHHHHHHHHHhCCCccEEEEecchhccCCcccc
Confidence            457788887 677788888773 111                 111247888888887773 444332221     2233


Q ss_pred             ceeeecCCCCChhHHHHhhccCCCCCCCCceEEEEC
Q psy7691          92 LAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFT  127 (165)
Q Consensus        92 ~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~  127 (165)
                      ..+|-||.-.+....+||.|| ||+ ++|.++++.+
T Consensus       494 ~lVIcYd~~snpIrmIQrrGR-gRa-~ns~~vll~t  527 (746)
T KOG0354|consen  494 NLVICYDYSSNPIRMVQRRGR-GRA-RNSKCVLLTT  527 (746)
T ss_pred             cEEEEecCCccHHHHHHHhcc-ccc-cCCeEEEEEc
Confidence            378999999999999999999 887 6677888877

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=94.58  E-value=0.032  Score=54.07  Aligned_cols=27  Identities=30%  Similarity=0.509  Sum_probs=23.1

Q ss_pred             ChhHHHHhhccCCCCCCCCceEEEECCC
Q psy7691         102 SSEDYIHRIGRTGRCASSGTAYTFFTPN  129 (165)
Q Consensus       102 ~~~~~i~r~gr~~r~~~~g~~~~~~~p~  129 (165)
                      +..+|+||.||+||.+ .|.|+.+++..
T Consensus       378 Skasa~QRaGRAGR~~-~G~cyRLyte~  404 (1283)
T TIGR01967       378 SQASANQRKGRCGRVA-PGICIRLYSEE  404 (1283)
T ss_pred             CHHHHHHHhhhhCCCC-CceEEEecCHH
Confidence            3468999999999997 89999998754

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.

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

Probab=93.82  E-value=0.12  Score=46.60  Aligned_cols=65  Identities=29%  Similarity=0.385  Sum_probs=41.5

Q ss_pred             CCCCCchHHHHHHHHH----HcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHH
Q psy7691          59 GFEEPTAIQAQGWPIA----LSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQA  134 (165)
Q Consensus        59 g~~~~t~~Q~~a~~~~----l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~  134 (165)
                      || .+.+.|.+.+..+    ..|..+++.|+||+|||++++   +|     -+... +     ..+..+.+.+.+ ..+.
T Consensus        13 ~~-~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL---~~-----al~~~-~-----~~~~~viist~t-~~lq   76 (654)
T COG1199          13 GF-EPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYL---LP-----ALAYA-R-----EEGKKVIISTRT-KALQ   76 (654)
T ss_pred             CC-CCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHH---HH-----HHHHH-H-----HcCCcEEEECCC-HHHH
Confidence            44 4888998766433    445559999999999999999   77     23222 1     122456666666 5554


Q ss_pred             HHHHH
Q psy7691         135 KELIA  139 (165)
Q Consensus       135 ~~i~~  139 (165)
                      .|+.+
T Consensus        77 ~q~~~   81 (654)
T COG1199          77 EQLLE   81 (654)
T ss_pred             HHHHH
Confidence            55443

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=93.70  E-value=0.064  Score=50.19  Aligned_cols=68  Identities=24%  Similarity=0.271  Sum_probs=48.0

Q ss_pred             CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHH
Q psy7691          58 QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL  137 (165)
Q Consensus        58 ~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i  137 (165)
                      .|.. |+++|..+--.+..|.  ++..+||+|||+++.   ||.    |++-.        .|..+.+++|+ ..++.+.
T Consensus        79 lgm~-~ydVQliGgl~L~~G~--IaEm~TGEGKTL~a~---lp~----~l~al--------~g~~VhIvT~n-dyLA~RD  139 (908)
T PRK13107         79 FEMR-HFDVQLLGGMVLDSNR--IAEMRTGEGKTLTAT---LPA----YLNAL--------TGKGVHVITVN-DYLARRD  139 (908)
T ss_pred             hCCC-cCchHHhcchHhcCCc--cccccCCCCchHHHH---HHH----HHHHh--------cCCCEEEEeCC-HHHHHHH
Confidence            4665 7889977544445553  579999999999998   883    44432        22348899999 7788877


Q ss_pred             HHHHHhc
Q psy7691         138 IAVLTEA  144 (165)
Q Consensus       138 ~~~l~~~  144 (165)
                      .+++...
T Consensus       140 ~e~m~~l  146 (908)
T PRK13107        140 AENNRPL  146 (908)
T ss_pred             HHHHHHH
Confidence            7776553

>PRK05580 primosome assembly protein PriA; Validated

Probab=93.68  E-value=0.13  Score=47.07  Aligned_cols=37  Identities=22%  Similarity=0.214  Sum_probs=28.3

Q ss_pred             eeecCCCCCh----------hHHHHhhccCCCCCCCCceEEEECCCc
Q psy7691          94 VINFDYPNSS----------EDYIHRIGRTGRCASSGTAYTFFTPNN  130 (165)
Q Consensus        94 ~~~~~lP~~~----------~~~i~r~gr~~r~~~~g~~~~~~~p~~  130 (165)
                      ++++|.+...          ..|+|+.||+||.+..|.+++....++
T Consensus       504 il~aD~~l~~pdfra~Er~~~~l~q~~GRagR~~~~g~viiqT~~p~  550 (679)
T PRK05580        504 VLDADLGLFSPDFRASERTFQLLTQVAGRAGRAEKPGEVLIQTYHPE  550 (679)
T ss_pred             EEcCchhccCCccchHHHHHHHHHHHHhhccCCCCCCEEEEEeCCCC
Confidence            4677777553          568999999999999998887665443

>KOG0951|consensus

Probab=93.50  E-value=0.14  Score=49.47  Aligned_cols=88  Identities=22%  Similarity=0.317  Sum_probs=62.4

Q ss_pred             CCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcC-CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCC-C---C
Q psy7691          45 GCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSG-RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCA-S---S  119 (165)
Q Consensus        45 l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G-~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~-~---~  119 (165)
                      +.+|++-..++.  |......+|..-.+.++++ .+++.|||||+|||.--+   +     +.++.+++..|.. .   .
T Consensus       294 selP~Wnq~aF~--g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAv---L-----tiLqel~~h~r~dgs~nl~  363 (1674)
T KOG0951|consen  294 SELPKWNQPAFF--GKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAV---L-----TILQELGNHLREDGSVNLA  363 (1674)
T ss_pred             cCCcchhhhhcc--cchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHH---H-----HHHHHHhcccccccceecc
Confidence            367777777776  5666889999999999888 579999999999998443   3     3888888754421 1   1


Q ss_pred             CceEEEECCCcHHHHHHHHHHHHh
Q psy7691         120 GTAYTFFTPNNGKQAKELIAVLTE  143 (165)
Q Consensus       120 g~~~~~~~p~~~~~~~~i~~~l~~  143 (165)
                      ..-+.++.|. ..++..+...+..
T Consensus       364 ~fKIVYIAPm-KaLvqE~VgsfSk  386 (1674)
T KOG0951|consen  364 PFKIVYIAPM-KALVQEMVGSFSK  386 (1674)
T ss_pred             cceEEEEeeH-HHHHHHHHHHHHh
Confidence            2257778887 6666666554443

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

Probab=93.46  E-value=0.085  Score=43.80  Aligned_cols=42  Identities=29%  Similarity=0.319  Sum_probs=30.7

Q ss_pred             CCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccc
Q psy7691          33 NNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTL   92 (165)
Q Consensus        33 ~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~   92 (165)
                      ..+|..+..|++|++|+-+.+.+..                 -+| =|++.+||||||+.
T Consensus        99 R~Ip~~i~~~e~LglP~i~~~~~~~-----------------~~G-LILVTGpTGSGKST  140 (353)
T COG2805          99 RLIPSKIPTLEELGLPPIVRELAES-----------------PRG-LILVTGPTGSGKST  140 (353)
T ss_pred             eccCccCCCHHHcCCCHHHHHHHhC-----------------CCc-eEEEeCCCCCcHHH
Confidence            3478888899999888887773321                 122 37899999999965

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

Probab=93.32  E-value=0.16  Score=39.12  Aligned_cols=63  Identities=24%  Similarity=0.196  Sum_probs=40.5

Q ss_pred             CchHHHHHHHHHHcCCC--eeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHH
Q psy7691          63 PTAIQAQGWPIALSGRD--MVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAV  140 (165)
Q Consensus        63 ~t~~Q~~a~~~~l~G~d--i~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~  140 (165)
                      .++-|.+++..++...|  .+++++.|+|||....          .+.+.-..     .|..+.+++|+ ...+..+.+.
T Consensus         2 L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l~----------~~~~~~~~-----~g~~v~~~apT-~~Aa~~L~~~   65 (196)
T PF13604_consen    2 LNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLLK----------ALAEALEA-----AGKRVIGLAPT-NKAAKELREK   65 (196)
T ss_dssp             S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHHH----------HHHHHHHH-----TT--EEEEESS-HHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHHH----------HHHHHHHh-----CCCeEEEECCc-HHHHHHHHHh
Confidence            57889999999876543  5577999999997533          12111111     35678999999 5556666655


Q ss_pred             H
Q psy7691         141 L  141 (165)
Q Consensus       141 l  141 (165)
                      +
T Consensus        66 ~   66 (196)
T PF13604_consen   66 T   66 (196)
T ss_dssp             H
T ss_pred             h
Confidence            4

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=92.94  E-value=0.056  Score=45.41  Aligned_cols=65  Identities=22%  Similarity=0.209  Sum_probs=40.1

Q ss_pred             ccccccCCCcHHHHHHHHhCCCC--C------CchHHH---------HHHHHHHcCCCeeeecccCCcccceeeecCCCC
Q psy7691          39 TQELTEGCFPNAVLQHLKGQGFE--E------PTAIQA---------QGWPIALSGRDMVGIAQTGSGKTLAVINFDYPN  101 (165)
Q Consensus        39 i~~f~~l~l~~~l~~~l~~~g~~--~------~t~~Q~---------~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~  101 (165)
                      ++.+.+..-.+.+.+.|++.|+.  .      ....++         .|++.+.+|.|+...         .++ ++ |.
T Consensus       276 LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~R~~~~~~~iLVaTdv~~rGiDi~~~---------~vi-~~-p~  344 (357)
T TIGR03158       276 AIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKDRERAMQFDILLGTSTVDVGVDFKRD---------WLI-FS-AR  344 (357)
T ss_pred             EEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHHHHHhccCCEEEEecHHhcccCCCCc---------eEE-EC-CC
Confidence            44555567777888888775432  1      011111         145556677776432         344 45 88


Q ss_pred             ChhHHHHhhccCC
Q psy7691         102 SSEDYIHRIGRTG  114 (165)
Q Consensus       102 ~~~~~i~r~gr~~  114 (165)
                      +.++|+||+||+|
T Consensus       345 ~~~~yiqR~GR~g  357 (357)
T TIGR03158       345 DAAAFWQRLGRLG  357 (357)
T ss_pred             CHHHHhhhcccCC
Confidence            9999999999985

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.

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

Probab=92.47  E-value=0.25  Score=41.77  Aligned_cols=20  Identities=35%  Similarity=0.539  Sum_probs=17.6

Q ss_pred             CeeeecccCCcccceeeecCCCC
Q psy7691          79 DMVGIAQTGSGKTLAVINFDYPN  101 (165)
Q Consensus        79 di~~~a~tgsGKt~~~~~~~lP~  101 (165)
                      +++++|+||||||.+++   +|.
T Consensus         1 H~lv~g~tGsGKt~~~v---iP~   20 (384)
T cd01126           1 HVLVFAPTRSGKGVGFV---IPN   20 (384)
T ss_pred             CeeEecCCCCCCccEEE---ccc
Confidence            47889999999999998   883

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.

>TIGR00595 priA primosomal protein N'

Probab=91.98  E-value=0.12  Score=45.69  Aligned_cols=47  Identities=21%  Similarity=0.246  Sum_probs=32.2

Q ss_pred             eecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691          82 GIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus        82 ~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      ..++||||||..++.         .+..+-.      .|..++++.|+ ..++.|+.+.+++.
T Consensus         2 L~g~TGsGKT~v~l~---------~i~~~l~------~g~~vLvlvP~-i~L~~Q~~~~l~~~   48 (505)
T TIGR00595         2 LFGVTGSGKTEVYLQ---------AIEKVLA------LGKSVLVLVPE-IALTPQMIQRFKYR   48 (505)
T ss_pred             ccCCCCCCHHHHHHH---------HHHHHHH------cCCeEEEEeCc-HHHHHHHHHHHHHH
Confidence            468999999997651         2222211      24468888898 88888888777653

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).

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

Probab=91.96  E-value=0.25  Score=43.98  Aligned_cols=65  Identities=26%  Similarity=0.378  Sum_probs=47.0

Q ss_pred             CCCCCchHHHHHHHHHHcC-----CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHH
Q psy7691          59 GFEEPTAIQAQGWPIALSG-----RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQ  133 (165)
Q Consensus        59 g~~~~t~~Q~~a~~~~l~G-----~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~  133 (165)
                      .|. |+--|-.||..+..|     ++-...+.||||||..+.|         .|.++.|+         .++++|. ..+
T Consensus        10 ~f~-PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~An---------VI~~~~rP---------tLV~AhN-KTL   69 (663)
T COG0556          10 PFK-PAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTMAN---------VIAKVQRP---------TLVLAHN-KTL   69 (663)
T ss_pred             CCC-CCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHHHH---------HHHHhCCC---------eEEEecc-hhH
Confidence            454 777888888877666     3455678999999986543         78888774         6777777 777


Q ss_pred             HHHHHHHHHh
Q psy7691         134 AKELIAVLTE  143 (165)
Q Consensus       134 ~~~i~~~l~~  143 (165)
                      +.|+..-+..
T Consensus        70 AaQLy~Efk~   79 (663)
T COG0556          70 AAQLYSEFKE   79 (663)
T ss_pred             HHHHHHHHHH
Confidence            7777766654

>COG5008 PilU Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=91.33  E-value=0.45  Score=39.19  Aligned_cols=97  Identities=21%  Similarity=0.320  Sum_probs=46.2

Q ss_pred             hhcCCHHHHHHHHhhcCcEEec--CCCC-CCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHH-------HHcCCCe
Q psy7691          11 AARLSESEVEAFRQKKEITVKG--NNIP-CPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPI-------ALSGRDM   80 (165)
Q Consensus        11 ~~~~~~~~~~~~~~~~~i~~~~--~~~p-~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~-------~l~G~di   80 (165)
                      .+-|+++.-++|++.++...--  .+.- -.+.-|-+-++..-+++.+... +  | .++..-+|.       .-||. +
T Consensus        56 ~~iM~~~q~~eF~~~~EcNfai~~~~~gRfRvnAf~qr~~~g~VlRrI~~~-I--P-t~eeL~LPevlk~la~~kRGL-v  130 (375)
T COG5008          56 FSIMSAKQREEFEETHECNFAISARDIGRFRVNAFYQRGLAGLVLRRIETK-I--P-TFEELKLPEVLKDLALAKRGL-V  130 (375)
T ss_pred             HHHhhHHHHHHHHhcccceEEEEcCCCceEEeehhhhcCcchhhhhhhhcc-C--C-cHHhcCCcHHHHHhhcccCce-E
Confidence            3457788888888777543321  1100 0122333334444444444321 1  1 111111111       12443 5


Q ss_pred             eeecccCCcccce------eeecCCC------CChhHHHHhhcc
Q psy7691          81 VGIAQTGSGKTLA------VINFDYP------NSSEDYIHRIGR  112 (165)
Q Consensus        81 ~~~a~tgsGKt~~------~~~~~lP------~~~~~~i~r~gr  112 (165)
                      +.+++|||||+..      +-|-+.+      .++..|+|...|
T Consensus       131 iiVGaTGSGKSTtmAaMi~yRN~~s~gHIiTIEDPIEfih~h~~  174 (375)
T COG5008         131 IIVGATGSGKSTTMAAMIGYRNKNSTGHIITIEDPIEFIHKHKR  174 (375)
T ss_pred             EEECCCCCCchhhHHHHhcccccCCCCceEEecChHHHHhcccc
Confidence            6799999999652      1111122      456778886654

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

Probab=91.32  E-value=0.8  Score=42.28  Aligned_cols=65  Identities=23%  Similarity=0.237  Sum_probs=42.7

Q ss_pred             CCchHHHHHHHHHHcC----CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALSG----RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL  137 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G----~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i  137 (165)
                      .....|..|...+...    .-.+..+.||||||..            |++-+...-+   .|..++++.|. -.+..|+
T Consensus       198 ~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEv------------Yl~~i~~~L~---~GkqvLvLVPE-I~Ltpq~  261 (730)
T COG1198         198 ALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEV------------YLEAIAKVLA---QGKQVLVLVPE-IALTPQL  261 (730)
T ss_pred             ccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHH------------HHHHHHHHHH---cCCEEEEEecc-ccchHHH
Confidence            4566788888877555    4578899999999975            5555543322   45678888887 4444444


Q ss_pred             HHHHH
Q psy7691         138 IAVLT  142 (165)
Q Consensus       138 ~~~l~  142 (165)
                      .+-+.
T Consensus       262 ~~rf~  266 (730)
T COG1198         262 LARFK  266 (730)
T ss_pred             HHHHH
Confidence            44443

>TIGR00376 DNA helicase, putative

Probab=91.02  E-value=0.51  Score=42.86  Aligned_cols=66  Identities=21%  Similarity=0.274  Sum_probs=42.8

Q ss_pred             CCchHHHHHHHHHHcC-CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALSG-RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAV  140 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G-~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~  140 (165)
                      .+...|..|+..++.. ..+++.+++|+|||.....         ++...-.      .|..+++++|+. ..+..+.+.
T Consensus       157 ~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~---------ii~~~~~------~g~~VLv~a~sn-~Avd~l~e~  220 (637)
T TIGR00376       157 NLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVE---------LIRQLVK------RGLRVLVTAPSN-IAVDNLLER  220 (637)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHH---------HHHHHHH------cCCCEEEEcCcH-HHHHHHHHH
Confidence            4578999999988876 4567999999999964331         2222211      234788888884 444455544


Q ss_pred             HHh
Q psy7691         141 LTE  143 (165)
Q Consensus       141 l~~  143 (165)
                      +..
T Consensus       221 l~~  223 (637)
T TIGR00376       221 LAL  223 (637)
T ss_pred             HHh
Confidence            443

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.

>TIGR00595 priA primosomal protein N'

Probab=90.83  E-value=0.34  Score=42.74  Aligned_cols=38  Identities=24%  Similarity=0.314  Sum_probs=26.9

Q ss_pred             eeeecCCCCC----------hhHHHHhhccCCCCCCCCceEEEE-CCCc
Q psy7691          93 AVINFDYPNS----------SEDYIHRIGRTGRCASSGTAYTFF-TPNN  130 (165)
Q Consensus        93 ~~~~~~lP~~----------~~~~i~r~gr~~r~~~~g~~~~~~-~p~~  130 (165)
                      .++++|....          ...|+|+.||+||.+..|.+++.. .|..
T Consensus       335 ~vl~aD~~l~~pd~ra~E~~~~ll~q~~GRagR~~~~g~viiqt~~p~~  383 (505)
T TIGR00595       335 GVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGQVIIQTYNPNH  383 (505)
T ss_pred             EEEcCcccccCcccchHHHHHHHHHHHHhccCCCCCCCEEEEEeCCCCC
Confidence            3578886332          356899999999999999877544 4443

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).

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

Probab=90.74  E-value=0.52  Score=43.02  Aligned_cols=69  Identities=14%  Similarity=0.092  Sum_probs=45.2

Q ss_pred             chHHHHHHHHH----Hc-----C-CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHH
Q psy7691          64 TAIQAQGWPIA----LS-----G-RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQ  133 (165)
Q Consensus        64 t~~Q~~a~~~~----l~-----G-~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~  133 (165)
                      -+.|..|+..+    .+     | +..++..+||||||+..+.         +.+++-+.    .....++++++. .++
T Consensus       240 r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~---------la~~l~~~----~~~~~vl~lvdR-~~L  305 (667)
T TIGR00348       240 RYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLF---------AARKALEL----LKNPKVFFVVDR-REL  305 (667)
T ss_pred             HHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHH---------HHHHHHhh----cCCCeEEEEECc-HHH
Confidence            44677777654    23     2 4578899999999985441         23333221    234567788877 889


Q ss_pred             HHHHHHHHHhcCC
Q psy7691         134 AKELIAVLTEASQ  146 (165)
Q Consensus       134 ~~~i~~~l~~~~~  146 (165)
                      ..|+.+.+.....
T Consensus       306 ~~Q~~~~f~~~~~  318 (667)
T TIGR00348       306 DYQLMKEFQSLQK  318 (667)
T ss_pred             HHHHHHHHHhhCC
Confidence            9999988887653

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

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

Probab=90.46  E-value=0.35  Score=41.80  Aligned_cols=52  Identities=23%  Similarity=0.373  Sum_probs=35.3

Q ss_pred             CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCC
Q psy7691          78 RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQP  147 (165)
Q Consensus        78 ~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~  147 (165)
                      .+++++|+||||||..++   +|.    .++   .      .+ .+++..|. .+++.....+++..+..
T Consensus        45 ~h~lvig~tgSGKt~~~v---iP~----ll~---~------~~-s~iV~D~K-gEl~~~t~~~r~~~G~~   96 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFV---IPN----LLN---Y------PG-SMIVTDPK-GELYEKTAGYRKKRGYK   96 (469)
T ss_pred             eEEEEEeCCCCCccceee---HhH----HHh---c------cC-CEEEEECC-CcHHHHHHHHHHHCCCE
Confidence            469999999999999999   883    221   1      11 45555555 67777666666665543

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

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=90.39  E-value=0.53  Score=42.59  Aligned_cols=21  Identities=38%  Similarity=0.604  Sum_probs=18.8

Q ss_pred             CCeeeecccCCcccceeeecCCCC
Q psy7691          78 RDMVGIAQTGSGKTLAVINFDYPN  101 (165)
Q Consensus        78 ~di~~~a~tgsGKt~~~~~~~lP~  101 (165)
                      .+++++|+||||||..++   +|.
T Consensus       159 ~hvLviapTgSGKg~g~V---IPn  179 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFV---IPN  179 (606)
T ss_pred             ceEEEEcCCCCCcceEEe---hhh
Confidence            468999999999999999   883

>TIGR00603 rad25 DNA repair helicase rad25

Probab=90.36  E-value=0.61  Score=43.08  Aligned_cols=61  Identities=11%  Similarity=0.174  Sum_probs=39.5

Q ss_pred             CchHHHHHHHHHH-cC--CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHH
Q psy7691          63 PTAIQAQGWPIAL-SG--RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIA  139 (165)
Q Consensus        63 ~t~~Q~~a~~~~l-~G--~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~  139 (165)
                      +.+.|.+|+..+. .|  +..+++.|||+|||+..+    -     .+.+++         ..+++++|+ ..++.|-.+
T Consensus       256 LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai----~-----aa~~l~---------k~tLILvps-~~Lv~QW~~  316 (732)
T TIGR00603       256 IRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGV----T-----AACTVK---------KSCLVLCTS-AVSVEQWKQ  316 (732)
T ss_pred             cCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHH----H-----HHHHhC---------CCEEEEeCc-HHHHHHHHH
Confidence            4568999988776 34  357789999999998544    1     333332         236788887 555555444


Q ss_pred             HHH
Q psy7691         140 VLT  142 (165)
Q Consensus       140 ~l~  142 (165)
                      .+.
T Consensus       317 ef~  319 (732)
T TIGR00603       317 QFK  319 (732)
T ss_pred             HHH
Confidence            443

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).

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

Probab=88.65  E-value=0.76  Score=38.96  Aligned_cols=66  Identities=21%  Similarity=0.144  Sum_probs=42.8

Q ss_pred             CCchHHHHHHHHH----HcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHH
Q psy7691          62 EPTAIQAQGWPIA----LSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL  137 (165)
Q Consensus        62 ~~t~~Q~~a~~~~----l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i  137 (165)
                      +.|+.|..+...+    -.-.|.++.|-||+|||..+.    +     -+..+-      +.|..+++.+|- .+....+
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEMif----~-----~i~~al------~~G~~vciASPR-vDVclEl  160 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEMIF----Q-----GIEQAL------NQGGRVCIASPR-VDVCLEL  160 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhhhH----H-----HHHHHH------hcCCeEEEecCc-ccchHHH
Confidence            3678888765544    455799999999999999764    2     333332      356678888887 4444444


Q ss_pred             HHHHHh
Q psy7691         138 IAVLTE  143 (165)
Q Consensus       138 ~~~l~~  143 (165)
                      ..-+.+
T Consensus       161 ~~Rlk~  166 (441)
T COG4098         161 YPRLKQ  166 (441)
T ss_pred             HHHHHH
Confidence            433333

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=88.62  E-value=0.73  Score=41.73  Aligned_cols=65  Identities=20%  Similarity=0.205  Sum_probs=40.2

Q ss_pred             CchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCC-CCCCCCceEEEECCCcHHHHHHHHHHH
Q psy7691          63 PTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTG-RCASSGTAYTFFTPNNGKQAKELIAVL  141 (165)
Q Consensus        63 ~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~-r~~~~g~~~~~~~p~~~~~~~~i~~~l  141 (165)
                      +++-|.+++.  ....++++.|..|||||...            ++|+.+.- ..+.....+++++-+ +..+.++.+-+
T Consensus         2 Ln~~Q~~av~--~~~~~~~V~Ag~GSGKT~~L------------~~ri~~ll~~~~~~p~~IL~vTFt-~~Aa~em~~Rl   66 (664)
T TIGR01074         2 LNPQQQEAVE--YVTGPCLVLAGAGSGKTRVI------------TNKIAYLIQNCGYKARNIAAVTFT-NKAAREMKERV   66 (664)
T ss_pred             CCHHHHHHHh--CCCCCEEEEecCCCCHHHHH------------HHHHHHHHHhcCCCHHHeEEEecc-HHHHHHHHHHH
Confidence            5678888764  23458999999999999743            34443322 122334467777777 45555555544


Q ss_pred             H
Q psy7691         142 T  142 (165)
Q Consensus       142 ~  142 (165)
                      .
T Consensus        67 ~   67 (664)
T TIGR01074        67 A   67 (664)
T ss_pred             H
Confidence            4

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

>KOG0353|consensus

Probab=88.55  E-value=0.5  Score=40.59  Aligned_cols=86  Identities=23%  Similarity=0.296  Sum_probs=55.1

Q ss_pred             cccccCCCcHHHHHHHHhCCCCCCc------------hHHHHHHHHHHcCC-C-eeeecccCCcc----cceeeecCCCC
Q psy7691          40 QELTEGCFPNAVLQHLKGQGFEEPT------------AIQAQGWPIALSGR-D-MVGIAQTGSGK----TLAVINFDYPN  101 (165)
Q Consensus        40 ~~f~~l~l~~~l~~~l~~~g~~~~t------------~~Q~~a~~~~l~G~-d-i~~~a~tgsGK----t~~~~~~~lP~  101 (165)
                      +..-..+-++.+.++|++.|+....            ..|..     ..|. - +++.-..|.|-    .-.|+|..+|.
T Consensus       322 iyc~sq~d~ekva~alkn~gi~a~~yha~lep~dks~~hq~w-----~a~eiqvivatvafgmgidkpdvrfvihhsl~k  396 (695)
T KOG0353|consen  322 IYCFSQKDCEKVAKALKNHGIHAGAYHANLEPEDKSGAHQGW-----IAGEIQVIVATVAFGMGIDKPDVRFVIHHSLPK  396 (695)
T ss_pred             EEEeccccHHHHHHHHHhcCccccccccccCccccccccccc-----cccceEEEEEEeeecccCCCCCeeEEEecccch
Confidence            3333446789999999999886421            12211     1121 1 22222333331    12688999999


Q ss_pred             ChhHHHH-------------------------------------------hhccCCCCCCCCceEEEECCCc
Q psy7691         102 SSEDYIH-------------------------------------------RIGRTGRCASSGTAYTFFTPNN  130 (165)
Q Consensus       102 ~~~~~i~-------------------------------------------r~gr~~r~~~~g~~~~~~~p~~  130 (165)
                      +.++|-+                                           ..||+||++.+..+++++.-.+
T Consensus       397 sienyyqasarillrmtkqknksdtggstqinilevctnfkiffavfsekesgragrd~~~a~cilyy~~~d  468 (695)
T KOG0353|consen  397 SIENYYQASARILLRMTKQKNKSDTGGSTQINILEVCTNFKIFFAVFSEKESGRAGRDDMKADCILYYGFAD  468 (695)
T ss_pred             hHHHHHHHHHHHHHHHhhhcccccCCCcceeehhhhhccceeeeeeecchhccccccCCCcccEEEEechHH
Confidence            9999999                                           6688888888888998887554

>PRK09694 helicase Cas3; Provisional

Probab=87.97  E-value=1.3  Score=41.74  Aligned_cols=65  Identities=20%  Similarity=0.251  Sum_probs=39.0

Q ss_pred             eeecCCCCChhHHHHhhccCCCCCCC----C---ceEEEECCCc-----------H-HHHHHHHHHHHhcC---CCCChH
Q psy7691          94 VINFDYPNSSEDYIHRIGRTGRCASS----G---TAYTFFTPNN-----------G-KQAKELIAVLTEAS---QPIPPQ  151 (165)
Q Consensus        94 ~~~~~lP~~~~~~i~r~gr~~r~~~~----g---~~~~~~~p~~-----------~-~~~~~i~~~l~~~~---~~~p~~  151 (165)
                      ++....|  .+.++||+||.+|.++.    |   +.+.++.|..           . ..+..-.+.+...+   ..+|..
T Consensus       642 lItdlaP--idsLiQRaGR~~R~~~~~rp~~~~~p~~~V~~p~~~~~~~~~~VY~~~~~L~rT~~~L~~~~~~~~~~P~~  719 (878)
T PRK09694        642 LITQLCP--VDLLFQRLGRLHRHHRKYRPAGFEIPVATVLLPDGEGYGRSGYIYGNTRVLWRTEQLLEEHNAASLFFPDA  719 (878)
T ss_pred             EEECCCC--HHHHHHHHhccCCCCCCCCCCCCcCceEEEEeccccccCCceeecCchHHHHHHHHHHHhcCCCCcCChHH
Confidence            4444455  67899999999998863    2   3344444432           1 23334445555554   557888


Q ss_pred             HHHHhhhCC
Q psy7691         152 LQDLANSNP  160 (165)
Q Consensus       152 ~~~~~~~~~  160 (165)
                      +..+....+
T Consensus       720 ~~~lve~vY  728 (878)
T PRK09694        720 YREWIESVY  728 (878)
T ss_pred             HHHHHHHHh
Confidence            777766544

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=87.50  E-value=0.91  Score=44.31  Aligned_cols=68  Identities=26%  Similarity=0.233  Sum_probs=42.4

Q ss_pred             CchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCc---HHHHHHHHH
Q psy7691          63 PTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN---GKQAKELIA  139 (165)
Q Consensus        63 ~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~---~~~~~~i~~  139 (165)
                      .|+.|.++|.  .+|.++++.|..|||||...+        +-+++.+-.    |..-..+++++=|+   .++-.+|.+
T Consensus         2 ~t~~Q~~ai~--~~~~~~lv~A~AGsGKT~~lv--------~r~~~~~~~----~~~~~~il~~tFt~~aa~e~~~ri~~   67 (1232)
T TIGR02785         2 WTDEQWQAIY--TRGQNILVSASAGSGKTAVLV--------ERIIKKILR----GVDIDRLLVVTFTNAAAREMKERIEE   67 (1232)
T ss_pred             CCHHHHHHHh--CCCCCEEEEecCCCcHHHHHH--------HHHHHHHhc----CCCHhhEEEEeccHHHHHHHHHHHHH
Confidence            5889999985  689999999999999997432        224444421    11212466777663   234445555


Q ss_pred             HHHhc
Q psy7691         140 VLTEA  144 (165)
Q Consensus       140 ~l~~~  144 (165)
                      .+...
T Consensus        68 ~l~~~   72 (1232)
T TIGR02785        68 ALQKA   72 (1232)
T ss_pred             HHHHH
Confidence            55443

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.

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=87.29  E-value=1.4  Score=39.79  Aligned_cols=70  Identities=21%  Similarity=0.219  Sum_probs=46.3

Q ss_pred             hHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691          65 AIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus        65 ~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      ..|..|+..++...-.++.+..|+|||..+..         ++..+-+.... ..+..+.+.+|| ...+.++.+.+...
T Consensus       148 ~~Qk~A~~~al~~~~~vitGgpGTGKTt~v~~---------ll~~l~~~~~~-~~~~~I~l~APT-GkAA~rL~e~~~~~  216 (586)
T TIGR01447       148 NWQKVAVALALKSNFSLITGGPGTGKTTTVAR---------LLLALVKQSPK-QGKLRIALAAPT-GKAAARLAESLRKA  216 (586)
T ss_pred             HHHHHHHHHHhhCCeEEEEcCCCCCHHHHHHH---------HHHHHHHhccc-cCCCcEEEECCc-HHHHHHHHHHHHhh
Confidence            57888998999998899999999999985431         22222111110 112468888998 66677777766554


Q ss_pred             C
Q psy7691         145 S  145 (165)
Q Consensus       145 ~  145 (165)
                      .
T Consensus       217 ~  217 (586)
T TIGR01447       217 V  217 (586)
T ss_pred             h
Confidence            3

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.

>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=87.27  E-value=0.51  Score=36.88  Aligned_cols=34  Identities=18%  Similarity=0.179  Sum_probs=24.6

Q ss_pred             CCchHHHHHHHHHHcCCCeeeecccCCcccceee
Q psy7691          62 EPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVI   95 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~   95 (165)
                      ..+..|..++..++.-.-+++.++.|+|||+..+
T Consensus         4 p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~   37 (205)
T PF02562_consen    4 PKNEEQKFALDALLNNDLVIVNGPAGTGKTFLAL   37 (205)
T ss_dssp             --SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHH
T ss_pred             CCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHH
Confidence            3577899999999966668899999999998543

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

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=86.99  E-value=1.6  Score=39.61  Aligned_cols=70  Identities=24%  Similarity=0.240  Sum_probs=47.5

Q ss_pred             chHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHh
Q psy7691          64 TAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTE  143 (165)
Q Consensus        64 t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~  143 (165)
                      ...|..|+-.++...-.++.+.+|+|||..+..         ++..+-+.  .+.....+.+..|+ ...+.++.+.+..
T Consensus       154 ~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~~---------ll~~l~~~--~~~~~~~i~l~APT-gkAA~rL~e~~~~  221 (615)
T PRK10875        154 VDWQKVAAAVALTRRISVISGGPGTGKTTTVAK---------LLAALIQL--ADGERCRIRLAAPT-GKAAARLTESLGK  221 (615)
T ss_pred             CHHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHH---------HHHHHHHh--cCCCCcEEEEECCc-HHHHHHHHHHHHh
Confidence            468999998888888899999999999985431         22222111  11123568888898 6777777777765


Q ss_pred             cC
Q psy7691         144 AS  145 (165)
Q Consensus       144 ~~  145 (165)
                      ..
T Consensus       222 ~~  223 (615)
T PRK10875        222 AL  223 (615)
T ss_pred             hh
Confidence            33

>PRK11054 helD DNA helicase IV; Provisional

Probab=86.94  E-value=2  Score=39.52  Aligned_cols=66  Identities=20%  Similarity=0.188  Sum_probs=39.7

Q ss_pred             CCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCC-CCCCCCceEEEECCCcHHHHHHHHH
Q psy7691          61 EEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTG-RCASSGTAYTFFTPNNGKQAKELIA  139 (165)
Q Consensus        61 ~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~-r~~~~g~~~~~~~p~~~~~~~~i~~  139 (165)
                      ..+++.|.+|+-  ....++++.|..|||||...            ++|++..- +.+..+..+++++-+ +..+..+.+
T Consensus       195 ~~L~~~Q~~av~--~~~~~~lV~agaGSGKT~vl------------~~r~ayLl~~~~~~~~~IL~ltft-~~AA~em~e  259 (684)
T PRK11054        195 SPLNPSQARAVV--NGEDSLLVLAGAGSGKTSVL------------VARAGWLLARGQAQPEQILLLAFG-RQAAEEMDE  259 (684)
T ss_pred             CCCCHHHHHHHh--CCCCCeEEEEeCCCCHHHHH------------HHHHHHHHHhCCCCHHHeEEEecc-HHHHHHHHH
Confidence            357889988763  33346889999999999742            33332211 112344567777777 555555544


Q ss_pred             HH
Q psy7691         140 VL  141 (165)
Q Consensus       140 ~l  141 (165)
                      -+
T Consensus       260 RL  261 (684)
T PRK11054        260 RI  261 (684)
T ss_pred             HH
Confidence            43

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

Probab=86.73  E-value=0.98  Score=41.14  Aligned_cols=82  Identities=20%  Similarity=0.248  Sum_probs=52.6

Q ss_pred             cHHHHHH-HHhCCCCCCchHHHHHHHHHHcC------CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCC
Q psy7691          48 PNAVLQH-LKGQGFEEPTAIQAQGWPIALSG------RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSG  120 (165)
Q Consensus        48 ~~~l~~~-l~~~g~~~~t~~Q~~a~~~~l~G------~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g  120 (165)
                      ...+++. +....|. +|..|.+++..+...      ++=+.++-=|||||+-..   +.     .+.-+       ..|
T Consensus       248 ~~~l~~~~~~~LPF~-LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~---la-----ml~ai-------~~G  311 (677)
T COG1200         248 NGELLAKFLAALPFK-LTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVAL---LA-----MLAAI-------EAG  311 (677)
T ss_pred             cHHHHHHHHHhCCCC-ccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHH---HH-----HHHHH-------HcC
Confidence            3344444 5667896 899999999988655      334568888999998333   22     22222       356


Q ss_pred             ceEEEECCCc---HHHHHHHHHHHHhcC
Q psy7691         121 TAYTFFTPNN---GKQAKELIAVLTEAS  145 (165)
Q Consensus       121 ~~~~~~~p~~---~~~~~~i~~~l~~~~  145 (165)
                      ..+.++.||+   ++.+..+.+++...+
T Consensus       312 ~Q~ALMAPTEILA~QH~~~~~~~l~~~~  339 (677)
T COG1200         312 YQAALMAPTEILAEQHYESLRKWLEPLG  339 (677)
T ss_pred             CeeEEeccHHHHHHHHHHHHHHHhhhcC
Confidence            7889999994   334444555555433

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=86.38  E-value=2.4  Score=39.19  Aligned_cols=35  Identities=20%  Similarity=0.142  Sum_probs=30.2

Q ss_pred             CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccce
Q psy7691          58 QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA   93 (165)
Q Consensus        58 ~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~   93 (165)
                      .++ ..++.|.+|+..+....-+++.+..|+|||..
T Consensus       320 ~~~-~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~  354 (720)
T TIGR01448       320 LRK-GLSEEQKQALDTAIQHKVVILTGGPGTGKTTI  354 (720)
T ss_pred             cCC-CCCHHHHHHHHHHHhCCeEEEECCCCCCHHHH
Confidence            455 47899999999998888889999999999974

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.

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=86.38  E-value=1  Score=41.32  Aligned_cols=21  Identities=29%  Similarity=0.468  Sum_probs=18.7

Q ss_pred             CCeeeecccCCcccceeeecCCCC
Q psy7691          78 RDMVGIAQTGSGKTLAVINFDYPN  101 (165)
Q Consensus        78 ~di~~~a~tgsGKt~~~~~~~lP~  101 (165)
                      .+++++|+||||||..++   +|.
T Consensus       140 ~hvlviApTgSGKgvg~V---IPn  160 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVV---IPT  160 (670)
T ss_pred             ceEEEEecCCCCceeeeh---HhH
Confidence            478999999999999998   783

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=86.16  E-value=1.4  Score=40.19  Aligned_cols=21  Identities=29%  Similarity=0.317  Sum_probs=18.9

Q ss_pred             CCeeeecccCCcccceeeecCCCC
Q psy7691          78 RDMVGIAQTGSGKTLAVINFDYPN  101 (165)
Q Consensus        78 ~di~~~a~tgsGKt~~~~~~~lP~  101 (165)
                      .++++.|+||+|||..++   +|.
T Consensus       225 ~H~Lv~ApTgsGKt~g~V---IPn  245 (641)
T PRK13822        225 THGLVFAGSGGFKTTSVV---VPT  245 (641)
T ss_pred             ceEEEEeCCCCCccceEe---hhh
Confidence            578999999999999998   883

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=85.72  E-value=0.82  Score=38.92  Aligned_cols=15  Identities=33%  Similarity=0.246  Sum_probs=13.1

Q ss_pred             CeeeecccCCcccce
Q psy7691          79 DMVGIAQTGSGKTLA   93 (165)
Q Consensus        79 di~~~a~tgsGKt~~   93 (165)
                      -++++++||||||..
T Consensus       151 lilI~G~TGSGKTT~  165 (372)
T TIGR02525       151 LGLICGETGSGKSTL  165 (372)
T ss_pred             EEEEECCCCCCHHHH
Confidence            578999999999874

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).

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=85.27  E-value=2.8  Score=40.09  Aligned_cols=64  Identities=22%  Similarity=0.212  Sum_probs=42.5

Q ss_pred             CCCCCCchHHHHHHHHHHcCCC-eeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHH
Q psy7691          58 QGFEEPTAIQAQGWPIALSGRD-MVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKE  136 (165)
Q Consensus        58 ~g~~~~t~~Q~~a~~~~l~G~d-i~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~  136 (165)
                      .|+ ..++-|.+|+..++.+.+ +++++..|+|||..+-          .+..+-+     ..|..+..+.|+ ...+..
T Consensus       343 ~g~-~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~l~----------~~~~~~e-----~~G~~V~~~ApT-GkAA~~  405 (988)
T PRK13889        343 RGL-VLSGEQADALAHVTDGRDLGVVVGYAGTGKSAMLG----------VAREAWE-----AAGYEVRGAALS-GIAAEN  405 (988)
T ss_pred             cCC-CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHHHH----------HHHHHHH-----HcCCeEEEecCc-HHHHHH
Confidence            455 379999999999998766 5689999999997422          1222211     135567788888 344444


Q ss_pred             HH
Q psy7691         137 LI  138 (165)
Q Consensus       137 i~  138 (165)
                      |.
T Consensus       406 L~  407 (988)
T PRK13889        406 LE  407 (988)
T ss_pred             Hh
Confidence            43

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=85.20  E-value=1.2  Score=40.72  Aligned_cols=66  Identities=21%  Similarity=0.211  Sum_probs=40.4

Q ss_pred             CchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCC-CCCCCCceEEEECCCcHHHHHHHHHHH
Q psy7691          63 PTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTG-RCASSGTAYTFFTPNNGKQAKELIAVL  141 (165)
Q Consensus        63 ~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~-r~~~~g~~~~~~~p~~~~~~~~i~~~l  141 (165)
                      +++.|.+|+..  ..-.+++.|..|||||...            ++|+.+-- ..|-....+++++-+ +..+..+.+-+
T Consensus         3 Ln~~Q~~av~~--~~g~~lV~AgpGSGKT~vL------------~~Ria~Li~~~~v~p~~IL~lTFT-~kAA~em~~Rl   67 (672)
T PRK10919          3 LNPGQQQAVEF--VTGPCLVLAGAGSGKTRVI------------TNKIAHLIRGCGYQARHIAAVTFT-NKAAREMKERV   67 (672)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHHH------------HHHHHHHHHhcCCCHHHeeeEech-HHHHHHHHHHH
Confidence            57889887643  3457889999999999743            33333211 112334467888877 55555555544


Q ss_pred             Hh
Q psy7691         142 TE  143 (165)
Q Consensus       142 ~~  143 (165)
                      ..
T Consensus        68 ~~   69 (672)
T PRK10919         68 AQ   69 (672)
T ss_pred             HH
Confidence            43

>KOG1802|consensus

Probab=85.03  E-value=3.3  Score=38.12  Aligned_cols=40  Identities=18%  Similarity=0.138  Sum_probs=33.3

Q ss_pred             HHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccce
Q psy7691          54 HLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA   93 (165)
Q Consensus        54 ~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~   93 (165)
                      .+...|+......|..|...++.--=-+.++|+|+|||..
T Consensus       402 ~~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvt  441 (935)
T KOG1802|consen  402 RFSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVT  441 (935)
T ss_pred             hhcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceeh
Confidence            4555677788889999999998887677899999999973

>KOG0947|consensus

Probab=84.91  E-value=1.4  Score=41.86  Aligned_cols=35  Identities=26%  Similarity=0.206  Sum_probs=31.7

Q ss_pred             hCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccc
Q psy7691          57 GQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTL   92 (165)
Q Consensus        57 ~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~   92 (165)
                      ...|. +-.+|++||-++.+|..+++.|.|-+|||+
T Consensus       293 ~~pFe-lD~FQk~Ai~~lerg~SVFVAAHTSAGKTv  327 (1248)
T KOG0947|consen  293 IYPFE-LDTFQKEAIYHLERGDSVFVAAHTSAGKTV  327 (1248)
T ss_pred             hCCCC-ccHHHHHHHHHHHcCCeEEEEecCCCCcch
Confidence            34675 788999999999999999999999999997

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=84.87  E-value=1.9  Score=39.32  Aligned_cols=21  Identities=29%  Similarity=0.496  Sum_probs=19.1

Q ss_pred             CCeeeecccCCcccceeeecCCCC
Q psy7691          78 RDMVGIAQTGSGKTLAVINFDYPN  101 (165)
Q Consensus        78 ~di~~~a~tgsGKt~~~~~~~lP~  101 (165)
                      .+++++|+||||||..++   +|.
T Consensus       176 ~HvlviapTgSGKgvg~V---iPn  196 (636)
T PRK13880        176 EHVLTYAPTRSGKGVGLV---VPT  196 (636)
T ss_pred             ceEEEEecCCCCCceEEE---ccc
Confidence            579999999999999999   884

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

Probab=84.80  E-value=0.5  Score=35.08  Aligned_cols=49  Identities=27%  Similarity=0.293  Sum_probs=32.1

Q ss_pred             eeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691          81 VGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus        81 ~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      +.--.+|+|||--++    |..+.+++.+-+          .++++.|+ |-.+..+.+.|...
T Consensus         8 ~~d~hpGaGKTr~vl----p~~~~~~i~~~~----------rvLvL~PT-Rvva~em~~aL~~~   56 (148)
T PF07652_consen    8 VLDLHPGAGKTRRVL----PEIVREAIKRRL----------RVLVLAPT-RVVAEEMYEALKGL   56 (148)
T ss_dssp             EEE--TTSSTTTTHH----HHHHHHHHHTT------------EEEEESS-HHHHHHHHHHTTTS
T ss_pred             EEecCCCCCCccccc----HHHHHHHHHccC----------eEEEeccc-HHHHHHHHHHHhcC
Confidence            344568999998664    754444443333          47899999 88888888888654

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 ....

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=84.34  E-value=3.7  Score=38.06  Aligned_cols=61  Identities=16%  Similarity=0.092  Sum_probs=40.1

Q ss_pred             CCchHHHHHHHHHHcC-CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALSG-RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELI  138 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G-~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~  138 (165)
                      ..++-|..|+..++.+ .-+++++..|+|||..+-    .     .++.+ .     ..|..+.+++|+ ...+..+.
T Consensus       352 ~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll~----~-----i~~~~-~-----~~g~~V~~~ApT-g~Aa~~L~  413 (744)
T TIGR02768       352 RLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTMLK----A-----AREAW-E-----AAGYRVIGAALS-GKAAEGLQ  413 (744)
T ss_pred             CCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHHH----H-----HHHHH-H-----hCCCeEEEEeCc-HHHHHHHH
Confidence            3789999999988875 446789999999997433    1     11111 1     134568888888 43444444

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.

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=84.26  E-value=1.8  Score=39.52  Aligned_cols=65  Identities=26%  Similarity=0.347  Sum_probs=44.2

Q ss_pred             CCCCCchHHHHHHHHHHcCC-----CeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHH
Q psy7691          59 GFEEPTAIQAQGWPIALSGR-----DMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQ  133 (165)
Q Consensus        59 g~~~~t~~Q~~a~~~~l~G~-----di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~  133 (165)
                      .|. |+-.|..++..+..|.     ..+..+.||||||+.+.+         .+++.+|         .+++++|+ ..+
T Consensus         7 ~~~-~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~a~---------~~~~~~~---------p~Lvi~~n-~~~   66 (655)
T TIGR00631         7 PFQ-PAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMAN---------VIAQVNR---------PTLVIAHN-KTL   66 (655)
T ss_pred             CCC-CChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHHHH---------HHHHhCC---------CEEEEECC-HHH
Confidence            353 8888998888775552     556789999999986442         4444444         47888888 666


Q ss_pred             HHHHHHHHHh
Q psy7691         134 AKELIAVLTE  143 (165)
Q Consensus       134 ~~~i~~~l~~  143 (165)
                      +.|+..-+..
T Consensus        67 A~ql~~el~~   76 (655)
T TIGR00631        67 AAQLYNEFKE   76 (655)
T ss_pred             HHHHHHHHHH
Confidence            6666655544

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

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=84.25  E-value=0.94  Score=38.31  Aligned_cols=18  Identities=28%  Similarity=0.217  Sum_probs=15.0

Q ss_pred             cCCCeeeecccCCcccce
Q psy7691          76 SGRDMVGIAQTGSGKTLA   93 (165)
Q Consensus        76 ~G~di~~~a~tgsGKt~~   93 (165)
                      .+.-++++++||||||..
T Consensus       133 ~~glilI~GpTGSGKTTt  150 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTL  150 (358)
T ss_pred             cCCEEEEECCCCCCHHHH
Confidence            455788999999999874

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.

