Citrus Sinensis ID: 037139

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-----
Protein Sequence
LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTIPDRPPRRNDTVFAH
Secondary Structure (PSIPRED)
cccEEEEEcccccHHHHHHHHHHHHcccccEEEEEEccccccccccccEEEccccccccccccccccccccccccEEEEEEcccccHHHHHHHHHHHHHccccccHHHHHcHHHHcccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccEEEEcccccHHHHHHHHHHHHcccccEEEEEcHHHccccccccEEEEEEcccccHHHHHEEccccccccccEEEEEEEccccHHHHHHHHHHHHHHcccccHHHHHHHHHHcccccccccccccccEEEEc
Coil and Loop (DISEMBL)
lgyrvttlhggksqeQREISLEGFRTKRYNVLVATdvagrgidipdvahvinydmpgniemythrigrtgragktgvaTTFLTFHDTDVFYDLKQMLiqsnspvppelakheaskfkpgtipdrpprrndtvfah
Flexible Loop (DISEMBL)
lgyrvttlhggksqeqreislegfrtkrYNVLVATdvagrgidipdvAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHeaskfkpgtipdrpprrndtvfah
Low Complexity Region (SEG)
LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTIPDRPPRRNDTVFAH
Disordered region (IsUnstruct)
********************LEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLI*************************************
Disordered Region (DISOPRED)
*GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPP*****************************
Disordered Region (DISEMBL)
******************ISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTIPDRPPRRNDTVFAH
Disordered Region (DISPRO)
*GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKF*******************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTIPDRPPRRNDTVFAH
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	135	2.2.26 [Sep-21-2011]
P93008	733	DEAD-box ATP-dependent RN	yes	no	0.977	0.180	0.878	1e-67
Q53RK8	736	DEAD-box ATP-dependent RN	yes	no	0.985	0.180	0.819	1e-64
Q9FZ92	622	Putative DEAD-box ATP-dep	no	no	0.896	0.194	0.760	4e-50
Q1DMX8	820	Pre-mRNA-splicing ATP-dep	N/A	no	0.874	0.143	0.638	3e-38
Q9BUQ8	820	Probable ATP-dependent RN	yes	no	0.985	0.162	0.6	5e-38
Q5RC67	820	Probable ATP-dependent RN	yes	no	0.985	0.162	0.6	6e-38
Q2HEB0	705	Pre-mRNA-splicing ATP-dep	N/A	no	0.874	0.167	0.613	4e-37
Q2UH00	803	Pre-mRNA-splicing ATP-dep	yes	no	0.874	0.146	0.621	6e-37
A1CX72	796	Pre-mRNA-splicing ATP-dep	N/A	no	0.874	0.148	0.621	8e-37
Q5BCU6	782	Pre-mRNA-splicing ATP-dep	yes	no	0.874	0.150	0.638	8e-37

>sp|P93008|RH21_ARATH DEAD-box ATP-dependent RNA helicase 21 OS=Arabidopsis thaliana GN=RH21 PE=2 SV=1

 Score =  254 bits (648), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 116/132 (87%), Positives = 126/132 (95%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           GYRVTTLHGGKSQEQREISLEGFR KRYNVLVATDV GRGIDIPDVAHVINYDMP +IEM
Sbjct: 600 GYRVTTLHGGKSQEQREISLEGFRAKRYNVLVATDVVGRGIDIPDVAHVINYDMPKHIEM 659

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTI 121
           YTHRIGRTGRAGK+GVAT+FLT HDT+VFYDLKQML+QSNS VPPELA+HEAS+FKPGT+
Sbjct: 660 YTHRIGRTGRAGKSGVATSFLTLHDTEVFYDLKQMLVQSNSAVPPELARHEASRFKPGTV 719

Query: 122 PDRPPRRNDTVF 133
           PDRPPR +DTV+
Sbjct: 720 PDRPPRHSDTVY 731

ATP-dependent RNA helicase involved in mRNA splicing. May destabilize the U1/5'-splice site duplex to permit an effective competition for the 5'-splice site by the U6 snRNA, resulting in the switch between U1 and U6 at the 5'-splice site. May also act to unwind the U4/U6 base-pairing interaction in the U4/U6/U5 snRNP, facilitating the first covalent step of splicing.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q53RK8|RH21_ORYSJ DEAD-box ATP-dependent RNA helicase 21 OS=Oryza sativa subsp. japonica GN=Os03g0708600 PE=2 SV=1

 Score =  244 bits (622), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 109/133 (81%), Positives = 125/133 (93%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G+RVTTLHGGKSQEQRE SL+GFR +R+ VLVATDVAGRGIDIPDVAHVINY+MP +I+ 
Sbjct: 602 GFRVTTLHGGKSQEQRETSLDGFRNRRFTVLVATDVAGRGIDIPDVAHVINYEMPSSIDT 661

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTI 121
           YTHRIGRTGRAGK G+AT+FLT  +TD+F+DLKQMLIQSNSPVPPELA+HEASKFKPG++
Sbjct: 662 YTHRIGRTGRAGKKGLATSFLTLENTDIFFDLKQMLIQSNSPVPPELARHEASKFKPGSV 721

Query: 122 PDRPPRRNDTVFA 134
           PDRPPRRNDTV+A
Sbjct: 722 PDRPPRRNDTVYA 734

ATP-dependent RNA helicase involved in mRNA splicing. May destabilize the U1/5'-splice site duplex to permit an effective competition for the 5'-splice site by the U6 snRNA, resulting in the switch between U1 and U6 at the 5'-splice site. May also act to unwind the U4/U6 base-pairing interaction in the U4/U6/U5 snRNP, facilitating the first covalent step of splicing.