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=83.93  E-value=1.6  Score=36.41  Aligned_cols=37  Identities=30%  Similarity=0.099  Sum_probs=24.7

Q ss_pred             HHhCCCCCCchHHHHHHHH-HHcCCCeeeecccCCcccce
Q psy7691          55 LKGQGFEEPTAIQAQGWPI-ALSGRDMVGIAQTGSGKTLA   93 (165)
Q Consensus        55 l~~~g~~~~t~~Q~~a~~~-~l~G~di~~~a~tgsGKt~~   93 (165)
                      +...|.  .++.|...+-. +..+.+++++++||||||..
T Consensus       123 lv~~g~--~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTl  160 (323)
T PRK13833        123 YVTSKI--MTEAQASVIRSAIDSRLNIVISGGTGSGKTTL  160 (323)
T ss_pred             HHHcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH
Confidence            444454  34555544433 45567999999999999973

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=83.71  E-value=1  Score=41.91  Aligned_cols=55  Identities=29%  Similarity=0.471  Sum_probs=39.8

Q ss_pred             CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCc
Q psy7691          58 QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN  130 (165)
Q Consensus        58 ~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~  130 (165)
                      .|.. |+++|..+-=.+..|.  ++.=.||+|||+...   +|.    |+.-        ..|..+-+++|++
T Consensus        77 ~g~~-~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~---l~a----~l~a--------l~G~~v~vvT~ne  131 (796)
T PRK12906         77 LGLR-PFDVQIIGGIVLHEGN--IAEMKTGEGKTLTAT---LPV----YLNA--------LTGKGVHVVTVNE  131 (796)
T ss_pred             hCCC-CchhHHHHHHHHhcCC--cccccCCCCCcHHHH---HHH----HHHH--------HcCCCeEEEeccH
Confidence            4775 8999988765667775  677889999999766   562    3332        2455788889985

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=83.69  E-value=1.6  Score=36.33  Aligned_cols=40  Identities=33%  Similarity=0.365  Sum_probs=26.9

Q ss_pred             HHHHHhCCCCCCchHHHHHHHH-HHcCCCeeeecccCCcccce
Q psy7691          52 LQHLKGQGFEEPTAIQAQGWPI-ALSGRDMVGIAQTGSGKTLA   93 (165)
Q Consensus        52 ~~~l~~~g~~~~t~~Q~~a~~~-~l~G~di~~~a~tgsGKt~~   93 (165)
                      +..|.+.|+  .++.|...+.. +..+.+++++++||||||..
T Consensus       124 l~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTl  164 (319)
T PRK13894        124 LDQYVERGI--MTAAQREAIIAAVRAHRNILVIGGTGSGKTTL  164 (319)
T ss_pred             HHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH
Confidence            344445555  34556555543 45668999999999999863

>PRK10536 hypothetical protein; Provisional

Probab=83.64  E-value=1.3  Score=36.01  Aligned_cols=37  Identities=19%  Similarity=0.107  Sum_probs=29.2

Q ss_pred             CCCCCchHHHHHHHHHHcCCCeeeecccCCcccceee
Q psy7691          59 GFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVI   95 (165)
Q Consensus        59 g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~   95 (165)
                      ++...+..|...+..+....-+++.++.|+|||...+
T Consensus        56 ~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~   92 (262)
T PRK10536         56 PILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISA   92 (262)
T ss_pred             cccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHH
Confidence            4455567888888888887778899999999998543

>PF13871 Helicase_C_4: Helicase_C-like

Probab=83.58  E-value=8.8  Score=31.45  Aligned_cols=73  Identities=25%  Similarity=0.426  Sum_probs=48.1

Q ss_pred             HHHHHcCC-CeeeecccC-Ccccce------------eeecCCCCChhHHHHhhccCCCCCCC-CceEEEECCC---cHH
Q psy7691          71 WPIALSGR-DMVGIAQTG-SGKTLA------------VINFDYPNSSEDYIHRIGRTGRCASS-GTAYTFFTPN---NGK  132 (165)
Q Consensus        71 ~~~~l~G~-di~~~a~tg-sGKt~~------------~~~~~lP~~~~~~i~r~gr~~r~~~~-g~~~~~~~p~---~~~  132 (165)
                      ...++.|. +|++++..| +|-.++            .+...+|-+.+..+|..||+-|.+.. .+.+.++...   ++.
T Consensus        54 ~~~F~~g~k~v~iis~AgstGiSlHAd~~~~nqr~Rv~i~le~pwsad~aiQ~~GR~hRsnQ~~~P~y~~l~t~~~gE~R  133 (278)
T PF13871_consen   54 KQAFMDGEKDVAIISDAGSTGISLHADRRVKNQRRRVHITLELPWSADKAIQQFGRTHRSNQVSAPEYRFLVTDLPGERR  133 (278)
T ss_pred             HHHHhCCCceEEEEecccccccchhccccCCCCCceEEEEeeCCCCHHHHHHHhccccccccccCCEEEEeecCCHHHHH
Confidence            34577774 777666554 676665            35577899999999999999999864 4445555433   244


Q ss_pred             HHHHHHHHHHh
Q psy7691         133 QAKELIAVLTE  143 (165)
Q Consensus       133 ~~~~i~~~l~~  143 (165)
                      .+.-+.+-+..
T Consensus       134 fas~va~rL~s  144 (278)
T PF13871_consen  134 FASTVARRLES  144 (278)
T ss_pred             HHHHHHHHHhh
Confidence            45555555443

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

Probab=83.25  E-value=1.4  Score=37.19  Aligned_cols=34  Identities=29%  Similarity=0.168  Sum_probs=28.2

Q ss_pred             CCCCCchHHHHHHHHHHcCC-CeeeecccCCcccc
Q psy7691          59 GFEEPTAIQAQGWPIALSGR-DMVGIAQTGSGKTL   92 (165)
Q Consensus        59 g~~~~t~~Q~~a~~~~l~G~-di~~~a~tgsGKt~   92 (165)
                      .|...++-|...+-.+.+++ ++++++.||||||.
T Consensus       154 ~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTT  188 (355)
T COG4962         154 IFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTT  188 (355)
T ss_pred             HcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHH
Confidence            57778888887776666665 99999999999987

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=83.01  E-value=2.3  Score=39.34  Aligned_cols=68  Identities=18%  Similarity=0.132  Sum_probs=43.0

Q ss_pred             chHHHHHHHHHHcC---C-CeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHH
Q psy7691          64 TAIQAQGWPIALSG---R-DMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIA  139 (165)
Q Consensus        64 t~~Q~~a~~~~l~G---~-di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~  139 (165)
                      .+.|..++..+.++   . .++..||||.|||.+.+   .+     ..+..-..   ......+..+.|. +....++.+
T Consensus       197 ~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl---~~-----a~~~~~~~---~~~~~r~i~vlP~-~t~ie~~~~  264 (733)
T COG1203         197 YELQEKALELILRLEKRSLLVVLEAPTGYGKTEASL---IL-----ALALLDEK---IKLKSRVIYVLPF-RTIIEDMYR  264 (733)
T ss_pred             hHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHH---HH-----HHHHhhcc---ccccceEEEEccH-HHHHHHHHH
Confidence            56777777777554   3 67789999999999877   44     33333221   1233345555565 777776666


Q ss_pred             HHHh
Q psy7691         140 VLTE  143 (165)
Q Consensus       140 ~l~~  143 (165)
                      .+..
T Consensus       265 r~~~  268 (733)
T COG1203         265 RAKE  268 (733)
T ss_pred             HHHh
Confidence            6654

>KOG1803|consensus

Probab=82.91  E-value=3.6  Score=37.21  Aligned_cols=61  Identities=16%  Similarity=0.251  Sum_probs=41.4

Q ss_pred             CchHHHHHHHHHHcCCC-eeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHH
Q psy7691          63 PTAIQAQGWPIALSGRD-MVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELI  138 (165)
Q Consensus        63 ~t~~Q~~a~~~~l~G~d-i~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~  138 (165)
                      .-+.|..|+..+..-++ .+..+|+|+|||..+.         .++++.--      .+..+++..|+.....+-+.
T Consensus       186 ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~Tlv---------EiI~qlvk------~~k~VLVcaPSn~AVdNive  247 (649)
T KOG1803|consen  186 LNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLV---------EIISQLVK------QKKRVLVCAPSNVAVDNIVE  247 (649)
T ss_pred             ccHHHHHHHHHHhccCCceEeeCCCCCCceeeHH---------HHHHHHHH------cCCeEEEEcCchHHHHHHHH
Confidence            34578888888777766 4478999999998654         15555532      34578888898554444444

>TIGR01075 uvrD DNA helicase II

Probab=82.78  E-value=1.7  Score=39.93  Aligned_cols=68  Identities=22%  Similarity=0.170  Sum_probs=39.9

Q ss_pred             CCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCC-CCCCCCceEEEECCCcHHHHHHHHH
Q psy7691          61 EEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTG-RCASSGTAYTFFTPNNGKQAKELIA  139 (165)
Q Consensus        61 ~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~-r~~~~g~~~~~~~p~~~~~~~~i~~  139 (165)
                      ..+++.|.+|+..  ....+++.|..|||||...            ++|+..-- ..|-....+++++-+ +..+..+.+
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~L------------~~Ria~Li~~~~v~p~~IL~lTFT-nkAA~em~~   67 (715)
T TIGR01075         3 DGLNDKQREAVAA--PPGNLLVLAGAGSGKTRVL------------THRIAWLLSVENASPHSIMAVTFT-NKAAAEMRH   67 (715)
T ss_pred             cccCHHHHHHHcC--CCCCEEEEecCCCCHHHHH------------HHHHHHHHHcCCCCHHHeEeeecc-HHHHHHHHH
Confidence            3478899987643  3458899999999999742            33332211 112233457777777 444444444


Q ss_pred             HHHh
Q psy7691         140 VLTE  143 (165)
Q Consensus       140 ~l~~  143 (165)
                      -+..
T Consensus        68 Rl~~   71 (715)
T TIGR01075        68 RIGA   71 (715)
T ss_pred             HHHH
Confidence            4433

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

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

Probab=82.59  E-value=0.57  Score=39.43  Aligned_cols=19  Identities=53%  Similarity=0.662  Sum_probs=15.9

Q ss_pred             HcCCCeeeecccCCcccce
Q psy7691          75 LSGRDMVGIAQTGSGKTLA   93 (165)
Q Consensus        75 l~G~di~~~a~tgsGKt~~   93 (165)
                      +.-.+++.++|||||||+.
T Consensus        95 L~KSNILLiGPTGsGKTlL  113 (408)
T COG1219          95 LSKSNILLIGPTGSGKTLL  113 (408)
T ss_pred             eeeccEEEECCCCCcHHHH
Confidence            4446899999999999984

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=82.56  E-value=1.7  Score=39.92  Aligned_cols=66  Identities=24%  Similarity=0.180  Sum_probs=39.6

Q ss_pred             CCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCC-CCCCCCceEEEECCCcHHHHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTG-RCASSGTAYTFFTPNNGKQAKELIAV  140 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~-r~~~~g~~~~~~~p~~~~~~~~i~~~  140 (165)
                      .+++-|.+|+..  ....+++.|..|||||...            ++|+.+-- ..|-....++.++-+ +..+..+.+-
T Consensus         9 ~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~vl------------~~Ria~Li~~~~v~p~~IL~lTFT-~kAA~Em~~R   73 (721)
T PRK11773          9 SLNDKQREAVAA--PLGNMLVLAGAGSGKTRVL------------VHRIAWLMQVENASPYSIMAVTFT-NKAAAEMRHR   73 (721)
T ss_pred             hcCHHHHHHHhC--CCCCEEEEecCCCCHHHHH------------HHHHHHHHHcCCCChhHeEeeecc-HHHHHHHHHH
Confidence            478899997642  3357899999999999742            33332211 112233457777777 4444444444


Q ss_pred             HH
Q psy7691         141 LT  142 (165)
Q Consensus       141 l~  142 (165)
                      +.
T Consensus        74 l~   75 (721)
T PRK11773         74 IE   75 (721)
T ss_pred             HH
Confidence            43

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=81.65  E-value=2.3  Score=34.93  Aligned_cols=38  Identities=29%  Similarity=0.319  Sum_probs=23.6

Q ss_pred             HHHhCCCCCCchHHHHHHHH-HHcCCCeeeecccCCcccce
Q psy7691          54 HLKGQGFEEPTAIQAQGWPI-ALSGRDMVGIAQTGSGKTLA   93 (165)
Q Consensus        54 ~l~~~g~~~~t~~Q~~a~~~-~l~G~di~~~a~tgsGKt~~   93 (165)
                      .|.+.|.  .++.|...+.. +..+.+++++++||||||..
T Consensus       110 ~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTl  148 (299)
T TIGR02782       110 DYVEAGI--MTAAQRDVLREAVLARKNILVVGGTGSGKTTL  148 (299)
T ss_pred             HHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH
Confidence            3444443  33444443333 44567899999999999874

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.

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

Probab=81.31  E-value=2.9  Score=38.02  Aligned_cols=21  Identities=33%  Similarity=0.431  Sum_probs=19.0

Q ss_pred             CCeeeecccCCcccceeeecCCCC
Q psy7691          78 RDMVGIAQTGSGKTLAVINFDYPN  101 (165)
Q Consensus        78 ~di~~~a~tgsGKt~~~~~~~lP~  101 (165)
                      .++++.|+||||||..++   +|.
T Consensus       212 ~H~lv~ApTgsGKgvg~V---IPn  232 (623)
T TIGR02767       212 THMIFFAGSGGFKTTSVV---VPT  232 (623)
T ss_pred             ceEEEEeCCCCCccceee---hhh
Confidence            589999999999999998   883

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.

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

Probab=81.17  E-value=5.1  Score=37.59  Aligned_cols=80  Identities=21%  Similarity=0.173  Sum_probs=50.6

Q ss_pred             CccccccC-CCcHHHHHHHHhCC-------CCCCchHHHHH-HHHHHcC-CCeeeecccC-----CcccceeeecCCCCC
Q psy7691          38 PTQELTEG-CFPNAVLQHLKGQG-------FEEPTAIQAQG-WPIALSG-RDMVGIAQTG-----SGKTLAVINFDYPNS  102 (165)
Q Consensus        38 ~i~~f~~l-~l~~~l~~~l~~~g-------~~~~t~~Q~~a-~~~~l~G-~di~~~a~tg-----sGKt~~~~~~~lP~~  102 (165)
                      ....|.+. ...+.+...|++.+       +...+.-|..- -..+.+| ...++|..+=     -|-...|++|.-|.+
T Consensus       255 ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TSSLELGIDiG~vdlVIq~~SP~s  334 (814)
T COG1201         255 TTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELGIDIGDIDLVIQLGSPKS  334 (814)
T ss_pred             cEEEEEeChHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcCCceEEEEccchhhccccCCceEEEEeCCcHH
Confidence            35677776 57777888888765       22344445432 2334455 2333333221     233347999999999


Q ss_pred             hhHHHHhhccCCCCC
Q psy7691         103 SEDYIHRIGRTGRCA  117 (165)
Q Consensus       103 ~~~~i~r~gr~~r~~  117 (165)
                      +...+||+||+|..-
T Consensus       335 V~r~lQRiGRsgHr~  349 (814)
T COG1201         335 VNRFLQRIGRAGHRL  349 (814)
T ss_pred             HHHHhHhcccccccc
Confidence            999999999988653

>PRK13764 ATPase; Provisional

Probab=80.68  E-value=1.4  Score=39.82  Aligned_cols=19  Identities=16%  Similarity=0.226  Sum_probs=15.6

Q ss_pred             HcCCCeeeecccCCcccce
Q psy7691          75 LSGRDMVGIAQTGSGKTLA   93 (165)
Q Consensus        75 l~G~di~~~a~tgsGKt~~   93 (165)
                      ..+..++++++||||||..
T Consensus       255 ~~~~~ILIsG~TGSGKTTl  273 (602)
T PRK13764        255 ERAEGILIAGAPGAGKSTF  273 (602)
T ss_pred             hcCCEEEEECCCCCCHHHH
Confidence            3456799999999999973

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=80.23  E-value=2.3  Score=39.96  Aligned_cols=65  Identities=26%  Similarity=0.356  Sum_probs=44.5

Q ss_pred             CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHH
Q psy7691          58 QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL  137 (165)
Q Consensus        58 ~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i  137 (165)
                      .|.+ |+++|..+-=.+..|  -++.-.||.|||+.+.   +|.    |++.+        .|..+-+++++ ..++.+-
T Consensus        73 lG~r-~ydvQlig~l~L~~G--~IaEm~TGEGKTL~a~---l~a----yl~aL--------~G~~VhVvT~N-dyLA~RD  133 (870)
T CHL00122         73 LGLR-HFDVQLIGGLVLNDG--KIAEMKTGEGKTLVAT---LPA----YLNAL--------TGKGVHIVTVN-DYLAKRD  133 (870)
T ss_pred             hCCC-CCchHhhhhHhhcCC--ccccccCCCCchHHHH---HHH----HHHHh--------cCCceEEEeCC-HHHHHHH
Confidence            5776 899998865344444  4678899999999888   784    66654        24568888888 4555444


Q ss_pred             HHHH
Q psy7691         138 IAVL  141 (165)
Q Consensus       138 ~~~l  141 (165)
                      .+.+
T Consensus       134 ~e~m  137 (870)
T CHL00122        134 QEWM  137 (870)
T ss_pred             HHHH
Confidence            4433

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	165
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		1e-22
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		7e-22
2jgn_A	185	Ddx3 Helicase Domain Length = 185		5e-13
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		1e-12
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		1e-09
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		3e-09
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		4e-09
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		1e-07
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		1e-07
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		2e-07
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-06
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-06
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		2e-06
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		2e-06
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		2e-06
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		2e-06
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		2e-06
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		4e-06
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		7e-06
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		1e-05
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		2e-05
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		5e-05
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		6e-05
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		2e-04
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		2e-04
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		2e-04
1t5i_A	172	Crystal Structure Of The C-Terminal Domain Of Uap56		3e-04

>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 =  102 bits (254), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 49/84 (58%), Positives = 60/84 (71%)
Query: 12 ARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGW 71
          AR +  EVE +R+ KEITV+G+N P P     E  FP  V+  +  Q F EPTAIQAQGW
Sbjct: 15 ARRTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGW 74
Query: 72 PIALSGRDMVGIAQTGSGKTLAVI 95
          P+ALSG DMVG+AQTGSGKTL+ +
Sbjct: 75 PVALSGLDMVGVAQTGSGKTLSYL 98

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 99.8 bits (247), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 47/78 (60%), Positives = 57/78 (73%)
Query: 18 EVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSG 77
          EVE +R+ KEITV+G+N P P     E  FP  V+  +  Q F EPTAIQAQGWP+ALSG
Sbjct: 7  EVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSG 66
Query: 78 RDMVGIAQTGSGKTLAVI 95
           DMVG+AQTGSGKTL+ +
Sbjct: 67 LDMVGVAQTGSGKTLSYL 84

>pdb|2JGN|A Chain A, Ddx3 Helicase Domain Length = 185

Iteration: 1
 Score = 70.1 bits (170), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 30/63 (47%), Positives = 42/63 (66%)
Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ 153
           VINFD P+  E+Y+HRIGRTGR  + G A +FF   N    K+L+ +L EA Q +P  L+
Sbjct: 118 VINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLE 177
Query: 154 DLA 156
           ++A
Sbjct: 178 NMA 180

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 68.9 bits (167), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 30/63 (47%), Positives = 42/63 (66%)
Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ 153
           VINFD P+  E+Y+HRIGRTGR  + G A +FF   N    K+L+ +L EA Q +P  L+
Sbjct: 348 VINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLE 407
Query: 154 DLA 156
           ++A
Sbjct: 408 NMA 410

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score = 58.9 bits (141), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 26/61 (42%), Positives = 40/61 (65%), Gaps = 1/61 (1%)
Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQ-AKELIAVLTEASQPIPPQL 152
           VIN+D P+  +DY+HRIGRTGR  ++G A +FF P   +  A +L+ +L  + Q +P  L
Sbjct: 372 VINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKILEGSGQTVPDFL 431
Query: 153 Q 153
           +
Sbjct: 432 R 432

>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain Length = 191

Iteration: 1
 Score = 57.8 bits (138), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 29/63 (46%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQA-KELIAVLTEASQPIPPQL 152
           VIN+D P   E+Y+HRIGRTG   ++G A TF      +    +L A+L EA Q +PP L
Sbjct: 126 VINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVL 185
Query: 153 QDL 155
           Q L
Sbjct: 186 QVL 188

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 57.4 bits (137), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 32/80 (40%), Positives = 49/80 (61%), Gaps = 4/80 (5%)
Query: 18 EVEAFRQKKEITVKGNNIPCPT---QELTEGCFPNA-VLQHLKGQGFEEPTAIQAQGWPI 73
          ++   R K +I V+G ++P P    Q+L +    N+ +LQ++   GF+ PT IQ Q  P+
Sbjct: 3  KINFLRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPV 62
Query: 74 ALSGRDMVGIAQTGSGKTLA 93
           L GR+++  A TGSGKTLA
Sbjct: 63 MLHGRELLASAPTGSGKTLA 82

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score = 52.8 bits (125), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 23/43 (53%), Positives = 32/43 (74%)
Query: 51 VLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
          +L+ L G+G   PT IQA   P+AL G+D++G A+TG+GKTLA
Sbjct: 12 ILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLA 54

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/63 (41%), Positives = 40/63 (63%), Gaps = 3/63 (4%)
Query: 35 IPCPTQELTEGC--FPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTL 92
          IP PT    +    +P+ +L+ +   G  +PT IQ+Q WPI L G D++ +AQTG+GKTL
Sbjct: 14 IPKPTCRFKDAFQQYPD-LLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTL 72
Query: 93 AVI 95
          + +
Sbjct: 73 SYL 75

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 22/43 (51%), Positives = 32/43 (74%)
Query: 51 VLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
          +L+ L G+G   PT I+A   P+AL G+D++G A+TG+GKTLA
Sbjct: 12 ILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLA 54

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 34/62 (54%)
Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ 153
           +IN+D PN+ E YIHRIGR+GR    G A  F   ++ +  +++    +     +P  + 
Sbjct: 312 IINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDIRVLRDIEQYYSTQIDEMPMNVA 371
Query: 154 DL 155
           DL
Sbjct: 372 DL 373

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 34/62 (54%)
Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ 153
           +IN+D PN+ E YIHRIGR+GR    G A  F   ++ +  +++    +     +P  + 
Sbjct: 312 IINYDLPNNRELYIHRIGRSGRYGRKGVAVNFVKNDDIRVLRDIEQYYSTQIDEMPMNVA 371
Query: 154 DL 155
           DL
Sbjct: 372 DL 373

>pdb|2WAX|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex With An Edc3-Fdf Peptide Length = 193

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/60 (38%), Positives = 32/60 (53%)
Query: 93  AVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQL 152
            VINFD+P  +E Y+HRIGR+GR    G A    T ++    K +   L    +PIP  +
Sbjct: 115 VVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNI 174

>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 = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 34/62 (54%)
Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ 153
           +IN+D PN+ E YIHRIGR+GR    G A  F   ++ +  +++    +     +P  + 
Sbjct: 349 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVA 408
Query: 154 DL 155
           DL
Sbjct: 409 DL 410

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 34/62 (54%)
Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ 153
           +IN+D PN+ E YIHRIGR+GR    G A  F   ++ +  +++    +     +P  + 
Sbjct: 348 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVA 407
Query: 154 DL 155
           DL
Sbjct: 408 DL 409

>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 = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 34/62 (54%)
Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ 153
           +IN+D PN+ E YIHRIGR+GR    G A  F   ++ +  +++    +     +P  + 
Sbjct: 349 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVA 408
Query: 154 DL 155
           DL
Sbjct: 409 DL 410

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 34/62 (54%)
Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ 153
           +IN+D PN+ E YIHRIGR+GR    G A  F   ++ +  +++    +     +P  + 
Sbjct: 327 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVA 386
Query: 154 DL 155
           DL
Sbjct: 387 DL 388

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 19/33 (57%), Positives = 27/33 (81%)
Query: 59 GFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKT 91
          G+ +PT IQ +  P+AL GRD++G+A+TGSGKT
Sbjct: 62 GWTKPTKIQIEAIPLALQGRDIIGLAETGSGKT 94

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 46.2 bits (108), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 20/33 (60%), Positives = 20/33 (60%)
Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFF 126
           VINFD P     YIHRIGRTGR    G A TF 
Sbjct: 288 VINFDAPQDLRTYIHRIGRTGRMGRKGEAITFI 320

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 18/38 (47%), Positives = 24/38 (63%)
Query: 93  AVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN 130
            VINFD+P ++E Y+HRIGR+GR    G A      N+
Sbjct: 329 VVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWND 366

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/51 (39%), Positives = 32/51 (62%)
Query: 41 ELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKT 91
          E  + C    +L  +   G+E+P+ IQ +  PIALSGRD++  A+ G+GK+
Sbjct: 4  EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKS 54

>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The Bacillus Subtilis Yxin Protein Length = 163

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 22/34 (64%)
Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFT 127
           VIN+D P   E Y+HR GRTGR  + G A +F T
Sbjct: 107 VINYDLPLEKESYVHRTGRTGRAGNKGKAISFVT 140

>pdb|2YJT|D Chain D, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound To Regulator Of Ribonuclease Activity A (Rraa) Length = 170

Iteration: 1
 Score = 43.5 bits (101), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 17/37 (45%), Positives = 22/37 (59%)
Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN 130
           V NFD P S + Y+HRIGRT R    GTA +    ++
Sbjct: 102 VFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHD 138

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 15/36 (41%), Positives = 21/36 (58%)
Query: 95  INFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN 130
            N+D P  S+ Y+HR+ R GR  + G A TF +  N
Sbjct: 322 FNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN 357

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 15/36 (41%), Positives = 21/36 (58%)
Query: 95  INFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN 130
            N+D P  S+ Y+HR+ R GR  + G A TF +  N
Sbjct: 323 FNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN 358

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 15/36 (41%), Positives = 21/36 (58%)
Query: 95  INFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN 130
            N+D P  S+ Y+HR+ R GR  + G A TF +  N
Sbjct: 323 FNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN 358

>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56 Length = 172

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 15/36 (41%), Positives = 21/36 (58%)
Query: 95  INFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN 130
            N+D P  S+ Y+HR+ R GR  + G A TF +  N
Sbjct: 104 FNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN 139

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	165
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	2e-42
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	2e-36
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	3e-34
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	7e-32
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	1e-32
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	1e-31
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	2e-31
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	4e-30
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	9e-29
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	3e-27
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	1e-16
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	2e-16
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	7e-16
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	9e-16
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	2e-15
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	2e-15
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	3e-15
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	5e-15
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	9e-14
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	7e-15
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	2e-14
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	3e-13
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	3e-14
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	3e-14
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	3e-13
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	3e-14
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	6e-14
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	4e-14
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	6e-14
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	2e-13
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	6e-14
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	1e-13
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	7e-14
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	2e-13
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	8e-14
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	8e-14
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	8e-14
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	6e-13
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	9e-14
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	9e-07
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	1e-13
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	2e-13
3bor_A	237	Human initiation factor 4A-II; translation initiat	2e-13
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	1e-12
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	3e-07
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	2e-12
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	2e-11
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	3e-12
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	5e-11
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	3e-12
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	7e-12
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	3e-10
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	9e-12
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	2e-11
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	7e-10
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	9e-11
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	6e-08
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	5e-05

>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 =  140 bits (355), Expect = 2e-42
 Identities = 47/82 (57%), Positives = 58/82 (70%)

Query: 12 ARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGW 71
          +  +  EVE +R+ KEITV+G+N P P     E  FP  V+  +  Q F EPTAIQAQGW
Sbjct: 1  SMRTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGW 60

Query: 72 PIALSGRDMVGIAQTGSGKTLA 93
          P+ALSG DMVG+AQTGSGKTL+
Sbjct: 61 PVALSGLDMVGVAQTGSGKTLS 82

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens} Length = 185

 Score =  123 bits (310), Expect = 2e-36
 Identities = 30/67 (44%), Positives = 43/67 (64%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ 153
           VINFD P+  E+Y+HRIGRTGR  + G A +FF   N    K+L+ +L EA Q +P  L+
Sbjct: 118 VINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLE 177

Query: 154 DLANSNP 160
           ++A  + 
Sbjct: 178 NMAYEHH 184

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  123 bits (310), Expect = 3e-34
 Identities = 31/72 (43%), Positives = 44/72 (61%), Gaps = 2/72 (2%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ 153
           VINFD P+  E+Y+HRIGRTGR  + G A +FF   N    K+L+ +L EA Q +P  L+
Sbjct: 348 VINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLE 407

Query: 154 DLANSNPNSKGG 165
           ++A    +   G
Sbjct: 408 NMAYE--HHYKG 417

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  116 bits (294), Expect = 7e-32
 Identities = 20/67 (29%), Positives = 33/67 (49%)

Query: 27 EITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQT 86
           +   GNN P   +  ++      ++ +++   +  PT +Q    PI    RD++  AQT
Sbjct: 2  MVEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQT 61

Query: 87 GSGKTLA 93
          GSGKT A
Sbjct: 62 GSGKTAA 68

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score =  113 bits (286), Expect = 1e-32
 Identities = 29/64 (45%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTP-NNGKQAKELIAVLTEASQPIPPQL 152
           VIN+D P   E+Y+HRIGRTG   ++G A TF     +     +L A+L EA Q +PP L
Sbjct: 126 VINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVL 185

Query: 153 QDLA 156
           Q L 
Sbjct: 186 QVLH 189

>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 =  112 bits (283), Expect = 1e-31
 Identities = 31/81 (38%), Positives = 46/81 (56%), Gaps = 4/81 (4%)

Query: 17 SEVEAFRQKKEITVKGNNIPCP----TQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWP 72
           ++   R K +I V+G ++P P     Q   E    + +LQ++   GF+ PT IQ Q  P
Sbjct: 2  MKINFLRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIP 61

Query: 73 IALSGRDMVGIAQTGSGKTLA 93
          + L GR+++  A TGSGKTLA
Sbjct: 62 VMLHGRELLASAPTGSGKTLA 82

>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 =  115 bits (291), Expect = 2e-31
 Identities = 28/91 (30%), Positives = 43/91 (47%), Gaps = 12/91 (13%)

Query: 15  SESEVEAFRQKK------------EITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEE 62
           S   +E F                 + V G+++P P Q  T     + ++ ++   G++ 
Sbjct: 19  SNDAIEIFSSGIASGIHFSKYNNIPVKVTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKI 78

Query: 63  PTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
           PT IQ    P+  SGRD++  AQTGSGKT A
Sbjct: 79  PTPIQKCSIPVISSGRDLMACAQTGSGKTAA 109

>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 =  112 bits (282), Expect = 4e-30
 Identities = 26/61 (42%), Positives = 40/61 (65%), Gaps = 1/61 (1%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTP-NNGKQAKELIAVLTEASQPIPPQL 152
           VIN+D P+  +DY+HRIGRTGR  ++G A +FF P  +   A +L+ +L  + Q +P  L
Sbjct: 372 VINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKILEGSGQTVPDFL 431

Query: 153 Q 153
           +
Sbjct: 432 R 432

>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 =  104 bits (263), Expect = 9e-29
 Identities = 25/67 (37%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 28 ITVKGNNIPCPTQELTE-GCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQT 86
           + +   IP PT    +       +L+ +   G  +PT IQ+Q WPI L G D++ +AQT
Sbjct: 7  KSGEKRLIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQT 66

Query: 87 GSGKTLA 93
          G+GKTL+
Sbjct: 67 GTGKTLS 73

>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 =  101 bits (254), Expect = 3e-27
 Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 2/69 (2%)

Query: 27 EITVKGNNIPCPT--QELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIA 84
           ++V G +       +   E      +  ++    ++ PT IQ    P  L  RD++  A
Sbjct: 8  PVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACA 67

Query: 85 QTGSGKTLA 93
          QTGSGKT A
Sbjct: 68 QTGSGKTAA 76

>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 = 72.6 bits (179), Expect = 1e-16
 Identities = 23/44 (52%), Positives = 32/44 (72%)

Query: 50 AVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
           +L+ L G+G   PT IQA   P+AL G+D++G A+TG+GKTLA
Sbjct: 11 EILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLA 54

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score = 72.6 bits (179), Expect = 2e-16
 Identities = 21/47 (44%), Positives = 29/47 (61%)

Query: 47 FPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
          F   +++ +K   F +PT IQ +  P AL G  MVG +QTG+GKT A
Sbjct: 11 FQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHA 57

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli} Length = 170

 Score = 69.9 bits (172), Expect = 7e-16
 Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 3/58 (5%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQ 151
           V NFD P S + Y+HRIGRT R    GTA +    ++     + +    E  +PI  +
Sbjct: 102 VFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGK-VGRYIE--EPIKAR 156

>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 = 70.7 bits (174), Expect = 9e-16
 Identities = 20/43 (46%), Positives = 28/43 (65%)

Query: 51 VLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
           L+ L+   +   T IQ Q   +AL G+D++G A+TGSGKTLA
Sbjct: 36 TLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLA 78

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score = 68.7 bits (169), Expect = 2e-15
 Identities = 18/36 (50%), Positives = 22/36 (61%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPN 129
           VIN+D P   E Y+HR GRTGR  + G A +F T  
Sbjct: 107 VINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAF 142

>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 = 69.5 bits (171), Expect = 2e-15
 Identities = 20/48 (41%), Positives = 31/48 (64%)

Query: 46 CFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
          C    +L  +   G+E+P+ IQ +  PIALSGRD++  A+ G+GK+ A
Sbjct: 9  CLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGA 56

>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 = 69.6 bits (171), Expect = 3e-15
 Identities = 26/98 (26%), Positives = 46/98 (46%), Gaps = 7/98 (7%)

Query: 1  MHNHAKTQERAARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPN-----AVLQHL 55
          MH+H          +E+      ++ +   + +      +E     F +      + +  
Sbjct: 1  MHHHHHHSSGVDLGTENLYFQSMEEHDSPTEASQPIVEEEETKT--FKDLGVTDVLCEAC 58

Query: 56 KGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
             G+ +PT IQ +  P+AL GRD++G+A+TGSGKT A
Sbjct: 59 DQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGA 96

>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 = 69.8 bits (172), Expect = 5e-15
 Identities = 17/44 (38%), Positives = 29/44 (65%)

Query: 50 AVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
           + Q ++  GF+  T +Q++  P+ L G+++V  A+TGSGKT A
Sbjct: 4  KIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAA 47

>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 = 66.4 bits (163), Expect = 9e-14
 Identities = 20/35 (57%), Positives = 20/35 (57%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTP 128
           VINFD P     YIHRIGRTGR    G A TF   
Sbjct: 288 VINFDAPQDLRTYIHRIGRTGRMGRKGEAITFILN 322

>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 = 68.9 bits (169), Expect = 7e-15
 Identities = 20/42 (47%), Positives = 26/42 (61%)

Query: 52  LQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
           L+ +K  GF   T IQ +     L GRD++  A+TGSGKTLA
Sbjct: 66  LKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLA 107

>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 = 68.4 bits (168), Expect = 2e-14
 Identities = 22/70 (31%), Positives = 32/70 (45%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ 153
           VINFD+P ++E Y+HRIGR+GR    G A      N+     ++   L      IP  + 
Sbjct: 330 VINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATID 389

Query: 154 DLANSNPNSK 163
                  N +
Sbjct: 390 KSLYVAENDE 399

>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 = 65.3 bits (160), Expect = 3e-13
 Identities = 18/43 (41%), Positives = 30/43 (69%)

Query: 51 VLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
          +L  +   GFE+P+ IQ +  P+A++GRD++  A+ G+GKT A
Sbjct: 32 LLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAA 74

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score = 65.7 bits (161), Expect = 3e-14
 Identities = 23/65 (35%), Positives = 32/65 (49%), Gaps = 2/65 (3%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEAS-QPIPPQL 152
           VIN+D P + E+YIHRIGR GR    G A  F T  +    +E +        + +P  +
Sbjct: 102 VINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRE-LEKFYSTQIEELPSDI 160

Query: 153 QDLAN 157
             L N
Sbjct: 161 ATLLN 165

>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 = 67.9 bits (167), Expect = 3e-14
 Identities = 18/48 (37%), Positives = 31/48 (64%), Gaps = 1/48 (2%)

Query: 47 FPNAVLQHLKGQGFEEPTAIQAQGWPIALSGR-DMVGIAQTGSGKTLA 93
            + +L  ++ +GFE+PT IQ +  P+ L+   ++V  A+TGSGKT +
Sbjct: 13 LSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTAS 60

>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 = 65.2 bits (160), Expect = 3e-13
 Identities = 16/36 (44%), Positives = 20/36 (55%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPN 129
           VIN+  P + E Y+HRIGRTGR    G A +     
Sbjct: 310 VINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRR 345

>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 = 67.9 bits (167), Expect = 3e-14
 Identities = 24/64 (37%), Positives = 33/64 (51%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ 153
           VIN+D P + E+YIHRIGR GR    G A  F T  +    +EL    +   + +P  + 
Sbjct: 331 VINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIA 390

Query: 154 DLAN 157
            L N
Sbjct: 391 TLLN 394

>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 = 67.2 bits (165), Expect = 6e-14
 Identities = 18/43 (41%), Positives = 28/43 (65%)

Query: 51 VLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
          +L+ + G GFEEP+AIQ +     + G D++  AQ+G+GKT  
Sbjct: 32 LLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGT 74

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A Length = 212

 Score = 66.2 bits (162), Expect = 4e-14
 Identities = 13/36 (36%), Positives = 19/36 (52%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPN 129
           V+++  P+ +E Y HR GRTGR    G     + P 
Sbjct: 103 VVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPR 138

>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 = 67.2 bits (165), Expect = 6e-14
 Identities = 16/43 (37%), Positives = 27/43 (62%)

Query: 51 VLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
          +L+ +   GFE+P+AIQ +     + G D++  AQ+G+GKT  
Sbjct: 51 LLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTAT 93

>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 = 65.7 bits (161), Expect = 2e-13
 Identities = 18/36 (50%), Positives = 21/36 (58%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPN 129
           VIN+D P + E+YIHRIGR GR    G A    T  
Sbjct: 352 VINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEE 387

>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 = 67.2 bits (165), Expect = 6e-14
 Identities = 16/43 (37%), Positives = 28/43 (65%)

Query: 51 VLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
          +L+ +   GFE+P+AIQ +     + GRD++  +Q+G+GKT  
Sbjct: 48 LLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTAT 90

>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 = 66.1 bits (162), Expect = 1e-13
 Identities = 18/36 (50%), Positives = 23/36 (63%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPN 129
           +IN+D PN+ E YIHRIGR+GR    G A  F   +
Sbjct: 348 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKND 383

>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 = 67.1 bits (164), Expect = 7e-14
 Identities = 18/79 (22%), Positives = 29/79 (36%), Gaps = 9/79 (11%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPN---------NGKQAKELIAVLTEA 144
           V+    P+   +YIHRIGRT R    G++  F   +         + K          E 
Sbjct: 414 VLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEKYEP 473

Query: 145 SQPIPPQLQDLANSNPNSK 163
           S+ I  ++ +     P   
Sbjct: 474 SEEIKSEVLEAVTEEPEDI 492

>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 = 66.0 bits (161), Expect = 2e-13
 Identities = 18/91 (19%), Positives = 32/91 (35%), Gaps = 3/91 (3%)

Query: 6   KTQERAARLSESEVEAFRQKKEITVKGNNIPCPTQEL-TEGCFPNAVLQHLKGQGFEEPT 64
                       +   F +   +  + N+       L  EG     + + +    F   T
Sbjct: 37  TRSREDDDEVHFDKTTFSKLIHVPKEDNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLT 96

Query: 65  AIQAQGWPIALSG--RDMVGIAQTGSGKTLA 93
            +Q +     LS    D++  A+TG+GKT A
Sbjct: 97  PVQQKTIKPILSSEDHDVIARAKTGTGKTFA 127

>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 = 65.3 bits (160), Expect = 8e-14
 Identities = 18/46 (39%), Positives = 28/46 (60%)

Query: 48 PNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
             +L+ + G GFEEP+AIQ +     + G D++  AQ+G+GKT  
Sbjct: 22 DENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGT 67

>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 = 65.3 bits (160), Expect = 8e-14
 Identities = 16/48 (33%), Positives = 27/48 (56%)

Query: 46 CFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
               VL+ L+  GFE P+ +Q +  P+   G D++  A++G+GKT  
Sbjct: 30 LLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCV 77

>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 = 66.8 bits (163), Expect = 8e-14
 Identities = 18/79 (22%), Positives = 29/79 (36%), Gaps = 9/79 (11%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPN---------NGKQAKELIAVLTEA 144
           V+    P+   +YIHRIGRT R    G++  F   +         + K          E 
Sbjct: 363 VLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEKYEP 422

Query: 145 SQPIPPQLQDLANSNPNSK 163
           S+ I  ++ +     P   
Sbjct: 423 SEEIKSEVLEAVTEEPEDI 441

>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 = 64.4 bits (157), Expect = 6e-13
 Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 2/46 (4%)

Query: 50 AVLQHLKGQGFEEPTAIQAQGWPIALSG--RDMVGIAQTGSGKTLA 93
           + + +    F   T +Q +     LS    D++  A+TG+GKT A
Sbjct: 31 EIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFA 76

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 66.7 bits (163), Expect = 9e-14
 Identities = 10/43 (23%), Positives = 16/43 (37%)

Query: 51 VLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
               K +  ++ T  Q       + G+    +A TG GKT  
Sbjct: 10 FRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTF 52

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 46.6 bits (111), Expect = 9e-07
 Identities = 10/63 (15%), Positives = 21/63 (33%), Gaps = 4/63 (6%)

Query: 94  VINFDYPNS--SEDYIHRIGRTGRCASSG--TAYTFFTPNNGKQAKELIAVLTEASQPIP 149
           VI +  P+      YI   GR+ R  +       +     + +  + L   L   ++   
Sbjct: 324 VIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFEEDEEIFESLKTRLLLIAEEEI 383

Query: 150 PQL 152
            + 
Sbjct: 384 IEE 386

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19 Length = 172

 Score = 64.1 bits (157), Expect = 1e-13
 Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEAS-QPIPPQL 152
             N+D P  S+ Y+HR+ R GR  + G A TF +  N  +    +    E +   +P ++
Sbjct: 103 AFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI 162

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus} Length = 300

 Score = 65.5 bits (160), Expect = 2e-13
 Identities = 13/36 (36%), Positives = 19/36 (52%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPN 129
           V+++  P+ +E Y HR GRTGR    G     + P 
Sbjct: 100 VVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPR 135

>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 = 64.9 bits (159), Expect = 2e-13
 Identities = 16/43 (37%), Positives = 27/43 (62%)

Query: 51 VLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
          +L+ +   GFE+P+AIQ +     + G D++  AQ+G+GKT  
Sbjct: 41 LLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTAT 83

>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 = 62.6 bits (153), Expect = 2e-12
 Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEAS-QPIPPQL 152
             N+D P  S+ Y+HR+ R GR  + G A TF +  N  +    +    E +   +P ++
Sbjct: 322 AFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI 381

>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 = 59.9 bits (146), Expect = 2e-11
 Identities = 15/48 (31%), Positives = 26/48 (54%)

Query: 46 CFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
               +L+ +   GFE P+ +Q +  P A+ G D++  A++G GKT  
Sbjct: 14 LLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAV 61

>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 = 62.6 bits (153), Expect = 3e-12
 Identities = 15/45 (33%), Positives = 28/45 (62%), Gaps = 2/45 (4%)

Query: 51 VLQHLKGQGFEEPTAIQAQGWPIALSG--RDMVGIAQTGSGKTLA 93
          +L+ +    F++P+ IQ +  P+ L    R+M+  +Q+G+GKT A
Sbjct: 16 LLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAA 60

>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 = 58.7 bits (143), Expect = 5e-11
 Identities = 21/71 (29%), Positives = 27/71 (38%), Gaps = 8/71 (11%)

Query: 94  VINFDYPNSS------EDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQ- 146
           V+N+D P  +        YIHRIGRTGR    G A +F    N       I       + 
Sbjct: 315 VVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEM 374

Query: 147 -PIPPQLQDLA 156
             +P    D  
Sbjct: 375 TRVPTDDWDEV 385

>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 = 61.1 bits (149), Expect = 3e-12
 Identities = 15/47 (31%), Positives = 26/47 (55%)

Query: 47 FPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
              +L+ +   GFE P+ +Q +  P A+ G D++  A++G GKT  
Sbjct: 21 LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAV 67

>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 = 61.4 bits (150), Expect = 7e-12
 Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 2/48 (4%)

Query: 48 PNAVLQHLKGQGFEEPTAIQAQGWPIALSG--RDMVGIAQTGSGKTLA 93
             +LQ +   GF  P+ IQ    P+ L+   ++++  +Q+G+GKT A
Sbjct: 33 KPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAA 80

>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 = 56.8 bits (138), Expect = 3e-10
 Identities = 18/43 (41%), Positives = 21/43 (48%), Gaps = 6/43 (13%)

Query: 94  VINFDYPNS------SEDYIHRIGRTGRCASSGTAYTFFTPNN 130
           VINFD P        +E Y+HRIGRTGR    G A       +
Sbjct: 338 VINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH 380

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens} Length = 175

 Score = 59.1 bits (144), Expect = 9e-12
 Identities = 17/42 (40%), Positives = 21/42 (50%), Gaps = 6/42 (14%)

Query: 94  VINFDYPNSS------EDYIHRIGRTGRCASSGTAYTFFTPN 129
           V+NFD P         E Y+HRIGRTGR    G A+     +
Sbjct: 106 VVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVD 147

>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 = 60.0 bits (146), Expect = 2e-11
 Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 2/45 (4%)

Query: 51  VLQHLKGQGFEEPTAIQAQGWPIALSG--RDMVGIAQTGSGKTLA 93
           +LQ +   GF  P+ IQ    P+ L+   ++++  +Q+G+GKT A
Sbjct: 103 LLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAA 147

>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 = 55.8 bits (135), Expect = 7e-10
 Identities = 18/43 (41%), Positives = 21/43 (48%), Gaps = 6/43 (13%)

Query: 94  VINFDYPNS------SEDYIHRIGRTGRCASSGTAYTFFTPNN 130
           VINFD P        +E Y+HRIGRTGR    G A       +
Sbjct: 405 VINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH 447

>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 = 57.8 bits (140), Expect = 9e-11
 Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 2/45 (4%)

Query: 51  VLQHLKGQGFEEPTAIQAQGWPIALSG--RDMVGIAQTGSGKTLA 93
           +LQ +   GF  P+ IQ    P+ L+   ++++  +Q+G+GKT A
Sbjct: 103 LLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAA 147

>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 = 49.8 bits (118), Expect = 6e-08
 Identities = 12/50 (24%), Positives = 18/50 (36%), Gaps = 1/50 (2%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTE 143
           V+ ++   S+   I R GRTGR    G            +A    +   E
Sbjct: 441 VVFYEPVPSAIRSIQRRGRTGR-HMPGRVIILMAKGTRDEAYYWSSRQKE 489

>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 = 5e-05
 Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 39 TQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
           +EL E    +  +  LK +G EE    QA+      SG++++    T +GKTL 
Sbjct: 3  VEELAES-ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLL 56

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	165
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.82
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.78
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.77
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.7
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.66
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.64
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.63
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.62
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.62
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.62
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.6
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.59
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.57
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.55
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.55
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.55
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.54
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.51
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.49
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.47
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.44
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.44
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.44
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.42
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.42
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.41
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.41
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.32
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.28
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.23
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.21
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.21
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.13
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.13
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.08
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.05
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.04
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	98.98
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	98.98
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	98.97
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	98.95
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	98.95
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	98.94
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	98.91
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	98.91
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	98.87
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	98.8
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	98.76
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	98.75
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	98.75
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	98.74
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	98.16
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	98.69
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	98.65
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	98.65
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	98.64
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	98.63
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	98.62
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	98.6
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	98.6
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	98.58
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	98.56
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	98.56
3b6e_A	216	Interferon-induced helicase C domain-containing P;	98.53
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	98.53
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	98.51
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	98.51
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	98.5
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	98.47
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	98.47
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	98.46
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	98.45
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	98.45
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	98.43
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	98.42
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	98.41
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	98.38
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	98.37
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	98.36
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	98.32
3jux_A	822	Protein translocase subunit SECA; protein transloc	98.28
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	98.27
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	98.26
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	98.23
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	98.22
4gl2_A	699	Interferon-induced helicase C domain-containing P;	98.22
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	98.21
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	98.18
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	98.18
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	98.15
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	98.13
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	98.11
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	98.08
1yks_A	440	Genome polyprotein [contains: flavivirin protease	98.05
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	98.04
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	98.03
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	98.02
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	98.0
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.0
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	98.0
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	97.98
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	97.98
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	97.94
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	97.89
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	97.87
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	97.87
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	97.85
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	97.83
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	97.82
1yks_A	440	Genome polyprotein [contains: flavivirin protease	97.79
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	97.78
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	97.75
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	97.74
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	97.64
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	97.62
4gl2_A	699	Interferon-induced helicase C domain-containing P;	97.56
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	97.54
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	97.53
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	97.41
3h1t_A	590	Type I site-specific restriction-modification syst	97.37
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	97.36
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	97.36
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	97.28
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	97.27
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	97.21
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	97.11
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	97.1
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	97.05
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	97.02
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	96.93
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	96.82
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	96.78
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	96.65
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	96.64
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	96.56
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	96.56
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	96.52
3h1t_A	590	Type I site-specific restriction-modification syst	96.13
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	95.92
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	95.71
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	95.62
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	95.52
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	95.37
3jux_A	822	Protein translocase subunit SECA; protein transloc	95.03
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	94.6
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	94.04
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	93.65
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	93.39
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	93.3
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	93.11
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	92.73
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	92.7
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	92.56
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	92.56
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	91.78
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	91.74
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	91.37
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	90.76
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	89.72
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	89.31
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	87.97
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	80.82

>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=99.82  E-value=6.2e-20  Score=143.44  Aligned_cols=123  Identities=45%  Similarity=0.687  Sum_probs=105.0

Q ss_pred             cCCHHHHHHHHhhcCcEEecCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccc
Q psy7691          13 RLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTL   92 (165)
Q Consensus        13 ~~~~~~~~~~~~~~~i~~~~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~   92 (165)
                      .+++++++.+++.+.+.+.|.+.|.|+..|+++++++.+.++|.+.||..|+++|.++++.++.|.|++++++||+|||+
T Consensus         2 ~~~~~~~~~~~~~~~i~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~   81 (242)
T 3fe2_A            2 MRTAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTL   81 (242)
T ss_dssp             ----CHHHHHHHHHTEEEESSCCCCCCSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHH
T ss_pred             CCCHHHHHHHHhcCceEEeCCCCCCccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHH
Confidence            45778999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeecCCCCChhHHHHhhccCCC-CCCCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691          93 AVINFDYPNSSEDYIHRIGRTGR-CASSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus        93 ~~~~~~lP~~~~~~i~r~gr~~r-~~~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      +|+   +|     .++++.+... ....+..+++++|+ ++++.|+.+.+...
T Consensus        82 ~~~---l~-----~l~~l~~~~~~~~~~~~~~lil~Pt-~~L~~Q~~~~~~~~  125 (242)
T 3fe2_A           82 SYL---LP-----AIVHINHQPFLERGDGPICLVLAPT-RELAQQVQQVAAEY  125 (242)
T ss_dssp             HHH---HH-----HHHHHHTSCCCCTTCCCSEEEECSS-HHHHHHHHHHHHHH
T ss_pred             HHH---HH-----HHHHHHhccccccCCCCEEEEEeCc-HHHHHHHHHHHHHH
Confidence            998   88     6776644322 12346678899999 88888887777653

>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=99.78  E-value=6.9e-19  Score=148.55  Aligned_cols=114  Identities=25%  Similarity=0.431  Sum_probs=98.9

Q ss_pred             hhcCcEEecCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCCh
Q psy7691          24 QKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSS  103 (165)
Q Consensus        24 ~~~~i~~~~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~  103 (165)
                      .+..+.+.|.+.|.|+..|+++++++.++++|.++||..||++|.+|||.++.|+|++++|+||||||++|+   +|   
T Consensus        40 ~~~~~~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~---lp---  113 (434)
T 2db3_A           40 NNIPVKVTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFL---LP---  113 (434)
T ss_dssp             GGSCEEEESSSCCCCCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHH---HH---
T ss_pred             cCceeEecCCCCCCCcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHH---HH---
Confidence            455788899999999999999999999999999999999999999999999999999999999999999998   88   


Q ss_pred             hHHHHhhccCCC-CCCCCceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         104 EDYIHRIGRTGR-CASSGTAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       104 ~~~i~r~gr~~r-~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                        .++++-.... ....+..+++++|+ ++++.|+.+.+.....
T Consensus       114 --il~~l~~~~~~~~~~~~~~lil~Pt-reLa~Q~~~~~~~~~~  154 (434)
T 2db3_A          114 --ILSKLLEDPHELELGRPQVVIVSPT-RELAIQIFNEARKFAF  154 (434)
T ss_dssp             --HHHHHHHSCCCCCTTCCSEEEECSS-HHHHHHHHHHHHHHTT
T ss_pred             --HHHHHHhcccccccCCccEEEEecC-HHHHHHHHHHHHHHhc
Confidence              7776644322 23456789999999 9999999888876543

>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=99.77  E-value=1.9e-18  Score=134.81  Aligned_cols=118  Identities=31%  Similarity=0.515  Sum_probs=105.0

Q ss_pred             HHHHHHHhhcCcEEecCCCCCCccccccC----CCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccc
Q psy7691          17 SEVEAFRQKKEITVKGNNIPCPTQELTEG----CFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTL   92 (165)
Q Consensus        17 ~~~~~~~~~~~i~~~~~~~p~~i~~f~~l----~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~   92 (165)
                      .+++.+|+++++.+.+.+.|.|+..|+++    ++++.++++|.+.||..|+++|.++++.++.|+|++++++||+|||+
T Consensus         2 ~~~~~~~~~~~i~~~~~~~p~~~~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~   81 (245)
T 3dkp_A            2 MKINFLRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTL   81 (245)
T ss_dssp             HHHHHHHHHTTEEEESSSCCCCCSSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHH
T ss_pred             hhHHHHHHhCceEecCCCCCCcccCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHH
Confidence            36889999999999999999999999987    89999999999999999999999999999999999999999999999


Q ss_pred             eeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691          93 AVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus        93 ~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      +|+   +|     .++++.+.   ...+..+++++|+ ++++.|+.+.+.....
T Consensus        82 ~~~---l~-----~l~~l~~~---~~~~~~~lil~Pt-~~L~~q~~~~~~~~~~  123 (245)
T 3dkp_A           82 AFS---IP-----ILMQLKQP---ANKGFRALIISPT-RELASQIHRELIKISE  123 (245)
T ss_dssp             HHH---HH-----HHHHHCSC---CSSSCCEEEECSS-HHHHHHHHHHHHHHTT
T ss_pred             HHH---HH-----HHHHHhhc---ccCCceEEEEeCC-HHHHHHHHHHHHHHhc
Confidence            988   88     77777432   2356678999999 9999999888877544

>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=99.70  E-value=6e-17  Score=131.04  Aligned_cols=109  Identities=19%  Similarity=0.342  Sum_probs=92.3

Q ss_pred             cCcEEecCCCCCC---ccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcC--CCeeeecccCCcccceeeecCCC
Q psy7691          26 KEITVKGNNIPCP---TQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSG--RDMVGIAQTGSGKTLAVINFDYP  100 (165)
Q Consensus        26 ~~i~~~~~~~p~~---i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G--~di~~~a~tgsGKt~~~~~~~lP  100 (165)
                      +.+.+.+.+.+.|   +..|+++++++.++++|..+||..||++|.+++|.++.|  +|++++|+||||||++|+   +|
T Consensus        75 ~~v~v~~~~~~~p~~~~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~---lp  151 (300)
T 3fmo_B           75 NQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFV---LA  151 (300)
T ss_dssp             SCEEEECSSTTCCCCCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHH---HH
T ss_pred             ccceeccCCCCCCcCCcCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHH---HH
Confidence            3455666665554   678999999999999999999999999999999999998  999999999999999998   88


Q ss_pred             CChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCC
Q psy7691         101 NSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQP  147 (165)
Q Consensus       101 ~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~  147 (165)
                           .++++...    ..++.+++++|+ ++++.|+.+.+......
T Consensus       152 -----~l~~l~~~----~~~~~~lil~Pt-reLa~Q~~~~~~~l~~~  188 (300)
T 3fmo_B          152 -----MLSQVEPA----NKYPQCLCLSPT-YELALQTGKVIEQMGKF  188 (300)
T ss_dssp             -----HHHHCCTT----SCSCCEEEECSS-HHHHHHHHHHHHHHTTT
T ss_pred             -----HHHhhhcc----CCCceEEEEcCc-HHHHHHHHHHHHHHHhh
Confidence                 88887543    345678899999 99999998888876543

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.66  E-value=3e-16  Score=121.61  Aligned_cols=118  Identities=25%  Similarity=0.336  Sum_probs=96.8

Q ss_pred             CHHHHHHHHhhcCcEEecCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCccccee
Q psy7691          15 SESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAV   94 (165)
Q Consensus        15 ~~~~~~~~~~~~~i~~~~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~   94 (165)
                      ++++++.+++++..     ..+.++..|+++++++.+.+.|.+.||..|+++|.++++.++.|.|++++++||+|||+++
T Consensus         5 ~~~~~~~~~~~~~~-----~~~~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~   79 (236)
T 2pl3_A            5 ERESISRLMQNYEK-----INVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAF   79 (236)
T ss_dssp             HHHHHHHHHHTTTT-----CCGGGCSBGGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHH
T ss_pred             cHhHHHHHHhcccc-----CCCcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHH
Confidence            45677777777663     2245678999999999999999999999999999999999999999999999999999998


Q ss_pred             eecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691          95 INFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus        95 ~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      +   +|     .++++.+.......+..+++++|+ ++++.|+.+.+.....
T Consensus        80 ~---~~-----~l~~l~~~~~~~~~~~~~lil~Pt-~~L~~q~~~~~~~~~~  122 (236)
T 2pl3_A           80 L---VP-----VLEALYRLQWTSTDGLGVLIISPT-RELAYQTFEVLRKVGK  122 (236)
T ss_dssp             H---HH-----HHHHHHHTTCCGGGCCCEEEECSS-HHHHHHHHHHHHHHTT
T ss_pred             H---HH-----HHHHHHhhcccccCCceEEEEeCC-HHHHHHHHHHHHHHhC
Confidence            8   78     666654432223456678999999 8999998888877554

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.64  E-value=3.3e-16  Score=129.60  Aligned_cols=109  Identities=24%  Similarity=0.373  Sum_probs=91.3

Q ss_pred             CcEEecCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHH
Q psy7691          27 EITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDY  106 (165)
Q Consensus        27 ~i~~~~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~  106 (165)
                      .+.+.|.++|.++..|+++++++.+.++|...||..|+++|.+++|.++.|.|++++++||+|||++|+   +|     .
T Consensus         2 ~~~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~---~~-----~   73 (417)
T 2i4i_A            2 MVEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFL---LP-----I   73 (417)
T ss_dssp             CEEEESTTCCCCCSSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHH---HH-----H
T ss_pred             CcccCCCcCCcccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHH---HH-----H
Confidence            466789999999999999999999999999999999999999999999999999999999999999988   77     5


Q ss_pred             HHhhccC------------CCC--CCCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691         107 IHRIGRT------------GRC--ASSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus       107 i~r~gr~------------~r~--~~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      ++++-..            ++.  ...+..+++++|+ ++++.|+.+.+...
T Consensus        74 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt-~~L~~q~~~~~~~~  124 (417)
T 2i4i_A           74 LSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPT-RELAVQIYEEARKF  124 (417)
T ss_dssp             HHHHHHHCCCHHHHHHHHCBTTBSCSBCCSEEEECSS-HHHHHHHHHHHHHH
T ss_pred             HHHHHhccccchhhccccccccccccCCccEEEECCc-HHHHHHHHHHHHHH
Confidence            5544211            111  1234678999999 89999888877653

>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=99.63  E-value=1.5e-16  Score=124.67  Aligned_cols=112  Identities=21%  Similarity=0.325  Sum_probs=93.3

Q ss_pred             hhcCcEEecCCCCC--CccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCC
Q psy7691          24 QKKEITVKGNNIPC--PTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPN  101 (165)
Q Consensus        24 ~~~~i~~~~~~~p~--~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~  101 (165)
                      .+..+.+.+.+.|.  ++..|+++++++.++++|...||..|+++|.++++.++.|.|++++++||+|||++++   +| 
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~---~~-   80 (253)
T 1wrb_A            5 DSIPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFL---IP-   80 (253)
T ss_dssp             CCCCCCEECCSSSCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHH---HH-
T ss_pred             hhCceeeeCCCCCCCCccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHH---HH-
Confidence            34567778888887  8999999999999999999999999999999999999999999999999999999988   78 


Q ss_pred             ChhHHHHhhccCCC-----CCCCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691         102 SSEDYIHRIGRTGR-----CASSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus       102 ~~~~~i~r~gr~~r-----~~~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                          .++++.....     ....+..+++++|+ ++++.|+.+.+...
T Consensus        81 ----~l~~l~~~~~~~~~~~~~~~~~~lil~Pt-~~L~~q~~~~~~~~  123 (253)
T 1wrb_A           81 ----IINHLVCQDLNQQRYSKTAYPKCLILAPT-RELAIQILSESQKF  123 (253)
T ss_dssp             ----HHHHHHTTCC------CCBCCSEEEECSS-HHHHHHHHHHHHHH
T ss_pred             ----HHHHHHhhccccccccccCCceEEEEECC-HHHHHHHHHHHHHH
Confidence                6666532211     12345678999999 88999888877664

>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=99.62  E-value=5.4e-16  Score=119.55  Aligned_cols=104  Identities=31%  Similarity=0.447  Sum_probs=87.0

Q ss_pred             cCCCCCCcccccc-CCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhh
Q psy7691          32 GNNIPCPTQELTE-GCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRI  110 (165)
Q Consensus        32 ~~~~p~~i~~f~~-l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~  110 (165)
                      +...|+|+..|++ +++++.++++|.+.||..|+++|.++++.++.|.|++++++||+|||++|+   +|     .++++
T Consensus        11 ~~~~p~p~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~---l~-----~~~~l   82 (228)
T 3iuy_A           11 KRLIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYL---MP-----GFIHL   82 (228)
T ss_dssp             CCCCCCCCCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHH---HH-----HHHHH
T ss_pred             cCcCCCChhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHH---HH-----HHHHH
Confidence            4668999999999 799999999999999999999999999999999999999999999999988   78     66655


Q ss_pred             ccC--CCCCCCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691         111 GRT--GRCASSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus       111 gr~--~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      ...  .+....+..+++++|+ ++++.|+.+.+...
T Consensus        83 ~~~~~~~~~~~~~~~lil~Pt-~~L~~q~~~~~~~~  117 (228)
T 3iuy_A           83 DSQPISREQRNGPGMLVLTPT-RELALHVEAECSKY  117 (228)
T ss_dssp             C---------CCCSEEEECSS-HHHHHHHHHHHHHH
T ss_pred             HhccchhhccCCCcEEEEeCC-HHHHHHHHHHHHHh
Confidence            322  1222456678999999 99999998888774

>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=99.62  E-value=1.3e-15  Score=117.97  Aligned_cols=102  Identities=22%  Similarity=0.361  Sum_probs=83.0

Q ss_pred             cCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhc
Q psy7691          32 GNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIG  111 (165)
Q Consensus        32 ~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~g  111 (165)
                      ++..|.+...|+++++++.+.++|.+.||..|+++|.++++.++.|.|++++++||+|||++|.   +|     .++++.
T Consensus        16 ~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~---l~-----~l~~l~   87 (230)
T 2oxc_A           16 GDVLLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFS---TI-----ALDSLV   87 (230)
T ss_dssp             --------CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHH---HH-----HHHHCC
T ss_pred             CCCCCCCCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHH---HH-----HHHHHH
Confidence            5666778889999999999999999999999999999999999999999999999999999988   77     777764


Q ss_pred             cCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         112 RTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       112 r~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      +.    ..+..+++++|+ ++++.|+.+.+.....
T Consensus        88 ~~----~~~~~~lil~Pt-~~L~~q~~~~~~~~~~  117 (230)
T 2oxc_A           88 LE----NLSTQILILAPT-REIAVQIHSVITAIGI  117 (230)
T ss_dssp             TT----SCSCCEEEECSS-HHHHHHHHHHHHHHTT
T ss_pred             hc----CCCceEEEEeCC-HHHHHHHHHHHHHHhc
Confidence            32    235678999999 8999999888877544

>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=99.62  E-value=8e-16  Score=119.76  Aligned_cols=105  Identities=21%  Similarity=0.315  Sum_probs=85.3

Q ss_pred             EEecCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHH
Q psy7691          29 TVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIH  108 (165)
Q Consensus        29 ~~~~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~  108 (165)
                      .+...+.++++..|+++++++.+.++|.+.||..|+++|.++++.++.|.|++++++||+|||++|+   +|     .++
T Consensus        19 ~~~~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~---l~-----~l~   90 (237)
T 3bor_A           19 GVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFA---IS-----ILQ   90 (237)
T ss_dssp             --------CCCCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHH---HH-----HHH
T ss_pred             CcccCCCCCccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHH---HH-----HHH
Confidence            3445667888999999999999999999999999999999999999999999999999999999988   77     777


Q ss_pred             hhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         109 RIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       109 r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      ++.+.    ..+..+++++|+ ++++.|+.+.+.....
T Consensus        91 ~l~~~----~~~~~~lil~Pt-~~L~~q~~~~~~~~~~  123 (237)
T 3bor_A           91 QLEIE----FKETQALVLAPT-RELAQQIQKVILALGD  123 (237)
T ss_dssp             HCCTT----SCSCCEEEECSS-HHHHHHHHHHHHHHTT
T ss_pred             HHHhc----CCCceEEEEECc-HHHHHHHHHHHHHHhh
Confidence            76432    245578899999 8999999888876543

>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=99.60  E-value=3.3e-15  Score=114.59  Aligned_cols=101  Identities=24%  Similarity=0.342  Sum_probs=87.5

Q ss_pred             cCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhc
Q psy7691          32 GNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIG  111 (165)
Q Consensus        32 ~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~g  111 (165)
                      ..+.++++..|+++++++.+.+.|.+.||..|+++|.++++.++.|.|++++++||+|||+++.   +|     .++++.
T Consensus         6 ~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~---~~-----~l~~l~   77 (224)
T 1qde_A            6 QTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFS---IA-----ALQRID   77 (224)
T ss_dssp             CBSCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHH---HH-----HHHHCC
T ss_pred             ccccCcccCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHH---HH-----HHHHHh
Confidence            3556788899999999999999999999999999999999999999999999999999999887   77     777774


Q ss_pred             cCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcC
Q psy7691         112 RTGRCASSGTAYTFFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus       112 r~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~  145 (165)
                      ..    ..+..+++++|+ ++++.|+.+.+....
T Consensus        78 ~~----~~~~~~lil~Pt-~~L~~q~~~~~~~~~  106 (224)
T 1qde_A           78 TS----VKAPQALMLAPT-RELALQIQKVVMALA  106 (224)
T ss_dssp             TT----CCSCCEEEECSS-HHHHHHHHHHHHHHT
T ss_pred             cc----CCCceEEEEECC-HHHHHHHHHHHHHHh
Confidence            32    345678899999 888888888777643

>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=99.59  E-value=5.6e-15  Score=111.77  Aligned_cols=95  Identities=27%  Similarity=0.495  Sum_probs=82.6

Q ss_pred             cccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCC
Q psy7691          40 QELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASS  119 (165)
Q Consensus        40 ~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~  119 (165)
                      ..|+++++++.++++|.+.||..|+++|.++++.++.|+|++++++||+|||++++   +|     .++++...    ..
T Consensus         3 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~---~~-----~~~~~~~~----~~   70 (206)
T 1vec_A            3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYL---IP-----LLERLDLK----KD   70 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHH---HH-----HHHHCCTT----SC
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHH---HH-----HHHHhccc----CC
Confidence            47999999999999999999999999999999999999999999999999999888   77     77776432    34


Q ss_pred             CceEEEECCCcHHHHHHHHHHHHhcCCC
Q psy7691         120 GTAYTFFTPNNGKQAKELIAVLTEASQP  147 (165)
Q Consensus       120 g~~~~~~~p~~~~~~~~i~~~l~~~~~~  147 (165)
                      +..+++++|+ ++++.|+.+.+......
T Consensus        71 ~~~~lil~Pt-~~L~~q~~~~~~~~~~~   97 (206)
T 1vec_A           71 NIQAMVIVPT-RELALQVSQICIQVSKH   97 (206)
T ss_dssp             SCCEEEECSC-HHHHHHHHHHHHHHTTT
T ss_pred             CeeEEEEeCc-HHHHHHHHHHHHHHHhh
Confidence            5678999999 89999988888765543

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.57  E-value=3.7e-15  Score=114.34  Aligned_cols=96  Identities=27%  Similarity=0.381  Sum_probs=81.7

Q ss_pred             CccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCC
Q psy7691          38 PTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCA  117 (165)
Q Consensus        38 ~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~  117 (165)
                      |+..|+++++++.+.++|.+.||..|+++|.++++.++.|.|++++++||+|||++|+   +|     .++++.+.    
T Consensus         2 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~---~~-----~l~~l~~~----   69 (219)
T 1q0u_A            2 AETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYL---LP-----IMEKIKPE----   69 (219)
T ss_dssp             --CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHH---HH-----HHHHCCTT----
T ss_pred             CCCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHH---HH-----HHHHHHhC----
Confidence            3568999999999999999999999999999999999999999999999999999988   78     77776432    


Q ss_pred             CCCceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         118 SSGTAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       118 ~~g~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      ..+..+++++|+ ++++.|+.+.+.....
T Consensus        70 ~~~~~~lil~Pt-~~L~~q~~~~~~~~~~   97 (219)
T 1q0u_A           70 RAEVQAVITAPT-RELATQIYHETLKITK   97 (219)
T ss_dssp             SCSCCEEEECSS-HHHHHHHHHHHHHHHT
T ss_pred             cCCceEEEEcCc-HHHHHHHHHHHHHHhh
Confidence            345678899998 8898888887766543

>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=99.55  E-value=6.1e-15  Score=116.75  Aligned_cols=98  Identities=31%  Similarity=0.442  Sum_probs=80.0

Q ss_pred             cccccCC--CcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCC
Q psy7691          40 QELTEGC--FPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCA  117 (165)
Q Consensus        40 ~~f~~l~--l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~  117 (165)
                      ..|+++.  +++.++++|.++||..|+++|.++++.++.|+|++++++||+|||++|+   +|     .++++.+.....
T Consensus        52 ~~f~~l~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~---l~-----~l~~l~~~~~~~  123 (262)
T 3ly5_A           52 TSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFL---IP-----AVELIVKLRFMP  123 (262)
T ss_dssp             GCC-----CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHH---HH-----HHHHHHHTTCCG
T ss_pred             CChhHhccccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHH---HH-----HHHHHHhccccc
Confidence            3556665  9999999999999999999999999999999999999999999999988   88     777665433333


Q ss_pred             CCCceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         118 SSGTAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       118 ~~g~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      ..+..+++++|+ ++++.|+.+.+.....
T Consensus       124 ~~~~~~lil~Pt-~~La~q~~~~~~~~~~  151 (262)
T 3ly5_A          124 RNGTGVLILSPT-RELAMQTFGVLKELMT  151 (262)
T ss_dssp             GGCCCEEEECSS-HHHHHHHHHHHHHHTT
T ss_pred             cCCceEEEEeCC-HHHHHHHHHHHHHHHh
Confidence            356678999999 9999999888877544

>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=99.55  E-value=1.5e-14  Score=110.65  Aligned_cols=97  Identities=18%  Similarity=0.276  Sum_probs=81.2

Q ss_pred             CCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCC
Q psy7691          37 CPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRC  116 (165)
Q Consensus        37 ~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~  116 (165)
                      .....|+++++++.+.++|.+.||..|+++|.++++.++.|.|++++++||+|||++++   +|     .++++.+.   
T Consensus        11 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~---~~-----~~~~~~~~---   79 (220)
T 1t6n_A           11 IHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFV---LA-----TLQQLEPV---   79 (220)
T ss_dssp             ---CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHH---HH-----HHHHCCCC---
T ss_pred             ccCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhh---HH-----HHHhhhcc---
Confidence            34567999999999999999999999999999999999999999999999999999988   77     66665331   


Q ss_pred             CCCCceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         117 ASSGTAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       117 ~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                       ..+..+++++|+ ++++.|+.+.+.....
T Consensus        80 -~~~~~~lil~Pt-~~L~~q~~~~~~~~~~  107 (220)
T 1t6n_A           80 -TGQVSVLVMCHT-RELAFQISKEYERFSK  107 (220)
T ss_dssp             -TTCCCEEEECSC-HHHHHHHHHHHHHHTT
T ss_pred             -CCCEEEEEEeCC-HHHHHHHHHHHHHHHh
Confidence             234578999999 8999998887776543

>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=99.55  E-value=2.2e-14  Score=108.46  Aligned_cols=96  Identities=32%  Similarity=0.529  Sum_probs=82.1

Q ss_pred             ccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCC
Q psy7691          41 ELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSG  120 (165)
Q Consensus        41 ~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g  120 (165)
                      .|+++++++.+.+.|.+.||..|+++|.++++.++.|.|++++++||+|||++++   +|     .++++... +....+
T Consensus         2 ~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~---~~-----~~~~l~~~-~~~~~~   72 (207)
T 2gxq_A            2 EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFA---LP-----IAERLAPS-QERGRK   72 (207)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHH---HH-----HHHHCCCC-CCTTCC
T ss_pred             ChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHH---HH-----HHHHHhhc-cccCCC
Confidence            6999999999999999999999999999999999999999999999999999887   77     67766432 222345


Q ss_pred             ceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         121 TAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       121 ~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      ..+++++|+ ++++.|+.+.+.....
T Consensus        73 ~~~lil~P~-~~L~~q~~~~~~~~~~   97 (207)
T 2gxq_A           73 PRALVLTPT-RELALQVASELTAVAP   97 (207)
T ss_dssp             CSEEEECSS-HHHHHHHHHHHHHHCT
T ss_pred             CcEEEEECC-HHHHHHHHHHHHHHhh
Confidence            678899999 8999998888877643

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=99.54  E-value=6.8e-15  Score=115.69  Aligned_cols=95  Identities=27%  Similarity=0.407  Sum_probs=81.6

Q ss_pred             CCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCC
Q psy7691          37 CPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRC  116 (165)
Q Consensus        37 ~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~  116 (165)
                      .++..|+++++++.+.++|...||..|+++|.++++.++.|+|++++++||+|||++++   +|     .++++.+.   
T Consensus        40 ~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~---~~-----il~~l~~~---  108 (249)
T 3ber_A           40 EETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFA---LP-----ILNALLET---  108 (249)
T ss_dssp             HHHCCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHH---HH-----HHHHHHHS---
T ss_pred             cccCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhH---HH-----HHHHHhcC---
Confidence            45788999999999999999999999999999999999999999999999999999988   77     66665432   


Q ss_pred             CCCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691         117 ASSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus       117 ~~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                       ..+..+++++|+ ++++.|+.+.+...
T Consensus       109 -~~~~~~lil~Pt-r~L~~q~~~~~~~~  134 (249)
T 3ber_A          109 -PQRLFALVLTPT-RELAFQISEQFEAL  134 (249)
T ss_dssp             -CCSSCEEEECSS-HHHHHHHHHHHHHH
T ss_pred             -CCCceEEEEeCC-HHHHHHHHHHHHHH
Confidence             234568899998 88888888776654

>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=99.51  E-value=4.3e-14  Score=116.89  Aligned_cols=103  Identities=20%  Similarity=0.281  Sum_probs=86.8

Q ss_pred             EecCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHh
Q psy7691          30 VKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHR  109 (165)
Q Consensus        30 ~~~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r  109 (165)
                      ....+.+++...|+++++++.+.++|...||..|+++|.++++.++.|.|++++++||+|||++++   +|     .++.
T Consensus        27 ~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~---~~-----~~~~   98 (410)
T 2j0s_A           27 FETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFS---IS-----VLQC   98 (410)
T ss_dssp             CCCCTTCCCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHH---HH-----HHHT
T ss_pred             cCCCCCccCCCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHH---HH-----HHHH
Confidence            334445567789999999999999999999999999999999999999999999999999999988   77     6666


Q ss_pred             hccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcC
Q psy7691         110 IGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus       110 ~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~  145 (165)
                      +..    ...+..+++++|+ ++++.|+.+.+....
T Consensus        99 l~~----~~~~~~~lil~Pt-~~L~~q~~~~~~~~~  129 (410)
T 2j0s_A           99 LDI----QVRETQALILAPT-RELAVQIQKGLLALG  129 (410)
T ss_dssp             CCT----TSCSCCEEEECSS-HHHHHHHHHHHHHHT
T ss_pred             Hhh----ccCCceEEEEcCc-HHHHHHHHHHHHHHh
Confidence            532    2345678999998 899999988887654

>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=99.49  E-value=4.7e-14  Score=119.63  Aligned_cols=105  Identities=21%  Similarity=0.360  Sum_probs=85.8

Q ss_pred             cEEecCCCCCC---ccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcC--CCeeeecccCCcccceeeecCCCCC
Q psy7691          28 ITVKGNNIPCP---TQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSG--RDMVGIAQTGSGKTLAVINFDYPNS  102 (165)
Q Consensus        28 i~~~~~~~p~~---i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G--~di~~~a~tgsGKt~~~~~~~lP~~  102 (165)
                      +.+.+.+.+.|   +..|+++++++.++++|..+||..|+++|.++++.++.|  .|++++++||||||++|+   +|  
T Consensus        77 ~~~~~~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~---l~--  151 (479)
T 3fmp_B           77 VEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFV---LA--  151 (479)
T ss_dssp             EEEECSSTTSCCCCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHH---HH--
T ss_pred             ceecCCCCCCCccCcCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHH---HH--
Confidence            33444444444   668999999999999999999999999999999999987  999999999999999988   77  


Q ss_pred             hhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcC
Q psy7691         103 SEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus       103 ~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~  145 (165)
                         .++++..    +..+..+++++|+ ++++.|+.+.+....
T Consensus       152 ---il~~l~~----~~~~~~~lil~Pt-~~La~Q~~~~~~~~~  186 (479)
T 3fmp_B          152 ---MLSQVEP----ANKYPQCLCLSPT-YELALQTGKVIEQMG  186 (479)
T ss_dssp             ---HHTTCCT----TSCSCCEEEECSS-HHHHHHHHHHHHHHH
T ss_pred             ---HHHHHhh----cCCCCcEEEEeCh-HHHHHHHHHHHHHHH
Confidence               6666643    2345578889998 999999877776643

>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=99.47  E-value=1.5e-13  Score=113.10  Aligned_cols=98  Identities=19%  Similarity=0.338  Sum_probs=84.1

Q ss_pred             CCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcC--CCeeeecccCCcccceeeecCCCCChhHHHHhhccCC
Q psy7691          37 CPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSG--RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTG  114 (165)
Q Consensus        37 ~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G--~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~  114 (165)
                      .++..|+++++++.++++|.+.||..|+++|.++++.++.|  .|++++++||+|||++++   +|     .++++.+. 
T Consensus        22 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~---~~-----~~~~~~~~-   92 (412)
T 3fht_A           22 YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFV---LA-----MLSQVEPA-   92 (412)
T ss_dssp             CCSSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHH---HH-----HHHHCCTT-
T ss_pred             cccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHH---HH-----HHHHhhhc-
Confidence            34778999999999999999999999999999999999998  999999999999999988   77     67766432 


Q ss_pred             CCCCCCceEEEECCCcHHHHHHHHHHHHhcCCC
Q psy7691         115 RCASSGTAYTFFTPNNGKQAKELIAVLTEASQP  147 (165)
Q Consensus       115 r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~  147 (165)
                         ..+..+++++|+ ++++.|+.+.+......
T Consensus        93 ---~~~~~~lil~P~-~~L~~q~~~~~~~~~~~  121 (412)
T 3fht_A           93 ---NKYPQCLCLSPT-YELALQTGKVIEQMGKF  121 (412)
T ss_dssp             ---SCSCCEEEECSS-HHHHHHHHHHHHHHTTT
T ss_pred             ---CCCCCEEEECCC-HHHHHHHHHHHHHHHhh
Confidence               345578889998 99999998888775543

>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=99.44  E-value=9.2e-14  Score=119.92  Aligned_cols=96  Identities=19%  Similarity=0.225  Sum_probs=81.0

Q ss_pred             ccccccC----CCcHHHHHHHHhCCCCCCchHHHHHHHHHH--cCCCeeeecccCCcccceeeecCCCCChhHHHHhhcc
Q psy7691          39 TQELTEG----CFPNAVLQHLKGQGFEEPTAIQAQGWPIAL--SGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGR  112 (165)
Q Consensus        39 i~~f~~l----~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l--~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr  112 (165)
                      ...|+++    .+++.++++|.+.||..|+++|.++++.++  .|+|++++++||+|||++|+   +|     .++++.+
T Consensus        67 ~~~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~---lp-----il~~l~~  138 (563)
T 3i5x_A           67 EVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFL---IP-----IFQHLIN  138 (563)
T ss_dssp             CCCHHHHHHTTSSCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHH---HH-----HHHHHHH
T ss_pred             CcCHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHH---HH-----HHHHHHh
Confidence            4456555    399999999999999999999999999999  67899999999999999998   88     7777765


Q ss_pred             CCCCCCCCceEEEECCCcHHHHHHHHHHHHh
Q psy7691         113 TGRCASSGTAYTFFTPNNGKQAKELIAVLTE  143 (165)
Q Consensus       113 ~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~  143 (165)
                      .......+..+++++|+ ++++.|+.+.+..
T Consensus       139 ~~~~~~~~~~~lil~Pt-r~La~Q~~~~~~~  168 (563)
T 3i5x_A          139 TKFDSQYMVKAVIVAPT-RDLALQIEAEVKK  168 (563)
T ss_dssp             TTTSSTTSCCEEEECSS-HHHHHHHHHHHHH
T ss_pred             ccccccCCeeEEEEcCc-HHHHHHHHHHHHH
Confidence            54444456678999999 8999888887766

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.44  E-value=9.4e-14  Score=120.86  Aligned_cols=99  Identities=18%  Similarity=0.209  Sum_probs=82.7

Q ss_pred             CCCccccccCC----CcHHHHHHHHhCCCCCCchHHHHHHHHHH--cCCCeeeecccCCcccceeeecCCCCChhHHHHh
Q psy7691          36 PCPTQELTEGC----FPNAVLQHLKGQGFEEPTAIQAQGWPIAL--SGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHR  109 (165)
Q Consensus        36 p~~i~~f~~l~----l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l--~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r  109 (165)
                      +.+...|+++.    +++.++++|...||..|+++|.++++.++  .|.|++++++||+|||++|+   +|     .+++
T Consensus        13 ~~~~~~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~---lp-----il~~   84 (579)
T 3sqw_A           13 NSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFL---IP-----IFQH   84 (579)
T ss_dssp             SCCCCCHHHHHHTTSSCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHH---HH-----HHHH
T ss_pred             CCCCcCHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHH---HH-----HHHH
Confidence            33445666553    99999999999999999999999999999  78999999999999999998   88     7777


Q ss_pred             hccCCCCCCCCceEEEECCCcHHHHHHHHHHHHh
Q psy7691         110 IGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTE  143 (165)
Q Consensus       110 ~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~  143 (165)
                      +.+....+..+..+++++|+ ++++.|+.+.+..
T Consensus        85 l~~~~~~~~~~~~~lvl~Pt-r~La~Q~~~~~~~  117 (579)
T 3sqw_A           85 LINTKFDSQYMVKAVIVAPT-RDLALQIEAEVKK  117 (579)
T ss_dssp             HHHTTTSSTTSCCEEEECSS-HHHHHHHHHHHHH
T ss_pred             HHhccccccCCCeEEEEcch-HHHHHHHHHHHHH
Confidence            76554444556788999999 8998888887775

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=99.44  E-value=3.1e-13  Score=110.32  Aligned_cols=95  Identities=22%  Similarity=0.415  Sum_probs=81.5

Q ss_pred             CccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcC--CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCC
Q psy7691          38 PTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSG--RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGR  115 (165)
Q Consensus        38 ~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G--~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r  115 (165)
                      ...+|+++++++.+.++|.+.||..|+++|.++++.++.|  .|++++++||+|||++++   +|     .++++...  
T Consensus         3 ~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~---~~-----~~~~~~~~--   72 (395)
T 3pey_A            3 MAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFS---LT-----MLTRVNPE--   72 (395)
T ss_dssp             -CCSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHH---HH-----HHHHCCTT--
T ss_pred             cccCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHH---HH-----HHHHhccC--
Confidence            3578999999999999999999999999999999999998  999999999999999888   67     66665332  


Q ss_pred             CCCCCceEEEECCCcHHHHHHHHHHHHhcC
Q psy7691         116 CASSGTAYTFFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus       116 ~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~  145 (165)
                        ..+..+++++|+ ++++.|+.+.+....
T Consensus        73 --~~~~~~lil~P~-~~L~~q~~~~~~~~~   99 (395)
T 3pey_A           73 --DASPQAICLAPS-RELARQTLEVVQEMG   99 (395)
T ss_dssp             --CCSCCEEEECSS-HHHHHHHHHHHHHHT
T ss_pred             --CCCccEEEECCC-HHHHHHHHHHHHHHh
Confidence              345578899999 899999888887744

>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=99.42  E-value=4.1e-13  Score=110.50  Aligned_cols=98  Identities=22%  Similarity=0.404  Sum_probs=81.0

Q ss_pred             CCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCC
Q psy7691          36 PCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGR  115 (165)
Q Consensus        36 p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r  115 (165)
                      ......|+++++++.+.++|.++||..|+++|.++++.++.|.|++++++||+|||++++   +|     .++.+..   
T Consensus        17 ~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~---~~-----~~~~~~~---   85 (400)
T 1s2m_A           17 NTKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFV---IP-----TLEKVKP---   85 (400)
T ss_dssp             ----CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHH---HH-----HHHHCCT---
T ss_pred             ccccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHH---HH-----HHHHHhh---
Confidence            345678999999999999999999999999999999999999999999999999999888   77     6665532   


Q ss_pred             CCCCCceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         116 CASSGTAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       116 ~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                       +..+..+++++|+ +.++.|+.+.+.....
T Consensus        86 -~~~~~~~lil~P~-~~L~~q~~~~~~~~~~  114 (400)
T 1s2m_A           86 -KLNKIQALIMVPT-RELALQTSQVVRTLGK  114 (400)
T ss_dssp             -TSCSCCEEEECSS-HHHHHHHHHHHHHHTT
T ss_pred             -ccCCccEEEEcCC-HHHHHHHHHHHHHHhc
Confidence             2345578899998 8888888888876544

>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=99.42  E-value=2.8e-13  Score=110.89  Aligned_cols=99  Identities=24%  Similarity=0.351  Sum_probs=85.1

Q ss_pred             CCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccC
Q psy7691          34 NIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRT  113 (165)
Q Consensus        34 ~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~  113 (165)
                      ...+++..|+++++++.+.++|...||..|+++|.++++.++.|.|++++++||+|||+++.   +|     .++++...
T Consensus        15 ~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~---~~-----~~~~l~~~   86 (394)
T 1fuu_A           15 NYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFS---IA-----ALQRIDTS   86 (394)
T ss_dssp             SSCCCCCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHH---HH-----HHHHCCTT
T ss_pred             hcccccCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHH---HH-----HHHHhhcc
Confidence            35567889999999999999999999999999999999999999999999999999999887   77     67766432


Q ss_pred             CCCCCCCceEEEECCCcHHHHHHHHHHHHhcC
Q psy7691         114 GRCASSGTAYTFFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus       114 ~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~  145 (165)
                          ..+..+++++|+ +.++.|+.+.+....
T Consensus        87 ----~~~~~~lil~P~-~~L~~q~~~~~~~~~  113 (394)
T 1fuu_A           87 ----VKAPQALMLAPT-RELALQIQKVVMALA  113 (394)
T ss_dssp             ----CCSCCEEEECSS-HHHHHHHHHHHHHHT
T ss_pred             ----CCCCCEEEEcCC-HHHHHHHHHHHHHHh
Confidence                345578999998 889888888776644

>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=99.41  E-value=3.9e-13  Score=110.04  Aligned_cols=94  Identities=18%  Similarity=0.287  Sum_probs=80.4

Q ss_pred             cccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCC
Q psy7691          40 QELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASS  119 (165)
Q Consensus        40 ~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~  119 (165)
                      ..|+++++++.+.++|.++||..|+++|.++++.++.|.|++++++||+|||++++   +|     .++.+.+.    ..
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~---~~-----~~~~l~~~----~~   75 (391)
T 1xti_A            8 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFV---LA-----TLQQLEPV----TG   75 (391)
T ss_dssp             -CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHH---HH-----HHHHCCCC----TT
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHH---HH-----HHHhhccc----CC
Confidence            57999999999999999999999999999999999999999999999999999988   77     66665332    34


Q ss_pred             CceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         120 GTAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       120 g~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      +..+++++|+ +.++.|+.+.+.....
T Consensus        76 ~~~~lil~P~-~~L~~q~~~~~~~~~~  101 (391)
T 1xti_A           76 QVSVLVMCHT-RELAFQISKEYERFSK  101 (391)
T ss_dssp             CCCEEEECSC-HHHHHHHHHHHHHHTT
T ss_pred             CeeEEEECCC-HHHHHHHHHHHHHHHh
Confidence            5578999999 8999988887776543

>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=99.41  E-value=7.3e-13  Score=109.18  Aligned_cols=100  Identities=22%  Similarity=0.339  Sum_probs=85.5

Q ss_pred             cCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhc
Q psy7691          32 GNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIG  111 (165)
Q Consensus        32 ~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~g  111 (165)
                      ..+.+..+..|+++++++.+.+.|.+.||..|+++|.++++.++.|.|++++++||+|||+++.   +|     .++++.
T Consensus        32 ~~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~---~~-----~~~~~~  103 (414)
T 3eiq_A           32 ESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFA---IS-----ILQQIE  103 (414)
T ss_dssp             CCCCCCCCCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHH---HH-----HHHHCC
T ss_pred             CCCccchhcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHH---HH-----HHHHHh
Confidence            3455667789999999999999999999999999999999999999999999999999999987   77     676664


Q ss_pred             cCCCCCCCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691         112 RTGRCASSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus       112 r~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      ..    ..+..+++++|+ +.++.|+.+.+...
T Consensus       104 ~~----~~~~~~lil~P~-~~L~~q~~~~~~~~  131 (414)
T 3eiq_A          104 LD----LKATQALVLAPT-RELAQQIQKVVMAL  131 (414)
T ss_dssp             TT----SCSCCEEEECSS-HHHHHHHHHHHHHH
T ss_pred             hc----CCceeEEEEeCh-HHHHHHHHHHHHHH
Confidence            32    245568999999 88888888887764

>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=99.32  E-value=2.9e-12  Score=103.49  Aligned_cols=92  Identities=27%  Similarity=0.452  Sum_probs=78.1

Q ss_pred             ccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcC-CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCC
Q psy7691          39 TQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSG-RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCA  117 (165)
Q Consensus        39 i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G-~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~  117 (165)
                      ...|+++++++.+.++|.+.||..|+++|.++++.++.| .+++++++||+|||++++   +|     .++.+..     
T Consensus         5 ~~~f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~---~~-----~~~~~~~-----   71 (367)
T 1hv8_A            5 YMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFA---IP-----LIELVNE-----   71 (367)
T ss_dssp             CCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHH---HH-----HHHHSCS-----
T ss_pred             cCchhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHH---HH-----HHHHhcc-----
Confidence            467999999999999999999999999999999999998 799999999999999887   66     4554422     


Q ss_pred             CCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691         118 SSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus       118 ~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      ..+..+++++|+ +.++.|+.+.+...
T Consensus        72 ~~~~~~lil~P~-~~L~~q~~~~~~~~   97 (367)
T 1hv8_A           72 NNGIEAIILTPT-RELAIQVADEIESL   97 (367)
T ss_dssp             SSSCCEEEECSC-HHHHHHHHHHHHHH
T ss_pred             cCCCcEEEEcCC-HHHHHHHHHHHHHH
Confidence            245678899998 88888888877664

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.28  E-value=8.8e-12  Score=94.58  Aligned_cols=112  Identities=34%  Similarity=0.473  Sum_probs=82.8

Q ss_pred             Ccccccc-CCCcHHHHHHHHhCCCCC------Cch-HHHHHHHHHH--------------cCCCeeeecccCCcccceee
Q psy7691          38 PTQELTE-GCFPNAVLQHLKGQGFEE------PTA-IQAQGWPIAL--------------SGRDMVGIAQTGSGKTLAVI   95 (165)
Q Consensus        38 ~i~~f~~-l~l~~~l~~~l~~~g~~~------~t~-~Q~~a~~~~l--------------~G~di~~~a~tgsGKt~~~~   95 (165)
                      +++.|.. ....+.+.+.|...|+..      .+. .+..++..+.              +|.|+..+.        .++
T Consensus        56 ~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~~~~~Gldi~~v~--------~VI  127 (191)
T 2p6n_A           56 PVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQ--------HVI  127 (191)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECHHHHTTCCCCCCS--------EEE
T ss_pred             CEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcCchhcCCCcccCC--------EEE
Confidence            4556654 467778888888777643      222 2333444444              444444333        799


Q ss_pred             ecCCCCChhHHHHhhccCCCCCCCCceEEEECCC-cHHHHHHHHHHHHhcCCCCChHHHHHhh
Q psy7691          96 NFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPN-NGKQAKELIAVLTEASQPIPPQLQDLAN  157 (165)
Q Consensus        96 ~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~-~~~~~~~i~~~l~~~~~~~p~~~~~~~~  157 (165)
                      +||+|.+.++|+||+||+||.|..|.+++++++. +...+..+.+.+....+++|+++.+++.
T Consensus       128 ~~d~p~~~~~~~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~~l~~~l~~~~~~~p~~l~~~~~  190 (191)
T 2p6n_A          128 NYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQVLHC  190 (191)
T ss_dssp             ESSCCSSHHHHHHHHTTSCC---CCEEEEEECTTSCHHHHHHHHHHHHHTTCCCCHHHHSTTC
T ss_pred             EeCCCCCHHHHHHHhCccccCCCCcEEEEEEcCchhHHHHHHHHHHHHHccCcCCHHHHhhcC
Confidence            9999999999999999999999999999999987 6788999999999999999999887654

>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=99.23  E-value=4.4e-12  Score=106.83  Aligned_cols=116  Identities=28%  Similarity=0.448  Sum_probs=83.7

Q ss_pred             ccccc-cCCCcHHHHHHHHhCCCCCC------c-hHHHHHHHHHHcCC-Ceeeec-ccCCcc----cceeeecCCCCChh
Q psy7691          39 TQELT-EGCFPNAVLQHLKGQGFEEP------T-AIQAQGWPIALSGR-DMVGIA-QTGSGK----TLAVINFDYPNSSE  104 (165)
Q Consensus        39 i~~f~-~l~l~~~l~~~l~~~g~~~~------t-~~Q~~a~~~~l~G~-di~~~a-~tgsGK----t~~~~~~~lP~~~~  104 (165)
                      ++.|. .....+.+.+.|.+.|+...      + ..+.+++..+..|. +++++. .-+.|=    ..+|+|||+|.+.+
T Consensus       303 ~lVF~~t~~~a~~l~~~L~~~~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v~~rGlDi~~v~~VI~~d~p~~~~  382 (434)
T 2db3_A          303 TIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKID  382 (434)
T ss_dssp             EEEECSSHHHHHHHHHHHHHTTCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECGGGTSSCCCTTCCEEEESSCCSSHH
T ss_pred             EEEEEeCcHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEchhhhCCCCcccCCEEEEECCCCCHH
Confidence            44444 45778888888988887531      1 22334444454442 232221 112221    12799999999999


Q ss_pred             HHHHhhccCCCCCCCCceEEEECCC-cHHHHHHHHHHHHhcCCCCChHHHH
Q psy7691         105 DYIHRIGRTGRCASSGTAYTFFTPN-NGKQAKELIAVLTEASQPIPPQLQD  154 (165)
Q Consensus       105 ~~i~r~gr~~r~~~~g~~~~~~~p~-~~~~~~~i~~~l~~~~~~~p~~~~~  154 (165)
                      +|+||+||+||.|+.|.+++++.|. +...+..+.+.+....+++|+|+.+
T Consensus       383 ~y~qriGR~gR~g~~G~a~~~~~~~~~~~~~~~l~~~l~~~~~~vp~~l~~  433 (434)
T 2db3_A          383 DYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKILEGSGQTVPDFLRT  433 (434)
T ss_dssp             HHHHHHTTSSCTTCCEEEEEEECTTTCGGGHHHHHHHHHHTTCCCCGGGC-
T ss_pred             HHHHHhcccccCCCCCEEEEEEeccccHHHHHHHHHHHHHcCCCCCHHHHh
Confidence            9999999999999999999999976 5778999999999999999999865

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens}

Probab=99.21  E-value=8.4e-12  Score=94.09  Aligned_cols=122  Identities=30%  Similarity=0.452  Sum_probs=88.3

Q ss_pred             CCcccccc-CCCcHHHHHHHHhCCCCCC-------chHHHHHHHHHHcCC-Ceeeec-ccCCcc----cceeeecCCCCC
Q psy7691          37 CPTQELTE-GCFPNAVLQHLKGQGFEEP-------TAIQAQGWPIALSGR-DMVGIA-QTGSGK----TLAVINFDYPNS  102 (165)
Q Consensus        37 ~~i~~f~~-l~l~~~l~~~l~~~g~~~~-------t~~Q~~a~~~~l~G~-di~~~a-~tgsGK----t~~~~~~~lP~~  102 (165)
                      ..++.|.. ....+.+.+.|...|+...       ...+..++..+..|. +++++. .-+.|-    ...+++||+|.+
T Consensus        47 ~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~s  126 (185)
T 2jgn_A           47 SLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSD  126 (185)
T ss_dssp             SCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHHHHHHTSSSEEEEEC------CCCSBSEEEESSCCSS
T ss_pred             CeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHHHcCCCeEEEEcChhhcCCCcccCCEEEEeCCCCC
Confidence            34556654 4778888888988887431       122333444555553 333322 222332    227899999999


Q ss_pred             hhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCChHHHHHhhh
Q psy7691         103 SEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQDLANS  158 (165)
Q Consensus       103 ~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p~~~~~~~~~  158 (165)
                      ..+|+||+||++|.|..|.+++++++.+...+..+.+.+....+++|.++.+++..
T Consensus       127 ~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~l~~~a~~  182 (185)
T 2jgn_A          127 IEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAYE  182 (185)
T ss_dssp             HHHHHHHHTTBCCTTSCEEEEEEECGGGGGGHHHHHHHHHHTTCCCCHHHHHHHC-
T ss_pred             HHHHHHHccccCCCCCCcEEEEEEchhhHHHHHHHHHHHHhccCCCCHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999998764

>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=99.21  E-value=2.8e-11  Score=96.77  Aligned_cols=80  Identities=26%  Similarity=0.449  Sum_probs=69.2

Q ss_pred             CcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEE
Q psy7691          47 FPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFF  126 (165)
Q Consensus        47 l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~  126 (165)
                      |++.+.++|+++||..|+++|.++++.++.|.+++++++||+|||++++   +|     .+++          +..++++
T Consensus         1 l~~~i~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~---~~-----~~~~----------~~~~liv   62 (337)
T 2z0m_A            1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYA---IP-----ILEL----------GMKSLVV   62 (337)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHH---HH-----HHHH----------TCCEEEE
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHH---HH-----HHhh----------cCCEEEE
Confidence            5789999999999999999999999999999999999999999999887   66     4443          3357888


Q ss_pred             CCCcHHHHHHHHHHHHhcC
Q psy7691         127 TPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus       127 ~p~~~~~~~~i~~~l~~~~  145 (165)
                      +|+ +.++.|+.+.+....
T Consensus        63 ~P~-~~L~~q~~~~~~~~~   80 (337)
T 2z0m_A           63 TPT-RELTRQVASHIRDIG   80 (337)
T ss_dssp             CSS-HHHHHHHHHHHHHHT
T ss_pred             eCC-HHHHHHHHHHHHHHh
Confidence            998 888888888887643

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=99.13  E-value=3.7e-11  Score=103.81  Aligned_cols=88  Identities=22%  Similarity=0.213  Sum_probs=75.6

Q ss_pred             cccccCCCcHHHHHHHHh-CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCC
Q psy7691          40 QELTEGCFPNAVLQHLKG-QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCAS  118 (165)
Q Consensus        40 ~~f~~l~l~~~l~~~l~~-~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~  118 (165)
                      ..|+++++++.+.+.|++ .||..++++|.++++.++.|.|++++++||+|||++|.   +|     .+.+-        
T Consensus         2 ~~fe~l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~---lp-----~l~~~--------   65 (523)
T 1oyw_A            2 AQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQ---IP-----ALLLN--------   65 (523)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHH---HH-----HHHSS--------
T ss_pred             CChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHH---HH-----HHHhC--------
Confidence            479999999999999999 89999999999999999999999999999999999988   78     44331        


Q ss_pred             CCceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         119 SGTAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       119 ~g~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                       | .+++++|+ +.++.+..+.+...+.
T Consensus        66 -g-~~lvi~P~-~aL~~q~~~~l~~~gi   90 (523)
T 1oyw_A           66 -G-LTVVVSPL-ISLMKDQVDQLQANGV   90 (523)
T ss_dssp             -S-EEEEECSC-HHHHHHHHHHHHHTTC
T ss_pred             -C-CEEEECCh-HHHHHHHHHHHHHcCC
Confidence             2 46888888 8888888888876543

>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=99.08  E-value=1.8e-10  Score=101.04  Aligned_cols=90  Identities=16%  Similarity=0.220  Sum_probs=75.0

Q ss_pred             CCccccc--cCCCcHHHHHHHHh-CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccC
Q psy7691          37 CPTQELT--EGCFPNAVLQHLKG-QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRT  113 (165)
Q Consensus        37 ~~i~~f~--~l~l~~~l~~~l~~-~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~  113 (165)
                      .....|+  ++++++.+.+.|++ .||..++++|.++++.++.|.|+++++|||+|||++|.   +|     .+.+    
T Consensus        16 ~~~~~w~~~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~---lp-----al~~----   83 (591)
T 2v1x_A           16 SSPAAWNKEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQ---LP-----ALCS----   83 (591)
T ss_dssp             CCGGGGCCSCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHH---HH-----HHTS----
T ss_pred             cchhccccccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHH---HH-----HHHc----
Confidence            3445665  47889999999999 69999999999999999999999999999999999988   78     4432    


Q ss_pred             CCCCCCCceEEEECCCcHHHHHHHHHHHHhcC
Q psy7691         114 GRCASSGTAYTFFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus       114 ~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~  145 (165)
                            +..+++++|+ ++++.|..+.+...+
T Consensus        84 ------~g~~lVisP~-~~L~~q~~~~l~~~g  108 (591)
T 2v1x_A           84 ------DGFTLVICPL-ISLMEDQLMVLKQLG  108 (591)
T ss_dssp             ------SSEEEEECSC-HHHHHHHHHHHHHHT
T ss_pred             ------CCcEEEEeCH-HHHHHHHHHHHHhcC
Confidence                  1267888898 888888888887753

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.05  E-value=2.4e-10  Score=94.28  Aligned_cols=115  Identities=31%  Similarity=0.498  Sum_probs=87.7

Q ss_pred             Cccccc-cCCCcHHHHHHHHhCCCCC------Cch-HHHHH--------------HHHHHcCCCeeeecccCCcccceee
Q psy7691          38 PTQELT-EGCFPNAVLQHLKGQGFEE------PTA-IQAQG--------------WPIALSGRDMVGIAQTGSGKTLAVI   95 (165)
Q Consensus        38 ~i~~f~-~l~l~~~l~~~l~~~g~~~------~t~-~Q~~a--------------~~~~l~G~di~~~a~tgsGKt~~~~   95 (165)
                      .++.|. .....+.+.+.|.+.|+..      .+. .+.+.              ++.+.+|.|+..+.        +++
T Consensus       278 ~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~Gidip~v~--------~Vi  349 (417)
T 2i4i_A          278 LTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVK--------HVI  349 (417)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECHHHHTTSCCCCEE--------EEE
T ss_pred             eEEEEECCHHHHHHHHHHHHHCCCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccCC--------EEE
Confidence            344554 4467778888888877643      122 22233              33344555655555        899


Q ss_pred             ecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCChHHHHHhhhCC
Q psy7691          96 NFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQDLANSNP  160 (165)
Q Consensus        96 ~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p~~~~~~~~~~~  160 (165)
                      +||+|.+..+|+||+||+||.|+.|.+++++.+.+...+.++.+.+....+++|.++..++....
T Consensus       350 ~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~~~~  414 (417)
T 2i4i_A          350 NFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAYEHH  414 (417)
T ss_dssp             ESSCCSSHHHHHHHHTTBCC--CCEEEEEEECGGGGGGHHHHHHHHHHTTCCCCHHHHHHHTCSC
T ss_pred             EEcCCCCHHHHHHhcCccccCCCCceEEEEEccccHHHHHHHHHHHHHhcCcCCHHHHHHHHhhh
Confidence            99999999999999999999999999999999999999999999999999999999999887653

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.04  E-value=2.7e-10  Score=101.26  Aligned_cols=89  Identities=21%  Similarity=0.266  Sum_probs=75.9

Q ss_pred             ccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHH-HHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCC
Q psy7691          39 TQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPI-ALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCA  117 (165)
Q Consensus        39 i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~-~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~  117 (165)
                      ...|+++++++.+.+++.+.||..++++|.++++. +..|.+++++++||||||+++.   +|     .++.+..     
T Consensus         7 ~~~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~---l~-----il~~~~~-----   73 (715)
T 2va8_A            7 WMPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAE---MG-----IISFLLK-----   73 (715)
T ss_dssp             CCBGGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHH---HH-----HHHHHHH-----
T ss_pred             cCcHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHH---HH-----HHHHHHH-----
Confidence            46899999999999999999999999999999998 7889999999999999999887   66     5554432     


Q ss_pred             CCCceEEEECCCcHHHHHHHHHHHH
Q psy7691         118 SSGTAYTFFTPNNGKQAKELIAVLT  142 (165)
Q Consensus       118 ~~g~~~~~~~p~~~~~~~~i~~~l~  142 (165)
                       .|..++++.|+ +.++.|+.+.++
T Consensus        74 -~~~~il~i~P~-r~La~q~~~~~~   96 (715)
T 2va8_A           74 -NGGKAIYVTPL-RALTNEKYLTFK   96 (715)
T ss_dssp             -SCSEEEEECSC-HHHHHHHHHHHG
T ss_pred             -CCCeEEEEeCc-HHHHHHHHHHHH
Confidence             13478899998 888888888774

>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=98.98  E-value=2e-10  Score=102.24  Aligned_cols=87  Identities=25%  Similarity=0.274  Sum_probs=74.3

Q ss_pred             ccccCCCcHHHHHHHHhCCCCCCchHHHHHHHH-HHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCC
Q psy7691          41 ELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPI-ALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASS  119 (165)
Q Consensus        41 ~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~-~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~  119 (165)
                      .|+++++++.+.+.+++.||..++++|.++++. +..|.+++++++||||||+++.   +|     .++.+...      
T Consensus         2 ~f~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~---l~-----il~~~~~~------   67 (720)
T 2zj8_A            2 RVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAE---IA-----MVHRILTQ------   67 (720)
T ss_dssp             BGGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHH---HH-----HHHHHHHH------
T ss_pred             cHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHH---HH-----HHHHHHhC------
Confidence            689999999999999999999999999999998 8899999999999999999876   66     55554321      


Q ss_pred             CceEEEECCCcHHHHHHHHHHHH
Q psy7691         120 GTAYTFFTPNNGKQAKELIAVLT  142 (165)
Q Consensus       120 g~~~~~~~p~~~~~~~~i~~~l~  142 (165)
                      |..++++.|+ +.++.|+.+.+.
T Consensus        68 ~~~~l~i~P~-raLa~q~~~~~~   89 (720)
T 2zj8_A           68 GGKAVYIVPL-KALAEEKFQEFQ   89 (720)
T ss_dssp             CSEEEEECSS-GGGHHHHHHHTG
T ss_pred             CCEEEEEcCc-HHHHHHHHHHHH
Confidence            3578899998 788888877774

>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase, translocation, secretion, protein transport; 2.18A {Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A 3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A

Probab=98.98  E-value=2.8e-10  Score=102.87  Aligned_cols=113  Identities=18%  Similarity=0.204  Sum_probs=78.8

Q ss_pred             cCChHhhcCCHHHHHHHHhhcCcEEecCCCCCCccccccCCCcHHHH---HH-HHhCCCCCCchHHHHHHHHHHcCCCee
Q psy7691           6 KTQERAARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVL---QH-LKGQGFEEPTAIQAQGWPIALSGRDMV   81 (165)
Q Consensus         6 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~p~~i~~f~~l~l~~~l~---~~-l~~~g~~~~t~~Q~~a~~~~l~G~di~   81 (165)
                      ...+.++.+|++++.......+......+      .+.++ +++.+.   ++ ....|| .||++|..++|.++.|+  +
T Consensus        31 ~~~~~~~~lsd~el~~~t~~~~~~~~~g~------~ld~~-l~ea~a~vrea~~r~lG~-~pt~VQ~~~ip~ll~G~--I  100 (844)
T 1tf5_A           31 AIRGDYENLSDDALKHKTIEFKERLEKGA------TTDDL-LVEAFAVVREASRRVTGM-FPFKVQLMGGVALHDGN--I  100 (844)
T ss_dssp             HTTHHHHTCCHHHHHHHHHHHHHHHHTTC------CHHHH-HHHHHHHHHHHHHHHHSC-CCCHHHHHHHHHHHTTS--E
T ss_pred             hhhHHHHhCCHHHHHHHHHHHHHHHhcCC------ChHHH-HHHHHHHHHHHHHHHcCC-CCcHHHHHhhHHHhCCC--E
Confidence            44578899999999666655443332211      11111 222211   11 224799 89999999999999998  8


Q ss_pred             eecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691          82 GIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus        82 ~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      +.++||+|||++|.   ||.    |++.+        .|..+.+++|+ +++|.|+.+.+...
T Consensus       101 aea~TGeGKTlaf~---LP~----~l~aL--------~g~~vlVltpt-reLA~qd~e~~~~l  147 (844)
T 1tf5_A          101 AEMKTGEGKTLTST---LPV----YLNAL--------TGKGVHVVTVN-EYLASRDAEQMGKI  147 (844)
T ss_dssp             EECCTTSCHHHHHH---HHH----HHHHT--------TSSCEEEEESS-HHHHHHHHHHHHHH
T ss_pred             EEccCCcHHHHHHH---HHH----HHHHH--------cCCCEEEEeCC-HHHHHHHHHHHHHH
Confidence            99999999999999   893    33433        23468999999 99999888877653

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=98.97  E-value=4.5e-10  Score=93.23  Aligned_cols=80  Identities=19%  Similarity=0.172  Sum_probs=64.3

Q ss_pred             HHHHHHHHh-CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEEC
Q psy7691          49 NAVLQHLKG-QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFT  127 (165)
Q Consensus        49 ~~l~~~l~~-~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~  127 (165)
                      +.+.+.+++ .|| .|+++|.++++.++.|.|++++++||+|||++++   +|     .++..       ..+..+++++
T Consensus         8 ~~~~~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l---~~-----~~~~~-------~~~~~~lil~   71 (414)
T 3oiy_A            8 EDFRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGM---MT-----ALWLA-------RKGKKSALVF   71 (414)
T ss_dssp             HHHHHHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHH---HH-----HHHHH-------TTTCCEEEEE
T ss_pred             HHHHHHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHH---HH-----HHHHh-------cCCCEEEEEE
Confidence            345556666 477 6999999999999999999999999999999777   56     44444       2345788999


Q ss_pred             CCcHHHHHHHHHHHHhcC
Q psy7691         128 PNNGKQAKELIAVLTEAS  145 (165)
Q Consensus       128 p~~~~~~~~i~~~l~~~~  145 (165)
                      |+ ++++.|+.+.+....
T Consensus        72 Pt-~~L~~q~~~~~~~~~   88 (414)
T 3oiy_A           72 PT-VTLVKQTLERLQKLA   88 (414)
T ss_dssp             SS-HHHHHHHHHHHHHHC
T ss_pred             CC-HHHHHHHHHHHHHHc
Confidence            99 999999998888843

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=98.95  E-value=8.6e-11  Score=86.51  Aligned_cols=117  Identities=23%  Similarity=0.321  Sum_probs=79.7

Q ss_pred             CCcccccc-CCCcHHHHHHHHhCCCCC------Cc-hHHHHHHHHHHcCC-Ceeeec-ccCCccc----ceeeecCCCCC
Q psy7691          37 CPTQELTE-GCFPNAVLQHLKGQGFEE------PT-AIQAQGWPIALSGR-DMVGIA-QTGSGKT----LAVINFDYPNS  102 (165)
Q Consensus        37 ~~i~~f~~-l~l~~~l~~~l~~~g~~~------~t-~~Q~~a~~~~l~G~-di~~~a-~tgsGKt----~~~~~~~lP~~  102 (165)
                      ..++.|.. ....+.+.+.|...|+..      .+ ..+...+..+..|. +++++. .-+.|-.    ..+++||+|.+
T Consensus        31 ~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G~d~~~~~~Vi~~~~p~~  110 (165)
T 1fuk_A           31 TQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPAN  110 (165)
T ss_dssp             SCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGGTTTCCCCSCSEEEESSCCSS
T ss_pred             CCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcChhhcCCCcccCCEEEEeCCCCC
Confidence            34555554 467788888898887643      12 23344555555553 333322 2233322    26899999999


Q ss_pred             hhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCChHHH
Q psy7691         103 SEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ  153 (165)
Q Consensus       103 ~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p~~~~  153 (165)
                      ..+|+||+||+||.|..|.+++++++.+...+..+.+.+....+++|.++.
T Consensus       111 ~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (165)
T 1fuk_A          111 KENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIA  161 (165)
T ss_dssp             GGGGGGSSCSCC-----CEEEEEEETTTHHHHHHHHHHSSCCCEECCSCCT
T ss_pred             HHHHHHHhcccccCCCCceEEEEEcchHHHHHHHHHHHHccCccccCccHH
Confidence            999999999999999999999999999999999999998888888876543

>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=98.95  E-value=1.3e-10  Score=103.25  Aligned_cols=86  Identities=22%  Similarity=0.249  Sum_probs=71.3

Q ss_pred             ccccCC--CcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCC
Q psy7691          41 ELTEGC--FPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCAS  118 (165)
Q Consensus        41 ~f~~l~--l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~  118 (165)
                      .|++++  +++.+.+++++.||..++++|.++++.++.|.+++++++||||||+++.   +|     .++.+.+      
T Consensus         2 ~f~~l~~~l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~---l~-----il~~~~~------   67 (702)
T 2p6r_A            2 KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAE---MA-----MVREAIK------   67 (702)
T ss_dssp             CSHHHHHHHHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHH---HH-----HHHHHHT------
T ss_pred             chhhhhhccCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHH---HH-----HHHHHHh------
Confidence            588888  9999999999999999999999999999999999999999999999887   66     5555432      


Q ss_pred             CCceEEEECCCcHHHHHHHHHHHH
Q psy7691         119 SGTAYTFFTPNNGKQAKELIAVLT  142 (165)
Q Consensus       119 ~g~~~~~~~p~~~~~~~~i~~~l~  142 (165)
                       +..++++.|+ +.++.|+.+.++
T Consensus        68 -~~~~l~i~P~-r~La~q~~~~~~   89 (702)
T 2p6r_A           68 -GGKSLYVVPL-RALAGEKYESFK   89 (702)
T ss_dssp             -TCCEEEEESS-HHHHHHHHHHHT
T ss_pred             -CCcEEEEeCc-HHHHHHHHHHHH
Confidence             3467888898 888988888874

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=98.94  E-value=5.3e-10  Score=82.13  Aligned_cols=111  Identities=22%  Similarity=0.258  Sum_probs=78.4

Q ss_pred             CCcccccc-CCCcHHHHHHHHhCCCCC------Cc-hHHHHHHHHHHcCC-Ceeeecc-cCCcc----cceeeecCCCCC
Q psy7691          37 CPTQELTE-GCFPNAVLQHLKGQGFEE------PT-AIQAQGWPIALSGR-DMVGIAQ-TGSGK----TLAVINFDYPNS  102 (165)
Q Consensus        37 ~~i~~f~~-l~l~~~l~~~l~~~g~~~------~t-~~Q~~a~~~~l~G~-di~~~a~-tgsGK----t~~~~~~~lP~~  102 (165)
                      ..++.|.. ....+.+.+.|...|+..      .+ ..+...+..+..|. +++++.. -+.|-    ...+++||+|.+
T Consensus        36 ~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gld~~~~~~Vi~~~~p~~  115 (163)
T 2hjv_A           36 DSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLE  115 (163)
T ss_dssp             SSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTTTCCCSCCSEEEESSCCSS
T ss_pred             CcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCCchhcCCEEEEeCCCCC
Confidence            34555654 467888888898887743      12 23334455555553 3443322 22332    227999999999


Q ss_pred             hhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCC
Q psy7691         103 SEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQP  147 (165)
Q Consensus       103 ~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~  147 (165)
                      ..+|+||+||++|.|..|.+++++.+.+...+..+.+.+.....+
T Consensus       116 ~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~  160 (163)
T 2hjv_A          116 KESYVHRTGRTGRAGNKGKAISFVTAFEKRFLADIEEYIGFEIQK  160 (163)
T ss_dssp             HHHHHHHTTTSSCTTCCEEEEEEECGGGHHHHHHHHHHHTSCCEE
T ss_pred             HHHHHHhccccCcCCCCceEEEEecHHHHHHHHHHHHHHCCCcCc
Confidence            999999999999999999999999999989899998887655443

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A

Probab=98.91  E-value=4.8e-10  Score=86.03  Aligned_cols=112  Identities=18%  Similarity=0.275  Sum_probs=79.4

Q ss_pred             CCcccccc-CCCcHHHHHHHHhCCCCC-------CchHHHHHHHHHHcCC-Ceeeec-ccCCccc----ceeeecCCCCC
Q psy7691          37 CPTQELTE-GCFPNAVLQHLKGQGFEE-------PTAIQAQGWPIALSGR-DMVGIA-QTGSGKT----LAVINFDYPNS  102 (165)
Q Consensus        37 ~~i~~f~~-l~l~~~l~~~l~~~g~~~-------~t~~Q~~a~~~~l~G~-di~~~a-~tgsGKt----~~~~~~~lP~~  102 (165)
                      .+++.|.. ....+.+.+.|...|+..       +...+..++..+..|. +++++. .-+.|-+    ..|++||+|.+
T Consensus        32 ~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~Gidi~~v~~Vi~~~~p~~  111 (212)
T 3eaq_A           32 DRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDR  111 (212)
T ss_dssp             SCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECTTTTCSSSCCCBSEEEESSCCSS
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecChhhcCCCCccCcEEEECCCCcC
Confidence            45666655 466778888888877643       2234555666666663 343322 2223322    27999999999


Q ss_pred             hhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCC
Q psy7691         103 SEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPI  148 (165)
Q Consensus       103 ~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~  148 (165)
                      ..+|+||+||+||.|+.|.+++++++.+......+.+.+......+
T Consensus       112 ~~~~~qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~~~~~~~~~~~  157 (212)
T 3eaq_A          112 AEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRFKRV  157 (212)
T ss_dssp             HHHHHHHHTTBCCCC--BEEEEEECGGGHHHHHHHHHHHSSCCEEC
T ss_pred             HHHHHHHhcccCCCCCCCeEEEEEchhHHHHHHHHHHHhcCcCeec
Confidence            9999999999999999999999999999888899988887665554

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}

Probab=98.91  E-value=2.7e-10  Score=84.56  Aligned_cols=113  Identities=19%  Similarity=0.272  Sum_probs=77.5

Q ss_pred             CCcccccc-CCCcHHHHHHHHhCCCCC------Cch-HHHHHHHHHHcCC-Ceeeecc-cCCccc----ceeeecCCC--
Q psy7691          37 CPTQELTE-GCFPNAVLQHLKGQGFEE------PTA-IQAQGWPIALSGR-DMVGIAQ-TGSGKT----LAVINFDYP--  100 (165)
Q Consensus        37 ~~i~~f~~-l~l~~~l~~~l~~~g~~~------~t~-~Q~~a~~~~l~G~-di~~~a~-tgsGKt----~~~~~~~lP--  100 (165)
                      .+++.|.. ....+.+.+.|...|+..      .++ .+...+..+..|. +++++.. -+.|-.    ..+++||+|  
T Consensus        35 ~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~Gid~~~~~~Vi~~d~p~~  114 (175)
T 2rb4_A           35 GQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVK  114 (175)
T ss_dssp             SEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECCSCCTTTCCTTEEEEEESSCCC-
T ss_pred             CCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEecchhcCCCcccCCEEEEeCCCCC
Confidence            34556654 467788888898887643      222 3344555666663 4443332 233422    268999999  


Q ss_pred             ----CChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCC
Q psy7691         101 ----NSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIP  149 (165)
Q Consensus       101 ----~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p  149 (165)
                          .+..+|+||+||+||.|..|.+++++.+.+...+..+.+.+.....++|
T Consensus       115 ~~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  167 (175)
T 2rb4_A          115 QGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNSSIKQLN  167 (175)
T ss_dssp             -CCSCCHHHHHHHHCBC----CCEEEEEEECGGGHHHHHHHHHHHTCCCEEEC
T ss_pred             ccccCCHHHHHHHhcccccCCCCceEEEEEccchHHHHHHHHHHhcCcccccC
Confidence                9999999999999999999999999999988888899888877666554

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19

Probab=98.87  E-value=2.2e-10  Score=85.16  Aligned_cols=118  Identities=20%  Similarity=0.275  Sum_probs=82.3

Q ss_pred             CCcccccc-CCCcHHHHHHHHhCCCCC------Cc-hHHHHHHHHHHcCC-Ceeeecc-cCCcc----cceeeecCCCCC
Q psy7691          37 CPTQELTE-GCFPNAVLQHLKGQGFEE------PT-AIQAQGWPIALSGR-DMVGIAQ-TGSGK----TLAVINFDYPNS  102 (165)
Q Consensus        37 ~~i~~f~~-l~l~~~l~~~l~~~g~~~------~t-~~Q~~a~~~~l~G~-di~~~a~-tgsGK----t~~~~~~~lP~~  102 (165)
                      .+++.|.. ....+.+.+.|...|+..      .+ ..+..++..+..|. +++++.. -+.|-    ...+++||+|.+
T Consensus        32 ~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldi~~~~~Vi~~d~p~~  111 (172)
T 1t5i_A           32 NQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPED  111 (172)
T ss_dssp             SSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSCCSTTCCGGGCSEEEESSCCSS
T ss_pred             CcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECCchhcCcchhhCCEEEEECCCCC
Confidence            34556654 477888888898887743      22 23345566666663 4443322 22332    237899999999


Q ss_pred             hhHHHHhhccCCCCCCCCceEEEECCCc-HHHHHHHHHHHHhcCCCCChHHHH
Q psy7691         103 SEDYIHRIGRTGRCASSGTAYTFFTPNN-GKQAKELIAVLTEASQPIPPQLQD  154 (165)
Q Consensus       103 ~~~~i~r~gr~~r~~~~g~~~~~~~p~~-~~~~~~i~~~l~~~~~~~p~~~~~  154 (165)
                      ..+|+||+||+||.|..|.+++++.+.+ ...+..+.+.+.....++|.++..
T Consensus       112 ~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~  164 (172)
T 1t5i_A          112 SDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDI  164 (172)
T ss_dssp             HHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEECC-----
T ss_pred             HHHHHHHhcccccCCCCcEEEEEEcChhHHHHHHHHHHHHhcchhhCChhhch
Confidence            9999999999999999999999999873 567889999988888888877543

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=98.80  E-value=1.9e-09  Score=87.33  Aligned_cols=113  Identities=19%  Similarity=0.294  Sum_probs=77.3

Q ss_pred             CCCccccccC-CCcHHHHHHHHhCCCCC-------CchHHHHHHHHHHcCC-Ceeeec-ccCCccc----ceeeecCCCC
Q psy7691          36 PCPTQELTEG-CFPNAVLQHLKGQGFEE-------PTAIQAQGWPIALSGR-DMVGIA-QTGSGKT----LAVINFDYPN  101 (165)
Q Consensus        36 p~~i~~f~~l-~l~~~l~~~l~~~g~~~-------~t~~Q~~a~~~~l~G~-di~~~a-~tgsGKt----~~~~~~~lP~  101 (165)
                      +.+++.|... ...+.+.+.|...|+..       +...|...+..+..|. +++++. .-+.|-+    .+|+|||+|.
T Consensus        28 ~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~va~~Gidi~~v~~VI~~d~p~  107 (300)
T 3i32_A           28 PDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPD  107 (300)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECSTTTCSTTCCCCSEEEESSCCS
T ss_pred             CCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEechhhcCccccceeEEEEcCCCC
Confidence            3456666654 66778888898888743       2334555666666553 443322 2233322    2799999999


Q ss_pred             ChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCC
Q psy7691         102 SSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPI  148 (165)
Q Consensus       102 ~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~  148 (165)
                      +..+|+||+||+||.|+.|.+++++++.+......+.+.+......+
T Consensus       108 s~~~y~Qr~GRagR~g~~G~~i~l~~~~e~~~~~~ie~~~~~~~~~~  154 (300)
T 3i32_A          108 RAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRFKRV  154 (300)
T ss_dssp             STTHHHHHHTCCC-----CEEEEEECSSTHHHHHHHHHHHTCCCEEC
T ss_pred             CHHHHHHHccCcCcCCCCceEEEEeChHHHHHHHHHHHHhCCcceEe
Confidence            99999999999999999999999999999888999998887765544

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=98.76  E-value=8.4e-09  Score=96.18  Aligned_cols=77  Identities=19%  Similarity=0.171  Sum_probs=62.5

Q ss_pred             HHHHHHh-CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCC
Q psy7691          51 VLQHLKG-QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPN  129 (165)
Q Consensus        51 l~~~l~~-~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~  129 (165)
                      +.+.+.. .|| .||++|.+|++.++.|+|++++|+||||||++++   +|     .++.+       ..|..+++++|+
T Consensus        67 ~~~~~~~~~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l---~~-----il~~~-------~~~~~~Lil~Pt  130 (1104)
T 4ddu_A           67 FRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGM---MT-----ALWLA-------RKGKKSALVFPT  130 (1104)
T ss_dssp             HHHHHHHHSSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHH---HH-----HHHHH-------TTTCCEEEEESS
T ss_pred             HHHHHHHhcCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHH---HH-----HHHHH-------hcCCeEEEEech
Confidence            3344443 689 4999999999999999999999999999999766   45     44444       245678999999


Q ss_pred             cHHHHHHHHHHHHhc
Q psy7691         130 NGKQAKELIAVLTEA  144 (165)
Q Consensus       130 ~~~~~~~i~~~l~~~  144 (165)
                       ++++.|+.+.+...
T Consensus       131 -reLa~Q~~~~l~~l  144 (1104)
T 4ddu_A          131 -VTLVKQTLERLQKL  144 (1104)
T ss_dssp             -HHHHHHHHHHHHTT
T ss_pred             -HHHHHHHHHHHHHh
Confidence             99999999999883

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=98.75  E-value=6.3e-09  Score=91.62  Aligned_cols=83  Identities=17%  Similarity=0.131  Sum_probs=61.3

Q ss_pred             HHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcH
Q psy7691          52 LQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNG  131 (165)
Q Consensus        52 ~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~  131 (165)
                      ...+..+||..|+++|.++++.++.|.|++++++||+|||++++   +|     .++.+.+. ..+ .+..+++++|+ +
T Consensus         3 ~~~l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~---~~-----i~~~l~~~-~~~-~~~~~lvl~Pt-~   71 (696)
T 2ykg_A            3 VSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSL---LI-----CEHHLKKF-PQG-QKGKVVFFANQ-I   71 (696)
T ss_dssp             ----CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHH---HH-----HHHHHHHS-CTT-CCCCEEEECSS-H
T ss_pred             CCcccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHH---HH-----HHHHHHhC-ccC-CCCeEEEEECC-H
Confidence            45678899999999999999999999999999999999999988   77     55555332 111 22467889998 7


Q ss_pred             HHHHHHHHHHHhcC
Q psy7691         132 KQAKELIAVLTEAS  145 (165)
Q Consensus       132 ~~~~~i~~~l~~~~  145 (165)
                      .++.|..+.+....
T Consensus        72 ~L~~Q~~~~~~~~~   85 (696)
T 2ykg_A           72 PVYEQNKSVFSKYF   85 (696)
T ss_dssp             HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHh
Confidence            88888877776654

>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=98.75  E-value=9.9e-09  Score=95.29  Aligned_cols=79  Identities=16%  Similarity=0.119  Sum_probs=63.6

Q ss_pred             HHHHHHh-CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCC
Q psy7691          51 VLQHLKG-QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPN  129 (165)
Q Consensus        51 l~~~l~~-~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~  129 (165)
                      +.+.+.+ .||. | ++|.++++.++.|+|++++++||||||+ |.   +|     .+.++..      .+..+++++|+
T Consensus        46 ~~~~~~~~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~---lp-----~l~~~~~------~~~~~lil~Pt  108 (1054)
T 1gku_B           46 FVEFFRKCVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FG---LA-----MSLFLAL------KGKRCYVIFPT  108 (1054)
T ss_dssp             HHHHHHTTTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HH---HH-----HHHHHHT------TSCCEEEEESC
T ss_pred             HHHHHHHhcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HH---HH-----HHHHHhh------cCCeEEEEecc
Confidence            3355544 7999 9 9999999999999999999999999997 66   77     6666533      34578899999


Q ss_pred             cHHHHHHHHHHHHhcCCC
Q psy7691         130 NGKQAKELIAVLTEASQP  147 (165)
Q Consensus       130 ~~~~~~~i~~~l~~~~~~  147 (165)
                       ++++.|+.+.+......
T Consensus       109 -reLa~Q~~~~l~~l~~~  125 (1054)
T 1gku_B          109 -SLLVIQAAETIRKYAEK  125 (1054)
T ss_dssp             -HHHHHHHHHHHHHHHTT
T ss_pred             -HHHHHHHHHHHHHHHhh
Confidence             99999988888765443

>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=98.74  E-value=1.9e-09  Score=88.60  Aligned_cols=118  Identities=21%  Similarity=0.335  Sum_probs=74.9

Q ss_pred             Cccccc-cCCCcHHHHHHHHhCCCCCC------ch-HHHHHHHHHHcCC-Ceeeecc-cCCccc----ceeeecCCCCCh
Q psy7691          38 PTQELT-EGCFPNAVLQHLKGQGFEEP------TA-IQAQGWPIALSGR-DMVGIAQ-TGSGKT----LAVINFDYPNSS  103 (165)
Q Consensus        38 ~i~~f~-~l~l~~~l~~~l~~~g~~~~------t~-~Q~~a~~~~l~G~-di~~~a~-tgsGKt----~~~~~~~lP~~~  103 (165)
                      .++.|. .....+.+.+.|...|+...      +. .+...+..+..|. +++++.. -+.|=.    ..|++||+|.+.
T Consensus       282 ~~lvf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~v~~Vi~~~~p~s~  361 (414)
T 3eiq_A          282 QAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNR  361 (414)
T ss_dssp             SCEEECSCHHHHHHHHHHHHTTTCCCEEC---CHHHHHHHHHHHHSCC---CEEECSSCC--CCGGGCSCEEESSCCSST
T ss_pred             cEEEEeCCHHHHHHHHHHHHhcCCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCccccCCCccCCCEEEEeCCCCCH
Confidence            344444 44677788888888777542      12 3344455555553 3332222 223322    268999999999


Q ss_pred             hHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCChHHHHH
Q psy7691         104 EDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQDL  155 (165)
Q Consensus       104 ~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p~~~~~~  155 (165)
                      .+|+||+||+||.|+.|.+++++.+.+...+..+.++++....++|..+.++
T Consensus       362 ~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  413 (414)
T 3eiq_A          362 ENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADL  413 (414)
T ss_dssp             HHHHHHSCCC-------CEEEEECSTHHHHHHHHHHHTTCCCEECCC-----
T ss_pred             HHhhhhcCcccCCCCCceEEEEEcHHHHHHHHHHHHHHcCCccccChhhhhc
Confidence            9999999999999999999999999999999999999999999999887765

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli}

Probab=98.16  E-value=1.7e-09  Score=79.94  Aligned_cols=103  Identities=22%  Similarity=0.340  Sum_probs=73.1

Q ss_pred             Ccccccc-CCCcHHHHHHHHhCCCCCC------ch-HHH--------------HHHHHHHcCCCeeeecccCCcccceee
Q psy7691          38 PTQELTE-GCFPNAVLQHLKGQGFEEP------TA-IQA--------------QGWPIALSGRDMVGIAQTGSGKTLAVI   95 (165)
Q Consensus        38 ~i~~f~~-l~l~~~l~~~l~~~g~~~~------t~-~Q~--------------~a~~~~l~G~di~~~a~tgsGKt~~~~   95 (165)
                      .++.|.. ....+.+.+.|...|+...      +. .+.              .|++.+.+|.|+..+.        .++
T Consensus        32 ~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gid~~~~~--------~Vi  103 (170)
T 2yjt_D           32 RSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVS--------HVF  103 (170)
Confidence            3445544 4666677777766655331      11 111              1344455666665555        799


Q ss_pred             ecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCC
Q psy7691          96 NFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPI  148 (165)
Q Consensus        96 ~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~  148 (165)
                      +||+|.+..+|+||+||+||.|..|.+++++.+.+...+..+.+.+.....+.
T Consensus       104 ~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (170)
T 2yjt_D          104 NFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGKVGRYIEEPIKAR  156 (170)
Confidence            99999999999999999999999999999999998888888888776655443

>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=98.69  E-value=2.5e-09  Score=88.19  Aligned_cols=113  Identities=20%  Similarity=0.292  Sum_probs=81.8

Q ss_pred             ccccc-cCCCcHHHHHHHHhCCCCC------Cch-HHHHHHHHHHcCC-Ceeeecc-cCCcc----cceeeecCCCCChh
Q psy7691          39 TQELT-EGCFPNAVLQHLKGQGFEE------PTA-IQAQGWPIALSGR-DMVGIAQ-TGSGK----TLAVINFDYPNSSE  104 (165)
Q Consensus        39 i~~f~-~l~l~~~l~~~l~~~g~~~------~t~-~Q~~a~~~~l~G~-di~~~a~-tgsGK----t~~~~~~~lP~~~~  104 (165)
                      ++.|. .....+.+.+.|.+.|+..      .+. .+...+..+..|. +++++.. -+.|=    ..++++||+|.+..
T Consensus       279 ~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~v~~Vi~~~~p~s~~  358 (410)
T 2j0s_A          279 AVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRE  358 (410)
T ss_dssp             EEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHH
T ss_pred             EEEEEcCHHHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECChhhCcCCcccCCEEEEECCCCCHH
Confidence            44454 4467778888898888754      122 2334455555553 3332222 22332    12789999999999


Q ss_pred             HHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCChH
Q psy7691         105 DYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQ  151 (165)
Q Consensus       105 ~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p~~  151 (165)
                      +|+||+||+||.|+.|.+++++.+.+...+..+.+++.....++|..
T Consensus       359 ~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~  405 (410)
T 2j0s_A          359 LYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN  405 (410)
T ss_dssp             HHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHHHHHHTTCCCEECCSC
T ss_pred             HHHHhcccccCCCCceEEEEEecHHHHHHHHHHHHHhCCCceecccc
Confidence            99999999999999999999999999999999999998888888754

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=98.65  E-value=2.7e-08  Score=84.47  Aligned_cols=72  Identities=19%  Similarity=0.197  Sum_probs=58.0

Q ss_pred             CCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVL  141 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l  141 (165)
                      .|+++|.++++.++.|.|++++++||+|||++++   +|     .++.+.+...  ..+..+++++|+ ++++.|..+.+
T Consensus         4 ~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~---~~-----~~~~~~~~~~--~~~~~~lil~P~-~~L~~q~~~~~   72 (555)
T 3tbk_A            4 KPRNYQLELALPAKKGKNTIICAPTGCGKTFVSL---LI-----CEHHLKKFPC--GQKGKVVFFANQ-IPVYEQQATVF   72 (555)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHH---HH-----HHHHHHTCCS--SCCCCEEEECSS-HHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHH---HH-----HHHHHHhccc--CCCCEEEEEeCC-HHHHHHHHHHH
Confidence            4899999999999999999999999999999988   77     6666644211  234568899999 88888877776


Q ss_pred             Hhc
Q psy7691         142 TEA  144 (165)
Q Consensus       142 ~~~  144 (165)
                      ...
T Consensus        73 ~~~   75 (555)
T 3tbk_A           73 SRY   75 (555)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A

Probab=98.65  E-value=1.3e-08  Score=92.52  Aligned_cols=109  Identities=22%  Similarity=0.349  Sum_probs=75.9

Q ss_pred             hHhhcCCHHHH----HHHHhhcCcEEecCCCCCCccccccCCCcHHHH---HHH-HhCCCCCCchHHHHHHHHHHcCCCe
Q psy7691           9 ERAARLSESEV----EAFRQKKEITVKGNNIPCPTQELTEGCFPNAVL---QHL-KGQGFEEPTAIQAQGWPIALSGRDM   80 (165)
Q Consensus         9 ~~~~~~~~~~~----~~~~~~~~i~~~~~~~p~~i~~f~~l~l~~~l~---~~l-~~~g~~~~t~~Q~~a~~~~l~G~di   80 (165)
                      +.+..+|++++    .+|++.....+.|.       ++.++ +++...   ++. ...|+ .||++|..++|.++.|.  
T Consensus        59 ~~~~~Lsd~eL~~kt~efk~rl~~~~~ge-------~ld~~-lpeafA~vrEa~~R~lG~-rP~~VQ~~~ip~Ll~G~--  127 (922)
T 1nkt_A           59 DDVEKLTDAELRAKTDEFKRRLADQKNPE-------TLDDL-LPEAFAVAREAAWRVLDQ-RPFDVQVMGAAALHLGN--  127 (922)
T ss_dssp             HHHHTSCHHHHHHHHHHHHHHHHCSSSCC-------CHHHH-HHHHHHHHHHHHHHHHSC-CCCHHHHHHHHHHHTTE--
T ss_pred             HHHHhCCHHHHHHHHHHHHHHHHhcccCC-------CHHHH-HHHHHHHHHHHHHHHcCC-CCCHHHHHHHHhHhcCC--
Confidence            56788899888    67775543211121       12222 333221   222 33688 79999999999999998  


Q ss_pred             eeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691          81 VGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus        81 ~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      ++.++||+|||++|.   ||.    |++.+.        |..+.+++|+ +.++.|+.+.+...
T Consensus       128 Iaem~TGeGKTLa~~---LP~----~l~aL~--------g~~v~VvTpT-reLA~Qdae~m~~l  175 (922)
T 1nkt_A          128 VAEMKTGEGKTLTCV---LPA----YLNALA--------GNGVHIVTVN-DYLAKRDSEWMGRV  175 (922)
T ss_dssp             EEECCTTSCHHHHTH---HHH----HHHHTT--------TSCEEEEESS-HHHHHHHHHHHHHH
T ss_pred             EEEecCCCccHHHHH---HHH----HHHHHh--------CCCeEEEeCC-HHHHHHHHHHHHHH
Confidence            899999999999999   883    455541        3468999999 88998888777653

>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=98.64  E-value=5.3e-09  Score=97.55  Aligned_cols=91  Identities=11%  Similarity=0.019  Sum_probs=73.2

Q ss_pred             cccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCC
Q psy7691          40 QELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASS  119 (165)
Q Consensus        40 ~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~  119 (165)
                      ..|..+.+++.+...+...++-.++++|.+|++.++.|.|++++++||||||+++.   +|     .++.+.       .
T Consensus       162 ~~~~~~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~---l~-----i~~~l~-------~  226 (1108)
T 3l9o_A          162 PNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAE---YA-----IAQSLK-------N  226 (1108)
T ss_dssp             SCCCSSTTTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHH---HH-----HHHHHH-------T
T ss_pred             CCcccCCCChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHH---HH-----HHHHHh-------c
Confidence            35666777777777776666667999999999999999999999999999999887   67     555542       2


Q ss_pred             CceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         120 GTAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       120 g~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      |..+++++|+ +.++.|+.+.+.....
T Consensus       227 g~rvlvl~Pt-raLa~Q~~~~l~~~~~  252 (1108)
T 3l9o_A          227 KQRVIYTSPI-KALSNQKYRELLAEFG  252 (1108)
T ss_dssp             TCEEEEEESS-HHHHHHHHHHHHHHTS
T ss_pred             CCeEEEEcCc-HHHHHHHHHHHHHHhC
Confidence            4468889998 9999998888877544

>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=98.63  E-value=3.1e-08  Score=84.30  Aligned_cols=75  Identities=19%  Similarity=0.180  Sum_probs=57.2

Q ss_pred             CCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHH
Q psy7691          59 GFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELI  138 (165)
Q Consensus        59 g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~  138 (165)
                      +.-.|+++|.++++.++.|.|++++++||+|||++++   +|     .++.+.+...  ..+..+++++|+ ++++.|..
T Consensus         4 ~~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~---~~-----~~~~~~~~~~--~~~~~~lil~P~-~~L~~q~~   72 (556)
T 4a2p_A            4 ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSI---LI-----CEHHFQNMPA--GRKAKVVFLATK-VPVYEQQK   72 (556)
T ss_dssp             ----CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHH---HH-----HHHHHHTCCS--SCCCCEEEECSS-HHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHH---HH-----HHHHHHhCcc--cCCCeEEEEeCC-HHHHHHHH
Confidence            3446999999999999999999999999999999988   77     6666644211  224568899998 88888877


Q ss_pred             HHHHhc
Q psy7691         139 AVLTEA  144 (165)
Q Consensus       139 ~~l~~~  144 (165)
                      +.+...
T Consensus        73 ~~~~~~   78 (556)
T 4a2p_A           73 NVFKHH   78 (556)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            776653

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=98.62  E-value=1e-09  Score=96.72  Aligned_cols=86  Identities=12%  Similarity=-0.017  Sum_probs=63.9

Q ss_pred             cccc-CCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCC
Q psy7691          41 ELTE-GCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASS  119 (165)
Q Consensus        41 ~f~~-l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~  119 (165)
                      .|.. +.+++.+.++|... .+.++|+|+.+++.++.|+|++++++||||||++|.   +|     +++++..      .
T Consensus       150 ~~~~~l~~~~~~~~~l~~~-~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~---lp-----il~~l~~------~  214 (618)
T 2whx_A          150 YGNGVVTKSGDYVSAITQA-ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRIL---PS-----IVREALK------R  214 (618)
T ss_dssp             CCC---------CEECBCC-CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHH---HH-----HHHHHHH------T
T ss_pred             cccccccchHHHHHHHhhc-cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHH---HH-----HHHHHHh------C
Confidence            3444 55666666666543 588999998899999999999999999999999988   78     7877643      3


Q ss_pred             CceEEEECCCcHHHHHHHHHHHH
Q psy7691         120 GTAYTFFTPNNGKQAKELIAVLT  142 (165)
Q Consensus       120 g~~~~~~~p~~~~~~~~i~~~l~  142 (165)
                      +..+++++|+ ++++.|+.+.+.
T Consensus       215 ~~~vLvl~Pt-reLa~Qi~~~l~  236 (618)
T 2whx_A          215 RLRTLILAPT-RVVAAEMEEALR  236 (618)
T ss_dssp             TCCEEEEESS-HHHHHHHHHHTT
T ss_pred             CCeEEEEcCh-HHHHHHHHHHhc
Confidence            4578888898 999999998875

>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=98.60  E-value=9.9e-09  Score=84.18  Aligned_cols=116  Identities=21%  Similarity=0.334  Sum_probs=84.6

Q ss_pred             ccccc-cCCCcHHHHHHHHhCCCCC------Cc-hHHHHHHHHHHcCC-Ceeeecc-cCCcccc----eeeecCCCCChh
Q psy7691          39 TQELT-EGCFPNAVLQHLKGQGFEE------PT-AIQAQGWPIALSGR-DMVGIAQ-TGSGKTL----AVINFDYPNSSE  104 (165)
Q Consensus        39 i~~f~-~l~l~~~l~~~l~~~g~~~------~t-~~Q~~a~~~~l~G~-di~~~a~-tgsGKt~----~~~~~~lP~~~~  104 (165)
                      ++.|. .....+.+.+.|.+.|+..      .+ ..+...+..+..|. +++++.. -+.|=.+    .+++||+|.+..
T Consensus       261 ~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~~~~Gidip~~~~Vi~~~~p~s~~  340 (400)
T 1s2m_A          261 AIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAE  340 (400)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSCCCTTEEEEEESSCCSSHH
T ss_pred             EEEEEecHHHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCccccCCCccCCCEEEEeCCCCCHH
Confidence            44444 4466778888888776642      22 33445566666664 4443332 2334222    689999999999


Q ss_pred             HHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCChHHHH
Q psy7691         105 DYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQD  154 (165)
Q Consensus       105 ~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p~~~~~  154 (165)
                      +|+||+||+||.|+.|.+++++.+.+...+.++.+.+.....++|.++.+
T Consensus       341 ~~~Qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~  390 (400)
T 1s2m_A          341 TYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATIDK  390 (400)
T ss_dssp             HHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHHHHHHTCCCEECCSSCCG
T ss_pred             HHHHhcchhcCCCCCceEEEEeccchHHHHHHHHHHhCCCcccccccccc
Confidence            99999999999999999999999999999999999998888888766544

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=98.60  E-value=5.8e-09  Score=88.34  Aligned_cols=68  Identities=13%  Similarity=0.053  Sum_probs=57.0

Q ss_pred             CCCCCchHHHHHHHHHHcCCCe-eeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHH
Q psy7691          59 GFEEPTAIQAQGWPIALSGRDM-VGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL  137 (165)
Q Consensus        59 g~~~~t~~Q~~a~~~~l~G~di-~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i  137 (165)
                      |+..|+++|+ ++|.++.|.|+ +++++||||||++|+   +|     ++++...      .|..++++.|+ ++++.|+
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~---~~-----~l~~~~~------~~~~~lvl~Pt-r~La~Q~   64 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRIL---PS-----IVREALL------RRLRTLILAPT-RVVAAEM   64 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHH---HH-----HHHHHHH------TTCCEEEEESS-HHHHHHH
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHH---HH-----HHHHHHh------cCCcEEEECCC-HHHHHHH
Confidence            7889999985 79999999998 899999999999988   78     6666533      34568888898 9999999


Q ss_pred             HHHHH
Q psy7691         138 IAVLT  142 (165)
Q Consensus       138 ~~~l~  142 (165)
                      .+.+.
T Consensus        65 ~~~l~   69 (451)
T 2jlq_A           65 EEALR   69 (451)
T ss_dssp             HHHTT
T ss_pred             HHHhc
Confidence            98874

>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=98.58  E-value=4.9e-08  Score=87.92  Aligned_cols=77  Identities=19%  Similarity=0.170  Sum_probs=57.6

Q ss_pred             hCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHH
Q psy7691          57 GQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKE  136 (165)
Q Consensus        57 ~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~  136 (165)
                      .+|+..|+++|.++++.++.|.|++++++||+|||++++   +|     .++.+.+. . ...+..+++++|+ +.++.|
T Consensus       243 ~~g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~---~~-----i~~~l~~~-~-~~~~~~~Lvl~Pt-~~L~~Q  311 (797)
T 4a2q_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSI---LI-----CEHHFQNM-P-AGRKAKVVFLATK-VPVYEQ  311 (797)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHH---HH-----HHHHHHTC-C-SSCCCCEEEECSS-HHHHHH
T ss_pred             hcCCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHH---HH-----HHHHHHhc-c-ccCCCeEEEEeCC-HHHHHH
Confidence            457889999999999999999999999999999999988   77     66666442 1 1224568899998 788887


Q ss_pred             HHHHHHhc
Q psy7691         137 LIAVLTEA  144 (165)
Q Consensus       137 i~~~l~~~  144 (165)
                      ..+.+...
T Consensus       312 ~~~~~~~~  319 (797)
T 4a2q_A          312 QKNVFKHH  319 (797)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHh
Confidence            76666553

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*

Probab=98.56  E-value=1.6e-08  Score=91.39  Aligned_cols=109  Identities=17%  Similarity=0.165  Sum_probs=72.6

Q ss_pred             hHhhcCCHHHHHHHHhhcCcEEecCCCCCCccccccCCCcHHHHHHHHh-----CCCCCCchHHHHHHHHHHcCCCeeee
Q psy7691           9 ERAARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKG-----QGFEEPTAIQAQGWPIALSGRDMVGI   83 (165)
Q Consensus         9 ~~~~~~~~~~~~~~~~~~~i~~~~~~~p~~i~~f~~l~l~~~l~~~l~~-----~g~~~~t~~Q~~a~~~~l~G~di~~~   83 (165)
                      +.+..+|++++...-...+.......      .+.++ ++ +....+.+     .|. .||++|..++|.++.|.  ++.
T Consensus        25 ~~~~~lsd~eL~~kt~~fk~rl~~g~------~ld~~-lp-eafA~vrea~~R~lg~-~p~~VQ~~~i~~ll~G~--Iae   93 (853)
T 2fsf_A           25 PEMEKLSDEELKGKTAEFRARLEKGE------VLENL-IP-EAFAVVREASKRVFGM-RHFDVQLLGGMVLNERC--IAE   93 (853)
T ss_dssp             HHHHHSCHHHHHHHHHHHHHHHHTTC------CHHHH-HH-HHHHHHHHHHHHHHSC-CCCHHHHHHHHHHHSSE--EEE
T ss_pred             HHHHhCCHHHHHHHHHHHHHHHHcCC------Chhhh-hH-HHHHHHHHHHHHHcCC-CCChHHHhhcccccCCe--eee
Confidence            45777888877654433332222211      12221 22 22222222     465 69999999999999998  899


Q ss_pred             cccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691          84 AQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus        84 a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      ++||+|||++|.   +|     .+...-       .|..+++++|+ ++++.|+.+.+...
T Consensus        94 m~TGsGKTlaf~---LP-----~l~~~l-------~g~~vlVltPT-reLA~Q~~e~~~~l  138 (853)
T 2fsf_A           94 MRTGEGKTLTAT---LP-----AYLNAL-------TGKGVHVVTVN-DYLAQRDAENNRPL  138 (853)
T ss_dssp             CCTTSCHHHHHH---HH-----HHHHHT-------TSSCCEEEESS-HHHHHHHHHHHHHH
T ss_pred             ecCCchHHHHHH---HH-----HHHHHH-------cCCcEEEEcCC-HHHHHHHHHHHHHH
Confidence            999999999999   89     443321       23468999999 99999888877654

>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=98.56  E-value=2.8e-08  Score=85.50  Aligned_cols=52  Identities=29%  Similarity=0.479  Sum_probs=47.1

Q ss_pred             eeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691          93 AVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus        93 ~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      +|++||+|.+.++|+||+||+||.|+.|.+++++.+.+...+..+.+.....
T Consensus       413 ~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~~~~~  464 (563)
T 3i5x_A          413 EVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIV  464 (563)
T ss_dssp             EEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHHHCCC
T ss_pred             EEEEECCCCchhhhhhhcCccccCCCCceEEEEEchhHHHHHHHHHHHhCCC
Confidence            7999999999999999999999999999999999999888888887765533

>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=98.53  E-value=2.7e-08  Score=74.74  Aligned_cols=76  Identities=16%  Similarity=0.141  Sum_probs=54.1

Q ss_pred             CCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHH-
Q psy7691          58 QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKE-  136 (165)
Q Consensus        58 ~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~-  136 (165)
                      .....+++.|.++++.++.|.++++.++||+|||++++   +|     ..+.+.+..+. ..+..+++++|+ +.++.| 
T Consensus        29 ~~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~---~~-----~~~~~~~~~~~-~~~~~~lil~p~-~~L~~q~   98 (216)
T 3b6e_A           29 EPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAV---YI-----AKDHLDKKKKA-SEPGKVIVLVNK-VLLVEQL   98 (216)
T ss_dssp             SCCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHH---HH-----HHHHHHHHHHT-TCCCCEEEEESS-HHHHHHH
T ss_pred             cCCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHH---HH-----HHHHHhhcccc-cCCCcEEEEECH-HHHHHHH
Confidence            34456999999999999999999999999999999887   55     33333221111 234467888888 777777 


Q ss_pred             HHHHHHh
Q psy7691         137 LIAVLTE  143 (165)
Q Consensus       137 i~~~l~~  143 (165)
                      +.+.+..
T Consensus        99 ~~~~~~~  105 (216)
T 3b6e_A           99 FRKEFQP  105 (216)
T ss_dssp             HHHTHHH
T ss_pred             HHHHHHH
Confidence            5554443

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=98.53  E-value=4.1e-08  Score=85.25  Aligned_cols=51  Identities=29%  Similarity=0.488  Sum_probs=46.6

Q ss_pred             eeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHh
Q psy7691          93 AVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTE  143 (165)
Q Consensus        93 ~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~  143 (165)
                      +|++||+|.+.++|+||+||+||.|+.|.+++++.+.+...+..+.+....
T Consensus       362 ~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~~~~  412 (579)
T 3sqw_A          362 EVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNI  412 (579)
T ss_dssp             EEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHHHCC
T ss_pred             EEEEcCCCCCHHHhhhhccccccCCCCceEEEEEcccHHHHHHHHHHHhCC
Confidence            799999999999999999999999999999999999988888888776543

>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=98.51  E-value=1.2e-08  Score=83.18  Aligned_cols=77  Identities=31%  Similarity=0.553  Sum_probs=0.0

Q ss_pred             HHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCC
Q psy7691          70 GWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIP  149 (165)
Q Consensus        70 a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p  149 (165)
                      |+..+.+|.|+..+.        .+++||+|.+..+|+||+||+||.|..|.+++++.+.+...+..+.+++.....++|
T Consensus       315 ~T~~~~~Gldi~~~~--------~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  386 (394)
T 1fuu_A          315 STDLLARGIDVQQVS--------LVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELP  386 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ECChhhcCCCcccCC--------EEEEeCCCCCHHHHHHHcCcccCCCCCceEEEEEchhHHHHHHHHHHHhCCcccccC
Confidence            444455666666555        789999999999999999999999999999999999988889999999888888888


Q ss_pred             hHHHH
Q psy7691         150 PQLQD  154 (165)
Q Consensus       150 ~~~~~  154 (165)
                      ..+.+
T Consensus       387 ~~~~~  391 (394)
T 1fuu_A          387 SDIAT  391 (394)
T ss_dssp             -----
T ss_pred             cchhh
Confidence            76544

>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=98.51  E-value=8e-08  Score=77.26  Aligned_cols=111  Identities=19%  Similarity=0.304  Sum_probs=79.0

Q ss_pred             cccc-ccCCCcHHHHHHHHhCCCCC------Cc-hHHHHHHHHHHcCC-Ceeeeccc-CCcc----cceeeecCCCCChh
Q psy7691          39 TQEL-TEGCFPNAVLQHLKGQGFEE------PT-AIQAQGWPIALSGR-DMVGIAQT-GSGK----TLAVINFDYPNSSE  104 (165)
Q Consensus        39 i~~f-~~l~l~~~l~~~l~~~g~~~------~t-~~Q~~a~~~~l~G~-di~~~a~t-gsGK----t~~~~~~~lP~~~~  104 (165)
                      +..| ........+.+.|.+.|+..      .+ ..+...+..+..|. +++++... +.|=    ...+++|++|.+..
T Consensus       241 ~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~  320 (367)
T 1hv8_A          241 GLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPE  320 (367)
T ss_dssp             EEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHCCCSCCSEEEESSCCSCHH
T ss_pred             EEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCCCcccCCEEEEecCCCCHH
Confidence            3444 44567778888888877643      12 23444555555553 34333221 1221    22789999999999


Q ss_pred             HHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCC
Q psy7691         105 DYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIP  149 (165)
Q Consensus       105 ~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p  149 (165)
                      +|+||+||++|.|+.|.+++++.+.+......+.+.+.....+++
T Consensus       321 ~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  365 (367)
T 1hv8_A          321 SYMHRIGRTGRAGKKGKAISIINRREYKKLRYIERAMKLKIKKLK  365 (367)
T ss_dssp             HHHHHSTTTCCSSSCCEEEEEECTTSHHHHHHHHHHHTCCCCCBC
T ss_pred             HhhhcccccccCCCccEEEEEEcHHHHHHHHHHHHHhCCCCceec
Confidence            999999999999999999999999999999999998887766654

>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase, translocation, secretion, protein transport; 2.18A {Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A 3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A

Probab=98.50  E-value=3.8e-08  Score=89.07  Aligned_cols=107  Identities=20%  Similarity=0.162  Sum_probs=68.8

Q ss_pred             CCcccccc-CCCcHHHHHHHHhCCCCCCc----hHHHHH---------------HHHHHcCCCeeeec-ccCCcccceee
Q psy7691          37 CPTQELTE-GCFPNAVLQHLKGQGFEEPT----AIQAQG---------------WPIALSGRDMVGIA-QTGSGKTLAVI   95 (165)
Q Consensus        37 ~~i~~f~~-l~l~~~l~~~l~~~g~~~~t----~~Q~~a---------------~~~~l~G~di~~~a-~tgsGKt~~~~   95 (165)
                      .|++.|.. ..-++.+.+.|...|+..-.    -.|.++               ++.+.||.||.... .-..| -++||
T Consensus       433 ~pvLVft~s~~~se~Ls~~L~~~gi~~~vLhg~~~~rEr~ii~~ag~~g~VlIATdmAgRG~DI~l~~~V~~~g-gl~VI  511 (844)
T 1tf5_A          433 QPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAVTIATNMAGRGTDIKLGEGVKELG-GLAVV  511 (844)
T ss_dssp             CCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTTSTTCEEEEETTSSTTCCCCCCTTSGGGT-SEEEE
T ss_pred             CcEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCccHHHHHHHHHcCCCCeEEEeCCccccCcCccccchhhhcC-CcEEE
Confidence            35556654 46788888889999986521    123333               22223444432000 00001 23899


Q ss_pred             ecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHH----HHHHHHHHHHhc
Q psy7691          96 NFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGK----QAKELIAVLTEA  144 (165)
Q Consensus        96 ~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~----~~~~i~~~l~~~  144 (165)
                      |||+|.+...|+||+|||||+|..|.+++|+++.+.-    ....+...+...
T Consensus       512 n~d~p~s~r~y~hr~GRTGRqG~~G~s~~~vs~eD~l~r~f~~~~~~~~~~~~  564 (844)
T 1tf5_A          512 GTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDELMRRFGAERTMAMLDRF  564 (844)
T ss_dssp             ESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSSGGGSSHHHHHHHHHHHH
T ss_pred             EecCCCCHHHHHhhcCccccCCCCCeEEEEecHHHHHHHHHhHHHHHHHHHhc
Confidence            9999999999999999999999999999999988731    123455555543

>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=98.47  E-value=1.5e-07  Score=91.02  Aligned_cols=88  Identities=19%  Similarity=0.325  Sum_probs=67.6

Q ss_pred             CcHHHHHHHHhCCCCCCchHHHHHHHHHH-cCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCC----CCCCCCc
Q psy7691          47 FPNAVLQHLKGQGFEEPTAIQAQGWPIAL-SGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTG----RCASSGT  121 (165)
Q Consensus        47 l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l-~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~----r~~~~g~  121 (165)
                      |++.....+  .||+.++++|.+++|.++ .+.|++++||||||||+++.   +|     .++++.+..    .....+.
T Consensus        66 Lp~~~~~~f--~g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~---l~-----il~~l~~~~~~~~~~~~~~~  135 (1724)
T 4f92_B           66 LPKYAQAGF--EGFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVAL---MC-----MLREIGKHINMDGTINVDDF  135 (1724)
T ss_dssp             SCGGGSTTC--TTCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHH---HH-----HHHHHGGGCCTTSSCCTTSC
T ss_pred             cCHHHHHhc--CCCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHH---HH-----HHHHHHhhccccccccCCCC
Confidence            555443333  289999999999999887 56899999999999999887   77     777775432    2234567


Q ss_pred             eEEEECCCcHHHHHHHHHHHHhcC
Q psy7691         122 AYTFFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus       122 ~~~~~~p~~~~~~~~i~~~l~~~~  145 (165)
                      .+++++|+ +.++.++.+.+....
T Consensus       136 k~lyiaP~-kALa~e~~~~l~~~~  158 (1724)
T 4f92_B          136 KIIYIAPM-RSLVQEMVGSFGKRL  158 (1724)
T ss_dssp             EEEEECSS-HHHHHHHHHHHHHHH
T ss_pred             EEEEECCH-HHHHHHHHHHHHHHH
Confidence            89999999 899998888776543

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=98.47  E-value=1.2e-07  Score=85.74  Aligned_cols=80  Identities=18%  Similarity=0.172  Sum_probs=63.7

Q ss_pred             HHHHHHHHhCCCCCCchHHHHHHHHHHcC------CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCce
Q psy7691          49 NAVLQHLKGQGFEEPTAIQAQGWPIALSG------RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTA  122 (165)
Q Consensus        49 ~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G------~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~  122 (165)
                      +.+.+.+...+| .+|++|.++++.++.+      +|++++++||||||++++   +|     .++.+.       .|..
T Consensus       356 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlval---l~-----il~~l~-------~g~q  419 (780)
T 1gm5_A          356 KLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQ---LA-----ILDNYE-------AGFQ  419 (780)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHH---HH-----HHHHHH-------HTSC
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHH---HH-----HHHHHH-------cCCe
Confidence            445555678899 7999999999999876      699999999999999988   77     555552       2356


Q ss_pred             EEEECCCcHHHHHHHHHHHHhcC
Q psy7691         123 YTFFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus       123 ~~~~~p~~~~~~~~i~~~l~~~~  145 (165)
                      +++++|+ +.++.|+.+.+....
T Consensus       420 vlvlaPt-r~La~Q~~~~l~~~~  441 (780)
T 1gm5_A          420 TAFMVPT-SILAIQHYRRTVESF  441 (780)
T ss_dssp             EEEECSC-HHHHHHHHHHHHHHH
T ss_pred             EEEEeCc-HHHHHHHHHHHHHHh
Confidence            8899999 888888887776543

>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=98.46  E-value=1.7e-07  Score=90.72  Aligned_cols=84  Identities=21%  Similarity=0.259  Sum_probs=67.1

Q ss_pred             CCcHHHHHHHHhCCCCCCchHHHHHHHHHHcC-CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEE
Q psy7691          46 CFPNAVLQHLKGQGFEEPTAIQAQGWPIALSG-RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYT  124 (165)
Q Consensus        46 ~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G-~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~  124 (165)
                      .+.....+++...+|..++|+|.++++.++.+ .|++++||||||||+++.   +|     .++.+-+.     .+..++
T Consensus       910 ~L~~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliae---la-----il~~l~~~-----~~~kav  976 (1724)
T 4f92_B          910 ALRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAE---FA-----ILRMLLQS-----SEGRCV  976 (1724)
T ss_dssp             GSCCHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHH---HH-----HHHHHHHC-----TTCCEE
T ss_pred             cccCHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHH---HH-----HHHHHHhC-----CCCEEE
Confidence            35567788888889999999999999999765 679999999999999877   77     66666431     233578


Q ss_pred             EECCCcHHHHHHHHHHHHh
Q psy7691         125 FFTPNNGKQAKELIAVLTE  143 (165)
Q Consensus       125 ~~~p~~~~~~~~i~~~l~~  143 (165)
                      +++|+ ++++.|+.+.+..
T Consensus       977 yi~P~-raLa~q~~~~~~~  994 (1724)
T 4f92_B          977 YITPM-EALAEQVYMDWYE  994 (1724)
T ss_dssp             EECSC-HHHHHHHHHHHHH
T ss_pred             EEcCh-HHHHHHHHHHHHH
Confidence            99999 8888888776654

>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=98.45  E-value=7.7e-08  Score=78.78  Aligned_cols=114  Identities=20%  Similarity=0.287  Sum_probs=77.4

Q ss_pred             Cccccc-cCCCcHHHHHHHHhCCCCC-------CchHHHHHHHHHHcCC-Ceeeeccc-CCccc----ceeeecCCC---
Q psy7691          38 PTQELT-EGCFPNAVLQHLKGQGFEE-------PTAIQAQGWPIALSGR-DMVGIAQT-GSGKT----LAVINFDYP---  100 (165)
Q Consensus        38 ~i~~f~-~l~l~~~l~~~l~~~g~~~-------~t~~Q~~a~~~~l~G~-di~~~a~t-gsGKt----~~~~~~~lP---  100 (165)
                      .++.|. .......+.+.|.+.|+..       +...+...+..+..|. +++++... +.|=.    -.|++||+|   
T Consensus       268 ~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~  347 (412)
T 3fht_A          268 QAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDK  347 (412)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTSSCCCTTEEEEEESSCCBCS
T ss_pred             CEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCccccCCCccCCCEEEEECCCCCC
Confidence            344554 4467788888888887643       2223444555555553 34332222 23322    268999999   


Q ss_pred             ---CChhHHHHhhccCCCCCCCCceEEEECCCc-HHHHHHHHHHHHhcCCCCChH
Q psy7691         101 ---NSSEDYIHRIGRTGRCASSGTAYTFFTPNN-GKQAKELIAVLTEASQPIPPQ  151 (165)
Q Consensus       101 ---~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~-~~~~~~i~~~l~~~~~~~p~~  151 (165)
                         .+..+|+||+||+||.|..|.+++++.+.+ ...+..+.+.+.....+++..
T Consensus       348 ~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~  402 (412)
T 3fht_A          348 DGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDTD  402 (412)
T ss_dssp             SSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHHHHHTCCCEEC---
T ss_pred             CCCcchheeecccCcccCCCCCceEEEEEcChhhHHHHHHHHHHHCCccccCCCc
Confidence               467899999999999999999999999875 677888888888887777543

>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=98.45  E-value=1.6e-07  Score=86.13  Aligned_cols=79  Identities=18%  Similarity=0.146  Sum_probs=57.0

Q ss_pred             HHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHH
Q psy7691          55 LKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQA  134 (165)
Q Consensus        55 l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~  134 (165)
                      ..-.|+..|+++|.++++.++.|.|++++++||+|||++++   +|     .++.+.+. .. ..+..+++++|+ +.++
T Consensus       241 ~~l~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~---~~-----i~~~l~~~-~~-~~~~~vLvl~Pt-~~L~  309 (936)
T 4a2w_A          241 PPVYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSI---LI-----CEHHFQNM-PA-GRKAKVVFLATK-VPVY  309 (936)
T ss_dssp             -------CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHH---HH-----HHTTTTTC-CS-SCCCCEEEECSS-HHHH
T ss_pred             ccccCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHH---HH-----HHHHHHhc-cc-cCCCeEEEEeCC-HHHH
Confidence            34457888999999999999999999999999999999988   77     66655442 11 224568899998 7788


Q ss_pred             HHHHHHHHhc
Q psy7691         135 KELIAVLTEA  144 (165)
Q Consensus       135 ~~i~~~l~~~  144 (165)
                      .|..+.+...
T Consensus       310 ~Q~~~~~~~~  319 (936)
T 4a2w_A          310 EQQKNVFKHH  319 (936)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            7776666553

>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=98.43  E-value=2.5e-08  Score=84.28  Aligned_cols=73  Identities=27%  Similarity=0.466  Sum_probs=0.0

Q ss_pred             HHHHHHcCCCeeeecccCCcccceeeecCCCC------ChhHHHHhhccCCCCCCCCceEEEECCCc-HHHHHHHHHHHH
Q psy7691          70 GWPIALSGRDMVGIAQTGSGKTLAVINFDYPN------SSEDYIHRIGRTGRCASSGTAYTFFTPNN-GKQAKELIAVLT  142 (165)
Q Consensus        70 a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~------~~~~~i~r~gr~~r~~~~g~~~~~~~p~~-~~~~~~i~~~l~  142 (165)
                      |+..+.+|.|+..+.        .|++||+|.      +..+|+||+||+||.|+.|.+++++.+.+ ...+..+.+.+.
T Consensus       389 ~T~~~~~GlDip~v~--------~VI~~d~p~~~~~~~s~~~~~Qr~GRagR~g~~G~~i~~~~~~~~~~~~~~i~~~~~  460 (479)
T 3fmp_B          389 TTNVCARGIDVEQVS--------VVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFN  460 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EccccccCCccccCC--------EEEEecCCCCCccCCCHHHHHHHhcccccCCCCceEEEEEcCcchHHHHHHHHHHhC
Confidence            556667777877776        799999994      56799999999999999999999999875 567778888887


Q ss_pred             hcCCCCCh
Q psy7691         143 EASQPIPP  150 (165)
Q Consensus       143 ~~~~~~p~  150 (165)
                      ....+++.
T Consensus       461 ~~~~~l~~  468 (479)
T 3fmp_B          461 KKIERLDT  468 (479)
T ss_dssp             --------
T ss_pred             CCceECCC
Confidence            77766653

>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=98.42  E-value=5.6e-08  Score=79.17  Aligned_cols=114  Identities=22%  Similarity=0.318  Sum_probs=80.7

Q ss_pred             Cccccc-cCCCcHHHHHHHHhCCCCC-------CchHHHHHHHHHHcCC-Ceeeeccc-CCcc----cceeeecCCCCCh
Q psy7691          38 PTQELT-EGCFPNAVLQHLKGQGFEE-------PTAIQAQGWPIALSGR-DMVGIAQT-GSGK----TLAVINFDYPNSS  103 (165)
Q Consensus        38 ~i~~f~-~l~l~~~l~~~l~~~g~~~-------~t~~Q~~a~~~~l~G~-di~~~a~t-gsGK----t~~~~~~~lP~~~  103 (165)
                      .++.|. .......+.+.|...|+..       +...+...+..+..|. +++++... +.|=    .-.+++||+|.+.
T Consensus       252 ~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gidi~~~~~Vi~~~~p~s~  331 (391)
T 1xti_A          252 QVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDS  331 (391)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCCCSSCBCCTTEEEEEESSCCSSH
T ss_pred             cEEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECChhhcCCCcccCCEEEEeCCCCCH
Confidence            344444 4567778888888887643       1223445555566653 34433322 2342    2368999999999


Q ss_pred             hHHHHhhccCCCCCCCCceEEEECCCc-HHHHHHHHHHHHhcCCCCChH
Q psy7691         104 EDYIHRIGRTGRCASSGTAYTFFTPNN-GKQAKELIAVLTEASQPIPPQ  151 (165)
Q Consensus       104 ~~~i~r~gr~~r~~~~g~~~~~~~p~~-~~~~~~i~~~l~~~~~~~p~~  151 (165)
                      .+|+||+||+||.|..|.+++++.+.+ ......+.+.+.....++|.+
T Consensus       332 ~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  380 (391)
T 1xti_A          332 DTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDE  380 (391)
T ss_dssp             HHHHHHHCBCSSSCCCCEEEEEECSHHHHHHHHHHHHHTTCCCEECCSC
T ss_pred             HHHHHhcccccCCCCceEEEEEEcccchHHHHHHHHHHhcCChhhCCcc
Confidence            999999999999999999999999874 466788888888888888765

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=98.41  E-value=5e-09  Score=93.23  Aligned_cols=76  Identities=22%  Similarity=0.183  Sum_probs=59.5

Q ss_pred             HHHhCCCC-----CCchHHH-----HHHHHHH------cCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCC
Q psy7691          54 HLKGQGFE-----EPTAIQA-----QGWPIAL------SGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCA  117 (165)
Q Consensus        54 ~l~~~g~~-----~~t~~Q~-----~a~~~~l------~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~  117 (165)
                      .|..+||.     .||++|.     ++||.++      .|+|++++++||||||++|+   +|     +++++..     
T Consensus       202 ~l~~~Gf~~~~~~~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~l---l~-----il~~l~~-----  268 (673)
T 2wv9_A          202 GLYGNGVILGNGAYVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRIL---PQ-----IIKDAIQ-----  268 (673)
T ss_dssp             EEEEEEEECSSSCEEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHH---HH-----HHHHHHH-----
T ss_pred             EeeeccccccCCCccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHH---HH-----HHHHHHh-----
Confidence            45566777     8999999     9999888      89999999999999999987   77     7766533     


Q ss_pred             CCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691         118 SSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus       118 ~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                       .+..+++++|+ ++++.|+.+.+...
T Consensus       269 -~~~~~lilaPT-r~La~Q~~~~l~~~  293 (673)
T 2wv9_A          269 -KRLRTAVLAPT-RVVAAEMAEALRGL  293 (673)
T ss_dssp             -TTCCEEEEESS-HHHHHHHHHHTTTS
T ss_pred             -CCCcEEEEccH-HHHHHHHHHHHhcC
Confidence             34568888898 99999999887643

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=98.38  E-value=1.5e-07  Score=85.72  Aligned_cols=69  Identities=20%  Similarity=0.250  Sum_probs=57.5

Q ss_pred             hCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHH
Q psy7691          57 GQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKE  136 (165)
Q Consensus        57 ~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~  136 (165)
                      ..|+ .||++|..++|.++.|.  ++.++||+|||+++.   +|.    |++.+        .|..+.+++|+ +.++.|
T Consensus        75 ~lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~---Lp~----~L~aL--------~G~qv~VvTPT-reLA~Q  135 (997)
T 2ipc_A           75 YLGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVAT---LAV----ALNAL--------TGKGVHVVTVN-DYLARR  135 (997)
T ss_dssp             HTCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHH---HHH----HHHHT--------TCSCCEEEESS-HHHHHH
T ss_pred             HhCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHH---HHH----HHHHH--------hCCCEEEEeCC-HHHHHH
Confidence            3799 79999999999999997  899999999999998   883    45554        13368899999 899998


Q ss_pred             HHHHHHhc
Q psy7691         137 LIAVLTEA  144 (165)
Q Consensus       137 i~~~l~~~  144 (165)
                      ..+.+...
T Consensus       136 dae~m~~l  143 (997)
T 2ipc_A          136 DAEWMGPV  143 (997)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            88877664

>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=98.37  E-value=2.3e-07  Score=73.80  Aligned_cols=61  Identities=44%  Similarity=0.605  Sum_probs=47.3

Q ss_pred             HHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHH
Q psy7691          73 IALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLT  142 (165)
Q Consensus        73 ~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~  142 (165)
                      .+.+|.|+..+.        .+++|+.|.+..+|+||+||+||.|..|.+++++. .+......+.+.+.
T Consensus       275 ~~~~Gid~~~~~--------~Vi~~~~~~s~~~~~Q~~GR~gR~g~~g~~~~~~~-~~~~~~~~i~~~~~  335 (337)
T 2z0m_A          275 VASRGLDIPLVE--------KVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFIL-NEYWLEKEVKKVSQ  335 (337)
T ss_dssp             HHHTTCCCCCBS--------EEEESSCCSSHHHHHHHHTTBCGGGCCEEEEEEES-SCHHHHHHHC----
T ss_pred             ccccCCCccCCC--------EEEEecCCCCHHHhhHhcCccccCCCCceEEEEEe-CcHHHHHHHHHHhc
Confidence            344555554444        79999999999999999999999999999999999 66777777776654

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=98.36  E-value=2.4e-07  Score=71.53  Aligned_cols=72  Identities=13%  Similarity=0.041  Sum_probs=53.4

Q ss_pred             CCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHH
Q psy7691          61 EEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAV  140 (165)
Q Consensus        61 ~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~  140 (165)
                      -..+++|.++++.+..|.+++++|+||||||.++.   +|     .++..-..++  ..+..++++.|+ +.++.++.+.
T Consensus        60 ~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~---~~-----~~~~~~~~~~--~~~~~~l~~~p~-~~la~q~~~~  128 (235)
T 3llm_A           60 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVP---QF-----ILDDFIQNDR--AAECNIVVTQPR-RISAVSVAER  128 (235)
T ss_dssp             SGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHH---HH-----HHHHHHHTTC--GGGCEEEEEESS-HHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHH---HH-----HhcchhhcCC--CCceEEEEeccc-hHHHHHHHHH
Confidence            34688999999999999999999999999998766   44     3333322222  234467778887 8888888777


Q ss_pred             HHh
Q psy7691         141 LTE  143 (165)
Q Consensus       141 l~~  143 (165)
                      +..
T Consensus       129 ~~~  131 (235)
T 3llm_A          129 VAF  131 (235)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>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=98.32  E-value=3.2e-07  Score=82.74  Aligned_cols=92  Identities=21%  Similarity=0.178  Sum_probs=68.3

Q ss_pred             CCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcC-CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCC
Q psy7691          37 CPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSG-RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGR  115 (165)
Q Consensus        37 ~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G-~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r  115 (165)
                      .++..|+.+++++.+.+.+...+ ..|+++|.++++.++.+ .+++++++||+|||..     +|.    ++...+..  
T Consensus        69 ~~~~~f~~~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTtl-----lp~----ll~~~~~~--  136 (773)
T 2xau_A           69 GKINPFTGREFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQ-----IPQ----FVLFDEMP--  136 (773)
T ss_dssp             SSBCTTTCSBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHH-----HHH----HHHHHHCG--
T ss_pred             CCCCCccccCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHHH-----HHH----HHHHhccc--
Confidence            35778999999999999999988 67999999999988765 5799999999999993     451    22222111  


Q ss_pred             CCCCCceEEEECCCcHHHHHHHHHHHH
Q psy7691         116 CASSGTAYTFFTPNNGKQAKELIAVLT  142 (165)
Q Consensus       116 ~~~~g~~~~~~~p~~~~~~~~i~~~l~  142 (165)
                       ...|..++++.|+ +.++.++.+.+.
T Consensus       137 -~~~g~~ilvl~P~-r~La~q~~~~l~  161 (773)
T 2xau_A          137 -HLENTQVACTQPR-RVAAMSVAQRVA  161 (773)
T ss_dssp             -GGGTCEEEEEESC-HHHHHHHHHHHH
T ss_pred             -cCCCceEEecCch-HHHHHHHHHHHH
Confidence             1124567778887 888887776553

>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=98.28  E-value=4.4e-07  Score=81.34  Aligned_cols=107  Identities=18%  Similarity=0.133  Sum_probs=70.4

Q ss_pred             CCcccccc-CCCcHHHHHHHHhCCCCCCc----hHHHHH---------------HHHHHcCCCeeee-cccCCcccceee
Q psy7691          37 CPTQELTE-GCFPNAVLQHLKGQGFEEPT----AIQAQG---------------WPIALSGRDMVGI-AQTGSGKTLAVI   95 (165)
Q Consensus        37 ~~i~~f~~-l~l~~~l~~~l~~~g~~~~t----~~Q~~a---------------~~~~l~G~di~~~-a~tgsGKt~~~~   95 (165)
                      .|++.|.. ..-++.+.+.|.+.|+..-.    -.|.++               ++.+.||.||..- .-..-| -++|+
T Consensus       475 qpVLVFt~S~e~sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g~VtVATdmAgRGtDI~lg~~V~~~G-glhVI  553 (822)
T 3jux_A          475 QPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKGMVTIATNMAGRGTDIKLGPGVAELG-GLCII  553 (822)
T ss_dssp             CCEEEEESSHHHHHHHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTTCEEEEETTTTTTCCCCCCTTTTTTT-SCEEE
T ss_pred             CCEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCCeEEEEcchhhCCcCccCCcchhhcC-CCEEE
Confidence            45666654 46788888889998886421    122222               2233344554200 000001 13899


Q ss_pred             ecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHH----HHHHHHHHHhc
Q psy7691          96 NFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQ----AKELIAVLTEA  144 (165)
Q Consensus        96 ~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~----~~~i~~~l~~~  144 (165)
                      ||++|.+...|+||+||+||+|..|.+++|+++.+.-+    ...+..++...
T Consensus       554 nte~Pes~r~y~qriGRTGRqG~~G~a~~fvsleD~l~r~fg~~~~~~~m~~~  606 (822)
T 3jux_A          554 GTERHESRRIDNQLRGRAGRQGDPGESIFFLSLEDDLLRIFGSEQIGKVMNIL  606 (822)
T ss_dssp             ESSCCSSHHHHHHHHTTSSCSSCCCEEEEEEETTSHHHHHTTHHHHHHHHHHS
T ss_pred             ecCCCCCHHHHHHhhCccccCCCCeeEEEEechhHHHHHhhhHHHHHHHHHHc
Confidence            99999999999999999999999999999999987332    34666666554

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=98.27  E-value=2.3e-07  Score=76.80  Aligned_cols=103  Identities=17%  Similarity=0.146  Sum_probs=72.8

Q ss_pred             CCcccccc-CCCcHHHHHHHHhCCCCCC---chHHHHHHHHHHcCC-Ceeee----cc-cCCc----c-cceeeecCCC-
Q psy7691          37 CPTQELTE-GCFPNAVLQHLKGQGFEEP---TAIQAQGWPIALSGR-DMVGI----AQ-TGSG----K-TLAVINFDYP-  100 (165)
Q Consensus        37 ~~i~~f~~-l~l~~~l~~~l~~~g~~~~---t~~Q~~a~~~~l~G~-di~~~----a~-tgsG----K-t~~~~~~~lP-  100 (165)
                      .+++.|.. ..-.+.+.+.|...|+...   ..-+.+ +..+..|. +++++    .. -+.|    . .-+|++||+| 
T Consensus       253 ~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~~r~-~~~f~~g~~~vLvat~s~T~~~~~GiDip~~v~~VI~~~~p~  331 (414)
T 3oiy_A          253 DGILIFAQTEEEGKELYEYLKRFKFNVGETWSEFEKN-FEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPS  331 (414)
T ss_dssp             SSEEEEESSHHHHHHHHHHHHHTTCCEEESSSCHHHH-HHHHHTTSCSEEEEECCTTCCCCCCCCCTTTCCEEEEESCCT
T ss_pred             CCEEEEECCHHHHHHHHHHHHHcCCceehhhcCcchH-HHHHhCCCCeEEEEecCcCchhhccCccccccCEEEEECCCC
Confidence            34455544 4677888888988887653   122444 66676663 55555    11 1233    1 3479999999 


Q ss_pred             -CChhHHHHhhccCCCCC----CCCceEEEECCCcHHHHHHHHHHHH
Q psy7691         101 -NSSEDYIHRIGRTGRCA----SSGTAYTFFTPNNGKQAKELIAVLT  142 (165)
Q Consensus       101 -~~~~~~i~r~gr~~r~~----~~g~~~~~~~p~~~~~~~~i~~~l~  142 (165)
                       .+..+|+||+||+||.|    +.|.+++++  .+...+..+.+.+.
T Consensus       332 ~~~~~~y~qr~GR~gR~g~~~~~~g~~i~~~--~~~~~~~~l~~~~~  376 (414)
T 3oiy_A          332 GPDVYTYIQASGRSSRILNGVLVKGVSVIFE--EDEEIFESLKTRLL  376 (414)
T ss_dssp             TTCHHHHHHHHGGGCCEETTEECCEEEEEEC--CCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhCccccCCCCCCcceEEEEEE--ccHHHHHHHHHHhc
Confidence             89999999999999998    478788777  66788888888888

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=98.26  E-value=5.5e-07  Score=83.40  Aligned_cols=72  Identities=15%  Similarity=0.180  Sum_probs=58.3

Q ss_pred             HhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHH
Q psy7691          56 KGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAK  135 (165)
Q Consensus        56 ~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~  135 (165)
                      ...+|. ++++|.+|++.+..|.+++++++||+|||+++.   +|     ..+.+.       .|..+++++|+ +.++.
T Consensus        81 ~~~~f~-L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~---la-----i~~~l~-------~g~rvL~l~Pt-kaLa~  143 (1010)
T 2xgj_A           81 RTYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAE---YA-----IAQSLK-------NKQRVIYTSPI-KALSN  143 (1010)
T ss_dssp             CCCSSC-CCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHH---HH-----HHHHHH-------TTCEEEEEESS-HHHHH
T ss_pred             HhCCCC-CCHHHHHHHHHHHcCCCEEEECCCCCChHHHHH---HH-----HHHHhc-------cCCeEEEECCh-HHHHH
Confidence            445886 999999999999999999999999999999876   55     444442       23578899998 88888


Q ss_pred             HHHHHHHhc
Q psy7691         136 ELIAVLTEA  144 (165)
Q Consensus       136 ~i~~~l~~~  144 (165)
                      |..+.+...
T Consensus       144 Q~~~~l~~~  152 (1010)
T 2xgj_A          144 QKYRELLAE  152 (1010)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            888777653

>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=98.23  E-value=6.7e-07  Score=70.71  Aligned_cols=109  Identities=11%  Similarity=0.040  Sum_probs=69.2

Q ss_pred             HHHHHHHhhcCcEEecCCCCCCccccccCCCc-HHHHHHHHhCCC------CCCchHHHHHHHHHHcCCCeeeecccCCc
Q psy7691          17 SEVEAFRQKKEITVKGNNIPCPTQELTEGCFP-NAVLQHLKGQGF------EEPTAIQAQGWPIALSGRDMVGIAQTGSG   89 (165)
Q Consensus        17 ~~~~~~~~~~~i~~~~~~~p~~i~~f~~l~l~-~~l~~~l~~~g~------~~~t~~Q~~a~~~~l~G~di~~~a~tgsG   89 (165)
                      +++..+.+.+++.+...+...+...     +. ...-+++....+      -.++++|.++++.++.+.+.+++++||+|
T Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~f~~~~~~~~~~~~~~~~~l~~~Q~~ai~~~l~~~~~ll~~~tGsG  140 (282)
T 1rif_A           66 GQIKKFCDNFGYKAWIDPQINEKEE-----LSRKDFDEWLSKLEIYSGNKRIEPHWYQKDAVFEGLVNRRRILNLPTSAG  140 (282)
T ss_dssp             GGHHHHHHHTTCCEEECGGGGCCCC-----CCHHHHHHHHHTCCCEETTEECCCCHHHHHHHHHHHHHSEEEECCCTTSC
T ss_pred             HHHHHHHHhcCCeeEecCccCCCCC-----CCHHHHHhHHhHHHHhcCCCccCccHHHHHHHHHHHhcCCeEEEcCCCCC
Confidence            4555555666665554332222111     22 233334443444      26899999999999888888889999999


Q ss_pred             ccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcC
Q psy7691          90 KTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus        90 Kt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~  145 (165)
                      ||.+++   ++     ..+.+.+      .+..+++++|+ +.++.|..+.+..-.
T Consensus       141 KT~~~~---~~-----~~~~~~~------~~~~~lil~Pt-~~L~~q~~~~l~~~~  181 (282)
T 1rif_A          141 RSLIQA---LL-----ARYYLEN------YEGKILIIVPT-TALTTQMADDFVDYR  181 (282)
T ss_dssp             HHHHHH---HH-----HHHHHHH------CSSEEEEECSS-HHHHHHHHHHHHHHT
T ss_pred             cHHHHH---HH-----HHHHHHc------CCCeEEEEECC-HHHHHHHHHHHHHhc
Confidence            999876   43     2222211      11258888898 888888888777654

>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=98.22  E-value=4.5e-07  Score=73.51  Aligned_cols=105  Identities=26%  Similarity=0.348  Sum_probs=71.4

Q ss_pred             Cccccc-cCCCcHHHHHHHHhCCCCC-------CchHHHHHHHHHHcCC-Ceeeecc-cCCcc----cceeeecCCCC--
Q psy7691          38 PTQELT-EGCFPNAVLQHLKGQGFEE-------PTAIQAQGWPIALSGR-DMVGIAQ-TGSGK----TLAVINFDYPN--  101 (165)
Q Consensus        38 ~i~~f~-~l~l~~~l~~~l~~~g~~~-------~t~~Q~~a~~~~l~G~-di~~~a~-tgsGK----t~~~~~~~lP~--  101 (165)
                      .++.|. .....+.+.+.|...|+..       +...+...+..+..|. +++++.. -+.|=    ...+++||+|.  
T Consensus       245 ~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~  324 (395)
T 3pey_A          245 SSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLA  324 (395)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGGGSSSCCCTTEEEEEESSCCBCT
T ss_pred             CEEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECChhhcCCCcccCCEEEEcCCCCCC
Confidence            344444 4567788888898887753       2234445555566553 3433322 22332    22789999998  


Q ss_pred             ----ChhHHHHhhccCCCCCCCCceEEEECCCc-HHHHHHHHHHHH
Q psy7691         102 ----SSEDYIHRIGRTGRCASSGTAYTFFTPNN-GKQAKELIAVLT  142 (165)
Q Consensus       102 ----~~~~~i~r~gr~~r~~~~g~~~~~~~p~~-~~~~~~i~~~l~  142 (165)
                          +..+|+||+||+||.|..|.+++++.+.+ ......+.+.+.
T Consensus       325 ~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~  370 (395)
T 3pey_A          325 NGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFG  370 (395)
T ss_dssp             TSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHHHHTT
T ss_pred             cCCCCHHHhhHhccccccCCCCceEEEEEechHHHHHHHHHHHHhC
Confidence                88999999999999999999999998764 455666666665

>4gl2_A Interferon-induced helicase C domain-containing P; MDA5, dsRNA, anti-viral signaling, RIG-I, MAVS, oligomerizat helicase, ATPase; HET: ANP; 3.56A {Homo sapiens}

Probab=98.22  E-value=1.8e-07  Score=82.42  Aligned_cols=73  Identities=18%  Similarity=0.167  Sum_probs=54.1

Q ss_pred             CCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHH-HHH
Q psy7691          62 EPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL-IAV  140 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i-~~~  140 (165)
                      .|++.|.++++.++.|.|++++++||+|||+++.   +|     .++.+.+. +....+..+++++|+ +.++.|. .+.
T Consensus         7 ~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~---~~-----i~~~l~~~-~~~~~~~~vlvl~P~-~~L~~Q~~~~~   76 (699)
T 4gl2_A            7 QLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAV---YI-----AKDHLDKK-KKASEPGKVIVLVNK-VLLVEQLFRKE   76 (699)
T ss_dssp             CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHH---HH-----HHHHHHHH-HHHTCCCCBCCEESC-SHHHHHHHHHT
T ss_pred             CccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHH---HH-----HHHHHHhc-cccCCCCeEEEEECC-HHHHHHHHHHH
Confidence            4899999999999999999999999999999988   77     44443221 111223457788998 7777777 665


Q ss_pred             HHhc
Q psy7691         141 LTEA  144 (165)
Q Consensus       141 l~~~  144 (165)
                      +...
T Consensus        77 l~~~   80 (699)
T 4gl2_A           77 FQPF   80 (699)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5543

>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=98.21  E-value=3.8e-07  Score=79.93  Aligned_cols=97  Identities=15%  Similarity=0.110  Sum_probs=66.3

Q ss_pred             Cccccc-cCCCcHHHHHHHHhCCCCC------Cc-hHHHHHHHHHHcCC-Ceee-ecccCCccc----ceeeecCCCCCh
Q psy7691          38 PTQELT-EGCFPNAVLQHLKGQGFEE------PT-AIQAQGWPIALSGR-DMVG-IAQTGSGKT----LAVINFDYPNSS  103 (165)
Q Consensus        38 ~i~~f~-~l~l~~~l~~~l~~~g~~~------~t-~~Q~~a~~~~l~G~-di~~-~a~tgsGKt----~~~~~~~lP~~~  103 (165)
                      +++.|. ...-.+.+.+.|...|+..      .+ ..+......+..|. +|++ +..-|.|-.    -.|++|++|.+.
T Consensus       269 ~~IVf~~sr~~~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~a~~~GID~p~V~~VI~~~~p~s~  348 (591)
T 2v1x_A          269 SGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSM  348 (591)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTTSCTTCCCSCEEEEEESSCCSSH
T ss_pred             CeEEEeCcHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhcCCCcccccEEEEeCCCCCH
Confidence            344454 4467788888898888743      22 23444555566663 3332 222233422    279999999999


Q ss_pred             hHHHHhhccCCCCCCCCceEEEECCCcHHHH
Q psy7691         104 EDYIHRIGRTGRCASSGTAYTFFTPNNGKQA  134 (165)
Q Consensus       104 ~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~  134 (165)
                      +.|+||+||+||.|..|.+++++.+.+...+
T Consensus       349 ~~y~Qr~GRaGR~G~~g~~i~l~~~~D~~~~  379 (591)
T 2v1x_A          349 ENYYQESGRAGRDDMKADCILYYGFGDIFRI  379 (591)
T ss_dssp             HHHHHHHTTSCTTSSCEEEEEEECHHHHHHH
T ss_pred             HHHHHHhccCCcCCCCceEEEEEChHHHHHH
Confidence            9999999999999999999999988764433

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=98.18  E-value=7.7e-07  Score=78.42  Aligned_cols=111  Identities=17%  Similarity=0.134  Sum_probs=72.7

Q ss_pred             Cccccc-cCCCcHHHHHHHHhCCCCCCc---hHHHH--------------HHHHHHcCCCeeeecc---cC---------
Q psy7691          38 PTQELT-EGCFPNAVLQHLKGQGFEEPT---AIQAQ--------------GWPIALSGRDMVGIAQ---TG---------   87 (165)
Q Consensus        38 ~i~~f~-~l~l~~~l~~~l~~~g~~~~t---~~Q~~--------------a~~~~l~G~di~~~a~---tg---------   87 (165)
                      .++.|. +..-.+.+.+.|...|+....   ..+.+              |++.+.+|.|+. +.-   .|         
T Consensus       357 ~~LVF~~s~~~a~~l~~~L~~~g~~v~~lhg~~R~~~l~~F~~g~~~VLVaTdv~~rGiDi~-v~~VId~g~~~~P~~~~  435 (618)
T 2whx_A          357 KTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTFDTEYPKTKLTDWDFVVTTDISEMGANFR-AGRVIDPRRCLKPVILT  435 (618)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHTTCCEEEECTTTHHHHTTHHHHSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEEEC
T ss_pred             CEEEEECChhHHHHHHHHHHHcCCcEEEEChHHHHHHHHhhcCCCcEEEEECcHHHcCcccC-ceEEEECcceecceecc
Confidence            344554 446777888888888775321   11222              344445666553 110   00         


Q ss_pred             CcccceeeecCCCCChhHHHHhhccCCCCCC-CCceEEEEC---CCcHHHHHHHHHHHHhcCCCCC
Q psy7691          88 SGKTLAVINFDYPNSSEDYIHRIGRTGRCAS-SGTAYTFFT---PNNGKQAKELIAVLTEASQPIP  149 (165)
Q Consensus        88 sGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~-~g~~~~~~~---p~~~~~~~~i~~~l~~~~~~~p  149 (165)
                      ...+-.++|||+|.+.++|+||+||+||.|. .|.++++++   +.+...+..+++.+.....++|
T Consensus       436 ~~~~~~~i~~d~P~s~~~yiQR~GRaGR~g~~~G~ai~l~~~~~~~d~~~l~~le~~i~l~~~~~~  501 (618)
T 2whx_A          436 DGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHWTEAKMLLDNIYTP  501 (618)
T ss_dssp             SSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTCHHHHHHHHHHTTCCCT
T ss_pred             cCCCceEEcccccCCHHHHHHhccccCCCCCCCCeEEEEccCCchhhHHHHHHHHhHhccccccCC
Confidence            0111234899999999999999999999975 899999998   7777788888887766555554

>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=98.18  E-value=4.4e-07  Score=78.24  Aligned_cols=98  Identities=19%  Similarity=0.261  Sum_probs=66.8

Q ss_pred             Cccccc-cCCCcHHHHHHHHhCCCCC------Cch-HHHHHHHHHHcCC-Ceeee-cccCCcc----cceeeecCCCCCh
Q psy7691          38 PTQELT-EGCFPNAVLQHLKGQGFEE------PTA-IQAQGWPIALSGR-DMVGI-AQTGSGK----TLAVINFDYPNSS  103 (165)
Q Consensus        38 ~i~~f~-~l~l~~~l~~~l~~~g~~~------~t~-~Q~~a~~~~l~G~-di~~~-a~tgsGK----t~~~~~~~lP~~~  103 (165)
                      +++.|. +..-.+.+.+.|...|+..      .++ ........+..|. +++++ ..-|.|-    .-.|++|++|.+.
T Consensus       238 ~~IVf~~sr~~~e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a~~~GiD~p~v~~VI~~~~p~s~  317 (523)
T 1oyw_A          238 SGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNI  317 (523)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCTTCCEEEESSCCSSH
T ss_pred             cEEEEeCCHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhCCCCccCccEEEEECCCCCH
Confidence            344454 4467788888898887743      222 2334455566664 33322 2234442    2379999999999


Q ss_pred             hHHHHhhccCCCCCCCCceEEEECCCcHHHHH
Q psy7691         104 EDYIHRIGRTGRCASSGTAYTFFTPNNGKQAK  135 (165)
Q Consensus       104 ~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~  135 (165)
                      ++|+||+||+||.|..|.+++++.+.+.....
T Consensus       318 ~~y~Qr~GRaGR~g~~~~~~l~~~~~d~~~~~  349 (523)
T 1oyw_A          318 ESYYQETGRAGRDGLPAEAMLFYDPADMAWLR  349 (523)
T ss_dssp             HHHHHHHTTSCTTSSCEEEEEEECHHHHHHHH
T ss_pred             HHHHHHhccccCCCCCceEEEEeCHHHHHHHH
Confidence            99999999999999999999999887654433

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=98.15  E-value=2.6e-06  Score=71.68  Aligned_cols=63  Identities=21%  Similarity=0.149  Sum_probs=52.0

Q ss_pred             CCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVL  141 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l  141 (165)
                      .+++.|.++++.++.+.+++++++||+|||+.++   ++      +...         +..+++++|+ +.++.|..+.+
T Consensus        93 ~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l---~~------i~~~---------~~~~Lvl~P~-~~L~~Q~~~~~  153 (472)
T 2fwr_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAM---AA------INEL---------STPTLIVVPT-LALAEQWKERL  153 (472)
T ss_dssp             CBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHH---HH------HHHH---------CSCEEEEESS-HHHHHHHHHHG
T ss_pred             CcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHH---HH------HHHc---------CCCEEEEECC-HHHHHHHHHHH
Confidence            5899999999999999999999999999999876   44      2222         3468888898 88888888887


Q ss_pred             Hh
Q psy7691         142 TE  143 (165)
Q Consensus       142 ~~  143 (165)
                      ..
T Consensus       154 ~~  155 (472)
T 2fwr_A          154 GI  155 (472)
T ss_dssp             GG
T ss_pred             Hh
Confidence            76

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=98.13  E-value=5.4e-06  Score=77.67  Aligned_cols=84  Identities=19%  Similarity=0.122  Sum_probs=62.8

Q ss_pred             CCcHHHHHHHH-hCCCCCCchHHHHHHHHHHc----CC--CeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCC
Q psy7691          46 CFPNAVLQHLK-GQGFEEPTAIQAQGWPIALS----GR--DMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCAS  118 (165)
Q Consensus        46 ~l~~~l~~~l~-~~g~~~~t~~Q~~a~~~~l~----G~--di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~  118 (165)
                      ..+..+.+.+. ..+|. +|+.|.+|++.++.    |.  |++++++||+|||++++   ++     ....+       .
T Consensus       587 ~~~~~~~~~~~~~f~~~-~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val---~a-----a~~~~-------~  650 (1151)
T 2eyq_A          587 KHDREQYQLFCDSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAM---RA-----AFLAV-------D  650 (1151)
T ss_dssp             CCCHHHHHHHHHTCCSC-CCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHH---HH-----HHHHH-------T
T ss_pred             CCCHHHHHHHHHhCCCC-CCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHH---HH-----HHHHH-------H
Confidence            45566666654 46997 79999999999876    65  99999999999998766   44     22222       1


Q ss_pred             CCceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         119 SGTAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       119 ~g~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      .|..+++++|+ +.++.|..+.+.....
T Consensus       651 ~g~~vlvlvPt-~~La~Q~~~~~~~~~~  677 (1151)
T 2eyq_A          651 NHKQVAVLVPT-TLLAQQHYDNFRDRFA  677 (1151)
T ss_dssp             TTCEEEEECSS-HHHHHHHHHHHHHHST
T ss_pred             hCCeEEEEech-HHHHHHHHHHHHHHhh
Confidence            34578999999 8889888888876443

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=98.11  E-value=1.6e-06  Score=80.27  Aligned_cols=72  Identities=19%  Similarity=0.165  Sum_probs=56.5

Q ss_pred             hCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHH
Q psy7691          57 GQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKE  136 (165)
Q Consensus        57 ~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~  136 (165)
                      ..+|. ++++|.++++.++.|.|++++++||+|||+++.   +|     +..-. +      .|..+++++|+ +.++.|
T Consensus        35 ~~~f~-l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~---~~-----i~~~~-~------~g~~vlvl~Pt-raLa~Q   97 (997)
T 4a4z_A           35 SWPFE-LDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAE---YA-----IAMAH-R------NMTKTIYTSPI-KALSNQ   97 (997)
T ss_dssp             CCSSC-CCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHH---HH-----HHHHH-H------TTCEEEEEESC-GGGHHH
T ss_pred             hCCCC-CCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHH---HH-----HHHHH-h------cCCeEEEEeCC-HHHHHH
Confidence            45786 899999999999999999999999999998765   44     22221 1      34567888998 888888


Q ss_pred             HHHHHHhcC
Q psy7691         137 LIAVLTEAS  145 (165)
Q Consensus       137 i~~~l~~~~  145 (165)
                      +.+.+....
T Consensus        98 ~~~~l~~~~  106 (997)
T 4a4z_A           98 KFRDFKETF  106 (997)
T ss_dssp             HHHHHHTTC
T ss_pred             HHHHHHHHc
Confidence            888887643

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=98.08  E-value=5.4e-06  Score=64.33  Aligned_cols=63  Identities=21%  Similarity=0.149  Sum_probs=50.4

Q ss_pred             CCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVL  141 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l  141 (165)
                      .+++.|.+++..++.+.+++++++||+|||..++   .+      +.+.         +..+++++|+ +.++.|+.+.+
T Consensus        93 ~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~---~~------~~~~---------~~~~liv~P~-~~L~~q~~~~~  153 (237)
T 2fz4_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAM---AA------INEL---------STPTLIVVPT-LALAEQWKERL  153 (237)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHH---HH------HHHS---------CSCEEEEESS-HHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHH---HH------HHHc---------CCCEEEEeCC-HHHHHHHHHHH
Confidence            5789999999999999999999999999999765   32      2222         2357888888 78888888877


Q ss_pred             Hh
Q psy7691         142 TE  143 (165)
Q Consensus       142 ~~  143 (165)
                      ..
T Consensus       154 ~~  155 (237)
T 2fz4_A          154 GI  155 (237)
T ss_dssp             GG
T ss_pred             Hh
Confidence            76

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=98.05  E-value=1.4e-06  Score=73.52  Aligned_cols=57  Identities=23%  Similarity=0.241  Sum_probs=46.5

Q ss_pred             eeecCCCCChhHHHHhhccCCCC-CCCCceEEEE---CCCcHHHHHHHHHHHHhcCCCCCh
Q psy7691          94 VINFDYPNSSEDYIHRIGRTGRC-ASSGTAYTFF---TPNNGKQAKELIAVLTEASQPIPP  150 (165)
Q Consensus        94 ~~~~~lP~~~~~~i~r~gr~~r~-~~~g~~~~~~---~p~~~~~~~~i~~~l~~~~~~~p~  150 (165)
                      +++|+.|.+..+|+||+||+||. +..|.+++++   ++.+...+..+...+.....++|.
T Consensus       263 vi~~~~p~~~~~~~Qr~GR~GR~g~~~g~~~~l~~~~~~~~~~~l~~l~~~~~~~~~~l~~  323 (440)
T 1yks_A          263 AIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPTSENNAHHVCWLEASMLLDNMEVRG  323 (440)
T ss_dssp             EEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTBHHHHHHHHHHTTSCCGG
T ss_pred             eeccccccCHHHHHHhccccCCCCCCCceEEEEeccCChhhhhhhhhhhHHhccccccccc
Confidence            34699999999999999999998 6899999996   677777778888877666666643

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*

Probab=98.04  E-value=1.2e-05  Score=72.92  Aligned_cols=53  Identities=15%  Similarity=0.261  Sum_probs=43.3

Q ss_pred             ceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHH----HHHHHHHHHhc
Q psy7691          92 LAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQ----AKELIAVLTEA  144 (165)
Q Consensus        92 ~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~----~~~i~~~l~~~  144 (165)
                      ++||||++|.+...|+||+||+||.|..|.+..|+++.+..+    ...+...+...
T Consensus       546 l~VI~te~pes~riy~qr~GRTGRqGd~G~s~~fls~eD~l~r~f~~~~~~~~~~~~  602 (853)
T 2fsf_A          546 LHIIGTERHESRRIDNQLRGRSGRQGDAGSSRFYLSMEDALMRIFASDRVSGMMRKL  602 (853)
T ss_dssp             EEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSGGGGTTCCHHHHTTGGGG
T ss_pred             cEEEEccCCCCHHHHHhhccccccCCCCeeEEEEecccHHHHHHhhHHHHHHHHHhh
Confidence            489999999999999999999999999999999999886322    23454455443

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=98.03  E-value=3.1e-06  Score=79.03  Aligned_cols=42  Identities=17%  Similarity=0.173  Sum_probs=33.5

Q ss_pred             ChhHHHHhhccCCCCCCCC--ceEEEECCCcHHHHHHHHHHHHh
Q psy7691         102 SSEDYIHRIGRTGRCASSG--TAYTFFTPNNGKQAKELIAVLTE  143 (165)
Q Consensus       102 ~~~~~i~r~gr~~r~~~~g--~~~~~~~p~~~~~~~~i~~~l~~  143 (165)
                      +.++|+||+|||||.+..|  ..++++...+..++..|.+.+..
T Consensus       461 d~~tYihr~GRtgR~~~gg~~~Glsi~~~~d~~~~~~l~~~~~~  504 (1104)
T 4ddu_A          461 DVYTYIQASGRSSRILNGVLVKGVSVIFEEDEEIFESLKTRLLL  504 (1104)
T ss_dssp             CHHHHHHHHHTTCCEETTEECCEEEEEECCCHHHHHHHHHHHHH
T ss_pred             ChhhhhcccCchhcccCCCcccceEEEEEecHHHHHHHHHHHhh
Confidence            7789999999999976544  45666677888888888888863

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=98.02  E-value=2.9e-06  Score=73.44  Aligned_cols=68  Identities=18%  Similarity=0.031  Sum_probs=54.1

Q ss_pred             CCCCCchHHHHHHHH----HHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHH
Q psy7691          59 GFEEPTAIQAQGWPI----ALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQA  134 (165)
Q Consensus        59 g~~~~t~~Q~~a~~~----~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~  134 (165)
                      || .+.+.|.+.+..    +..|.|+++.|+||+|||++|+   +|     .++          .+..+++++|+ ++++
T Consensus         1 ~~-~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l---~p-----~l~----------~~~~v~i~~pt-~~l~   60 (551)
T 3crv_A            1 MV-KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSL---LV-----SLE----------VKPKVLFVVRT-HNEF   60 (551)
T ss_dssp             CC-SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHH---HH-----HHH----------HCSEEEEEESS-GGGH
T ss_pred             CC-CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHH---HH-----HHh----------CCCeEEEEcCC-HHHH
Confidence            45 478999886653    4688999999999999999999   88     554          24578999999 8888


Q ss_pred             HHHHHHHHhcCC
Q psy7691         135 KELIAVLTEASQ  146 (165)
Q Consensus       135 ~~i~~~l~~~~~  146 (165)
                      .|+.+-+.....
T Consensus        61 ~q~~~~~~~l~~   72 (551)
T 3crv_A           61 YPIYRDLTKIRE   72 (551)
T ss_dssp             HHHHHHHTTCCC
T ss_pred             HHHHHHHHHHhh
Confidence            899888876644

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.00  E-value=4e-06  Score=72.55  Aligned_cols=67  Identities=18%  Similarity=0.097  Sum_probs=49.6

Q ss_pred             CCCCCCchHHHHHHH----HHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHH
Q psy7691          58 QGFEEPTAIQAQGWP----IALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQ  133 (165)
Q Consensus        58 ~g~~~~t~~Q~~a~~----~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~  133 (165)
                      .|| .+++.|.+++.    .+..|.|+++.++||+|||++++   +|     .++.          +..+++++|+ +.+
T Consensus         4 ~~~-~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l---~~-----~~~~----------~~~~~~~~~t-~~l   63 (540)
T 2vl7_A            4 LKL-QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVE---VL-----GMQL----------KKKVLIFTRT-HSQ   63 (540)
T ss_dssp             ------CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHH---HH-----HHHH----------TCEEEEEESC-HHH
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHH---HH-----HHhC----------CCcEEEEcCC-HHH
Confidence            478 68999998754    44688999999999999999988   77     3332          3478888898 888


Q ss_pred             HHHHHHHHHhc
Q psy7691         134 AKELIAVLTEA  144 (165)
Q Consensus       134 ~~~i~~~l~~~  144 (165)
                      +.|+.+-+...
T Consensus        64 ~~q~~~~~~~l   74 (540)
T 2vl7_A           64 LDSIYKNAKLL   74 (540)
T ss_dssp             HHHHHHHHGGG
T ss_pred             HHHHHHHHHhc
Confidence            88888877663

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=98.00  E-value=3.1e-06  Score=71.86  Aligned_cols=68  Identities=13%  Similarity=0.070  Sum_probs=54.5

Q ss_pred             CCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVL  141 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l  141 (165)
                      .+++.|.+|++.++.+.|++++++||+|||+.++   +|     ....+..      .+..+++++|+ +.++.|..+.+
T Consensus       113 ~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~---~~-----~~~~~~~------~~~~vlvl~P~-~~L~~Q~~~~~  177 (510)
T 2oca_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQA---LL-----ARYYLEN------YEGKILIIVPT-TALTTQMADDF  177 (510)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHH---HH-----HHHHHHH------CSSEEEEEESS-HHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHH---HH-----HHHHHhC------CCCeEEEEECc-HHHHHHHHHHH
Confidence            6899999999999999999999999999999887   55     3333311      11278899998 88888888888


Q ss_pred             Hhc
Q psy7691         142 TEA  144 (165)
Q Consensus       142 ~~~  144 (165)
                      ..-
T Consensus       178 ~~~  180 (510)
T 2oca_A          178 VDY  180 (510)
T ss_dssp             HHT
T ss_pred             HHh
Confidence            665

>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=97.98  E-value=2.4e-06  Score=72.56  Aligned_cols=94  Identities=13%  Similarity=0.132  Sum_probs=43.4

Q ss_pred             CCccccccC-CCcHHHHHHHHhC------------CCC-------CCchHHHHHHHHHHc-C-CCeeeeccc-CCcc---
Q psy7691          37 CPTQELTEG-CFPNAVLQHLKGQ------------GFE-------EPTAIQAQGWPIALS-G-RDMVGIAQT-GSGK---   90 (165)
Q Consensus        37 ~~i~~f~~l-~l~~~l~~~l~~~------------g~~-------~~t~~Q~~a~~~~l~-G-~di~~~a~t-gsGK---   90 (165)
                      ..++.|.+. ...+.+.+.|...            |..       .+...+..++..+.. | .+++++... +.|=   
T Consensus       391 ~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~GiDip  470 (556)
T 4a2p_A          391 TRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIV  470 (556)
T ss_dssp             CCEEEEESSHHHHHHHHHHHTTCSGGGSCCEEC------------------------------CCEEEEEC---------
T ss_pred             ceEEEEEccHHHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHhcccCceEEEEEcCchhcCCCch
Confidence            456666654 5666777777654            221       122233445555555 4 234332221 2222   


Q ss_pred             -cceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHH
Q psy7691          91 -TLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGK  132 (165)
Q Consensus        91 -t~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~  132 (165)
                       .-+|++||+|.+..+|+||+|| ||. +.|.++.++++.+.+
T Consensus       471 ~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~  511 (556)
T 4a2p_A          471 QCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVV  511 (556)
T ss_dssp             --CEEEEETCCSCHHHHHHC----------CCEEEEESCHHHH
T ss_pred             hCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCcchH
Confidence             1279999999999999999999 998 889999999887643

>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=97.98  E-value=5e-06  Score=68.48  Aligned_cols=67  Identities=16%  Similarity=0.166  Sum_probs=52.6

Q ss_pred             CCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVL  141 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l  141 (165)
                      .|++.|.++++.++.+ ++++.++||+|||+.++   ++     ..+.+.      ..+..+++++|+ +.++.|..+.+
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~---~~-----~~~~~~------~~~~~~liv~P~-~~L~~q~~~~~   72 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAM---MI-----AEYRLT------KYGGKVLMLAPT-KPLVLQHAESF   72 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHH---HH-----HHHHHH------HSCSCEEEECSS-HHHHHHHHHHH
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHH---HH-----HHHHHh------cCCCeEEEEECC-HHHHHHHHHHH
Confidence            4899999999999999 99999999999999887   55     333332      123468899998 78888777777


Q ss_pred             Hhc
Q psy7691         142 TEA  144 (165)
Q Consensus       142 ~~~  144 (165)
                      ...
T Consensus        73 ~~~   75 (494)
T 1wp9_A           73 RRL   75 (494)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>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=97.94  E-value=5e-05  Score=69.27  Aligned_cols=54  Identities=20%  Similarity=0.233  Sum_probs=44.8

Q ss_pred             ceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHH----HHHHHHHHhcC
Q psy7691          92 LAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQA----KELIAVLTEAS  145 (165)
Q Consensus        92 ~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~----~~i~~~l~~~~  145 (165)
                      ++||||++|.+...|+||+||+||.|..|.+..|+++.+.-+-    ..+..++....
T Consensus       580 lhVI~te~pes~riy~qr~GRTGRqGdpG~s~fflSleD~l~r~f~~~~~~~~~~~~~  637 (922)
T 1nkt_A          580 LYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGDELMRRFNGAALETLLTRLN  637 (922)
T ss_dssp             EEEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTSHHHHHTTHHHHHHHHHHTT
T ss_pred             cEEEeccCCCCHHHHHHHhcccccCCCCeeEEEEechhHHHHHHhhhHHHHHHHHHhC
Confidence            5899999999999999999999999999999999998864332    35666665543

>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=97.89  E-value=5.3e-06  Score=77.08  Aligned_cols=43  Identities=21%  Similarity=0.325  Sum_probs=38.0

Q ss_pred             CChhHHHHhhccCCCCCCCC--ceEEEECCCcHHHHHHHHHHHHh
Q psy7691         101 NSSEDYIHRIGRTGRCASSG--TAYTFFTPNNGKQAKELIAVLTE  143 (165)
Q Consensus       101 ~~~~~~i~r~gr~~r~~~~g--~~~~~~~p~~~~~~~~i~~~l~~  143 (165)
                      .+..+|+||+||+||.|..|  .+++++.+.+...+..+.+.+..
T Consensus       424 ~~~~~yiQr~GRagR~g~~g~~~g~~~~~~~d~~~~~~l~~~l~~  468 (1054)
T 1gku_B          424 PDLRTYIQGSGRTSRLFAGGLTKGASFLLEDDSELLSAFIERAKL  468 (1054)
T ss_dssp             ECHHHHHHHHHTTCCEETTEECCEEEEEECSCHHHHHHHHHHHHT
T ss_pred             CcHHHHhhhhchhhhccCCCCceEEEEEEecCHHHHHHHHHHHhh
Confidence            68999999999999988776  48889999888899999988886

>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=97.87  E-value=5.7e-06  Score=69.90  Aligned_cols=91  Identities=20%  Similarity=0.182  Sum_probs=55.1

Q ss_pred             Ccccccc-CCCcHHHHHHHHhCCCCCC---chHHHHHHHHHHcCC-Ceeeecc-cCCccc---ceeeecC----------
Q psy7691          38 PTQELTE-GCFPNAVLQHLKGQGFEEP---TAIQAQGWPIALSGR-DMVGIAQ-TGSGKT---LAVINFD----------   98 (165)
Q Consensus        38 ~i~~f~~-l~l~~~l~~~l~~~g~~~~---t~~Q~~a~~~~l~G~-di~~~a~-tgsGKt---~~~~~~~----------   98 (165)
                      +++.|.. ..-.+.+.+.|...|+...   ...+...+..+..|. +++++.. -+.|=+   ..|+|||          
T Consensus       190 ~~lVF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~~~~~f~~g~~~vLVaT~v~~~GiDip~~~VI~~~~~~~~~~d~~  269 (451)
T 2jlq_A          190 KTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTFDTEYPKTKLTDWDFVVTTDISEMGANFRAGRVIDPRRCLKPVILTD  269 (451)
T ss_dssp             CEEEECSSHHHHHHHHHHHHTTTCCEEEECTTTHHHHGGGGGSSCCSEEEECGGGGSSCCCCCSEEEECCEEEEEEEECS
T ss_pred             CEEEEcCCHHHHHHHHHHHHHcCCeEEECCHHHHHHHHHhhccCCceEEEECCHHHhCcCCCCCEEEECCCccccccccc
Confidence            4445543 4567788888888777531   112333333333342 2222111 111111   3789988          


Q ss_pred             ----------CCCChhHHHHhhccCCCCCC-CCceEEEECC
Q psy7691          99 ----------YPNSSEDYIHRIGRTGRCAS-SGTAYTFFTP  128 (165)
Q Consensus        99 ----------lP~~~~~~i~r~gr~~r~~~-~g~~~~~~~p  128 (165)
                                .|.+..+|+||+||+||.|. .|.++++...
T Consensus       270 ~~~~l~~~~~~p~s~~~y~Qr~GRaGR~g~~~g~~~~~~~~  310 (451)
T 2jlq_A          270 GPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGD  310 (451)
T ss_dssp             SSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSC
T ss_pred             ccceeeecccccCCHHHHHHhccccCCCCCCCccEEEEeCC
Confidence                      99999999999999999998 7777666543

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=97.87  E-value=6.4e-06  Score=73.29  Aligned_cols=52  Identities=19%  Similarity=0.193  Sum_probs=40.1

Q ss_pred             cCCCCChhHHHHhhccCCCC-CCCCceEEEE---CCCcHHHHHHHHHHHHhcCCCC
Q psy7691          97 FDYPNSSEDYIHRIGRTGRC-ASSGTAYTFF---TPNNGKQAKELIAVLTEASQPI  148 (165)
Q Consensus        97 ~~lP~~~~~~i~r~gr~~r~-~~~g~~~~~~---~p~~~~~~~~i~~~l~~~~~~~  148 (165)
                      ||+|.+.++|+||+||+||. +..|.+++++   .+.+...+..++..+.....++
T Consensus       500 ~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~~~~~~~d~~~l~~ie~~~~l~~~~~  555 (673)
T 2wv9_A          500 VPSAITSASAAQRRGRVGRNPSQIGDEYHYGGGTSEDDTMLAHWTEAKILLDNIHL  555 (673)
T ss_dssp             CSEECCHHHHHHHHTTSSCCSSCCCEEEEECSCCCCCCTTBHHHHHHHHHHHTSCB
T ss_pred             ccCCCCHHHHHHHhhccCCCCCCCCEEEEEEecCChhHHHHHHHHHHHHhhhhccC
Confidence            78999999999999999999 7899999996   5666666666666554433333

>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=97.85  E-value=2.8e-06  Score=72.00  Aligned_cols=55  Identities=20%  Similarity=0.162  Sum_probs=44.8

Q ss_pred             HHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHH
Q psy7691          73 IALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLT  142 (165)
Q Consensus        73 ~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~  142 (165)
                      .+..|.|++++++||||||++|+   +|     +++++..      .+..+++++|+ ++++.|+.+.+.
T Consensus        17 ~l~~~~~vlv~a~TGsGKT~~~~---l~-----il~~~~~------~~~~~lvl~Pt-r~La~Q~~~~l~   71 (459)
T 2z83_A           17 MLRKRQMTVLDLHPGSGKTRKIL---PQ-----IIKDAIQ------QRLRTAVLAPT-RVVAAEMAEALR   71 (459)
T ss_dssp             GGSTTCEEEECCCTTSCTTTTHH---HH-----HHHHHHH------TTCCEEEEECS-HHHHHHHHHHTT
T ss_pred             HHhcCCcEEEECCCCCCHHHHHH---HH-----HHHHHHh------CCCcEEEECch-HHHHHHHHHHhc
Confidence            46778999999999999999988   78     7766532      24568888898 999999998876

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=97.83  E-value=1.4e-06  Score=73.84  Aligned_cols=99  Identities=13%  Similarity=0.165  Sum_probs=59.3

Q ss_pred             CCccccccC-CCcHHHHHHHHhCCC-------------------CCCchHHHHHHHHHHc-C-CCeeeeccc-CCccc--
Q psy7691          37 CPTQELTEG-CFPNAVLQHLKGQGF-------------------EEPTAIQAQGWPIALS-G-RDMVGIAQT-GSGKT--   91 (165)
Q Consensus        37 ~~i~~f~~l-~l~~~l~~~l~~~g~-------------------~~~t~~Q~~a~~~~l~-G-~di~~~a~t-gsGKt--   91 (165)
                      ..++.|.+. ...+.+.+.|...|+                   ..+...+..++..+.. | .+++++... +.|=.  
T Consensus       390 ~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~GlDlp  469 (555)
T 3tbk_A          390 TKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDNNILIATSVADEGIDIA  469 (555)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC--------------------------CCSEEEECCCTTCCEETT
T ss_pred             ceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHhcCCCeeEEEEcchhhcCCccc
Confidence            456667654 677788888887642                   1122344456666666 5 355544332 23422  


Q ss_pred             --ceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHH
Q psy7691          92 --LAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL  137 (165)
Q Consensus        92 --~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i  137 (165)
                        -.|++||+|.+..+|+||+|| ||. +.|.++.++++.+.+....+
T Consensus       470 ~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~~~~~~  515 (555)
T 3tbk_A          470 ECNLVILYEYVGNVIKMIQTRGR-GRA-RDSKCFLLTSSADVIEKEKA  515 (555)
T ss_dssp             SCSEEEEESCCSSCCCEECSSCC-CTT-TSCEEEEEESCHHHHHHHHH
T ss_pred             cCCEEEEeCCCCCHHHHHHhcCc-CcC-CCceEEEEEcCCCHHHHHHH
Confidence              279999999999999999999 898 88999999998875544444

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=97.82  E-value=8.5e-06  Score=71.79  Aligned_cols=67  Identities=15%  Similarity=0.150  Sum_probs=50.7

Q ss_pred             CchHHHHHHH----HHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHH
Q psy7691          63 PTAIQAQGWP----IALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELI  138 (165)
Q Consensus        63 ~t~~Q~~a~~----~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~  138 (165)
                      |.+.|.+.+.    .+..|.|+++.|+||+|||++++   +|     .+..+..      .+..+++++|+ ++++.|+.
T Consensus         4 ~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l---~p-----~l~~~~~------~~~kvli~t~T-~~l~~Qi~   68 (620)
T 4a15_A            4 NRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMAL---KS-----ALQYSSE------RKLKVLYLVRT-NSQEEQVI   68 (620)
T ss_dssp             -CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHH---HH-----HHHHHHH------HTCEEEEEESS-HHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHH---HH-----HHHhhhh------cCCeEEEECCC-HHHHHHHH
Confidence            6788877654    45789999999999999999999   88     5655532      23478889998 77888887


Q ss_pred             HHHHhc
Q psy7691         139 AVLTEA  144 (165)
Q Consensus       139 ~~l~~~  144 (165)
                      +-+...
T Consensus        69 ~el~~l   74 (620)
T 4a15_A           69 KELRSL   74 (620)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            766543

>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=97.79  E-value=5e-06  Score=70.14  Aligned_cols=56  Identities=16%  Similarity=0.150  Sum_probs=45.4

Q ss_pred             HHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHh
Q psy7691          73 IALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTE  143 (165)
Q Consensus        73 ~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~  143 (165)
                      .++.|+|++++++||||||++|+   +|     +++++..      .+..+++++|+ ++++.|+.+.+..
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l---~~-----~l~~~~~------~~~~~lil~Pt-r~La~Q~~~~l~~   59 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFL---PQ-----ILAECAR------RRLRTLVLAPT-RVVLSEMKEAFHG   59 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHH---HH-----HHHHHHH------TTCCEEEEESS-HHHHHHHHHHTTT
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHH---HH-----HHHHHHh------cCCeEEEEcch-HHHHHHHHHHHhc
Confidence            36789999999999999999987   77     6666533      24578888898 9999999988764

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=97.78  E-value=1.1e-06  Score=77.27  Aligned_cols=99  Identities=14%  Similarity=0.219  Sum_probs=46.2

Q ss_pred             CCccccccC-CCcHHHHHHHHhCC----CC--------------C-CchHHHHHHHHHHc-CC-Cee-eecccCCccc--
Q psy7691          37 CPTQELTEG-CFPNAVLQHLKGQG----FE--------------E-PTAIQAQGWPIALS-GR-DMV-GIAQTGSGKT--   91 (165)
Q Consensus        37 ~~i~~f~~l-~l~~~l~~~l~~~g----~~--------------~-~t~~Q~~a~~~~l~-G~-di~-~~a~tgsGKt--   91 (165)
                      ..++.|... ...+.+.+.|...|    +.              . +...|.+.+..+.. |. +++ +...-|.|=+  
T Consensus       399 ~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~~~vLVaT~v~~~GiDip  478 (696)
T 2ykg_A          399 TITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIA  478 (696)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC-----------------------------CCSCSEEEESSCCC---C
T ss_pred             CcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHHhcCCccEEEEechhhcCCcCc
Confidence            346667654 67778888888876    21              1 12235556666665 52 433 3333344432  


Q ss_pred             --ceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHH
Q psy7691          92 --LAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL  137 (165)
Q Consensus        92 --~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i  137 (165)
                        ..|++||+|.+.++|+||+|| ||. +.|.++.++...+......+
T Consensus       479 ~v~~VI~~d~p~s~~~~~Qr~GR-GR~-~~g~~~~l~~~~~~~~~~~~  524 (696)
T 2ykg_A          479 QCNLVILYEYVGNVIKMIQTRGR-GRA-RGSKCFLLTSNAGVIEKEQI  524 (696)
T ss_dssp             CCSEEEEESCC--CCCC-----------CCCEEEEEESCHHHHHHHHH
T ss_pred             cCCEEEEeCCCCCHHHHHHhhcc-CcC-CCceEEEEecCCCHHHHHHH
Confidence              279999999999999999999 998 77888888877655443333

>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=97.75  E-value=5.1e-06  Score=70.40  Aligned_cols=33  Identities=27%  Similarity=0.390  Sum_probs=31.0

Q ss_pred             cCCCCChhHHHHhhccCCCCCC-CCceEEEECCC
Q psy7691          97 FDYPNSSEDYIHRIGRTGRCAS-SGTAYTFFTPN  129 (165)
Q Consensus        97 ~~lP~~~~~~i~r~gr~~r~~~-~g~~~~~~~p~  129 (165)
                      ||.|.+..+|+||+||+||.|. .|.+++++.+.
T Consensus       280 ~d~p~s~~~~~QR~GRaGR~g~~~G~~~~~~~~~  313 (459)
T 2z83_A          280 NPSPITSASAAQRRGRVGRNPNQVGDEYHYGGAT  313 (459)
T ss_dssp             SCEECCHHHHHHHHTTSSCCTTCCCEEEEECSCC
T ss_pred             cCCCCCHHHHHHhccccCCCCCCCCeEEEEEccc
Confidence            8899999999999999999997 89999999886

>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=97.74  E-value=1.4e-05  Score=70.78  Aligned_cols=96  Identities=17%  Similarity=0.081  Sum_probs=63.6

Q ss_pred             ccccc-cCCCcHHHHHHHHhCCCCCC------c-hHHHHHHHHHHcC-CCeeee-cccCCccc----ceeeecCC-----
Q psy7691          39 TQELT-EGCFPNAVLQHLKGQGFEEP------T-AIQAQGWPIALSG-RDMVGI-AQTGSGKT----LAVINFDY-----   99 (165)
Q Consensus        39 i~~f~-~l~l~~~l~~~l~~~g~~~~------t-~~Q~~a~~~~l~G-~di~~~-a~tgsGKt----~~~~~~~l-----   99 (165)
                      ++.|. +....+.+.+.|.+.|+...      + ..+...+..+..| .++++. ..-+.|=.    -+|++||.     
T Consensus       448 vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~GlDip~v~lVi~~d~d~~G~  527 (661)
T 2d7d_A          448 VLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGF  527 (661)
T ss_dssp             EEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTTCCCTTEEEEEETTTTCCTT
T ss_pred             EEEEECCHHHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCCcccCCCCEEEEeCcccccC
Confidence            44444 45677888888988887431      1 1233344445545 344432 12233322    26899997     


Q ss_pred             CCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHH
Q psy7691         100 PNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAK  135 (165)
Q Consensus       100 P~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~  135 (165)
                      |.+..+|+||+||+||. ..|.+++++.+.+..+..
T Consensus       528 p~s~~~~iQr~GRagR~-~~G~~i~~~~~~~~~~~~  562 (661)
T 2d7d_A          528 LRSERSLIQTIGRAARN-AEGRVIMYADKITKSMEI  562 (661)
T ss_dssp             TTSHHHHHHHHHTTTTS-TTCEEEEECSSCCHHHHH
T ss_pred             CCCHHHHHHHhCcccCC-CCCEEEEEEeCCCHHHHH
Confidence            99999999999999998 789999999998755444

>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=97.64  E-value=5.6e-06  Score=73.56  Aligned_cols=102  Identities=19%  Similarity=0.240  Sum_probs=63.9

Q ss_pred             Cccccc-cCCCcHHHHHHHHhCCCCCC------chHHH--------HHHHHHHcCCCeeeec---ccCCcccceeeecC-
Q psy7691          38 PTQELT-EGCFPNAVLQHLKGQGFEEP------TAIQA--------QGWPIALSGRDMVGIA---QTGSGKTLAVINFD-   98 (165)
Q Consensus        38 ~i~~f~-~l~l~~~l~~~l~~~g~~~~------t~~Q~--------~a~~~~l~G~di~~~a---~tgsGKt~~~~~~~-   98 (165)
                      .++.|. ...-.+.+.+.|.+.|+...      +..+.        .|++.+.+|.|+. +.   ..|..|. .++||| 
T Consensus       398 ~vLVFv~Tr~~ae~la~~L~~~g~~v~~lHG~l~q~er~~~~~~VLVATdVaerGIDId-V~~VI~~Gl~~~-~ViNyDy  475 (666)
T 3o8b_A          398 RHLIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSVIPTIGDVVVVATDALMTGYTGD-FDSVIDCNTCVT-QTVDFSL  475 (666)
T ss_dssp             EEEEECSCHHHHHHHHHHHHTTTCCEEEECTTSCGGGSCSSSCEEEEECTTHHHHCCCC-BSEEEECCEEEE-EEEECCC
T ss_pred             cEEEEeCCHHHHHHHHHHHHhCCCcEEEecCCCCHHHHHhCCCcEEEECChHHccCCCC-CcEEEecCcccc-ccccccc
Confidence            444554 44677788888888877431      11111        2455566676643 22   0011111 355899 


Q ss_pred             ----------CCCChhHHHHhhccCCCCCCCCceEEEECCCcHHH--H--HHHHHHHHh
Q psy7691          99 ----------YPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQ--A--KELIAVLTE  143 (165)
Q Consensus        99 ----------lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~--~--~~i~~~l~~  143 (165)
                                +|.+.++|+||+||+|| ++.|. +.++.+.+...  +  ..+.+.+..
T Consensus       476 dP~~gl~~~~~P~s~~syiQRiGRtGR-g~~G~-i~lvt~~e~~~~~l~~~~i~~~~~~  532 (666)
T 3o8b_A          476 DPTFTIETTTVPQDAVSRSQRRGRTGR-GRRGI-YRFVTPGERPSGMFDSSVLCECYDA  532 (666)
T ss_dssp             SSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEE-EEESCCCCBCSSBCCHHHHHHHHHH
T ss_pred             ccccccccccCcCCHHHHHHHhccCCC-CCCCE-EEEEecchhhcccccHHHHHHHhcC
Confidence                      99999999999999999 99998 88888876443  2  444444443

>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=97.62  E-value=1.5e-05  Score=71.63  Aligned_cols=93  Identities=13%  Similarity=0.138  Sum_probs=45.8

Q ss_pred             CCccccccC-CCcHHHHHHHHhC------------CCC-------CCchHHHHHHHHHHc-CC-Ceeeeccc-CCcc---
Q psy7691          37 CPTQELTEG-CFPNAVLQHLKGQ------------GFE-------EPTAIQAQGWPIALS-GR-DMVGIAQT-GSGK---   90 (165)
Q Consensus        37 ~~i~~f~~l-~l~~~l~~~l~~~------------g~~-------~~t~~Q~~a~~~~l~-G~-di~~~a~t-gsGK---   90 (165)
                      ..++.|.+. ...+.+.+.|...            |+.       .+...+...+..+.. |. +++++... |.|=   
T Consensus       632 ~kvLIF~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F~~~g~~~vLVaT~~~~~GIDlp  711 (797)
T 4a2q_A          632 TRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIV  711 (797)
T ss_dssp             CCEEEEESSHHHHHHHHHHHHTCSTTCSCCCEEC----------------------------CCSEEEEECC-------C
T ss_pred             CeEEEEECcHHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHhhccCCceEEEEcCchhcCCCch
Confidence            456677654 6777777878663            221       122234455555655 53 44433322 2332   


Q ss_pred             -cceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcH
Q psy7691          91 -TLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNG  131 (165)
Q Consensus        91 -t~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~  131 (165)
                       .-.|++||+|.+...|+||+|| ||. +.|.++.++++.+.
T Consensus       712 ~v~~VI~yd~p~s~~~~iQr~GR-GR~-~~g~~i~l~~~~~~  751 (797)
T 4a2q_A          712 QCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEV  751 (797)
T ss_dssp             CCSEEEEESCCSCHHHHHTC---------CCCEEEEECCHHH
T ss_pred             hCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCCcH
Confidence             2279999999999999999999 998 88999999988754

>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=97.56  E-value=5.6e-05  Score=66.42  Aligned_cols=92  Identities=13%  Similarity=0.159  Sum_probs=54.7

Q ss_pred             CCCcccccc-CCCcHHHHHHHHhC------CCC---------------CCchHHHHHHHHHHcCC-Ceee-ecccCCccc
Q psy7691          36 PCPTQELTE-GCFPNAVLQHLKGQ------GFE---------------EPTAIQAQGWPIALSGR-DMVG-IAQTGSGKT   91 (165)
Q Consensus        36 p~~i~~f~~-l~l~~~l~~~l~~~------g~~---------------~~t~~Q~~a~~~~l~G~-di~~-~a~tgsGKt   91 (165)
                      ...++.|.. ....+.+.+.|...      |+.               .+...+.+.+..+..|. +|++ +..-|.|=.
T Consensus       400 ~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~~~~~GID  479 (699)
T 4gl2_A          400 SARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLD  479 (699)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEECSCCTTSC
T ss_pred             CCcEEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCc
Confidence            345566655 46777888888765      543               22334555666666553 3332 222233422


Q ss_pred             c----eeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCc
Q psy7691          92 L----AVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN  130 (165)
Q Consensus        92 ~----~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~  130 (165)
                      +    .|++||+|.+..+|+||+||+||.   |.++.++.+.+
T Consensus       480 ip~v~~VI~~d~p~s~~~~~Qr~GRArr~---g~~~~l~~~~~  519 (699)
T 4gl2_A          480 IKECNIVIRYGLVTNEIAMVQARGRARAD---ESTYVLVAHSG  519 (699)
T ss_dssp             CCSCCCCEEESCCCCHHHHHHHHTTSCSS---SCEEEEEEESS
T ss_pred             cccCCEEEEeCCCCCHHHHHHHcCCCCCC---CceEEEEEeCC
Confidence            2    689999999999999999996443   45666665543

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=97.54  E-value=2.6e-05  Score=65.54  Aligned_cols=52  Identities=19%  Similarity=0.181  Sum_probs=41.3

Q ss_pred             cCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHH
Q psy7691          76 SGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLT  142 (165)
Q Consensus        76 ~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~  142 (165)
                      .|.|++++++||||||++++   +|     +++++-.      .|..+++++|+ +.++.|+.+.+.
T Consensus         1 kg~~~lv~a~TGsGKT~~~l---~~-----~l~~~~~------~g~~~lvl~Pt-~~La~Q~~~~~~   52 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVL---PQ-----LVREAVK------KRLRTVILAPT-RVVASEMYEALR   52 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHH---HH-----HHHHHHH------TTCCEEEEESS-HHHHHHHHHHTT
T ss_pred             CCCEEEEEcCCCCCHHHHHH---HH-----HHHHHHh------CCCCEEEECcH-HHHHHHHHHHhC
Confidence            37899999999999999987   67     6655432      34578888898 899999988875

>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=97.53  E-value=3.8e-05  Score=68.12  Aligned_cols=99  Identities=16%  Similarity=0.096  Sum_probs=64.4

Q ss_pred             ccccc-cCCCcHHHHHHHHhCCCCCC------c-hHHHHHHHHHHcC-CCeeee-cccCCccc----ceeeecCC-----
Q psy7691          39 TQELT-EGCFPNAVLQHLKGQGFEEP------T-AIQAQGWPIALSG-RDMVGI-AQTGSGKT----LAVINFDY-----   99 (165)
Q Consensus        39 i~~f~-~l~l~~~l~~~l~~~g~~~~------t-~~Q~~a~~~~l~G-~di~~~-a~tgsGKt----~~~~~~~l-----   99 (165)
                      ++.|. +....+.+.+.|.+.|+...      + ..+.+.+..+..| .++++. ..-+.|=.    -.|++||.     
T Consensus       442 vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~GlDip~v~lVI~~d~d~~G~  521 (664)
T 1c4o_A          442 TLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGF  521 (664)
T ss_dssp             EEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTTTSCSG
T ss_pred             EEEEECCHHHHHHHHHHHHhcCCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhcCccCCCCCEEEEeCCcccCC
Confidence            34444 44677888888888887531      1 2233444445555 344432 13333422    26899997     


Q ss_pred             CCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHH
Q psy7691         100 PNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELI  138 (165)
Q Consensus       100 P~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~  138 (165)
                      |.+..+|+||+||+||.+ .|.+++++.+.+..+...|.
T Consensus       522 p~s~~~~iQr~GRagR~~-~G~~i~~~~~~~~~~~~~i~  559 (664)
T 1c4o_A          522 LRSERSLIQTIGRAARNA-RGEVWLYADRVSEAMQRAIE  559 (664)
T ss_dssp             GGSHHHHHHHHGGGTTST-TCEEEEECSSCCHHHHHHHH
T ss_pred             CCCHHHHHHHHCccCcCC-CCEEEEEEcCCCHHHHHHHH
Confidence            889999999999999984 79999999887765444333

>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=97.41  E-value=3.6e-05  Score=63.30  Aligned_cols=96  Identities=17%  Similarity=0.161  Sum_probs=67.1

Q ss_pred             CCCcccccc-CCCcHHHHHHHHhCCCC---------------CCchHHHHHHHHHHcCC-Ceeeeccc-CCccc----ce
Q psy7691          36 PCPTQELTE-GCFPNAVLQHLKGQGFE---------------EPTAIQAQGWPIALSGR-DMVGIAQT-GSGKT----LA   93 (165)
Q Consensus        36 p~~i~~f~~-l~l~~~l~~~l~~~g~~---------------~~t~~Q~~a~~~~l~G~-di~~~a~t-gsGKt----~~   93 (165)
                      ...++.|.+ ......+.+.|...|+.               .+...+.+.+..+..|. +++++... |.|=+    ..
T Consensus       361 ~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~~~~vLv~T~~~~~Gldl~~~~~  440 (494)
T 1wp9_A          361 NSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDL  440 (494)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECGGGGGGGGSTTCCE
T ss_pred             CCeEEEEEccHHHHHHHHHHHHHcCCCcEEEeccccccccccCCHHHHHHHHHHHhcCCceEEEECCccccCCCchhCCE
Confidence            344566665 46777888888887663               12234556677776664 45443322 33432    26


Q ss_pred             eeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHH
Q psy7691          94 VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGK  132 (165)
Q Consensus        94 ~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~  132 (165)
                      |++||.|.+...|+||+||++|.|. |.++.++++.+.+
T Consensus       441 Vi~~d~~~~~~~~~Qr~GR~~R~g~-g~~~~l~~~~t~e  478 (494)
T 1wp9_A          441 VVFYEPVPSAIRSIQRRGRTGRHMP-GRVIILMAKGTRD  478 (494)
T ss_dssp             EEESSCCHHHHHHHHHHTTSCSCCC-SEEEEEEETTSHH
T ss_pred             EEEeCCCCCHHHHHHHHhhccCCCC-ceEEEEEecCCHH
Confidence            8999999999999999999999998 9999999988643

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=97.37  E-value=7.3e-05  Score=64.73  Aligned_cols=71  Identities=15%  Similarity=0.156  Sum_probs=42.7

Q ss_pred             CCchHHHHHHHHHHc----C-CCeeeecccCCcccceeeecCCCCChhHHHHhhccCC---CCCCCCceEEEECCCcHHH
Q psy7691          62 EPTAIQAQGWPIALS----G-RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTG---RCASSGTAYTFFTPNNGKQ  133 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~----G-~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~---r~~~~g~~~~~~~p~~~~~  133 (165)
                      .+++.|.+|++.++.    | .+++++++||+|||++++    +     ++.++-+.+   .....+..+++++|+ +++
T Consensus       178 ~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~----~-----~~~~l~~~~~~~~~~~~~~~vlil~P~-~~L  247 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAF----Q-----ISWKLWSARWNRTGDYRKPRILFLADR-NVL  247 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH----H-----HHHHHHHTTCCSSCSSSCCCEEEEEC-----
T ss_pred             CchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHH----H-----HHHHHHhcccccccccCCCeEEEEeCC-HHH
Confidence            589999999998875    5 558999999999999754    3     555553332   111245678999998 788


Q ss_pred             HHHHH-HHHH
Q psy7691         134 AKELI-AVLT  142 (165)
Q Consensus       134 ~~~i~-~~l~  142 (165)
                      +.|.. +.+.
T Consensus       248 ~~Q~~~~~~~  257 (590)
T 3h1t_A          248 VDDPKDKTFT  257 (590)
T ss_dssp             -------CCT
T ss_pred             HHHHHHHHHH
Confidence            88877 4444

>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=97.36  E-value=1.3e-05  Score=71.16  Aligned_cols=61  Identities=21%  Similarity=0.158  Sum_probs=44.2

Q ss_pred             chHHHHHHH-HHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHH
Q psy7691          64 TAIQAQGWP-IALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLT  142 (165)
Q Consensus        64 t~~Q~~a~~-~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~  142 (165)
                      ...|+++++ .+..+.|++++|+||||||.+|.   +|     +++          .|..++++.|+ ++++.|+.+.+.
T Consensus       218 ~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~---l~-----ll~----------~g~~vLVl~PT-ReLA~Qia~~l~  278 (666)
T 3o8b_A          218 VFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVP---AA-----YAA----------QGYKVLVLNPS-VAATLGFGAYMS  278 (666)
T ss_dssp             SCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHH---HH-----HHH----------TTCCEEEEESC-HHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHH---HH-----HHH----------CCCeEEEEcch-HHHHHHHHHHHH
Confidence            333444444 44577899999999999999887   55     443          13468899999 899999987664


Q ss_pred             h
Q psy7691         143 E  143 (165)
Q Consensus       143 ~  143 (165)
                      .
T Consensus       279 ~  279 (666)
T 3o8b_A          279 K  279 (666)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=97.36  E-value=4.7e-05  Score=69.90  Aligned_cols=94  Identities=13%  Similarity=0.132  Sum_probs=46.1

Q ss_pred             CCCccccccC-CCcHHHHHHHHhC------------CCC-------CCchHHHHHHHHHHc-CC-Ceeeec-ccCCcc--
Q psy7691          36 PCPTQELTEG-CFPNAVLQHLKGQ------------GFE-------EPTAIQAQGWPIALS-GR-DMVGIA-QTGSGK--   90 (165)
Q Consensus        36 p~~i~~f~~l-~l~~~l~~~l~~~------------g~~-------~~t~~Q~~a~~~~l~-G~-di~~~a-~tgsGK--   90 (165)
                      ...++.|... ...+.+.+.|...            |..       .+...+.+.+..+.. |. +++++. .-|.|=  
T Consensus       631 ~~rvLIF~~t~~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~Fr~~g~~~VLVaT~~~~eGIDl  710 (936)
T 4a2w_A          631 QTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDI  710 (936)
T ss_dssp             TCCEEEEESSHHHHHHHHHHHHHCSTTSSCCCEEC----------------------------CCSEEEEECC------C
T ss_pred             CCeEEEEeCCHHHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHhhccCCeeEEEEeCchhcCCcc
Confidence            3456677654 6788888888875            321       122234455555655 53 444322 222332  


Q ss_pred             --cceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcH
Q psy7691          91 --TLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNG  131 (165)
Q Consensus        91 --t~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~  131 (165)
                        .-.|++||+|.+..+|+||+|| ||. +.|.++.+++..+.
T Consensus       711 p~v~~VI~yD~p~s~~~~iQr~GR-GR~-~~g~vi~Li~~~t~  751 (936)
T 4a2w_A          711 VQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEV  751 (936)
T ss_dssp             CCCSEEEEESCCSCSHHHHCC---------CCCEEEEESCHHH
T ss_pred             hhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCCEEEEEEeCCCH
Confidence              2279999999999999999999 998 78889888887654

>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=97.28  E-value=9.5e-05  Score=68.13  Aligned_cols=107  Identities=13%  Similarity=0.123  Sum_probs=70.1

Q ss_pred             CCccccccC-CCcHHHHHHHHh-CCCCC------Cch-HHHHHHHHHHcC---CCeeeeccc-CCcc----cceeeecCC
Q psy7691          37 CPTQELTEG-CFPNAVLQHLKG-QGFEE------PTA-IQAQGWPIALSG---RDMVGIAQT-GSGK----TLAVINFDY   99 (165)
Q Consensus        37 ~~i~~f~~l-~l~~~l~~~l~~-~g~~~------~t~-~Q~~a~~~~l~G---~di~~~a~t-gsGK----t~~~~~~~l   99 (165)
                      ..++.|... ...+.+.+.|.. .|+..      .+. .....+..+..|   .+++++... +.|-    ...+++||+
T Consensus       504 ~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~~~~~~R~~~l~~F~~g~~~~~vLvaT~v~~~GlDl~~~~~VI~~d~  583 (968)
T 3dmq_A          504 QKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDL  583 (968)
T ss_dssp             SCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTTSCTTHHHHHHHHHHSTTSSCEEEECSCCTTCSSCCTTCCEEECSSC
T ss_pred             CCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCcccEEEecchhhcCCCcccCcEEEEecC
Confidence            345566654 566777778884 47642      222 334566667777   355544322 2332    236899999


Q ss_pred             CCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHh
Q psy7691         100 PNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTE  143 (165)
Q Consensus       100 P~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~  143 (165)
                      |.+...|.|++||++|.|..+.+.++....+...-..|.+.+..
T Consensus       584 p~~~~~~~Q~~GR~~R~Gq~~~v~v~~~~~~~t~ee~i~~~~~~  627 (968)
T 3dmq_A          584 PFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQSVLVRWYHE  627 (968)
T ss_dssp             CSSHHHHHHHHHTTSCSSSCSCCEEEEEEETTSHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhhccccCCCCceEEEEEecCCChHHHHHHHHHHh
Confidence            99999999999999999999987777655544444556666643

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=97.27  E-value=0.00018  Score=64.00  Aligned_cols=76  Identities=21%  Similarity=0.167  Sum_probs=50.2

Q ss_pred             cHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEEC
Q psy7691          48 PNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFT  127 (165)
Q Consensus        48 ~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~  127 (165)
                      +.+.++++.+.  ..|  .|+......+.|+|++++|+||||||..            .++++...+    .|   +++.
T Consensus       130 ~~d~l~~i~dl--~~p--~~~~p~ar~l~rk~vlv~apTGSGKT~~------------al~~l~~~~----~g---l~l~  186 (677)
T 3rc3_A          130 CKDDLRKISDL--RIP--PNWYPDARAMQRKIIFHSGPTNSGKTYH------------AIQKYFSAK----SG---VYCG  186 (677)
T ss_dssp             CHHHHHHHTBC--CCG--GGGCHHHHTSCCEEEEEECCTTSSHHHH------------HHHHHHHSS----SE---EEEE
T ss_pred             CHHHHHHHhhc--cCh--hhhCHHHHhcCCCEEEEEcCCCCCHHHH------------HHHHHHhcC----Ce---EEEe
Confidence            44445555433  333  3444445578999999999999999982            344443321    12   6778


Q ss_pred             CCcHHHHHHHHHHHHhcCCC
Q psy7691         128 PNNGKQAKELIAVLTEASQP  147 (165)
Q Consensus       128 p~~~~~~~~i~~~l~~~~~~  147 (165)
                      |+ ++++.|+.+.+...+..
T Consensus       187 Pt-R~LA~Qi~~~l~~~g~~  205 (677)
T 3rc3_A          187 PL-KLLAHEIFEKSNAAGVP  205 (677)
T ss_dssp             SS-HHHHHHHHHHHHHTTCC
T ss_pred             CH-HHHHHHHHHHHHhcCCc
Confidence            88 99999999998876443

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=97.21  E-value=0.00024  Score=63.24  Aligned_cols=107  Identities=17%  Similarity=0.149  Sum_probs=60.3

Q ss_pred             ccccccCCCcHHHHHHHHhCCCCC------CchHHH-HHHHHHHc--C-CCeeeec-ccCCcccc---eeeecCC-----
Q psy7691          39 TQELTEGCFPNAVLQHLKGQGFEE------PTAIQA-QGWPIALS--G-RDMVGIA-QTGSGKTL---AVINFDY-----   99 (165)
Q Consensus        39 i~~f~~l~l~~~l~~~l~~~g~~~------~t~~Q~-~a~~~~l~--G-~di~~~a-~tgsGKt~---~~~~~~l-----   99 (165)
                      ++.|....-.+.+.+.|.+.|+..      .++.++ +....+..  | .+|+++. .-+.|=++   .|++|++     
T Consensus       324 iIf~~s~~~ie~la~~L~~~g~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi~v~~VI~~~~~k~~~  403 (677)
T 3rc3_A          324 CIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNLSIRRIIFYSLIKPSI  403 (677)
T ss_dssp             EEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCCCBSEEEESCSBC---
T ss_pred             EEEEcCHHHHHHHHHHHHhcCCCeeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCcCccEEEECCcccccc
Confidence            333333344667777888777643      222222 33334444  4 3444332 22344332   6889999     


Q ss_pred             ---------CCChhHHHHhhccCCCCCCCCc--eEEEECCCcHHHHHHHHHHHHhcCCCC
Q psy7691         100 ---------PNSSEDYIHRIGRTGRCASSGT--AYTFFTPNNGKQAKELIAVLTEASQPI  148 (165)
Q Consensus       100 ---------P~~~~~~i~r~gr~~r~~~~g~--~~~~~~p~~~~~~~~i~~~l~~~~~~~  148 (165)
                               |.+..+|+||+||+||.|..|.  .+.++.+.+..   .+.+++.....++
T Consensus       404 ~~~G~~~~~p~s~~~~~QR~GRAGR~g~~g~~G~v~~l~~~d~~---~~~~~~~~~~~~i  460 (677)
T 3rc3_A          404 NEKGERELEPITTSQALQIAGRAGRFSSRFKEGEVTTMNHEDLS---LLKEILKRPVDPI  460 (677)
T ss_dssp             --------CBCCHHHHHHHHTTBTCTTSSCSSEEEEESSTTHHH---HHHHHHHSCCCCC
T ss_pred             ccCCccccccCCHHHHHHHhcCCCCCCCCCCCEEEEEEecchHH---HHHHHHhcCcchh
Confidence                     7789999999999999997632  44445555333   3444454444443

>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=97.11  E-value=0.0002  Score=64.70  Aligned_cols=45  Identities=11%  Similarity=0.126  Sum_probs=35.7

Q ss_pred             eeeecCCCC-ChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHH
Q psy7691          93 AVINFDYPN-SSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL  137 (165)
Q Consensus        93 ~~~~~~lP~-~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i  137 (165)
                      .+++||.|. +...|.||+||+||.|..|.+++++.|.+......+
T Consensus       660 ~VIi~d~~r~~l~~l~Qr~GRaGR~g~~g~~ill~~~~~~~~~~rl  705 (780)
T 1gm5_A          660 VMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEEAMERL  705 (780)
T ss_dssp             EEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCCHHHHHHH
T ss_pred             EEEEeCCCCCCHHHHHHHhcccCcCCCCCEEEEEECCCChHHHHHH
Confidence            688999986 567788999999999999999999886554433333

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=97.10  E-value=0.00029  Score=65.27  Aligned_cols=37  Identities=27%  Similarity=0.389  Sum_probs=32.8

Q ss_pred             eeee----cCC----CCChhHHHHhhccCCCCCC--CCceEEEECCC
Q psy7691          93 AVIN----FDY----PNSSEDYIHRIGRTGRCAS--SGTAYTFFTPN  129 (165)
Q Consensus        93 ~~~~----~~l----P~~~~~~i~r~gr~~r~~~--~g~~~~~~~p~  129 (165)
                      .|++    ||.    |.+..+|+||+||+||.|.  .|.+++++.+.
T Consensus       453 vVI~~~~kfd~~~~rp~s~~~y~Qr~GRAGR~G~d~~G~vi~l~~~~  499 (1010)
T 2xgj_A          453 VVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEK  499 (1010)
T ss_dssp             EEESCSEEECSSCEEECCHHHHHHHHTTBCCTTTCSSEEEEEEECSC
T ss_pred             EEEeCCcccCCcCCccCCHHHHhHhhhhcccCCCCCceEEEEEECCC
Confidence            5888    999    8899999999999999996  58888888876

>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=97.05  E-value=0.00026  Score=65.81  Aligned_cols=70  Identities=16%  Similarity=-0.041  Sum_probs=51.2

Q ss_pred             CCchHHHHHHHHHHc--------------CCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEEC
Q psy7691          62 EPTAIQAQGWPIALS--------------GRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFT  127 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~--------------G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~  127 (165)
                      .|++.|.+|++.++.              +.+.+++++||||||++++    +     .++.+.+.    .....+++++
T Consensus       271 ~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~~----~-----l~~ll~~~----~~~~rvLvlv  337 (1038)
T 2w00_A          271 VMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTSF----K-----AARLATEL----DFIDKVFFVV  337 (1038)
T ss_dssp             ECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHHH----H-----HHHHHTTC----TTCCEEEEEE
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHHH----H-----HHHHHHhc----CCCceEEEEe
Confidence            489999999998865              3689999999999999864    3     33333221    1234788899


Q ss_pred             CCcHHHHHHHHHHHHhcC
Q psy7691         128 PNNGKQAKELIAVLTEAS  145 (165)
Q Consensus       128 p~~~~~~~~i~~~l~~~~  145 (165)
                      |+ ++++.|+.+.+..-.
T Consensus       338 pr-~eL~~Q~~~~f~~f~  354 (1038)
T 2w00_A          338 DR-KDLDYQTMKEYQRFS  354 (1038)
T ss_dssp             CG-GGCCHHHHHHHHTTS
T ss_pred             Cc-HHHHHHHHHHHHHhc
Confidence            87 788888877766543

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=97.02  E-value=0.00026  Score=59.41  Aligned_cols=35  Identities=14%  Similarity=0.124  Sum_probs=28.3

Q ss_pred             eeeecCCCCChhHHHHhhccCCCCCCCCceEEEEC
Q psy7691          93 AVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFT  127 (165)
Q Consensus        93 ~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~  127 (165)
                      .+++|+.|.+..+|+||+||+||.|..+.+++++.
T Consensus       254 ~vi~~~~p~~~~~~~Qr~GR~GR~g~~~~~~~~~~  288 (431)
T 2v6i_A          254 VSMQGPIAITPASAAQRRGRIGRNPEKLGDIYAYS  288 (431)
T ss_dssp             EEEEEEEECCHHHHHHHHTTSSCCTTCCCCEEEEC
T ss_pred             eeecccccCCHHHHHHhhhccCCCCCCCCeEEEEc
Confidence            37899999999999999999999986544444444

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=96.93  E-value=0.0015  Score=57.17  Aligned_cols=66  Identities=24%  Similarity=0.262  Sum_probs=50.1

Q ss_pred             chHHHHHHHHHHcCCCeeeecccCCcccc--eeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHH
Q psy7691          64 TAIQAQGWPIALSGRDMVGIAQTGSGKTL--AVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVL  141 (165)
Q Consensus        64 t~~Q~~a~~~~l~G~di~~~a~tgsGKt~--~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l  141 (165)
                      ++.|..|++.++.+.++++++++|+|||.  +++   ++     .+.+...     ..+..+++++|+ ...+.++.+.+
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~l---l~-----~l~~~~~-----~~~~~vll~APT-g~AA~~L~e~~  216 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKL---LA-----ALIQMAD-----GERCRIRLAAPT-GKAAARLTESL  216 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHH---HH-----HHHHTCS-----SCCCCEEEEBSS-HHHHHHHHHHH
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHH---HH-----HHHHhhh-----cCCCeEEEEeCC-hhHHHHHHHHH
Confidence            68899999999999999999999999994  444   44     4444421     235678889999 77788887766


Q ss_pred             Hh
Q psy7691         142 TE  143 (165)
Q Consensus       142 ~~  143 (165)
                      ..
T Consensus       217 ~~  218 (608)
T 1w36_D          217 GK  218 (608)
T ss_dssp             TH
T ss_pred             HH
Confidence            53

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=96.82  E-value=0.0004  Score=54.95  Aligned_cols=94  Identities=13%  Similarity=0.058  Sum_probs=47.1

Q ss_pred             CCccccccC-CCcHHHHHHHHhC-CCCCC-------chHHHHHHHHHHcCC--Ceeeec--ccCCcccc----eeeecCC
Q psy7691          37 CPTQELTEG-CFPNAVLQHLKGQ-GFEEP-------TAIQAQGWPIALSGR--DMVGIA--QTGSGKTL----AVINFDY   99 (165)
Q Consensus        37 ~~i~~f~~l-~l~~~l~~~l~~~-g~~~~-------t~~Q~~a~~~~l~G~--di~~~a--~tgsGKt~----~~~~~~l   99 (165)
                      ..++.|++. ...+.+...|... |+...       ......++..+..|.  .++.++  .-|.|-.+    .+++||+
T Consensus       113 ~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~st~~~g~Glnl~~a~~VI~~d~  192 (271)
T 1z5z_A          113 DKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFDR  192 (271)
T ss_dssp             CCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCTTCCCCCCTTCSEEEECSC
T ss_pred             CeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEEehhhhcCCcCcccCCEEEEECC
Confidence            346777765 5666677777663 66432       123334566676663  323222  22344332    6899999


Q ss_pred             CCChhHHHHhhccCCCCCCCCce--EEEECCCc
Q psy7691         100 PNSSEDYIHRIGRTGRCASSGTA--YTFFTPNN  130 (165)
Q Consensus       100 P~~~~~~i~r~gr~~r~~~~g~~--~~~~~p~~  130 (165)
                      |-++..|+||+||++|.|..+.+  +.+++..+
T Consensus       193 ~wnp~~~~Q~~gR~~R~Gq~~~v~v~~li~~~T  225 (271)
T 1z5z_A          193 WWNPAVEDQATDRVYRIGQTRNVIVHKLISVGT  225 (271)
T ss_dssp             CSCTTTC--------------CCEEEEEEETTS
T ss_pred             CCChhHHHHHHHhccccCCCCceEEEEEeeCCC
Confidence            99999999999999999987765  44555554

>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=96.78  E-value=0.00026  Score=66.16  Aligned_cols=37  Identities=24%  Similarity=0.346  Sum_probs=28.4

Q ss_pred             eeeecCCC--------CChhHHHHhhccCCCCC--CCCceEEEECCC
Q psy7691          93 AVINFDYP--------NSSEDYIHRIGRTGRCA--SSGTAYTFFTPN  129 (165)
Q Consensus        93 ~~~~~~lP--------~~~~~~i~r~gr~~r~~--~~g~~~~~~~p~  129 (165)
                      .|++|+.|        .+..+|+||+||+||.|  ..|.+++++.+.
T Consensus       551 ~VI~~~~~~d~~~~r~iS~~eyiQr~GRAGR~G~d~~G~~ill~~~~  597 (1108)
T 3l9o_A          551 VVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEK  597 (1108)
T ss_dssp             EEESCSEEESSSCEEECCHHHHHHHHHHSCCSSSCSSEEEEEEECCC
T ss_pred             EEEecCcccCccccccCCHHHHHHhhcccCCCCCCCceEEEEEecCC
Confidence            57877664        35667999999999999  566677777665

>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=96.65  E-value=0.00023  Score=64.14  Aligned_cols=36  Identities=28%  Similarity=0.570  Sum_probs=31.1

Q ss_pred             eeeecCC------------------CCChhHHHHhhccCCCCCCCCceEEEECCC
Q psy7691          93 AVINFDY------------------PNSSEDYIHRIGRTGRCASSGTAYTFFTPN  129 (165)
Q Consensus        93 ~~~~~~l------------------P~~~~~~i~r~gr~~r~~~~g~~~~~~~p~  129 (165)
                      .|++|++                  |.+..+|+||+||+||. ..|.++.++++.
T Consensus       390 ~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~-~~G~~~~l~~~~  443 (773)
T 2xau_A          390 YVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEE  443 (773)
T ss_dssp             EEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSS-SSEEEEESSCHH
T ss_pred             EEEeCCCccceeeccccCccccccccCCHHHHHhhccccCCC-CCCEEEEEecHH
Confidence            7899888                  88999999999999999 788888777644

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=96.64  E-value=0.00067  Score=57.37  Aligned_cols=90  Identities=17%  Similarity=0.074  Sum_probs=56.2

Q ss_pred             CccccccCCCcHHHHHHHHhCCCC------CCch-HHHHHHHHHHcCC-Ceeeec-c-cCCcc----cceeeecCCCCCh
Q psy7691          38 PTQELTEGCFPNAVLQHLKGQGFE------EPTA-IQAQGWPIALSGR-DMVGIA-Q-TGSGK----TLAVINFDYPNSS  103 (165)
Q Consensus        38 ~i~~f~~l~l~~~l~~~l~~~g~~------~~t~-~Q~~a~~~~l~G~-di~~~a-~-tgsGK----t~~~~~~~lP~~~  103 (165)
                      .++.|....-++.+.+.|.+.|..      ..+. .+.+.+..+..|. +++++. . -+.|=    ...+++++.|.+.
T Consensus       350 ~~ivf~~~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~GiDip~v~~vi~~~~~~s~  429 (510)
T 2oca_A          350 AFVMFKHVSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFSTGISVKNLHHVVLAHGVKSK  429 (510)
T ss_dssp             EEEEESSHHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHHSCCCCSEEEEEESSCCCSC
T ss_pred             eEEEEecHHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhcccccccCcEEEEeCCCCCH
Confidence            456676665666788888876442      1122 2333444444553 444333 1 12221    1268899999999


Q ss_pred             hHHHHhhccCCCCCCCCceEEEEC
Q psy7691         104 EDYIHRIGRTGRCASSGTAYTFFT  127 (165)
Q Consensus       104 ~~~i~r~gr~~r~~~~g~~~~~~~  127 (165)
                      .+|+|++||+||.|..+..+.++.
T Consensus       430 ~~~~Q~~GR~gR~g~~~~~v~i~~  453 (510)
T 2oca_A          430 IIVLQTIGRVLRKHGSKTIATVWD  453 (510)
T ss_dssp             CHHHHHHHHHHTTTCCCCCCEEEE
T ss_pred             HHHHHHHhcccccCCCCceEEEEE
Confidence            999999999999998875555554

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=96.56  E-value=0.00087  Score=59.31  Aligned_cols=65  Identities=17%  Similarity=0.172  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHcC-CCeeeeccc-CCcccc----eeee----cC-------CCCChhHHHHhhccCCCCCC--CCceEEEE
Q psy7691          66 IQAQGWPIALSG-RDMVGIAQT-GSGKTL----AVIN----FD-------YPNSSEDYIHRIGRTGRCAS--SGTAYTFF  126 (165)
Q Consensus        66 ~Q~~a~~~~l~G-~di~~~a~t-gsGKt~----~~~~----~~-------lP~~~~~~i~r~gr~~r~~~--~g~~~~~~  126 (165)
                      .|......+..| ..++++..+ +.|-++    .|++    ||       .|.+..+|+||+||+||.|.  .|.++.++
T Consensus       326 ~r~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~  405 (715)
T 2va8_A          326 LRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGRPGFDQIGESIVVV  405 (715)
T ss_dssp             HHHHHHHHHHTTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHHHHTTBCCTTTCSCEEEEEEC
T ss_pred             HHHHHHHHHHcCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEe
Confidence            344444445555 344433322 233222    5777    88       89999999999999999984  66677777


Q ss_pred             CCCc
Q psy7691         127 TPNN  130 (165)
Q Consensus       127 ~p~~  130 (165)
                      .+.+
T Consensus       406 ~~~~  409 (715)
T 2va8_A          406 RDKE  409 (715)
T ss_dssp             SCGG
T ss_pred             CCch
Confidence            6653

>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=96.56  E-value=0.00074  Score=59.89  Aligned_cols=65  Identities=17%  Similarity=0.129  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHcC-CCeeeeccc-CCcccc----eeee----cC----CCCChhHHHHhhccCCCCCC--CCceEEEECCC
Q psy7691          66 IQAQGWPIALSG-RDMVGIAQT-GSGKTL----AVIN----FD----YPNSSEDYIHRIGRTGRCAS--SGTAYTFFTPN  129 (165)
Q Consensus        66 ~Q~~a~~~~l~G-~di~~~a~t-gsGKt~----~~~~----~~----lP~~~~~~i~r~gr~~r~~~--~g~~~~~~~p~  129 (165)
                      .+......+..| .+++++..+ +.|-++    .|++    ||    .|.+..+|+||+||+||.|.  .|.+++++++.
T Consensus       308 ~R~~v~~~f~~g~~~vlvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~  387 (720)
T 2zj8_A          308 ERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSD  387 (720)
T ss_dssp             HHHHHHHHHHTTSSCEEEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCTTTCSEEEEEEECSSS
T ss_pred             HHHHHHHHHHCCCCeEEEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCCCCCCCceEEEEecCc
Confidence            344445555555 345444333 233222    4676    77    58889999999999999984  57788887776


Q ss_pred             c
Q psy7691         130 N  130 (165)
Q Consensus       130 ~  130 (165)
                      +
T Consensus       388 ~  388 (720)
T 2zj8_A          388 D  388 (720)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=96.52  E-value=0.00092  Score=55.95  Aligned_cols=93  Identities=14%  Similarity=0.088  Sum_probs=53.3

Q ss_pred             CCccccccC-CCcHHHHHHHHhCCC--CCCchHHHHHHHHHHcCC-Ceeeeccc-CCccc----ceeeecCCCCChhHHH
Q psy7691          37 CPTQELTEG-CFPNAVLQHLKGQGF--EEPTAIQAQGWPIALSGR-DMVGIAQT-GSGKT----LAVINFDYPNSSEDYI  107 (165)
Q Consensus        37 ~~i~~f~~l-~l~~~l~~~l~~~g~--~~~t~~Q~~a~~~~l~G~-di~~~a~t-gsGKt----~~~~~~~lP~~~~~~i  107 (165)
                      ..++.|.+. ...+.+.+.|.-..+  ..+...+.+.+..+..|. +++++... +.|=.    ..+++||.|.+...|+
T Consensus       350 ~k~lvF~~~~~~~~~l~~~l~~~~~~g~~~~~~R~~~~~~F~~g~~~vLv~T~~~~~Gldlp~~~~Vi~~~~~~s~~~~~  429 (472)
T 2fwr_A          350 DKIIIFTRHNELVYRISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYI  429 (472)
T ss_dssp             SCBCCBCSCHHHHHHHHHHTTCCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSCSCCBSEEEEECCSSCCHHHH
T ss_pred             CcEEEEECCHHHHHHHHHHhCcceeeCCCCHHHHHHHHHHHhCCCCCEEEEcCchhcCcccccCcEEEEECCCCCHHHHH
Confidence            345566553 455555555532222  223344555566665553 44432211 23322    2689999999999999


Q ss_pred             HhhccCCCCCCC-CceEE--EECCC
Q psy7691         108 HRIGRTGRCASS-GTAYT--FFTPN  129 (165)
Q Consensus       108 ~r~gr~~r~~~~-g~~~~--~~~p~  129 (165)
                      ||+||++|.|.. +.+++  +++..
T Consensus       430 Q~~GR~~R~g~~k~~~~i~~lv~~~  454 (472)
T 2fwr_A          430 QRLGRILRPSKGKKEAVLYELISRG  454 (472)
T ss_dssp             HHHHHSBCCCTTTCCEEEEEEEECS
T ss_pred             HHHhhccCCCCCCceEEEEEEEeCC
Confidence            999999999954 44443  44433

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=96.13  E-value=0.0017  Score=56.11  Aligned_cols=90  Identities=10%  Similarity=0.038  Sum_probs=55.3

Q ss_pred             Ccccccc-CCCcHHHHHHHHhCCC-------------CCCchH-HHHHHHHHHcCC-C---eeeec-ccCCccc----ce
Q psy7691          38 PTQELTE-GCFPNAVLQHLKGQGF-------------EEPTAI-QAQGWPIALSGR-D---MVGIA-QTGSGKT----LA   93 (165)
Q Consensus        38 ~i~~f~~-l~l~~~l~~~l~~~g~-------------~~~t~~-Q~~a~~~~l~G~-d---i~~~a-~tgsGKt----~~   93 (165)
                      .++.|.. ...++.+.+.|.+.+.             ..-++. ....+..+..|. +   ++++. .-+.|=.    ..
T Consensus       441 k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~~~r~~~l~~F~~~~~~~~~ilvtt~~l~~GiDip~v~~  520 (590)
T 3h1t_A          441 KTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEGKIGKGHLSRFQELETSTPVILTTSQLLTTGVDAPTCKN  520 (590)
T ss_dssp             EEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTHHHHHHHHHHHHCTTCCCCCEEEESSTTTTTCCCTTEEE
T ss_pred             cEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCChHHHHHHHHHHhCCCCCCCEEEEECChhhcCccchheeE
Confidence            3445554 4566777777765432             112222 445666666663 2   44432 3345532    36


Q ss_pred             eeecCCCCChhHHHHhhccCCCCCC--CCceEEEEC
Q psy7691          94 VINFDYPNSSEDYIHRIGRTGRCAS--SGTAYTFFT  127 (165)
Q Consensus        94 ~~~~~lP~~~~~~i~r~gr~~r~~~--~g~~~~~~~  127 (165)
                      +++|+.|.+...|+|++||++|.+.  ....++++.
T Consensus       521 Vi~~~~~~s~~~~~Q~iGR~~R~~~~~~k~~~~I~D  556 (590)
T 3h1t_A          521 VVLARVVNSMSEFKQIVGRGTRLREDYGKLWFNIID  556 (590)
T ss_dssp             EEEESCCCCHHHHHHHHTTSCCCBGGGTBSCEEEEE
T ss_pred             EEEEecCCChHHHHHHHhhhcccCccCCCCEEEEEe
Confidence            8899999999999999999999886  344444544

>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=95.92  E-value=0.0024  Score=56.49  Aligned_cols=65  Identities=22%  Similarity=0.275  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHcCC-Ceeeeccc-CCcccc----eeee----cC---CCCChhHHHHhhccCCCCCC--CCceEEEECCCc
Q psy7691          66 IQAQGWPIALSGR-DMVGIAQT-GSGKTL----AVIN----FD---YPNSSEDYIHRIGRTGRCAS--SGTAYTFFTPNN  130 (165)
Q Consensus        66 ~Q~~a~~~~l~G~-di~~~a~t-gsGKt~----~~~~----~~---lP~~~~~~i~r~gr~~r~~~--~g~~~~~~~p~~  130 (165)
                      .|......+..|. .++++..+ +.|-++    .|++    ||   .|.+..+|+||+||+||.|.  .|.++.++.+.+
T Consensus       310 ~R~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~  389 (702)
T 2p6r_A          310 QRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRD  389 (702)
T ss_dssp             HHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGG
T ss_pred             HHHHHHHHHHCCCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEecCcc
Confidence            3444455566663 45444333 234332    4666    55   68889999999999999984  666777777664

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=95.71  E-value=0.0057  Score=56.60  Aligned_cols=27  Identities=19%  Similarity=0.310  Sum_probs=20.6

Q ss_pred             CCChhHHHHhhccCCCCCCCCc--eEEEE
Q psy7691         100 PNSSEDYIHRIGRTGRCASSGT--AYTFF  126 (165)
Q Consensus       100 P~~~~~~i~r~gr~~r~~~~g~--~~~~~  126 (165)
                      |.+..+|+||+||+||.|..+.  ++++.
T Consensus       461 ~~s~~~y~Qr~GRAGR~G~~~~G~vi~l~  489 (997)
T 4a4z_A          461 ELTPGEFTQMAGRAGRRGLDSTGTVIVMA  489 (997)
T ss_dssp             ECCHHHHHHHHGGGCCTTTCSSEEEEEEC
T ss_pred             CCCHHHHhHHhcccccCCCCcceEEEEec
Confidence            4489999999999999995444  44444

>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=95.62  E-value=0.01  Score=49.83  Aligned_cols=67  Identities=19%  Similarity=0.180  Sum_probs=44.5

Q ss_pred             CCchHHHHHHHHH----HcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHH
Q psy7691          62 EPTAIQAQGWPIA----LSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL  137 (165)
Q Consensus        62 ~~t~~Q~~a~~~~----l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i  137 (165)
                      .+.|.|.++++.+    ..|.+++..++||+|||+..+    .     ++....+.+    ....+++++|..  ++.|.
T Consensus        37 ~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai----~-----~i~~~~~~~----~~~~~LIv~P~~--l~~qw  101 (500)
T 1z63_A           37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTI----A-----VFSDAKKEN----ELTPSLVICPLS--VLKNW  101 (500)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHH----H-----HHHHHHHTT----CCSSEEEEECST--THHHH
T ss_pred             cchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHH----H-----HHHHHHhcC----CCCCEEEEccHH--HHHHH
Confidence            4889999998765    467889999999999999755    2     344332211    123578888863  44555


Q ss_pred             HHHHHh
Q psy7691         138 IAVLTE  143 (165)
Q Consensus       138 ~~~l~~  143 (165)
                      .+.+..
T Consensus       102 ~~e~~~  107 (500)
T 1z63_A          102 EEELSK  107 (500)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            554444

>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=95.52  E-value=0.0063  Score=51.18  Aligned_cols=93  Identities=14%  Similarity=0.049  Sum_probs=55.5

Q ss_pred             CccccccC-CCcHHHHHHHHhC-CCCCC-------chHHHHHHHHHHcCCC---eeee-cccCCcccc----eeeecCCC
Q psy7691          38 PTQELTEG-CFPNAVLQHLKGQ-GFEEP-------TAIQAQGWPIALSGRD---MVGI-AQTGSGKTL----AVINFDYP  100 (165)
Q Consensus        38 ~i~~f~~l-~l~~~l~~~l~~~-g~~~~-------t~~Q~~a~~~~l~G~d---i~~~-a~tgsGKt~----~~~~~~lP  100 (165)
                      .++.|.+. ...+.+.+.|... |+...       .....+.+..+..|.+   ++++ ..-|.|-.+    .+++||+|
T Consensus       343 k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~~~~~Glnl~~~~~vi~~d~~  422 (500)
T 1z63_A          343 KIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFDRW  422 (500)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECCCC-CCCCCTTCSEEEESSCC
T ss_pred             cEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEecccccCCCchhhCCEEEEeCCC
Confidence            45666664 4556666667653 55431       2334456666777632   3333 223345333    68999999


Q ss_pred             CChhHHHHhhccCCCCCCCCce--EEEECCCc
Q psy7691         101 NSSEDYIHRIGRTGRCASSGTA--YTFFTPNN  130 (165)
Q Consensus       101 ~~~~~~i~r~gr~~r~~~~g~~--~~~~~p~~  130 (165)
                      -++..|+|++||++|.|....+  +-+++..+
T Consensus       423 ~~~~~~~Q~~gR~~R~Gq~~~v~v~~lv~~~t  454 (500)
T 1z63_A          423 WNPAVEDQATDRVYRIGQTRNVIVHKLISVGT  454 (500)
T ss_dssp             SCC---CHHHHTTTTTTTTSCEEEEEEEETTS
T ss_pred             CCcchHHHHHHHHHHcCCCCeeEEEEEEeCCC
Confidence            9999999999999999987765  33444443

>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=95.37  E-value=0.0067  Score=56.94  Aligned_cols=91  Identities=10%  Similarity=-0.073  Sum_probs=55.1

Q ss_pred             cccccc-CCCcHHHHHHHHhC--CC------CCCchH-HHHHHHHHHcC-CCeeeeccc-CCccc----ceeeecCC-CC
Q psy7691          39 TQELTE-GCFPNAVLQHLKGQ--GF------EEPTAI-QAQGWPIALSG-RDMVGIAQT-GSGKT----LAVINFDY-PN  101 (165)
Q Consensus        39 i~~f~~-l~l~~~l~~~l~~~--g~------~~~t~~-Q~~a~~~~l~G-~di~~~a~t-gsGKt----~~~~~~~l-P~  101 (165)
                      +..|.. ..-.+.+.+.|.+.  ++      ...+.. +.+.+..+..| .+++++... +.|=.    ..++.++. +.
T Consensus       815 vlvf~~~v~~~~~l~~~L~~~~p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~v~e~GiDip~v~~VIi~~~~~~  894 (1151)
T 2eyq_A          815 VYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHF  894 (1151)
T ss_dssp             EEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEEETTTTSS
T ss_pred             EEEEECCHHHHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECCcceeeecccCCcEEEEeCCCCC
Confidence            444543 45667777777664  33      222333 33455555555 355544322 23321    14565655 34


Q ss_pred             ChhHHHHhhccCCCCCCCCceEEEECCC
Q psy7691         102 SSEDYIHRIGRTGRCASSGTAYTFFTPN  129 (165)
Q Consensus       102 ~~~~~i~r~gr~~r~~~~g~~~~~~~p~  129 (165)
                      +..+|.||+||+||.|..|.+++++.+.
T Consensus       895 ~l~~l~Qr~GRvgR~g~~g~~~ll~~~~  922 (1151)
T 2eyq_A          895 GLAQLHQLRGRVGRSHHQAYAWLLTPHP  922 (1151)
T ss_dssp             CHHHHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             CHHHHHHHHhccCcCCCceEEEEEECCc
Confidence            6788999999999999999999888764

>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=95.03  E-value=0.026  Score=50.90  Aligned_cols=68  Identities=28%  Similarity=0.367  Sum_probs=52.0

Q ss_pred             hCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHH
Q psy7691          57 GQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKE  136 (165)
Q Consensus        57 ~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~  136 (165)
                      ..|.+ |+++|..+.-.+..|+  ++.-.||+|||+++.   +|.    |++-+        .|..+.+++|+ +.+|.+
T Consensus        71 ~lg~r-~~dvQligg~~L~~G~--iaEM~TGEGKTLva~---lp~----~lnAL--------~G~~vhVvT~n-dyLA~r  131 (822)
T 3jux_A           71 TLGMR-PFDVQVMGGIALHEGK--VAEMKTGEGKTLAAT---MPI----YLNAL--------IGKGVHLVTVN-DYLARR  131 (822)
T ss_dssp             HTSCC-CCHHHHHHHHHHHTTC--EEECCTTSCHHHHTH---HHH----HHHHT--------TSSCEEEEESS-HHHHHH
T ss_pred             HhCCC-CcHHHHHHHHHHhCCC--hhhccCCCCccHHHH---HHH----HHHHh--------cCCceEEEecc-HHHHHh
Confidence            35886 8999999888888886  678889999999888   883    66644        24568889999 777776


Q ss_pred             HHHHHHh
Q psy7691         137 LIAVLTE  143 (165)
Q Consensus       137 i~~~l~~  143 (165)
                      -.+.+..
T Consensus       132 dae~m~~  138 (822)
T 3jux_A          132 DALWMGP  138 (822)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            6555544

>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=94.60  E-value=0.022  Score=50.00  Aligned_cols=93  Identities=11%  Similarity=0.070  Sum_probs=59.0

Q ss_pred             CccccccC-CCcHHHHHHHHhCCCCC-------CchHHHHHHHHHHcCCC---eeeec--ccCCcccc----eeeecCCC
Q psy7691          38 PTQELTEG-CFPNAVLQHLKGQGFEE-------PTAIQAQGWPIALSGRD---MVGIA--QTGSGKTL----AVINFDYP  100 (165)
Q Consensus        38 ~i~~f~~l-~l~~~l~~~l~~~g~~~-------~t~~Q~~a~~~~l~G~d---i~~~a--~tgsGKt~----~~~~~~lP  100 (165)
                      .++.|++. ...+.+.+.|...|+..       +.....+.+..+..|..   ++.++  .-|.|=++    .+++||+|
T Consensus       418 k~lIFs~~~~~~~~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~v~L~st~a~g~Glnl~~a~~Vi~~d~~  497 (644)
T 1z3i_X          418 KVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPD  497 (644)
T ss_dssp             EEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTTEEEEEECSCC
T ss_pred             EEEEEEccHHHHHHHHHHHHHCCCCEEEEeCCCCHHHHHHHHHHhcCCCCCcEEEEEecccccCCcccccCCEEEEECCC
Confidence            45667765 45556666677666632       12233456667777643   23222  22344332    68999999


Q ss_pred             CChhHHHHhhccCCCCCCCCceEE--EECCCc
Q psy7691         101 NSSEDYIHRIGRTGRCASSGTAYT--FFTPNN  130 (165)
Q Consensus       101 ~~~~~~i~r~gr~~r~~~~g~~~~--~~~p~~  130 (165)
                      -++..|.|++||+.|.|.+..+.+  +++..+
T Consensus       498 wnp~~~~Qa~gR~~R~Gq~~~v~v~~lv~~~t  529 (644)
T 1z3i_X          498 WNPANDEQAMARVWRDGQKKTCYIYRLLSTGT  529 (644)
T ss_dssp             SSHHHHHHHHTTSSSTTCCSCEEEEEEEETTS
T ss_pred             CCccHHHHHHHhhhhcCCCCceEEEEEEECCC
Confidence            999999999999999998766443  455543

>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=94.04  E-value=0.037  Score=50.94  Aligned_cols=65  Identities=12%  Similarity=0.067  Sum_probs=42.8

Q ss_pred             CCchHHHHHHHHHHcC--CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALSG--RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIA  139 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G--~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~  139 (165)
                      .+.+.|.+++..++..  ..++.+++||+|||...+   .      .++..-+.++.    ..+++++|+  .++.|-.+
T Consensus       153 ~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai---~------~i~~l~~~g~~----~rvLIVvP~--sLl~Qw~~  217 (968)
T 3dmq_A          153 SLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAG---M------ILHQQLLSGAA----ERVLIIVPE--TLQHQWLV  217 (968)
T ss_dssp             CCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHH---H------HHHHHHHTSSC----CCEEEECCT--TTHHHHHH
T ss_pred             CCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHH---H------HHHHHHHhCCC----CeEEEEeCH--HHHHHHHH
Confidence            4789999999887763  478889999999998665   2      33333222221    248899998  34444433


Q ss_pred             HH
Q psy7691         140 VL  141 (165)
Q Consensus       140 ~l  141 (165)
                      -+
T Consensus       218 E~  219 (968)
T 3dmq_A          218 EM  219 (968)
T ss_dssp             HH
T ss_pred             HH
Confidence            33

>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=93.65  E-value=0.021  Score=53.13  Aligned_cols=38  Identities=24%  Similarity=0.257  Sum_probs=29.6

Q ss_pred             ccceeeecCCCCChhHHHHhhccCCCCCCC----CceEEEEC
Q psy7691          90 KTLAVINFDYPNSSEDYIHRIGRTGRCASS----GTAYTFFT  127 (165)
Q Consensus        90 Kt~~~~~~~lP~~~~~~i~r~gr~~r~~~~----g~~~~~~~  127 (165)
                      ..+.++++|.|.....|+|++||++|.+..    |.++.++.
T Consensus       666 P~l~tlylDkpl~~~~liQaIGRtnR~~~~~K~~G~IVdf~~  707 (1038)
T 2w00_A          666 PTLNTLFVDKNLRYHGLMQAFSRTNRIYDATKTFGNIVTFRD  707 (1038)
T ss_dssp             TTEEEEEEESCCCHHHHHHHHHTTCCCCCTTCCSEEEEESSC
T ss_pred             ccccEEEEccCCCccceeehhhccCcCCCCCCCcEEEEEccc
Confidence            345688899999999999999999998864    44454443

>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=93.39  E-value=0.13  Score=44.94  Aligned_cols=70  Identities=13%  Similarity=0.162  Sum_probs=47.9

Q ss_pred             CCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHH
Q psy7691          60 FEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIA  139 (165)
Q Consensus        60 ~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~  139 (165)
                      +....+.|..|+..++...-.++.+++|+|||..+..         .+..+-+.     .+..+++++|+ ...+.++.+
T Consensus       178 ~~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~~---------~i~~l~~~-----~~~~ilv~a~t-n~A~~~l~~  242 (624)
T 2gk6_A          178 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSAT---------IVYHLARQ-----GNGPVLVCAPS-NIAVDQLTE  242 (624)
T ss_dssp             SCCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHHH---------HHHHHHTS-----SSCCEEEEESS-HHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHHH---------HHHHHHHc-----CCCeEEEEeCc-HHHHHHHHH
Confidence            3456789999998888776778999999999975331         22222221     34578888888 566667766


Q ss_pred             HHHhc
Q psy7691         140 VLTEA  144 (165)
Q Consensus       140 ~l~~~  144 (165)
                      .+...
T Consensus       243 ~l~~~  247 (624)
T 2gk6_A          243 KIHQT  247 (624)
T ss_dssp             HHHTT
T ss_pred             HHHhc
Confidence            66543

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=93.30  E-value=0.11  Score=45.39  Aligned_cols=65  Identities=23%  Similarity=0.283  Sum_probs=43.0

Q ss_pred             CchHHHHHHHHHHcCCC-eeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHH
Q psy7691          63 PTAIQAQGWPIALSGRD-MVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVL  141 (165)
Q Consensus        63 ~t~~Q~~a~~~~l~G~d-i~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l  141 (165)
                      ..+.|.+|+..++...+ .++.+|+|||||..++.         .+..+-.      .|..+++++|+. ..+..|.+-+
T Consensus       190 LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~---------~I~~l~~------~~~~ILv~a~TN-~AvD~i~erL  253 (646)
T 4b3f_X          190 LDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVE---------IILQAVK------QGLKVLCCAPSN-IAVDNLVERL  253 (646)
T ss_dssp             CCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHH---------HHHHHHH------TTCCEEEEESSH-HHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHH---------HHHHHHh------CCCeEEEEcCch-HHHHHHHHHH
Confidence            46789999998887776 46899999999975431         2322222      234689999984 4445555444


Q ss_pred             Hh
Q psy7691         142 TE  143 (165)
Q Consensus       142 ~~  143 (165)
                      ..
T Consensus       254 ~~  255 (646)
T 4b3f_X          254 AL  255 (646)
T ss_dssp             HH
T ss_pred             Hh
Confidence            43

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=93.11  E-value=0.088  Score=47.34  Aligned_cols=94  Identities=14%  Similarity=0.134  Sum_probs=59.9

Q ss_pred             CCccccccC-CCcHHHHHHHHhCCCCC-------CchHHHHHHHHHHcCC-C---eeeec-ccCCcccc----eeeecCC
Q psy7691          37 CPTQELTEG-CFPNAVLQHLKGQGFEE-------PTAIQAQGWPIALSGR-D---MVGIA-QTGSGKTL----AVINFDY   99 (165)
Q Consensus        37 ~~i~~f~~l-~l~~~l~~~l~~~g~~~-------~t~~Q~~a~~~~l~G~-d---i~~~a-~tgsGKt~----~~~~~~l   99 (165)
                      ..++.|++. .+...+...|...|+..       +...+..++..+..+. +   ++++. .-|.|=++    .+++||.
T Consensus       573 ~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F~~~~~~~~v~LlSt~agg~GlNL~~a~~VI~~D~  652 (800)
T 3mwy_W          573 HRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLMTADTVVIFDS  652 (800)
T ss_dssp             CCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTTSSTTCSCCCEEEEHHHHTTTCCCTTCCEEEESSC
T ss_pred             CeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhCCCCCceEEEEecccccCCCCccccceEEEecC
Confidence            357788876 56667777787777743       2233444555555432 2   22222 22344322    6899999


Q ss_pred             CCChhHHHHhhccCCCCCCCCceEE--EECCCc
Q psy7691         100 PNSSEDYIHRIGRTGRCASSGTAYT--FFTPNN  130 (165)
Q Consensus       100 P~~~~~~i~r~gr~~r~~~~g~~~~--~~~p~~  130 (165)
                      |-++..++|++||+.|.|.+..+.+  +++..+
T Consensus       653 ~wnp~~~~Qa~gR~~RiGQ~k~V~Vyrlv~~~T  685 (800)
T 3mwy_W          653 DWNPQADLQAMARAHRIGQKNHVMVYRLVSKDT  685 (800)
T ss_dssp             CSCSHHHHHHHTTTSCSSCCSCEEEEEEEETTS
T ss_pred             CCChhhHHHHHHHHHhcCCCceEEEEEEecCCC
Confidence            9999999999999999998766543  455543

>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=92.73  E-value=0.11  Score=43.51  Aligned_cols=71  Identities=20%  Similarity=0.220  Sum_probs=44.9

Q ss_pred             HhCCCCCCchHHHHHHHHHHcC----C-CeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCc
Q psy7691          56 KGQGFEEPTAIQAQGWPIALSG----R-DMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN  130 (165)
Q Consensus        56 ~~~g~~~~t~~Q~~a~~~~l~G----~-di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~  130 (165)
                      .-+.|..+++.|.+++..++..    . .+++.|+.|||||....      .   .+..+.+.+.     ..+++++|+ 
T Consensus        19 ~p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll~------~---~~~~l~~~~~-----~~il~~a~T-   83 (459)
T 3upu_A           19 SHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLTK------F---IIEALISTGE-----TGIILAAPT-   83 (459)
T ss_dssp             --CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHHH------H---HHHHHHHTTC-----CCEEEEESS-
T ss_pred             CCCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHHH------H---HHHHHHhcCC-----ceEEEecCc-
Confidence            3356888999999998876432    3 78899999999996432      0   2222222111     367888888 


Q ss_pred             HHHHHHHHHHH
Q psy7691         131 GKQAKELIAVL  141 (165)
Q Consensus       131 ~~~~~~i~~~l  141 (165)
                      ...+..+.+.+
T Consensus        84 ~~Aa~~l~~~~   94 (459)
T 3upu_A           84 HAAKKILSKLS   94 (459)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHhhh
Confidence            45555555444

>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=92.70  E-value=0.1  Score=45.11  Aligned_cols=68  Identities=22%  Similarity=0.207  Sum_probs=42.7

Q ss_pred             CCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCC-CCCCCceEEEECCCcHHHHHHHHH
Q psy7691          61 EEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGR-CASSGTAYTFFTPNNGKQAKELIA  139 (165)
Q Consensus        61 ~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r-~~~~g~~~~~~~p~~~~~~~~i~~  139 (165)
                      ..+++.|.+++.  .....+++.|+.|||||...            ++|+...-. .+.....+++++++ ...+.++.+
T Consensus         8 ~~Ln~~Q~~av~--~~~~~~lV~a~aGsGKT~~l------------~~ri~~l~~~~~~~~~~iL~ltft-~~aa~e~~~   72 (647)
T 3lfu_A            8 DSLNDKQREAVA--APRSNLLVLAGAGSGKTRVL------------VHRIAWLMSVENCSPYSIMAVTFT-NKAAAEMRH   72 (647)
T ss_dssp             TTCCHHHHHHHT--CCSSCEEEEECTTSCHHHHH------------HHHHHHHHHTSCCCGGGEEEEESS-HHHHHHHHH
T ss_pred             hcCCHHHHHHHh--CCCCCEEEEECCCCCHHHHH------------HHHHHHHHHhCCCChhhEEEEecc-HHHHHHHHH
Confidence            357889999875  33557889999999999743            333322111 12234578889988 555555555


Q ss_pred             HHHh
Q psy7691         140 VLTE  143 (165)
Q Consensus       140 ~l~~  143 (165)
                      -+..
T Consensus        73 rl~~   76 (647)
T 3lfu_A           73 RIGQ   76 (647)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4443

>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=92.56  E-value=0.12  Score=48.72  Aligned_cols=66  Identities=23%  Similarity=0.175  Sum_probs=43.7

Q ss_pred             CCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccC---CCCCCCCceEEEECCCcHHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRT---GRCASSGTAYTFFTPNNGKQAKELI  138 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~---~r~~~~g~~~~~~~p~~~~~~~~i~  138 (165)
                      .+|+-|.++|.  ..+.++++.|..|||||..            .++|+.+-   ++.+.....+++++.+ ...+..+.
T Consensus        10 ~~t~eQ~~~i~--~~~~~~~v~a~AGSGKT~v------------l~~ri~~ll~~~~~~~~~~~il~~Tft-~~aa~e~~   74 (1232)
T 3u4q_A           10 TWTDDQWNAIV--STGQDILVAAAAGSGKTAV------------LVERMIRKITAEENPIDVDRLLVVTFT-NASAAEMK   74 (1232)
T ss_dssp             CCCHHHHHHHH--CCSSCEEEEECTTCCHHHH------------HHHHHHHHHSCSSSCCCGGGEEEECSS-HHHHHHHH
T ss_pred             CCCHHHHHHHh--CCCCCEEEEecCCCcHHHH------------HHHHHHHHHhcCCCCCCccceEEEecc-HHHHHHHH
Confidence            47899999874  4588999999999999974            24444322   2222345579999999 44444444


Q ss_pred             HHHH
Q psy7691         139 AVLT  142 (165)
Q Consensus       139 ~~l~  142 (165)
                      +-+.
T Consensus        75 ~ri~   78 (1232)
T 3u4q_A           75 HRIA   78 (1232)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4443

>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=92.56  E-value=0.19  Score=45.42  Aligned_cols=70  Identities=13%  Similarity=0.154  Sum_probs=48.4

Q ss_pred             CCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHH
Q psy7691          61 EEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAV  140 (165)
Q Consensus        61 ~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~  140 (165)
                      ....+.|.+|+..++.+.-.++.+++|+|||..+..         .+..+-+.     .+..+++++|+ ...+.++.+.
T Consensus       355 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti~~---------~i~~l~~~-----~~~~ilv~a~t-n~A~~~l~~~  419 (800)
T 2wjy_A          355 PDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSAT---------IVYHLARQ-----GNGPVLVCAPS-NIAVDQLTEK  419 (800)
T ss_dssp             CCCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHHHH---------HHHHHHTT-----CSSCEEEEESS-HHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHHHH---------HHHHHHHc-----CCCcEEEEcCc-HHHHHHHHHH
Confidence            346789999999888776778999999999975431         22222221     34578888998 5666777776


Q ss_pred             HHhcC
Q psy7691         141 LTEAS  145 (165)
Q Consensus       141 l~~~~  145 (165)
                      +...+
T Consensus       420 l~~~g  424 (800)
T 2wjy_A          420 IHQTG  424 (800)
T ss_dssp             HHTTT
T ss_pred             HHHhC
Confidence            65543

>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=91.78  E-value=0.17  Score=43.99  Aligned_cols=63  Identities=22%  Similarity=0.163  Sum_probs=44.5

Q ss_pred             CchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHH
Q psy7691          63 PTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVL  141 (165)
Q Consensus        63 ~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l  141 (165)
                      .++.|..++..++.+..+++.++.|+|||..+..         .+.....      .|..+++++|+ ...+..+.+.+
T Consensus       190 L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i~~---------l~~~l~~------~g~~Vl~~ApT-~~Aa~~L~e~~  252 (574)
T 3e1s_A          190 LSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTKA---------VADLAES------LGLEVGLCAPT-GKAARRLGEVT  252 (574)
T ss_dssp             CCHHHHHHHHHHTTCSEEEEECCTTSCHHHHHHH---------HHHHHHH------TTCCEEEEESS-HHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHHHH---------HHHHHHh------cCCeEEEecCc-HHHHHHhHhhh
Confidence            6789999999999888899999999999974320         2222211      34567888898 55566665543

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=91.74  E-value=0.4  Score=43.05  Aligned_cols=86  Identities=15%  Similarity=0.234  Sum_probs=50.7

Q ss_pred             CccCChHhhcCCHHHHHHHHhhcCcEE---ecCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHH----c
Q psy7691           4 HAKTQERAARLSESEVEAFRQKKEITV---KGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIAL----S   76 (165)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~i~~---~~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l----~   76 (165)
                      +|-....+.....+.++.|........   .....+.....|..+...+...     .+. .+.+.|.+++..++    .
T Consensus       181 tWe~~~~~~~~~~~~i~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~-----~~~-~Lr~yQ~egv~~l~~~~~~  254 (800)
T 3mwy_W          181 TWENATDIVKLAPEQVKHFQNRENSKILPQYSSNYTSQRPRFEKLSVQPPFI-----KGG-ELRDFQLTGINWMAFLWSK  254 (800)
T ss_dssp             BCCBHHHHTTTCHHHHHHHHHTTTCTTCSTTCCCCCSCCCCCCCCSSCCTTC-----CSS-CCCTHHHHHHHHHHHHHTT
T ss_pred             cccchhhhhhhhHHHHHHHHHhhhcccCCcchhcccccCCcccccccCCCcc-----CCC-CcCHHHHHHHHHHHHHhhc
Confidence            344445566677788888865332111   1111122233455443322211     122 57889999987554    8


Q ss_pred             CCCeeeecccCCcccceee
Q psy7691          77 GRDMVGIAQTGSGKTLAVI   95 (165)
Q Consensus        77 G~di~~~a~tgsGKt~~~~   95 (165)
                      |...+....+|.|||+..+
T Consensus       255 ~~~~ILademGlGKT~~ai  273 (800)
T 3mwy_W          255 GDNGILADEMGLGKTVQTV  273 (800)
T ss_dssp             TCCEEECCCTTSSTTHHHH
T ss_pred             CCCEEEEeCCCcchHHHHH
Confidence            8899999999999998654

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=91.37  E-value=0.18  Score=45.66  Aligned_cols=70  Identities=16%  Similarity=0.194  Sum_probs=46.0

Q ss_pred             CCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHH
Q psy7691          60 FEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIA  139 (165)
Q Consensus        60 ~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~  139 (165)
                      +....+.|.+|+..++.+.-.++.|++|+|||..+..         .+.++-+.     .+..+++++|+ ...+..+.+
T Consensus       358 ~~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~~---------~i~~l~~~-----~~~~ILv~a~t-n~A~d~l~~  422 (802)
T 2xzl_A          358 FAQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSAT---------IVYHLSKI-----HKDRILVCAPS-NVAVDHLAA  422 (802)
T ss_dssp             SCCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHH---------HHHHHHHH-----HCCCEEEEESS-HHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHH---------HHHHHHhC-----CCCeEEEEcCc-HHHHHHHHH
Confidence            3446789999998888766678999999999975431         22222110     23468888888 555556655


Q ss_pred             HHHhc
Q psy7691         140 VLTEA  144 (165)
Q Consensus       140 ~l~~~  144 (165)
                      .+...
T Consensus       423 rL~~~  427 (802)
T 2xzl_A          423 KLRDL  427 (802)
T ss_dssp             HHHHT
T ss_pred             HHHhh
Confidence            55443

>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=90.76  E-value=0.24  Score=43.75  Aligned_cols=67  Identities=27%  Similarity=0.364  Sum_probs=46.2

Q ss_pred             CCCCCCchHHHHHHHHHHc----CC-CeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHH
Q psy7691          58 QGFEEPTAIQAQGWPIALS----GR-DMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGK  132 (165)
Q Consensus        58 ~g~~~~t~~Q~~a~~~~l~----G~-di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~  132 (165)
                      .+| .|+..|..++..+..    |. .....+.||||||+.+.+         .+.+.++         .+++++|+ ..
T Consensus         5 ~~~-~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a~---------~~~~~~~---------~~lvv~~~-~~   64 (664)
T 1c4o_A            5 RGP-SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAK---------VIEALGR---------PALVLAPN-KI   64 (664)
T ss_dssp             CSC-CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH---------HHHHHTC---------CEEEEESS-HH
T ss_pred             CCC-CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHHH---------HHHHhCC---------CEEEEecC-HH
Confidence            367 699999998876543    32 356789999999986541         4455433         37888888 66


Q ss_pred             HHHHHHHHHHhc
Q psy7691         133 QAKELIAVLTEA  144 (165)
Q Consensus       133 ~~~~i~~~l~~~  144 (165)
                      ++.|+..-+..-
T Consensus        65 ~A~ql~~el~~~   76 (664)
T 1c4o_A           65 LAAQLAAEFREL   76 (664)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            666666666554

>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=89.72  E-value=0.27  Score=43.03  Aligned_cols=72  Identities=17%  Similarity=0.107  Sum_probs=43.2

Q ss_pred             CCchHHHHHHHHHH---------cCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCC-CCCCceEEEECCCc-
Q psy7691          62 EPTAIQAQGWPIAL---------SGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRC-ASSGTAYTFFTPNN-  130 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l---------~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~-~~~g~~~~~~~p~~-  130 (165)
                      .+.|.|.+++..+.         .+...+....+|.|||+..+   .      ++...-+.+.. +.....+++++|.. 
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i---~------~i~~l~~~~~~~~p~~~~~LiV~P~sl  125 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCI---T------LIWTLLKQSPDCKPEIDKVIVVSPSSL  125 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHH---H------HHHHHHHCCTTSSCSCSCEEEEECHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHH---H------HHHHHHHhCccccCCCCcEEEEecHHH
Confidence            47889999988763         34567888999999998665   1      33333222211 12234578888873 


Q ss_pred             -HHHHHHHHHHHH
Q psy7691         131 -GKQAKELIAVLT  142 (165)
Q Consensus       131 -~~~~~~i~~~l~  142 (165)
                       .....++.+++.
T Consensus       126 l~qW~~E~~~~~~  138 (644)
T 1z3i_X          126 VRNWYNEVGKWLG  138 (644)
T ss_dssp             HHHHHHHHHHHHG
T ss_pred             HHHHHHHHHHHcC
Confidence             223344555543

>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=89.31  E-value=0.21  Score=43.77  Aligned_cols=67  Identities=22%  Similarity=0.230  Sum_probs=42.1

Q ss_pred             CCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCC-CCCCCceEEEECCCcHHHHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGR-CASSGTAYTFFTPNNGKQAKELIAV  140 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r-~~~~g~~~~~~~p~~~~~~~~i~~~  140 (165)
                      .+++.|.+++..  .+..+++.|..|||||...            ++|+.+.-. .+.....+++++.+ +..+..+.+-
T Consensus         2 ~L~~~Q~~av~~--~~~~~lV~AgaGSGKT~~l------------~~ri~~ll~~~~~~~~~IL~lTfT-~~Aa~em~~R   66 (673)
T 1uaa_A            2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVI------------TNKIAHLIRGCGYQARHIAAVTFT-NKAAREMKER   66 (673)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHH------------HHHHHHHHHHHCCCGGGEEEEESS-HHHHHHHHHH
T ss_pred             CCCHHHHHHHhC--CCCCEEEEeCCCCChHHHH------------HHHHHHHHHhcCCCHHHeEEEecc-HHHHHHHHHH
Confidence            367899998753  3567889999999999743            233221111 02233468888888 5566666655


Q ss_pred             HHh
Q psy7691         141 LTE  143 (165)
Q Consensus       141 l~~  143 (165)
                      +..
T Consensus        67 l~~   69 (673)
T 1uaa_A           67 VGQ   69 (673)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            554

>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=87.97  E-value=0.56  Score=41.63  Aligned_cols=63  Identities=22%  Similarity=0.147  Sum_probs=39.3

Q ss_pred             CCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCC-CCCCCceEEEECCCcHHHHHHHH
Q psy7691          61 EEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGR-CASSGTAYTFFTPNNGKQAKELI  138 (165)
Q Consensus        61 ~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r-~~~~g~~~~~~~p~~~~~~~~i~  138 (165)
                      ..+++.|.+|+..  ....+++.|..|||||...            ++|+.+.-. .+-....+++++-+ ...+..+.
T Consensus        10 ~~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL------------~~ri~~ll~~~~~~p~~IL~vTFT-nkAA~Em~   73 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVL------------THRIAYLMAEKHVAPWNILAITFT-NKAAREMR   73 (724)
T ss_dssp             TTSCHHHHHHHHC--CSSCEEEEECTTSCHHHHH------------HHHHHHHHHTTCCCGGGEEEEESS-HHHHHHHH
T ss_pred             hhCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHH------------HHHHHHHHHhcCCCHHHeEEEecc-HHHHHHHH
Confidence            4578999998753  3568899999999999743            333322111 12234468888888 43333333

>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=80.82  E-value=1.2  Score=31.76  Aligned_cols=18  Identities=28%  Similarity=0.481  Sum_probs=15.6

Q ss_pred             cCCCeeeecccCCcccce
Q psy7691          76 SGRDMVGIAQTGSGKTLA   93 (165)
Q Consensus        76 ~G~di~~~a~tgsGKt~~   93 (165)
                      .|..++..+++|+|||..
T Consensus        37 ~g~~~~l~G~~G~GKTtL   54 (180)
T 3ec2_A           37 EGKGLTFVGSPGVGKTHL   54 (180)
T ss_dssp             GCCEEEECCSSSSSHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            477889999999999974

---

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	165
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	1e-13
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	5e-13
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	1e-12
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	3e-11
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	6e-11
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	6e-11
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	8e-11
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	1e-10
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	3e-10
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	5e-10
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	5e-10
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	7e-10
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	1e-09
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	2e-09
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	4e-09
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	4e-09
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	4e-09
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	1e-08
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	3e-08
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	7e-08
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	3e-07
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	8e-07
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	2e-06
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	2e-05
d2p6ra4	201	c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglob	6e-05
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	0.002

>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 = 64.2 bits (155), Expect = 1e-13
 Identities = 19/71 (26%), Positives = 30/71 (42%)

Query: 27 EITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQT 86
           +T    +     +   E      +  ++    ++ PT IQ    P  L  RD++  AQT
Sbjct: 8  SVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQT 67

Query: 87 GSGKTLAVINF 97
          GSGKT A +  
Sbjct: 68 GSGKTAAFLIP 78

>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 = 62.2 bits (150), Expect = 5e-13
 Identities = 18/75 (24%), Positives = 31/75 (41%)

Query: 34  NIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
           N         +     ++L+ +   GFE+P+AIQ +     + G D++  AQ+G+GKT  
Sbjct: 6   NWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTAT 65

Query: 94  VINFDYPNSSEDYIH 108
                      D   
Sbjct: 66  FAISILQQIELDLKA 80

>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 = 61.1 bits (147), Expect = 1e-12
 Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 39 TQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTL 92
           +EL E    +  +  LK +G EE    QA+      SG++++    T +GKTL
Sbjct: 3  VEELAES-ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTL 55

>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 = 57.2 bits (137), Expect = 3e-11
 Identities = 16/62 (25%), Positives = 28/62 (45%)

Query: 47  FPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDY 106
               +L+ +   GFE+P+AIQ +     + GRD++  +Q+G+GKT               
Sbjct: 24  LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV 83

Query: 107 IH 108
             
Sbjct: 84  RE 85

>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 = 56.1 bits (134), Expect = 6e-11
 Identities = 18/62 (29%), Positives = 31/62 (50%)

Query: 47  FPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDY 106
               +L  +   GFE+P+ IQ +  P+A++GRD++  A+ G+GKT A +           
Sbjct: 8   LKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKL 67

Query: 107 IH 108
             
Sbjct: 68  NK 69

>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 = 56.2 bits (134), Expect = 6e-11
 Identities = 21/62 (33%), Positives = 31/62 (50%)

Query: 47  FPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDY 106
           F   +++ +K   F +PT IQ +  P AL G  MVG +QTG+GKT A +         + 
Sbjct: 8   FQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPER 67

Query: 107 IH 108
             
Sbjct: 68  AE 69

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 286

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 = 56.8 bits (136), Expect = 8e-11
 Identities = 10/37 (27%), Positives = 14/37 (37%), Gaps = 1/37 (2%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN 130
           V+ ++   S+   I R GRTGR    G          
Sbjct: 241 VVFYEPVPSAIRSIQRRGRTGR-HMPGRVIILMAKGT 276

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 162

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 = 54.9 bits (131), Expect = 1e-10
 Identities = 24/64 (37%), Positives = 33/64 (51%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ 153
           VIN+D P + E+YIHRIGR GR    G A  F T  +    +EL    +   + +P  + 
Sbjct: 99  VINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIA 158

Query: 154 DLAN 157
            L N
Sbjct: 159 TLLN 162

>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 = 54.4 bits (130), Expect = 3e-10
 Identities = 19/60 (31%), Positives = 31/60 (51%)

Query: 34 NIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
          N      +  +      +L+ + G GFEEP+AIQ +     + G D++  AQ+G+GKT  
Sbjct: 4  NYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGT 63

>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 = 54.1 bits (129), Expect = 5e-10
 Identities = 12/46 (26%), Positives = 14/46 (30%)

Query: 50 AVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVI 95
                  +   EP AIQ       L        A TG GKT   +
Sbjct: 31 KEFVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGL 76

>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 = 53.7 bits (128), Expect = 5e-10
 Identities = 15/45 (33%), Positives = 26/45 (57%)

Query: 47 FPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKT 91
              +L+ +   GFE P+ +Q +  P A+ G D++  A++G GKT
Sbjct: 8  LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKT 52

>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 = 53.4 bits (127), Expect = 7e-10
 Identities = 19/62 (30%), Positives = 32/62 (51%)

Query: 47  FPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDY 106
               +L  +   G+E+P+ IQ +  PIALSGRD++  A+ G+GK+ A +           
Sbjct: 10  LKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKK 69

Query: 107 IH 108
            +
Sbjct: 70  DN 71

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]} 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: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 53.0 bits (126), Expect = 1e-09
 Identities = 9/41 (21%), Positives = 15/41 (36%), Gaps = 3/41 (7%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTA---YTFFTPNNG 131
            +      S+ +YI R+GR  R +        Y   +   G
Sbjct: 160 GVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRGTG 200

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 299

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

 Score = 53.0 bits (127), Expect = 2e-09
 Identities = 8/48 (16%), Positives = 12/48 (25%), Gaps = 1/48 (2%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVL 141
           +     P  +     R GRTGR    G               +   + 
Sbjct: 121 IETTTLPQDAVSRTQRRGRTGRGK-PGIYRFVAPGERPSGMFDSSVLC 167

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 155

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 = 50.7 bits (120), Expect = 4e-09
 Identities = 17/44 (38%), Positives = 24/44 (54%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL 137
           VIN+  P + E Y+HRIGRTGR    G A +       K+ + +
Sbjct: 100 VINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYI 143

>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 = 51.2 bits (121), Expect = 4e-09
 Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 48 PNAVLQHLKGQ-GFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKT 91
           +   Q L+   G+++    Q +     LSGRD + +  TG GK+
Sbjct: 10 ESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKS 54

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 138

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

 Score = 50.1 bits (119), Expect = 4e-09
 Identities = 15/91 (16%), Positives = 22/91 (24%), Gaps = 2/91 (2%)

Query: 39  TQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFD 98
             EL        +      +G +           +  +   M G             +  
Sbjct: 48  CDELAAKLVALGINAVAYYRGLDVSVIPTNGDVVVVATDALMTGFTGDFDSVIDCNTSDG 107

Query: 99  YPNSSEDYIHRIGRTGRCASSGTAYTFFTPN 129
            P  +     R GRTGR       Y F  P 
Sbjct: 108 KPQDAVSRTQRRGRTGRGKPG--IYRFVAPG 136

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 168

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 = 49.6 bits (117), Expect = 1e-08
 Identities = 21/62 (33%), Positives = 34/62 (54%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ 153
           +IN+D PN+ E YIHRIGR+GR    G A  F   ++ +  +++    +     +P  + 
Sbjct: 106 IINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVA 165

Query: 154 DL 155
           DL
Sbjct: 166 DL 167

>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 = 48.9 bits (116), Expect = 3e-08
 Identities = 28/114 (24%), Positives = 48/114 (42%), Gaps = 2/114 (1%)

Query: 47  FPNAVLQHLKGQGFEEPTAIQAQGWPIALSGR-DMVGIAQTGSGKTLAVINFDYPNSSED 105
             + +L  ++ +GFE+PT IQ +  P+ L+   ++V  A+TGSGKT +         +E+
Sbjct: 11  LSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN 70

Query: 106 YIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQDLANSN 159
                                   + K  K L        + I PQ++ L N+N
Sbjct: 71  NGIEAIILTPTRELAIQV-ADEIESLKGNKNLKIAKIYGGKAIYPQIKALKNAN 123

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 248

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 = 48.2 bits (114), Expect = 7e-08
 Identities = 5/84 (5%), Positives = 19/84 (22%), Gaps = 4/84 (4%)

Query: 76  SGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAK 135
                +        +    +    P+    +   I      +        +   N  + +
Sbjct: 78  HYYGTLVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLLAYLYRNVDEIE 133

Query: 136 ELIAVLTEASQPIPPQLQDLANSN 159
            L+  +      +   L+ +    
Sbjct: 134 RLLPAVERHIDEVREILKKVMGKE 157

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 171

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 = 45.8 bits (107), Expect = 3e-07
 Identities = 21/59 (35%), Positives = 30/59 (50%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQL 152
           VINFD+P ++E Y+HRIGR+GR    G A      N+     ++   L      IP  +
Sbjct: 104 VINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATI 162

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]} Length = 305

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

 Score = 44.1 bits (103), Expect = 2e-06
 Identities = 7/40 (17%), Positives = 13/40 (32%)

Query: 88  SGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFT 127
            G+   ++    P +      R GR GR   +      + 
Sbjct: 259 DGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYM 298

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 168

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 = 40.8 bits (94), Expect = 2e-05
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 94  VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN-GKQAKELIAVLTEASQPIPPQL 152
             N+D P  S+ Y+HR+ R GR  + G A TF +  N  K   ++          +P ++
Sbjct: 99  AFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI 158

Query: 153 Q 153
            
Sbjct: 159 D 159

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 201

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 = 39.5 bits (91), Expect = 6e-05
 Identities = 8/43 (18%), Positives = 13/43 (30%), Gaps = 2/43 (4%)

Query: 96  NFDYPNSSEDYIHRIGRTGRC--ASSGTAYTFFTPNNGKQAKE 136
            +       +Y    GR GR      G A       + + A +
Sbjct: 151 GYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDREIAVK 193

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 34.8 bits (78), Expect = 0.002
 Identities = 8/38 (21%), Positives = 15/38 (39%), Gaps = 1/38 (2%)

Query: 58 QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVI 95
          +   +P   Q   +       + + +  TG GKTL  +
Sbjct: 5  RDLIQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAM 41

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	165
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.82
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.81
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.8
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.8
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.79
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.78
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.68
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.68
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.67
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.45
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.43
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.31
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.28
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.26
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.24
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.23
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.15
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.14
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.0
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	98.54
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	98.42
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	98.29
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	98.12
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	98.1
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	97.82
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	97.67
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	97.52
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	97.51
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	97.35
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	97.21
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	97.06
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	96.86
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.85
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	96.59
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	96.34
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	96.18
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	95.17
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	95.07
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	94.15
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	93.2
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	92.78
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	87.05
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	84.13
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	83.62
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	82.97
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	82.33
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	80.86

>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=99.82  E-value=1e-20  Score=144.79  Aligned_cols=102  Identities=24%  Similarity=0.330  Sum_probs=92.7

Q ss_pred             cCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhc
Q psy7691          32 GNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIG  111 (165)
Q Consensus        32 ~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~g  111 (165)
                      +.+.|+++.+|+++++++.++++|+++||..||++|.+|||.++.|+|++++|+||||||++|+   +|     .++++.
T Consensus         2 ~~~~~~~~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~---lp-----~i~~l~   73 (212)
T d1qdea_           2 QTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFS---IA-----ALQRID   73 (212)
T ss_dssp             CBSCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHH---HH-----HHHHCC
T ss_pred             CCCCcccccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhH---hh-----hHhhhh
Confidence            5788999999999999999999999999999999999999999999999999999999999999   99     899986


Q ss_pred             cCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         112 RTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       112 r~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      +.    ..++.+++++|+ ++++.|+...+.....
T Consensus        74 ~~----~~~~~~lil~pt-~el~~q~~~~~~~~~~  103 (212)
T d1qdea_          74 TS----VKAPQALMLAPT-RELALQIQKVVMALAF  103 (212)
T ss_dssp             TT----CCSCCEEEECSS-HHHHHHHHHHHHHHTT
T ss_pred             cc----CCCcceEEEccc-HHHhhhhhhhhccccc
Confidence            53    456788899999 8999999888876543

>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=99.81  E-value=1.5e-20  Score=144.41  Aligned_cols=102  Identities=22%  Similarity=0.329  Sum_probs=91.8

Q ss_pred             CCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhcc
Q psy7691          33 NNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGR  112 (165)
Q Consensus        33 ~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr  112 (165)
                      ++.++++.+|+++++++.++++|.++||..||++|.+|||.++.|+|++++|+||||||++|+   +|     .++++.+
T Consensus         5 ~~~~e~i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayl---lp-----~l~~i~~   76 (218)
T d2g9na1           5 SNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFA---IS-----ILQQIEL   76 (218)
T ss_dssp             CCCCCCCCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHH---HH-----HHHHCCT
T ss_pred             CCCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhh---hh-----hhheecc
Confidence            456889999999999999999999999999999999999999999999999999999999999   99     8998855


Q ss_pred             CCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCC
Q psy7691         113 TGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQP  147 (165)
Q Consensus       113 ~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~  147 (165)
                      .    ..++.+++++|+ ++++.|+.+.+......
T Consensus        77 ~----~~~~~alil~Pt-~eL~~Q~~~~~~~~~~~  106 (218)
T d2g9na1          77 D----LKATQALVLAPT-RELAQQIQKVVMALGDY  106 (218)
T ss_dssp             T----CCSCCEEEECSS-HHHHHHHHHHHHHHHTT
T ss_pred             c----ccCccEEEEccc-chhhhhHHHHHhhhccc
Confidence            3    467789999999 99999999888775443

>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=99.80  E-value=3.9e-20  Score=142.64  Aligned_cols=103  Identities=20%  Similarity=0.271  Sum_probs=89.4

Q ss_pred             cCCCCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhc
Q psy7691          32 GNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIG  111 (165)
Q Consensus        32 ~~~~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~g  111 (165)
                      ..+..+...+|++++|++.++++|+++||..||++|.+|||.++.|+|++++|+||||||+||+   +|     .++++.
T Consensus         9 ~~~~~~~~~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayl---lP-----il~~l~   80 (222)
T d2j0sa1           9 TSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFS---IS-----VLQCLD   80 (222)
T ss_dssp             CCTTCCCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHH---HH-----HHHTCC
T ss_pred             cCCCCCCCCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhc---cc-----cccccc
Confidence            3344456779999999999999999999999999999999999999999999999999999999   99     888885


Q ss_pred             cCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCC
Q psy7691         112 RTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQP  147 (165)
Q Consensus       112 r~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~  147 (165)
                      +.    ...+..++++|+ ++++.|+.+.+......
T Consensus        81 ~~----~~~~~~lil~Pt-reLa~Qi~~~~~~l~~~  111 (222)
T d2j0sa1          81 IQ----VRETQALILAPT-RELAVQIQKGLLALGDY  111 (222)
T ss_dssp             TT----SCSCCEEEECSS-HHHHHHHHHHHHHHTTT
T ss_pred             cc----ccCceeEEecch-HHHHHHHHHHHHHHhCc
Confidence            53    344567888998 99999999988776543

>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=99.80  E-value=4.6e-20  Score=140.51  Aligned_cols=96  Identities=18%  Similarity=0.279  Sum_probs=86.0

Q ss_pred             cccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCC
Q psy7691          40 QELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASS  119 (165)
Q Consensus        40 ~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~  119 (165)
                      ..|++++|+++++++|.++||..||++|.+|||.++.|+|++++|+||||||++|+   +|     .++++.+.    ..
T Consensus         1 s~F~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~---lp-----~l~~~~~~----~~   68 (207)
T d1t6na_           1 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFV---LA-----TLQQLEPV----TG   68 (207)
T ss_dssp             CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHH---HH-----HHHHCCCC----TT
T ss_pred             CCccccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccc---cc-----eeeeeccc----CC
Confidence            36999999999999999999999999999999999999999999999999999999   99     88887542    45


Q ss_pred             CceEEEECCCcHHHHHHHHHHHHhcCCCC
Q psy7691         120 GTAYTFFTPNNGKQAKELIAVLTEASQPI  148 (165)
Q Consensus       120 g~~~~~~~p~~~~~~~~i~~~l~~~~~~~  148 (165)
                      ++..++++|+ ++++.|+.+.++......
T Consensus        69 ~~~~lil~Pt-reL~~qi~~~~~~~~~~~   96 (207)
T d1t6na_          69 QVSVLVMCHT-RELAFQISKEYERFSKYM   96 (207)
T ss_dssp             CCCEEEECSC-HHHHHHHHHHHHHHTTTS
T ss_pred             CceEEEEecc-chhhHHHHHHHHHHHhhC
Confidence            5678899998 999999999988766544

>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=99.79  E-value=1.1e-19  Score=138.30  Aligned_cols=94  Identities=28%  Similarity=0.504  Sum_probs=85.0

Q ss_pred             cccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCC
Q psy7691          40 QELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASS  119 (165)
Q Consensus        40 ~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~  119 (165)
                      .+|++++++++++++|.++||..||++|.+|||.++.|+|++++|+||||||++|+   +|     .++++.+.    ..
T Consensus         3 ~~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayl---lP-----~l~~~~~~----~~   70 (206)
T d1veca_           3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYL---IP-----LLERLDLK----KD   70 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHH---HH-----HHHHCCTT----SC
T ss_pred             CChhccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccc---cc-----hhhccccc----cc
Confidence            58999999999999999999999999999999999999999999999999999999   99     88887543    45


Q ss_pred             CceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         120 GTAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       120 g~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      +..+++++|+ ++++.|+.+.+.....
T Consensus        71 ~~~~lil~pt-~el~~q~~~~~~~~~~   96 (206)
T d1veca_          71 NIQAMVIVPT-RELALQVSQICIQVSK   96 (206)
T ss_dssp             SCCEEEECSC-HHHHHHHHHHHHHHTT
T ss_pred             CcceEEEeec-chhhHHHHHHHHHHhh
Confidence            6788999999 9999999988876543

>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=99.78  E-value=3.5e-20  Score=144.09  Aligned_cols=114  Identities=23%  Similarity=0.332  Sum_probs=93.8

Q ss_pred             CcEEecCC--CCCCccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChh
Q psy7691          27 EITVKGNN--IPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSE  104 (165)
Q Consensus        27 ~i~~~~~~--~p~~i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~  104 (165)
                      .+...+.+  .++++.+|++++++++++++|.++||..||++|.+|||.++.|+|++++|+||||||++|+   +|    
T Consensus         6 ~~~~~~~~~~~~~~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayl---lp----   78 (238)
T d1wrba1           6 PVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFL---IP----   78 (238)
T ss_dssp             CCCEECCSSSCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHH---HH----
T ss_pred             ceeeeCCCCCCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeH---HH----
Confidence            34444544  4567899999999999999999999999999999999999999999999999999999999   99    


Q ss_pred             HHHHhhccC-----CCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCC
Q psy7691         105 DYIHRIGRT-----GRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIP  149 (165)
Q Consensus       105 ~~i~r~gr~-----~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p  149 (165)
                       .++++-..     .+....++.+++++|+ ++++.|+.+.+.......|
T Consensus        79 -~l~~l~~~~~~~~~~~~~~~~~alil~pt-~el~~q~~~~~~~~~~~~~  126 (238)
T d1wrba1          79 -IINHLVCQDLNQQRYSKTAYPKCLILAPT-RELAIQILSESQKFSLNTP  126 (238)
T ss_dssp             -HHHHHHTTCC------CCBCCSEEEECSS-HHHHHHHHHHHHHHHTTSS
T ss_pred             -HHHHHHhcccccccccCCCCceEEEeccc-hhhhcchheeeeecccCCC
Confidence             78876221     1233467789999999 9999999988877655543

>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=99.68  E-value=2.2e-17  Score=124.63  Aligned_cols=91  Identities=29%  Similarity=0.393  Sum_probs=75.7

Q ss_pred             cccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCC
Q psy7691          40 QELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASS  119 (165)
Q Consensus        40 ~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~  119 (165)
                      +.|+++++++.++++|++.||..||++|.+|||.++.|+|++++|+||||||++|+   +|     .++++.+.    ..
T Consensus         1 t~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayl---lp-----~l~~~~~~----~~   68 (209)
T d1q0ua_           1 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYL---LP-----IMEKIKPE----RA   68 (209)
T ss_dssp             CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHH---HH-----HHHHCCTT----SC
T ss_pred             CccccCCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeee---ee-----eccccccc----cc
Confidence            37999999999999999999999999999999999999999999999999999998   89     88877553    33


Q ss_pred             CceEEEECCCcHHHHHHHHHHHHh
Q psy7691         120 GTAYTFFTPNNGKQAKELIAVLTE  143 (165)
Q Consensus       120 g~~~~~~~p~~~~~~~~i~~~l~~  143 (165)
                      ....+++.|. .....+....+..
T Consensus        69 ~~~~~~~~~~-~~~~~~~~~~~~~   91 (209)
T d1q0ua_          69 EVQAVITAPT-RELATQIYHETLK   91 (209)
T ss_dssp             SCCEEEECSS-HHHHHHHHHHHHH
T ss_pred             cccccccccc-cchhHHHHHHHHh
Confidence            4455666666 5555555555544

>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=99.68  E-value=4.5e-17  Score=123.30  Aligned_cols=93  Identities=24%  Similarity=0.436  Sum_probs=78.7

Q ss_pred             ccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCC
Q psy7691          41 ELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSG  120 (165)
Q Consensus        41 ~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g  120 (165)
                      +|+++++++.++++|+++||..||++|.+|||.++.|+|++++|+||||||++|+   +|     .++++.+.    ..+
T Consensus         2 sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~---lp-----~i~~~~~~----~~~   69 (206)
T d1s2ma1           2 TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFV---IP-----TLEKVKPK----LNK   69 (206)
T ss_dssp             CGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHH---HH-----HHHHCCTT----SCS
T ss_pred             ChHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhc---cc-----cccccccc----ccc
Confidence            7999999999999999999999999999999999999999999999999999998   88     78877543    334


Q ss_pred             ceEEEECCCcHHHHHHHHHHHHhcCC
Q psy7691         121 TAYTFFTPNNGKQAKELIAVLTEASQ  146 (165)
Q Consensus       121 ~~~~~~~p~~~~~~~~i~~~l~~~~~  146 (165)
                      ...+++.|+ ..++.+....+.....
T Consensus        70 ~~~~~~~~~-~~~~~~~~~~~~~~~~   94 (206)
T d1s2ma1          70 IQALIMVPT-RELALQTSQVVRTLGK   94 (206)
T ss_dssp             CCEEEECSS-HHHHHHHHHHHHHHTT
T ss_pred             ccceeeccc-hhhhhhhhhhhhhccc
Confidence            556677777 7777777766655433

>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=99.67  E-value=4.3e-17  Score=123.73  Aligned_cols=92  Identities=27%  Similarity=0.468  Sum_probs=80.8

Q ss_pred             cccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCC-CeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCC
Q psy7691          40 QELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGR-DMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCAS  118 (165)
Q Consensus        40 ~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~-di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~  118 (165)
                      .+|+++++++.++++|.++||..||++|.++||.+++|. |++++|+||+|||++|+   +|     .+++..+     .
T Consensus         4 msf~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~---l~-----~~~~~~~-----~   70 (208)
T d1hv8a1           4 MNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFA---IP-----LIELVNE-----N   70 (208)
T ss_dssp             CCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHH---HH-----HHHHSCS-----S
T ss_pred             cCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceee---cc-----ccccccc-----c
Confidence            589999999999999999999999999999999999985 99999999999999998   77     6665533     3


Q ss_pred             CCceEEEECCCcHHHHHHHHHHHHhcC
Q psy7691         119 SGTAYTFFTPNNGKQAKELIAVLTEAS  145 (165)
Q Consensus       119 ~g~~~~~~~p~~~~~~~~i~~~l~~~~  145 (165)
                      .++.+++++|+ ++++.|+.+.++...
T Consensus        71 ~~~~~lil~pt-~~l~~q~~~~~~~~~   96 (208)
T d1hv8a1          71 NGIEAIILTPT-RELAIQVADEIESLK   96 (208)
T ss_dssp             SSCCEEEECSC-HHHHHHHHHHHHHHH
T ss_pred             cCcceEEEeec-cccchhhhhhhhhhc
Confidence            56778899999 899999888887653

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.45  E-value=5.8e-15  Score=108.03  Aligned_cols=110  Identities=25%  Similarity=0.408  Sum_probs=82.6

Q ss_pred             Cccccc-cCCCcHHHHHHHHhCCCCCC------chHHH-H--------------HHHHHHcCCCeeeecccCCcccceee
Q psy7691          38 PTQELT-EGCFPNAVLQHLKGQGFEEP------TAIQA-Q--------------GWPIALSGRDMVGIAQTGSGKTLAVI   95 (165)
Q Consensus        38 ~i~~f~-~l~l~~~l~~~l~~~g~~~~------t~~Q~-~--------------a~~~~l~G~di~~~a~tgsGKt~~~~   95 (165)
                      ..+.|. +....+.+.+.|...|+...      +.-|+ .              |++.+.+|.|+..+.        +|+
T Consensus        29 k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Tdv~~rGiDi~~v~--------~VI  100 (162)
T d1fuka_          29 QAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVS--------LVI  100 (162)
T ss_dssp             CEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGGTTTCCCCSCS--------EEE
T ss_pred             cEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhcccceeeccccccccccCCCce--------EEE
Confidence            345554 45788899999999888542      22222 2              344555666666665        899


Q ss_pred             ecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCChHHHHH
Q psy7691          96 NFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQDL  155 (165)
Q Consensus        96 ~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p~~~~~~  155 (165)
                      |||+|.+.+.|+||+||+||.|..|.+++++++.+...+..|.+.+....+++|.++.++
T Consensus       101 ~~d~P~~~~~yihR~GR~gR~g~~g~~i~~~~~~d~~~~~~i~~~~~~~~~~ip~~~~~l  160 (162)
T d1fuka_         101 NYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATL  160 (162)
T ss_dssp             ESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHHHHHHHHHHSSCCCEECCSCCTTT
T ss_pred             EeccchhHHHHHhhccccccCCCccEEEEEcCHHHHHHHHHHHHHHcCcCCCCChHHHHh
Confidence            999999999999999999999999999999999999999999999999999999876554

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.43  E-value=1.3e-14  Score=106.68  Aligned_cols=109  Identities=21%  Similarity=0.373  Sum_probs=85.2

Q ss_pred             Cccccc-cCCCcHHHHHHHHhCCCCCC------chHHH-H--------------HHHHHHcCCCeeeecccCCcccceee
Q psy7691          38 PTQELT-EGCFPNAVLQHLKGQGFEEP------TAIQA-Q--------------GWPIALSGRDMVGIAQTGSGKTLAVI   95 (165)
Q Consensus        38 ~i~~f~-~l~l~~~l~~~l~~~g~~~~------t~~Q~-~--------------a~~~~l~G~di~~~a~tgsGKt~~~~   95 (165)
                      .++.|. .....+.+...|...|+...      +.-|+ .              |++.+.+|.|+..+.        .|+
T Consensus        36 k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~fk~g~~~iLv~Td~~~rGiDi~~v~--------~VI  107 (168)
T d2j0sa2          36 QAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVS--------LII  107 (168)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCCCTTEE--------EEE
T ss_pred             ceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHHhcCCccEEeccchhcccccccCcc--------eEE
Confidence            344554 45778888888999988652      22232 2              344555666666666        899


Q ss_pred             ecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCChHHHH
Q psy7691          96 NFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQD  154 (165)
Q Consensus        96 ~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p~~~~~  154 (165)
                      |||+|.+.+.|+||+||+||.|+.|.+++++.+.+...+..|.+.+....+++|..+.+
T Consensus       108 n~d~P~~~~~yihR~GR~gR~g~~G~~i~~~~~~d~~~~~~i~~~~~~~i~e~p~~~~d  166 (168)
T d2j0sa2         108 NYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVAD  166 (168)
T ss_dssp             ESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHHHHHHTTCCCEECCSCCTT
T ss_pred             EecCCcCHHHHHhhhccccccCCCcEEEEEECHHHHHHHHHHHHHHcCcCCCCCcChHH
Confidence            99999999999999999999999999999999999888899998888788888866544

>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=99.31  E-value=8.2e-13  Score=98.73  Aligned_cols=88  Identities=20%  Similarity=0.196  Sum_probs=74.4

Q ss_pred             ccccCCCcHHHHHHHHhC-CCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCC
Q psy7691          41 ELTEGCFPNAVLQHLKGQ-GFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASS  119 (165)
Q Consensus        41 ~f~~l~l~~~l~~~l~~~-g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~  119 (165)
                      .++.++|++...+.|++. ||..++|.|.+|++.++.|+|+++++|||+|||++|.   +|     .+.+.         
T Consensus         3 ~~e~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~---~~-----~~~~~---------   65 (206)
T d1oywa2           3 QAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQ---IP-----ALLLN---------   65 (206)
T ss_dssp             CCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHH---HH-----HHHSS---------
T ss_pred             chhhCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhh---hh-----hhhcc---------
Confidence            567789999999999997 9999999999999999999999999999999999987   66     44332         


Q ss_pred             CceEEEECCCcHHHHHHHHHHHHhcCCC
Q psy7691         120 GTAYTFFTPNNGKQAKELIAVLTEASQP  147 (165)
Q Consensus       120 g~~~~~~~p~~~~~~~~i~~~l~~~~~~  147 (165)
                       ...+++.|+ ..+..+..+.++..+..
T Consensus        66 -~~~~~v~P~-~~L~~q~~~~l~~~~~~   91 (206)
T d1oywa2          66 -GLTVVVSPL-ISLMKDQVDQLQANGVA   91 (206)
T ss_dssp             -SEEEEECSC-HHHHHHHHHHHHHTTCC
T ss_pred             -CceEEeccc-hhhhhhHHHHHHhhccc
Confidence             246788888 88888888888776544

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.28  E-value=1.7e-12  Score=93.70  Aligned_cols=102  Identities=21%  Similarity=0.313  Sum_probs=76.5

Q ss_pred             Cccccc-cCCCcHHHHHHHHhCCCCCC------ch-HHHHHHHHHHcC--------------CCeeeecccCCcccceee
Q psy7691          38 PTQELT-EGCFPNAVLQHLKGQGFEEP------TA-IQAQGWPIALSG--------------RDMVGIAQTGSGKTLAVI   95 (165)
Q Consensus        38 ~i~~f~-~l~l~~~l~~~l~~~g~~~~------t~-~Q~~a~~~~l~G--------------~di~~~a~tgsGKt~~~~   95 (165)
                      ..+.|. +...++.+.+.|...|+...      +. .+..++..+..|              .|+..+.        +++
T Consensus        30 k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~~~~~Gid~~~v~--------~Vi  101 (155)
T d1hv8a2          30 YGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLN--------CVI  101 (155)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHCCCSCCS--------EEE
T ss_pred             CEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhhhhcccceeeeehhHHhhhhhhccCc--------EEE
Confidence            344554 45778889999999988542      12 233444444444              4444443        799


Q ss_pred             ecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCC
Q psy7691          96 NFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQP  147 (165)
Q Consensus        96 ~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~  147 (165)
                      |||+|.+...|+||+||+||.|..|.+++++.+.+...+..|.+.+.....+
T Consensus       102 ~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~d~~~~~~i~~~~~~~i~~  153 (155)
T d1hv8a2         102 NYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIERAMKLKIKK  153 (155)
T ss_dssp             ESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHHHHHHHHHHHTCCCCC
T ss_pred             EecCCCCHHHHHHHHHhcCcCCCCceEEEEEchHHHHHHHHHHHHHCCCccc
Confidence            9999999999999999999999999999999999988888888877665444

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.26  E-value=5.8e-13  Score=97.72  Aligned_cols=117  Identities=21%  Similarity=0.314  Sum_probs=85.8

Q ss_pred             Ccccccc-CCCcHHHHHHHHhCCCCCC------ch-HHHHHHHHHHcCC-Ceeeeccc-CCcc----cceeeecCCCCCh
Q psy7691          38 PTQELTE-GCFPNAVLQHLKGQGFEEP------TA-IQAQGWPIALSGR-DMVGIAQT-GSGK----TLAVINFDYPNSS  103 (165)
Q Consensus        38 ~i~~f~~-l~l~~~l~~~l~~~g~~~~------t~-~Q~~a~~~~l~G~-di~~~a~t-gsGK----t~~~~~~~lP~~~  103 (165)
                      .++.|.. ....+.+...|...|+...      +. .+.+++..+..|. +++++... +.|=    .-+++|||+|.+.
T Consensus        34 k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~~~~Gid~~~v~~VI~~d~p~~~  113 (171)
T d1s2ma2          34 QAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTA  113 (171)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSCCCTTEEEEEESSCCSSH
T ss_pred             ceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhcccCccccccchhHhhhccccceeEEEEecCCcchH
Confidence            4556654 4677888888998888653      11 2234444444442 33333222 2221    1279999999999


Q ss_pred             hHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCChHHHH
Q psy7691         104 EDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQD  154 (165)
Q Consensus       104 ~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p~~~~~  154 (165)
                      +.|+||+||+||.|..|.+++++.+.+...+..+.+.+.....++|.++..
T Consensus       114 ~~y~qr~GR~gR~g~~g~~i~~v~~~e~~~~~~i~~~l~~~~~~~p~~~d~  164 (171)
T d1s2ma2         114 ETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATIDK  164 (171)
T ss_dssp             HHHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHHHHHHTCCCEECCSSCCG
T ss_pred             HHHHHHhhhcccCCCccEEEEEeCHHHHHHHHHHHHHHCCCCCCCCcccch
Confidence            999999999999999999999999999999999999999988889877554

>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=99.24  E-value=3.1e-12  Score=97.67  Aligned_cols=89  Identities=17%  Similarity=0.095  Sum_probs=67.7

Q ss_pred             ccccccCCCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCC
Q psy7691          39 TQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCAS  118 (165)
Q Consensus        39 i~~f~~l~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~  118 (165)
                      ...|.+..+.+.+.+ +.+.++..|+++|.++++.++.|+|++++||||+|||++++   +|     .++...       
T Consensus        21 ~~~~~~~~~~~~~~~-~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~---~~-----~~~~~~-------   84 (237)
T d1gkub1          21 LCLFPEDFLLKEFVE-FFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGL---AM-----SLFLAL-------   84 (237)
T ss_dssp             CSCCTTHHHHHHHHH-HHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHH---HH-----HHHHHT-------
T ss_pred             cccCccchhHHHHHH-HHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHH---HH-----HHHHHH-------
Confidence            445555555555544 45568889999999999999999999999999999999877   55     444432       


Q ss_pred             CCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691         119 SGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus       119 ~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      .|..++++.|+ +.++.|+.+.+...
T Consensus        85 ~~~rvliv~Pt-~~La~Q~~~~l~~~  109 (237)
T d1gkub1          85 KGKRCYVIFPT-SLLVIQAAETIRKY  109 (237)
T ss_dssp             TSCCEEEEESC-HHHHHHHHHHHHHH
T ss_pred             hcCeEEEEecc-HHHHHHHHHHHHHH
Confidence            23457899999 88888888777654

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=99.15  E-value=5.5e-12  Score=94.97  Aligned_cols=98  Identities=19%  Similarity=0.247  Sum_probs=67.1

Q ss_pred             ccccccCCCcHHHHHHHHhCCCCCC------chH-HHHHHHHHHcCCC-ee-eecccCCcc----cceeeecCCCCChhH
Q psy7691          39 TQELTEGCFPNAVLQHLKGQGFEEP------TAI-QAQGWPIALSGRD-MV-GIAQTGSGK----TLAVINFDYPNSSED  105 (165)
Q Consensus        39 i~~f~~l~l~~~l~~~l~~~g~~~~------t~~-Q~~a~~~~l~G~d-i~-~~a~tgsGK----t~~~~~~~lP~~~~~  105 (165)
                      |+.+.+....+.+...|...|+...      +.. ...+...+..|.. ++ +....|.|=    .-+|+|||+|.+.++
T Consensus        34 IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd~~~~GiD~p~v~~VI~~~~P~~~~~  113 (200)
T d1oywa3          34 IIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIES  113 (200)
T ss_dssp             EEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCTTCCEEEESSCCSSHHH
T ss_pred             EEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhcccceEEEecchhhhccCCCCCCEEEECCCccchHH
Confidence            4444556788888899999888542      222 2334444444432 22 222222221    228999999999999


Q ss_pred             HHHhhccCCCCCCCCceEEEECCCcHHHHHH
Q psy7691         106 YIHRIGRTGRCASSGTAYTFFTPNNGKQAKE  136 (165)
Q Consensus       106 ~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~  136 (165)
                      |+||+||+||.|..|.+++++.|.+...+.+
T Consensus       114 y~qr~GR~gR~g~~g~ai~~~~~~d~~~l~~  144 (200)
T d1oywa3         114 YYQETGRAGRDGLPAEAMLFYDPADMAWLRR  144 (200)
T ss_dssp             HHHHHTTSCTTSSCEEEEEEECHHHHHHHHH
T ss_pred             HHHHhhhhhcCCCCceEEEecCHHHHHHHHh
Confidence            9999999999999999999999876655443

>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=99.14  E-value=6.5e-12  Score=93.64  Aligned_cols=83  Identities=20%  Similarity=0.207  Sum_probs=66.5

Q ss_pred             CCcHHHHHHHHhCCCCCCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEE
Q psy7691          46 CFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTF  125 (165)
Q Consensus        46 ~l~~~l~~~l~~~g~~~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~  125 (165)
                      .+++.+...|.+.||..++|+|.+|++.++.|.|+++++|||+|||.++.   ++     .++...+.       ..+++
T Consensus         9 ~~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~---l~-----i~~~~~~~-------~~vl~   73 (202)
T d2p6ra3           9 SISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAE---MA-----MVREAIKG-------GKSLY   73 (202)
T ss_dssp             HHHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHH---HH-----HHHHHHTT-------CCEEE
T ss_pred             hhhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHH---HH-----HHHHhhcc-------Cccee
Confidence            47889999999999999999999999999999999999999999998765   55     55555432       24678


Q ss_pred             ECCCcHHHHHHHHHHHHhc
Q psy7691         126 FTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus       126 ~~p~~~~~~~~i~~~l~~~  144 (165)
                      +.|+ +.++.|..+.+...
T Consensus        74 l~P~-~~L~~q~~~~~~~~   91 (202)
T d2p6ra3          74 VVPL-RALAGEKYESFKKW   91 (202)
T ss_dssp             EESS-HHHHHHHHHHHTTT
T ss_pred             eccc-HHHHHHHHHHHHHH
Confidence            8999 88888888887654

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.00  E-value=3e-10  Score=82.81  Aligned_cols=114  Identities=22%  Similarity=0.330  Sum_probs=82.9

Q ss_pred             cccccc-CCCcHHHHHHHHhCCCCC-------CchHHHHHHHHHHcCC-Ceeeeccc-CCcc----cceeeecCCCCChh
Q psy7691          39 TQELTE-GCFPNAVLQHLKGQGFEE-------PTAIQAQGWPIALSGR-DMVGIAQT-GSGK----TLAVINFDYPNSSE  104 (165)
Q Consensus        39 i~~f~~-l~l~~~l~~~l~~~g~~~-------~t~~Q~~a~~~~l~G~-di~~~a~t-gsGK----t~~~~~~~lP~~~~  104 (165)
                      ++.|.. ....+.+.+.|.+.|+..       +...+.+++..+..|. +++++... +.|-    .-++++||+|.+.+
T Consensus        30 ~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~~~~Gid~~~~~~vi~~~~p~~~~  109 (168)
T d1t5ia_          30 VVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSD  109 (168)
T ss_dssp             EEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSCCSTTCCGGGCSEEEESSCCSSHH
T ss_pred             EEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhccccceeeeccccccchhhcccchhhhhhhcccchh
Confidence            455554 467778888899998864       2234556677677663 45544432 3342    23689999999999


Q ss_pred             HHHHhhccCCCCCCCCceEEEECCCc-HHHHHHHHHHHHhcCCCCChHH
Q psy7691         105 DYIHRIGRTGRCASSGTAYTFFTPNN-GKQAKELIAVLTEASQPIPPQL  152 (165)
Q Consensus       105 ~~i~r~gr~~r~~~~g~~~~~~~p~~-~~~~~~i~~~l~~~~~~~p~~~  152 (165)
                      .|+||+||+||.|..|.+++++++.+ ...+..+.+.+.....++|..+
T Consensus       110 ~yiqr~GR~gR~g~~g~~i~l~~~~~~~~~~~~i~~~~~~~~~elp~~~  158 (168)
T d1t5ia_         110 TYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI  158 (168)
T ss_dssp             HHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEECC---
T ss_pred             hHhhhhhhcccCCCccEEEEEECchHHHHHHHHHHHHHcCCcccCCchh
Confidence            99999999999999999999999863 5677788888888888898776

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=98.54  E-value=5.3e-09  Score=73.95  Aligned_cols=83  Identities=19%  Similarity=0.244  Sum_probs=55.6

Q ss_pred             Ccccc-ccCCCcHHHHHHHHhCCCCCCchH----H----------HHHHHHHHcCCCeeeecccCCcccceeee----cC
Q psy7691          38 PTQEL-TEGCFPNAVLQHLKGQGFEEPTAI----Q----------AQGWPIALSGRDMVGIAQTGSGKTLAVIN----FD   98 (165)
Q Consensus        38 ~i~~f-~~l~l~~~l~~~l~~~g~~~~t~~----Q----------~~a~~~~l~G~di~~~a~tgsGKt~~~~~----~~   98 (165)
                      ..+.| .+...++.+.+.|...|+....-.    |          ..|++.+.+|.| +.+.        .|+|    |+
T Consensus        37 k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~~~~~~~~~~vlvaTd~~~~GiD-~~v~--------~Vi~~~~~~~  107 (138)
T d1jr6a_          37 RHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTNGDVVVVATDALMTGFT-GDFD--------SVIDCNTSDG  107 (138)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCSCCCTTSSCEEEEESSSSCSSSC-CCBS--------EEEECSEETT
T ss_pred             CEEEEeCcHHHHHHHHHHHhccccchhhhhccchhhhhhhhhcceeehhHHHHhccc-cccc--------eEEEEEecCC
Confidence            34445 455788999999999888642111    0          013333444444 3222        5666    55


Q ss_pred             CCCChhHHHHhhccCCCCCCCCceEEEECCCcH
Q psy7691          99 YPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNG  131 (165)
Q Consensus        99 lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~  131 (165)
                      +|.+.++|+||+||+|| |+.| .+.+++|.++
T Consensus       108 ~P~~~~~y~qr~GR~gR-g~~G-~~~~i~~~er  138 (138)
T d1jr6a_         108 KPQDAVSRTQRRGRTGR-GKPG-IYRFVAPGER  138 (138)
T ss_dssp             EECCHHHHHHHHTTBCS-SSCE-EEEECCSSCC
T ss_pred             CCCCHHHHHhHhccccC-CCCc-EEEEEcCCCC
Confidence            69999999999999999 9999 4778888763

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=98.42  E-value=9.7e-08  Score=70.19  Aligned_cols=73  Identities=22%  Similarity=0.196  Sum_probs=50.3

Q ss_pred             cccccc-CCCcHHHHHHHHhCCCCCC------ch-HHHHHHHHH--------------HcCCCeeeecccCCcccceeee
Q psy7691          39 TQELTE-GCFPNAVLQHLKGQGFEEP------TA-IQAQGWPIA--------------LSGRDMVGIAQTGSGKTLAVIN   96 (165)
Q Consensus        39 i~~f~~-l~l~~~l~~~l~~~g~~~~------t~-~Q~~a~~~~--------------l~G~di~~~a~tgsGKt~~~~~   96 (165)
                      ++.|.. ..-.+.+...|.+.|+..-      +. ...+++..+              .+|.|++.+.        +|+|
T Consensus        34 ~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~~rGiDip~v~--------~VI~  105 (181)
T d1t5la2          34 TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVS--------LVAI  105 (181)
T ss_dssp             EEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCCSSSCCCTTEE--------EEEE
T ss_pred             EEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHHHccCCCCCCC--------EEEE
Confidence            455554 4677888888999999542      22 223333334              4555555555        8999


Q ss_pred             cCCCC-----ChhHHHHhhccCCCCCCC
Q psy7691          97 FDYPN-----SSEDYIHRIGRTGRCASS  119 (165)
Q Consensus        97 ~~lP~-----~~~~~i~r~gr~~r~~~~  119 (165)
                      ||+|.     +..+|+||+||+||.|..
T Consensus       106 ~d~p~~~~~~s~~~yi~R~GRagR~g~~  133 (181)
T d1t5la2         106 LDADKEGFLRSERSLIQTIGRAARNANG  133 (181)
T ss_dssp             TTTTSCSGGGSHHHHHHHHGGGTTSTTC
T ss_pred             ecCCcccccccHHHHHHHHHhhccccCc
Confidence            99996     478999999999998753

>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=98.29  E-value=2.1e-07  Score=68.04  Aligned_cols=85  Identities=19%  Similarity=0.184  Sum_probs=56.9

Q ss_pred             cccc-ccCCCcHHHHHHHHhCCCCCC------ch-HHHHHHHHHH--------------cCCCeeeecccCCcccceeee
Q psy7691          39 TQEL-TEGCFPNAVLQHLKGQGFEEP------TA-IQAQGWPIAL--------------SGRDMVGIAQTGSGKTLAVIN   96 (165)
Q Consensus        39 i~~f-~~l~l~~~l~~~l~~~g~~~~------t~-~Q~~a~~~~l--------------~G~di~~~a~tgsGKt~~~~~   96 (165)
                      ++.| .+...++.+.+.|.+.|+..-      +. .-.+.+..+.              +|.|++.+.        +++|
T Consensus        34 ~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~GiDip~V~--------~Vi~  105 (174)
T d1c4oa2          34 TLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVS--------LVAI  105 (174)
T ss_dssp             EEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEE--------EEEE
T ss_pred             EEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeeeeeccCCCCc--------EEEE
Confidence            4445 456899999999999999652      11 2223333444              445555555        8999


Q ss_pred             cCCCC-----ChhHHHHhhccCCCCCCCCceEEEECCCcHH
Q psy7691          97 FDYPN-----SSEDYIHRIGRTGRCASSGTAYTFFTPNNGK  132 (165)
Q Consensus        97 ~~lP~-----~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~  132 (165)
                      ||+|.     +.++|+||+||+||.++ |.++++....+..
T Consensus       106 ~~~~~~~~~~~~~~~iq~~GR~gR~~~-g~~~~~~~~~~~~  145 (174)
T d1c4oa2         106 LDADKEGFLRSERSLIQTIGRAARNAR-GEVWLYADRVSEA  145 (174)
T ss_dssp             TTTTSCSGGGSHHHHHHHHGGGTTSTT-CEEEEECSSCCHH
T ss_pred             eccccccccchhHHHHHHhhhhhhcCC-CeeEEeecCCCHH
Confidence            99775     45789999999999876 6566555554433

>d1wp9a2 c.37.1.19 (A:201-486) 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=98.12  E-value=2.6e-07  Score=71.50  Aligned_cols=94  Identities=17%  Similarity=0.164  Sum_probs=64.4

Q ss_pred             CccccccC-CCcHHHHHHHHhCCCCCCc---------------hHHHHHHHHHHcCC-Ceeeec-ccCCc----ccceee
Q psy7691          38 PTQELTEG-CFPNAVLQHLKGQGFEEPT---------------AIQAQGWPIALSGR-DMVGIA-QTGSG----KTLAVI   95 (165)
Q Consensus        38 ~i~~f~~l-~l~~~l~~~l~~~g~~~~t---------------~~Q~~a~~~~l~G~-di~~~a-~tgsG----Kt~~~~   95 (165)
                      .++.|.+. ...+.+.+.|.+.|+....               ..|..++..+..|. +++++. .-|.|    ..-+|+
T Consensus       163 k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv~T~~~~~Gld~~~~~~Vi  242 (286)
T d1wp9a2         163 KIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVV  242 (286)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECGGGGGGGGSTTCCEEE
T ss_pred             cEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEEEccceeccccCCCCCEEE
Confidence            45566654 6777888889888776422               13556666666553 443322 11223    122799


Q ss_pred             ecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHH
Q psy7691          96 NFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGK  132 (165)
Q Consensus        96 ~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~  132 (165)
                      +||+|.++..|+||+||+||.+ .|.++.++++.+.+
T Consensus       243 ~~d~~~~~~~~~Qr~GR~gR~~-~~~~~~l~~~~~~e  278 (286)
T d1wp9a2         243 FYEPVPSAIRSIQRRGRTGRHM-PGRVIILMAKGTRD  278 (286)
T ss_dssp             ESSCCHHHHHHHHHHTTSCSCC-CSEEEEEEETTSHH
T ss_pred             EeCCCCCHHHHHHHHHhCCCCC-CCEEEEEEeCCCHH
Confidence            9999999999999999999964 68888899888654

>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=98.10  E-value=1.1e-06  Score=63.81  Aligned_cols=68  Identities=16%  Similarity=0.162  Sum_probs=49.1

Q ss_pred             CCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVL  141 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l  141 (165)
                      +|.+.|.+++..+. +.|++++++||+|||+.++   ++     ..+++-+      .+..+++++|+ +.++.|..+.+
T Consensus         9 ~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~---~~-----~~~~~~~------~~~~il~i~P~-~~L~~q~~~~~   72 (200)
T d1wp9a1           9 QPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAM---MI-----AEYRLTK------YGGKVLMLAPT-KPLVLQHAESF   72 (200)
T ss_dssp             CCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHH---HH-----HHHHHHH------SCSCEEEECSS-HHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHH---HH-----HHHHHHh------cCCcEEEEcCc-hHHHHHHHHHH
Confidence            58999999988765 5689999999999998655   33     2222211      12357888998 88888877777


Q ss_pred             HhcC
Q psy7691         142 TEAS  145 (165)
Q Consensus       142 ~~~~  145 (165)
                      ....
T Consensus        73 ~~~~   76 (200)
T d1wp9a1          73 RRLF   76 (200)
T ss_dssp             HHHB
T ss_pred             HHhh
Confidence            6643

>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=97.82  E-value=1.9e-06  Score=66.11  Aligned_cols=61  Identities=16%  Similarity=0.115  Sum_probs=45.0

Q ss_pred             HHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCCCC
Q psy7691          74 ALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIP  149 (165)
Q Consensus        74 ~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p  149 (165)
                      +..|+++++.++||||||++|+   +|     +++..-.      .|..++++.|+ ++++.|+.+.+........
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l---~~-----~~~~~~~------~~~~~lvi~Pt-r~La~q~~~~l~~~~~~~~   66 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYL---PA-----IVREAIK------RGLRTLILAPT-RVVAAEMEEALRGLPIRYQ   66 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHH---HH-----HHHHHHH------HTCCEEEEESS-HHHHHHHHHHTTTSCCBCC
T ss_pred             hhcCCcEEEEECCCCCHHHHHH---HH-----HHHHHHh------cCCEEEEEccH-HHHHHHHHHHHhcCCccee
Confidence            5678999999999999999876   45     4443311      12357888898 9999999988877655443

>d1a1va2 c.37.1.14 (A:326-624) 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=97.67  E-value=5.8e-06  Score=64.71  Aligned_cols=92  Identities=15%  Similarity=0.108  Sum_probs=59.0

Q ss_pred             Ccccccc-CCCcHHHHHHHHhCCCCCCchH----H-------------HHHHHHHHcC-CCeeeecc-cC-------Ccc
Q psy7691          38 PTQELTE-GCFPNAVLQHLKGQGFEEPTAI----Q-------------AQGWPIALSG-RDMVGIAQ-TG-------SGK   90 (165)
Q Consensus        38 ~i~~f~~-l~l~~~l~~~l~~~g~~~~t~~----Q-------------~~a~~~~l~G-~di~~~a~-tg-------sGK   90 (165)
                      .++.|.+ ...++++.+.|.+.|++....+    |             ..++..+..| .|+++..- ..       ...
T Consensus        38 k~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~g~~giDid~  117 (299)
T d1a1va2          38 RHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSLDP  117 (299)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEEEEEECCCSS
T ss_pred             CEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhccCCCCCCCc
Confidence            3456655 5789999999999998642111    1             1122223333 24443221 11       123


Q ss_pred             cceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCc
Q psy7691          91 TLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNN  130 (165)
Q Consensus        91 t~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~  130 (165)
                      +..|++||+|.++++|+||+||+|| |+.|...+++..+.
T Consensus       118 V~~VI~~d~P~SvesyIQRiGRTGR-Gr~G~~~~l~~~t~  156 (299)
T d1a1va2         118 TFTIETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVAPGER  156 (299)
T ss_dssp             SCEEEEEEEECBHHHHHHHHTTBCS-SSCEEEEESCSCCB
T ss_pred             ceEEEeCCCCCCHHHHHhhccccCC-CCCceEEEEecCCC
Confidence            4479999999999999999999999 99998776666554

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.52  E-value=1.9e-05  Score=58.76  Aligned_cols=54  Identities=13%  Similarity=0.159  Sum_probs=39.7

Q ss_pred             eeeecCCCCChhHHHHh-hccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhcCCC
Q psy7691          93 AVINFDYPNSSEDYIHR-IGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQP  147 (165)
Q Consensus        93 ~~~~~~lP~~~~~~i~r-~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~~~~  147 (165)
                      ++++|+.|..-.+++|+ .||.||.+..|.|++++.+........+ +.+......
T Consensus       111 ~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l~~~~~~~~~~~rl-~~~~~~~dG  165 (206)
T d1gm5a4         111 VMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEEAMERL-RFFTLNTDG  165 (206)
T ss_dssp             EEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCCHHHHHHH-HHHHTCCCS
T ss_pred             EEEEEccCCccHHHHHhhhhheeeccccceeEeeeccccccchhhh-hhccccCCC
Confidence            68889999876667776 6999999999999999888755544444 444444433

>d1gkub2 c.37.1.16 (B:251-498) 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=97.51  E-value=2e-07  Score=71.09  Aligned_cols=93  Identities=10%  Similarity=0.020  Sum_probs=64.3

Q ss_pred             ccccc-cCCCcHHHHHHHHhCCCCCCchHHH-HHHHHHHcCC-Ceeeeccc-----CCc----c-cceeeecCCCCChhH
Q psy7691          39 TQELT-EGCFPNAVLQHLKGQGFEEPTAIQA-QGWPIALSGR-DMVGIAQT-----GSG----K-TLAVINFDYPNSSED  105 (165)
Q Consensus        39 i~~f~-~l~l~~~l~~~l~~~g~~~~t~~Q~-~a~~~~l~G~-di~~~a~t-----gsG----K-t~~~~~~~lP~~~~~  105 (165)
                      .+.|. .....+.+...|....+...+..+. +.+..+..|. |+++....     +-|    + .-.|+|||+|.    
T Consensus        28 ~iif~~~~~~~~~l~~~l~~~~hg~~~~~~R~~~~~~f~~g~~~vLVaT~a~~~v~~rGlDip~~v~~VI~~d~P~----  103 (248)
T d1gkub2          28 GIIYARTGEEAEEIYESLKNKFRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPS----  103 (248)
T ss_dssp             EEEEESSHHHHHHHHHTTTTSSCEEECTTSSSHHHHHHHHTSCSEEEEECC------CCSCCTTTCCEEEEESCCE----
T ss_pred             EEEEECCHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhCCCeEEEEeccccchhhhccCccccccEEEEeCCCc----
Confidence            34444 4467778888887766655555443 4556676774 66654421     345    4 45799999995    


Q ss_pred             HHHhhccCCCCCCCCceEEEECCCcHHHHH
Q psy7691         106 YIHRIGRTGRCASSGTAYTFFTPNNGKQAK  135 (165)
Q Consensus       106 ~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~  135 (165)
                      |.||+||+||.|..|.+++++.+.+.....
T Consensus       104 ~~~r~gR~~R~g~~~~~~~~~~~~~~~~~~  133 (248)
T d1gkub2         104 FRVTIEDIDSLSPQMVKLLAYLYRNVDEIE  133 (248)
T ss_dssp             EEEECSCGGGSCHHHHHHHHTTTSCHHHHH
T ss_pred             chhhhhhhhccCcceEeeeeccHhhHHHHH
Confidence            999999999999999998888887655443

>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=97.35  E-value=0.0001  Score=54.04  Aligned_cols=64  Identities=20%  Similarity=0.135  Sum_probs=47.9

Q ss_pred             CCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVL  141 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l  141 (165)
                      .+.+.|.+++..++.+...++.++||+|||+..+    -     ++.+.+         ..+++++|. ..+..|..+.+
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~----~-----~~~~~~---------~~~Liv~p~-~~L~~q~~~~~  130 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAM----A-----AINELS---------TPTLIVVPT-LALAEQWKERL  130 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHH----H-----HHHHSC---------SCEEEEESS-HHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHH----h-----HHHHhc---------CceeEEEcc-cchHHHHHHHH
Confidence            3678999999999888888889999999998543    1     344332         136778887 78888888777


Q ss_pred             Hhc
Q psy7691         142 TEA  144 (165)
Q Consensus       142 ~~~  144 (165)
                      +.-
T Consensus       131 ~~~  133 (206)
T d2fz4a1         131 GIF  133 (206)
T ss_dssp             GGG
T ss_pred             Hhh
Confidence            653

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.21  E-value=3.9e-05  Score=56.49  Aligned_cols=35  Identities=20%  Similarity=0.322  Sum_probs=26.6

Q ss_pred             cCCCCChhHHHHhhccCCCCCC--CCceEEEECCCcH
Q psy7691          97 FDYPNSSEDYIHRIGRTGRCAS--SGTAYTFFTPNNG  131 (165)
Q Consensus        97 ~~lP~~~~~~i~r~gr~~r~~~--~g~~~~~~~p~~~  131 (165)
                      ++.|.+..+|+|++||+||.|.  .|.++++..+.+.
T Consensus       152 ~~~~~~~~~~~q~~GRAGR~g~~~~G~~~l~~~~~~~  188 (201)
T d2p6ra4         152 YSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDR  188 (201)
T ss_dssp             SEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGGH
T ss_pred             CcCCCCHHHHHHHhcccCCCCCCCeeEEEEEeCCCCh
Confidence            6678889999999999999985  4556655555433

>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=97.06  E-value=9.6e-05  Score=49.42  Aligned_cols=55  Identities=16%  Similarity=0.138  Sum_probs=38.0

Q ss_pred             HHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHh
Q psy7691          74 ALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTE  143 (165)
Q Consensus        74 ~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~  143 (165)
                      +..|.+++.+++||+|||..++   ..     +++...+      .+..++++.|+ +.++.|..+.+..
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~---~~-----~~~~~~~------~~~~vli~~p~-~~l~~q~~~~~~~   58 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFL---PQ-----ILAECAR------RRLRTLVLAPT-RVVLSEMKEAFHG   58 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHH---HH-----HHHHHHH------TTCCEEEEESS-HHHHHHHHHHTTT
T ss_pred             HHcCCcEEEEcCCCCChhHHHH---HH-----HHHHhhh------cCceeeeeecc-hhHHHHHHHHhhh
Confidence            3468899999999999997543   11     3333322      34567888888 7888888776644

>d2fwra1 c.37.1.19 (A:257-456) 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=96.86  E-value=0.00019  Score=52.06  Aligned_cols=83  Identities=16%  Similarity=0.087  Sum_probs=51.8

Q ss_pred             CccccccC-CCcHHHHHHHHhCCCCCCch--HHHHHHHHHHcCC-CeeeecccC-Cccc----ceeeecCCCCChhHHHH
Q psy7691          38 PTQELTEG-CFPNAVLQHLKGQGFEEPTA--IQAQGWPIALSGR-DMVGIAQTG-SGKT----LAVINFDYPNSSEDYIH  108 (165)
Q Consensus        38 ~i~~f~~l-~l~~~l~~~l~~~g~~~~t~--~Q~~a~~~~l~G~-di~~~a~tg-sGKt----~~~~~~~lP~~~~~~i~  108 (165)
                      .++.|.+. ...+.+.+.|....+..-++  .....+..+..|. +++++...+ .|=.    -.++.||.|.+..+|+|
T Consensus        95 k~lvf~~~~~~~~~l~~~l~~~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~~~~~Gidl~~~~~vi~~~~~~s~~~~~Q  174 (200)
T d2fwra1          95 KIIIFTRHNELVYRISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQ  174 (200)
T ss_dssp             CBCCBCSCHHHHHHHHHHTTCCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHH
T ss_pred             cEEEEeCcHHHHHHHHhhcCcceeeCCCCHHHHHHHHHHhhcCCeeeeeecchhhcccCCCCCCEEEEeCCCCCHHHHHH
Confidence            45567653 55566666665554443332  3344566666663 444433322 3322    26788999999999999


Q ss_pred             hhccCCCCCCCC
Q psy7691         109 RIGRTGRCASSG  120 (165)
Q Consensus       109 r~gr~~r~~~~g  120 (165)
                      |+||.+|.|...
T Consensus       175 ~iGR~~R~~~~k  186 (200)
T d2fwra1         175 RLGRILRPSKGK  186 (200)
T ss_dssp             HHHHSBCCCTTT
T ss_pred             HHHhcCCCCCCC
Confidence            999999998644

>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=96.85  E-value=0.0018  Score=48.54  Aligned_cols=86  Identities=19%  Similarity=0.122  Sum_probs=59.6

Q ss_pred             CcHHHHHHHHh-CCCCCCchHHHHHHHHHH----cC--CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCC
Q psy7691          47 FPNAVLQHLKG-QGFEEPTAIQAQGWPIAL----SG--RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASS  119 (165)
Q Consensus        47 l~~~l~~~l~~-~g~~~~t~~Q~~a~~~~l----~G--~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~  119 (165)
                      .+.+..+.+.+ .-|. +|+-|..++..+.    ++  ++.+.++.||||||..++            +-+-..   -..
T Consensus        40 ~~~~~~~~~~~~lP~~-lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~------------~a~~~~---~~~  103 (233)
T d2eyqa3          40 HDREQYQLFCDSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAM------------RAAFLA---VDN  103 (233)
T ss_dssp             CCHHHHHHHHHTCCSC-CCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHH------------HHHHHH---HTT
T ss_pred             CCHHHHHhhhhccccc-cchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHH------------HHHHHH---HHc
Confidence            34555555544 5675 7999999888763    33  478999999999998654            211111   135


Q ss_pred             CceEEEECCCcHHHHHHHHHHHHhcCCCCC
Q psy7691         120 GTAYTFFTPNNGKQAKELIAVLTEASQPIP  149 (165)
Q Consensus       120 g~~~~~~~p~~~~~~~~i~~~l~~~~~~~p  149 (165)
                      |..++++.|+ .-++.|..+.+..-...+|
T Consensus       104 g~qv~~l~Pt-~~La~Q~~~~~~~~~~~~~  132 (233)
T d2eyqa3         104 HKQVAVLVPT-TLLAQQHYDNFRDRFANWP  132 (233)
T ss_dssp             TCEEEEECSS-HHHHHHHHHHHHHHSTTTT
T ss_pred             CCceEEEccH-HHhHHHHHHHHHHHHhhCC
Confidence            6789999998 8888888888877544443

>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=96.59  E-value=0.00073  Score=51.83  Aligned_cols=68  Identities=13%  Similarity=0.082  Sum_probs=47.9

Q ss_pred             CCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVL  141 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l  141 (165)
                      .|.+.|.+|+..++.....+.+++||+|||+...   +      .+......     ....+++++|+ ..++.|..+-+
T Consensus       113 ~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~---~------i~~~~~~~-----~~~k~Liivp~-~~Lv~Q~~~~f  177 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQA---L------LARYYLEN-----YEGKILIIVPT-TALTTQMADDF  177 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHH---H------HHHHHHHH-----CSSEEEEECSS-HHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHhcCCceeEEEcccCccHHHH---H------HHHHhhhc-----ccceEEEEEcC-chhHHHHHHHH
Confidence            3788999999999888888899999999997433   1      12111111     11257888888 78888888777


Q ss_pred             Hhc
Q psy7691         142 TEA  144 (165)
Q Consensus       142 ~~~  144 (165)
                      ..-
T Consensus       178 ~~~  180 (282)
T d1rifa_         178 VDY  180 (282)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            654

>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=96.34  E-value=0.002  Score=49.13  Aligned_cols=78  Identities=18%  Similarity=0.186  Sum_probs=52.9

Q ss_pred             HHHHHHHhCCCCCCchHHHHHHHHHHc----C--CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceE
Q psy7691          50 AVLQHLKGQGFEEPTAIQAQGWPIALS----G--RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAY  123 (165)
Q Consensus        50 ~l~~~l~~~g~~~~t~~Q~~a~~~~l~----G--~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~  123 (165)
                      ...+.+....|. +|..|..|+..+..    +  ++.+.++-+|||||.-++   .-     ...-+       ..|..+
T Consensus        72 l~~~f~~~LPFe-LT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~---~a-----~~~~~-------~~g~q~  135 (264)
T d1gm5a3          72 LAEEFIKSLPFK-LTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQ---LA-----ILDNY-------EAGFQT  135 (264)
T ss_dssp             HHHHHHHHSSSC-CCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHH---HH-----HHHHH-------HHTSCE
T ss_pred             HHHHHHhhcccc-CCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHH---HH-----HHHHH-------hcccce
Confidence            334445667886 89999999988742    2  577899999999998544   11     11111       245578


Q ss_pred             EEECCCcHHHHHHHHHHHHhc
Q psy7691         124 TFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus       124 ~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      .+++|+ .-++.|..+.+..-
T Consensus       136 ~~m~Pt-~~La~Qh~~~~~~~  155 (264)
T d1gm5a3         136 AFMVPT-SILAIQHYRRTVES  155 (264)
T ss_dssp             EEECSC-HHHHHHHHHHHHHH
T ss_pred             eEEeeh-HhhhHHHHHHHHHh
Confidence            999999 66666666555553

>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=96.18  E-value=0.0023  Score=42.90  Aligned_cols=47  Identities=23%  Similarity=0.150  Sum_probs=32.6

Q ss_pred             CeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHHhc
Q psy7691          79 DMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEA  144 (165)
Q Consensus        79 di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~~~  144 (165)
                      ..+.+++||+|||..+.         .++..         .|..++++.|+ +.++.|..+.+...
T Consensus        10 ~~ll~apTGsGKT~~~~---------~~~~~---------~~~~vli~~P~-~~l~~q~~~~~~~~   56 (136)
T d1a1va1          10 VAHLHAPTGSGKSTKVP---------AAYAA---------QGYKVLVLNPS-VAATLGFGAYMSKA   56 (136)
T ss_dssp             EEEEECCTTSCTTTHHH---------HHHHT---------TTCCEEEEESC-HHHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHH---------HHHHH---------cCCcEEEEcCh-HHHHHHHHHHHHHH
Confidence            46789999999997432         02322         23458888888 88888888777654

>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=95.17  E-value=0.0081  Score=44.96  Aligned_cols=31  Identities=19%  Similarity=0.328  Sum_probs=25.1

Q ss_pred             CCCChhHHHHhhccCCCCCCCCceEEEECCC
Q psy7691          99 YPNSSEDYIHRIGRTGRCASSGTAYTFFTPN  129 (165)
Q Consensus        99 lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~  129 (165)
                      .|.+..+|+||+||+||.|..+....++...
T Consensus       270 ~~~s~~~~~Qr~GR~GR~~~~~~~~~~~~~~  300 (305)
T d2bmfa2         270 MPVTHSSAAQRRGRVGRNPKNENDQYIYMGE  300 (305)
T ss_dssp             EECCHHHHHHHHTTSSCSSSCCCEEEEECSC
T ss_pred             ccCCHHHHhhhhcCcCcCCCCceEEEEECCC
Confidence            4566789999999999999988877766543

>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=95.07  E-value=0.0079  Score=44.96  Aligned_cols=68  Identities=22%  Similarity=0.171  Sum_probs=41.9

Q ss_pred             CchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHH
Q psy7691          63 PTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLT  142 (165)
Q Consensus        63 ~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~  142 (165)
                      ++|.|.+|+..  ....+++.|+.|||||...++-     +..++++.+      .....+++++.+ +..+..+...+.
T Consensus         2 L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~r-----v~~ll~~~~------~~~~~ILvlt~t-n~a~~~i~~~~~   67 (306)
T d1uaaa1           2 LNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNK-----IAHLIRGCG------YQARHIAAVTFT-NKAAREMKERVG   67 (306)
T ss_dssp             CCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHH-----HHHHHHHHC------CCGGGEEEEESS-HHHHHHHHHHHH
T ss_pred             cCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHHH-----HHHHHHhcC------CChhHEEEEeCc-HHHHHHHHHHHH
Confidence            57889998853  3345889999999999753310     001111211      122358888988 666776666665


Q ss_pred             hc
Q psy7691         143 EA  144 (165)
Q Consensus       143 ~~  144 (165)
                      ..
T Consensus        68 ~~   69 (306)
T d1uaaa1          68 QT   69 (306)
T ss_dssp             HH
T ss_pred             Hh
Confidence            43

>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=94.15  E-value=0.027  Score=42.36  Aligned_cols=67  Identities=21%  Similarity=0.139  Sum_probs=41.4

Q ss_pred             CCchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCC-CCCceEEEECCCcHHHHHHHHHH
Q psy7691          62 EPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCA-SSGTAYTFFTPNNGKQAKELIAV  140 (165)
Q Consensus        62 ~~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~-~~g~~~~~~~p~~~~~~~~i~~~  140 (165)
                      ..++.|.+++..  .+..+++.|+.|||||...            ++|+.+--..+ .....+++++.+ +..+..+...
T Consensus        11 ~L~~eQ~~~v~~--~~g~~lV~g~aGSGKTt~l------------~~ri~~ll~~~~~~p~~il~lt~t-~~aa~~~~~~   75 (318)
T d1pjra1          11 HLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVL------------THRIAYLMAEKHVAPWNILAITFT-NKAAREMRER   75 (318)
T ss_dssp             TSCHHHHHHHHC--CSSCEEEEECTTSCHHHHH------------HHHHHHHHHTTCCCGGGEEEEESS-HHHHHHHHHH
T ss_pred             hCCHHHHHHHhC--CCCCEEEEecCCccHHHHH------------HHHHHHHHHcCCCCHHHeEeEecc-HHHHHHHHHH
Confidence            367899998863  3457999999999999743            33332111111 123467888888 5555555555


Q ss_pred             HHh
Q psy7691         141 LTE  143 (165)
Q Consensus       141 l~~  143 (165)
                      +..
T Consensus        76 ~~~   78 (318)
T d1pjra1          76 VQS   78 (318)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            543

>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=93.20  E-value=0.12  Score=40.37  Aligned_cols=69  Identities=23%  Similarity=0.224  Sum_probs=46.9

Q ss_pred             CchHHHHHHHHHHcCCCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHHHHHHH
Q psy7691          63 PTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLT  142 (165)
Q Consensus        63 ~t~~Q~~a~~~~l~G~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i~~~l~  142 (165)
                      .+..|.+|+..++.+.-.++.++.|+|||..+..      ....+.+...     ..+..+.+.+|+ ...+..+.+.+.
T Consensus       149 ~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~~------~l~~l~~~~~-----~~~~~I~l~ApT-gkAA~~L~e~~~  216 (359)
T d1w36d1         149 EINWQKVAAAVALTRRISVISGGPGTGKTTTVAK------LLAALIQMAD-----GERCRIRLAAPT-GKAAARLTESLG  216 (359)
T ss_dssp             SCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHH------HHHHHHHTCS-----SCCCCEEEEBSS-HHHHHHHHHHHT
T ss_pred             cccHHHHHHHHHHcCCeEEEEcCCCCCceehHHH------HHHHHHHHHh-----ccCCeEEEecCc-HHHHHHHHHHHH
Confidence            4567999999999888888999999999975431      0012333322     356679999999 555666665554


Q ss_pred             h
Q psy7691         143 E  143 (165)
Q Consensus       143 ~  143 (165)
                      .
T Consensus       217 ~  217 (359)
T d1w36d1         217 K  217 (359)
T ss_dssp             H
T ss_pred             H
Confidence            3

>d1tf5a4 c.37.1.19 (A:396-570) 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=87.05  E-value=0.59  Score=32.81  Aligned_cols=108  Identities=20%  Similarity=0.204  Sum_probs=66.6

Q ss_pred             CCccccc-cCCCcHHHHHHHHhCCCCC--Cch--HHHHHHHHHHcC---CCeeeecccCCc------------ccceeee
Q psy7691          37 CPTQELT-EGCFPNAVLQHLKGQGFEE--PTA--IQAQGWPIALSG---RDMVGIAQTGSG------------KTLAVIN   96 (165)
Q Consensus        37 ~~i~~f~-~l~l~~~l~~~l~~~g~~~--~t~--~Q~~a~~~~l~G---~di~~~a~tgsG------------Kt~~~~~   96 (165)
                      .|+..+. +..-.+.+.+.|.+.|+..  ...  ...++-=..-.|   .=+++....|-|            =-++|+.
T Consensus        35 rPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea~II~~Ag~~g~VtIATNmAGRGtDikl~~~v~~~GGLhVI~  114 (175)
T d1tf5a4          35 QPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAVTIATNMAGRGTDIKLGEGVKELGGLAVVG  114 (175)
T ss_dssp             CCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTTSTTCEEEEETTSSTTCCCCCCTTSGGGTSEEEEE
T ss_pred             CCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHHHHHHhccCCCceeehhhHHHcCCCccchHHHHhCCCcEEEE
Confidence            3544444 4577888888899888764  222  222221111122   123333333433            1347887


Q ss_pred             cCCCCChhHHHHhhccCCCCCCCCceEEEECCCcH----HHHHHHHHHHHhc
Q psy7691          97 FDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNG----KQAKELIAVLTEA  144 (165)
Q Consensus        97 ~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~----~~~~~i~~~l~~~  144 (165)
                      -..|.+.--..|-.||+||.|..|....+++-.+.    .....+.+++...
T Consensus       115 t~~~~s~Rid~Ql~GR~gRQGdpGs~~~~~sleD~l~~~f~~~~~~~~~~~~  166 (175)
T d1tf5a4         115 TERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDELMRRFGAERTMAMLDRF  166 (175)
T ss_dssp             SSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSSGGGSSHHHHHHHHHHHH
T ss_pred             eccCcchhHHHHHhcchhhhCCCcccEEEEEcCHHHHHHHhHHHHHHHHHHh
Confidence            77888887788889999999999999999977652    1245666666554

>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=84.13  E-value=0.2  Score=38.46  Aligned_cols=21  Identities=33%  Similarity=0.368  Sum_probs=17.9

Q ss_pred             HHHcCCCeeeecccCCcccce
Q psy7691          73 IALSGRDMVGIAQTGSGKTLA   93 (165)
Q Consensus        73 ~~l~G~di~~~a~tgsGKt~~   93 (165)
                      .+..+.+++++++||||||..
T Consensus       162 ~v~~~~nili~G~tgSGKTT~  182 (323)
T d1g6oa_         162 GIAIGKNVIVCGGTGSGKTTY  182 (323)
T ss_dssp             HHHHTCCEEEEESTTSSHHHH
T ss_pred             HHHhCCCEEEEeeccccchHH
Confidence            456778999999999999973

>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=83.62  E-value=0.16  Score=40.81  Aligned_cols=17  Identities=35%  Similarity=0.495  Sum_probs=15.3

Q ss_pred             CCCeeeecccCCcccce
Q psy7691          77 GRDMVGIAQTGSGKTLA   93 (165)
Q Consensus        77 G~di~~~a~tgsGKt~~   93 (165)
                      -.+++.++|||+|||+.
T Consensus        49 ksNILliGPTGvGKTlL   65 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEI   65 (443)
T ss_dssp             CCCEEEECCTTSSHHHH
T ss_pred             cccEEEECCCCCCHHHH
Confidence            46899999999999984

>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=82.97  E-value=0.65  Score=36.79  Aligned_cols=62  Identities=24%  Similarity=0.354  Sum_probs=41.2

Q ss_pred             CchHHHHHHHHHH----cC-CCeeeecccCCcccceeeecCCCCChhHHHHhhccCCCCCCCCceEEEECCCcHHHHHHH
Q psy7691          63 PTAIQAQGWPIAL----SG-RDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL  137 (165)
Q Consensus        63 ~t~~Q~~a~~~~l----~G-~di~~~a~tgsGKt~~~~~~~lP~~~~~~i~r~gr~~r~~~~g~~~~~~~p~~~~~~~~i  137 (165)
                      |+--|=+||..+.    .| ++.+..+.||||||+.+.         ..+.+.+|         .+++++|+ ...|.++
T Consensus        12 p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA---------~l~~~~~r---------p~LVVt~n-~~~A~qL   72 (413)
T d1t5la1          12 PQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTIS---------NVIAQVNK---------PTLVIAHN-KTLAGQL   72 (413)
T ss_dssp             CCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHHH---------HHHHHHTC---------CEEEECSS-HHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHHH---------HHHHHhCC---------CEEEEeCC-HHHHHHH
Confidence            5556666665544    44 467788999999997543         14555544         47889988 6666666


Q ss_pred             HHHHHh
Q psy7691         138 IAVLTE  143 (165)
Q Consensus       138 ~~~l~~  143 (165)
                      .+-+..
T Consensus        73 ~~dL~~   78 (413)
T d1t5la1          73 YSELKE   78 (413)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            666654

>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=82.33  E-value=0.79  Score=33.08  Aligned_cols=24  Identities=25%  Similarity=0.415  Sum_probs=18.7

Q ss_pred             HHHh-hccCCCCCCCCceEEEECCC
Q psy7691         106 YIHR-IGRTGRCASSGTAYTFFTPN  129 (165)
Q Consensus       106 ~i~r-~gr~~r~~~~g~~~~~~~p~  129 (165)
                      -+|+ -||.||.+..+.|+++..+.
T Consensus       117 QLhQLRGRVGR~~~~s~c~l~~~~~  141 (211)
T d2eyqa5         117 QLHQLRGRVGRSHHQAYAWLLTPHP  141 (211)
T ss_dssp             HHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             ccccccceeeecCccceEEEEecCC
Confidence            3555 49999999999999888653

>d1z3ix1 c.37.1.19 (X:390-735) 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=80.86  E-value=1.2  Score=34.21  Aligned_cols=93  Identities=11%  Similarity=0.072  Sum_probs=56.7

Q ss_pred             CccccccC-CCcHHHHHHHHhCCCCC-----Cch--HHHHHHHHHHcCCC---eee-eccc-CCcccc----eeeecCCC
Q psy7691          38 PTQELTEG-CFPNAVLQHLKGQGFEE-----PTA--IQAQGWPIALSGRD---MVG-IAQT-GSGKTL----AVINFDYP  100 (165)
Q Consensus        38 ~i~~f~~l-~l~~~l~~~l~~~g~~~-----~t~--~Q~~a~~~~l~G~d---i~~-~a~t-gsGKt~----~~~~~~lP  100 (165)
                      .++.|++. ..-+.+.+.|...|+..     .++  --..++..+..+..   ++. .... |.|=++    .++.||.+
T Consensus       120 KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~vlLls~~agg~GlnL~~a~~vi~~d~~  199 (346)
T d1z3ix1         120 KVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPD  199 (346)
T ss_dssp             EEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTTEEEEEECSCC
T ss_pred             ceeEEeehhhhhHHHHHHHhhhhccccccccchhHHHHHHHHHhhhcccccceeeeecchhhhhccccccceEEEEecCC
Confidence            35667764 34455666677767632     222  22345666665532   333 3222 235433    58899999


Q ss_pred             CChhHHHHhhccCCCCCCCCceE--EEECCCc
Q psy7691         101 NSSEDYIHRIGRTGRCASSGTAY--TFFTPNN  130 (165)
Q Consensus       101 ~~~~~~i~r~gr~~r~~~~g~~~--~~~~p~~  130 (165)
                      -++..+.|++||.-|.|.+..+.  -+++..+
T Consensus       200 wnp~~~~Qa~~R~~R~GQ~~~V~v~rli~~~T  231 (346)
T d1z3ix1         200 WNPANDEQAMARVWRDGQKKTCYIYRLLSTGT  231 (346)
T ss_dssp             SSHHHHHHHHTTSSSTTCCSCEEEEEEEETTS
T ss_pred             CccchHhHhhhcccccCCCCceEEEEEEeCCC
Confidence            99999999999999999876653  3344443