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9FZ92|RH44_ARATH Putative DEAD-box ATP-dependent RNA helicase 44 OS=Arabidopsis thaliana GN=RH44 PE=5 SV=2

 Score =  196 bits (498), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 92/121 (76%), Positives = 102/121 (84%)

Query: 4   RVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYT 63
           RVTTLH GKSQEQR+ SLE F+ KR+NVLV TDV GRG+DI D+A VINYDMP  +++YT
Sbjct: 498 RVTTLHAGKSQEQRDYSLEEFKKKRFNVLVTTDVLGRGLDILDLAQVINYDMPNTMDLYT 557

Query: 64  HRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTIPD 123
           HRIGRTGRAGKTGVATTFLT  D DVFY LKQ L + NS VPPELA+HEASKFKPGT PD
Sbjct: 558 HRIGRTGRAGKTGVATTFLTLEDKDVFYGLKQKLNECNSLVPPELARHEASKFKPGTFPD 617

Query: 124 R 124
           R
Sbjct: 618 R 618

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q1DMX8|PRP28_COCIM Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 OS=Coccidioides immitis (strain RS) GN=PRP28 PE=3 SV=2

 Score =  156 bits (395), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 76/119 (63%), Positives = 92/119 (77%), Gaps = 1/119 (0%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
           +GY   TLHG K+QEQRE +L   R    +VLVATD+AGRGID+PDV+ V+N++M  NIE
Sbjct: 678 MGYSSVTLHGSKTQEQREAALASVRNGNTDVLVATDLAGRGIDVPDVSLVVNFNMATNIE 737

Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSN-SPVPPELAKHEASKFKP 118
            YTHRIGRTGRAGK+GVA TFL   D DV YDLKQML++S+ S VP EL KHEA++ KP
Sbjct: 738 SYTHRIGRTGRAGKSGVAITFLGNEDADVMYDLKQMLMKSSISRVPEELRKHEAAQSKP 796

ATP-dependent RNA helicase involved in mRNA splicing. May destabilize the U1/5'-splice site duplex to permit an effective competition for the 5'-splice site by the U6 snRNA, resulting in the switch between U1 and U6 at the 5'-splice site. May also act to unwind the U4/U6 base-pairing interaction in the U4/U6/U5 snRNP, facilitating the first covalent step of splicing.

Coccidioides immitis (strain RS) (taxid: 246410)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9BUQ8|DDX23_HUMAN Probable ATP-dependent RNA helicase DDX23 OS=Homo sapiens GN=DDX23 PE=1 SV=3

 Score =  155 bits (393), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 81/135 (60%), Positives = 99/135 (73%), Gaps = 2/135 (1%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
           +GY   TLHGGK QEQRE +L   +    ++LVATDVAGRGIDI DV+ V+NYDM  NIE
Sbjct: 687 MGYNACTLHGGKGQEQREFALSNLKAGAKDILVATDVAGRGIDIQDVSMVVNYDMAKNIE 746

Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSN-SPVPPELAKHEASKFKPG 119
            Y HRIGRTGRAGK+GVA TFLT  D+ VFY+LKQ +++S  S  PPELA H  ++ KPG
Sbjct: 747 DYIHRIGRTGRAGKSGVAITFLTKEDSAVFYELKQAILESPVSSCPPELANHPDAQHKPG 806

Query: 120 TIPDRPPRRNDTVFA 134
           TI  +  RR +T+FA
Sbjct: 807 TILTK-KRREETIFA 820

Involved in pre-mRNA splicing and its phosphorylated form (by SRPK2) is required for spliceosomal B complex formation.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5RC67|DDX23_PONAB Probable ATP-dependent RNA helicase DDX23 OS=Pongo abelii GN=DDX23 PE=2 SV=1

 Score =  155 bits (392), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 81/135 (60%), Positives = 99/135 (73%), Gaps = 2/135 (1%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
           +GY   TLHGGK QEQRE +L   +    ++LVATDVAGRGIDI DV+ V+NYDM  NIE
Sbjct: 687 MGYNACTLHGGKGQEQREFALSNLKAGAKDILVATDVAGRGIDIQDVSMVVNYDMAKNIE 746

Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSN-SPVPPELAKHEASKFKPG 119
            Y HRIGRTGRAGK+GVA TFLT  D+ VFY+LKQ +++S  S  PPELA H  ++ KPG
Sbjct: 747 DYIHRIGRTGRAGKSGVAITFLTKEDSAVFYELKQAILESPVSSCPPELANHPDAQHKPG 806

Query: 120 TIPDRPPRRNDTVFA 134
           TI  +  RR +T+FA
Sbjct: 807 TILTK-KRREETIFA 820

Involved in pre-mRNA splicing and its phosphorylated form (by SRPK2) is required for spliceosomal B complex formation.

Pongo abelii (taxid: 9601)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q2HEB0|PRP28_CHAGB Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 OS=Chaetomium globosum (strain ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970) GN=PRP28 PE=3 SV=1

 Score =  152 bits (385), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 73/119 (61%), Positives = 92/119 (77%), Gaps = 1/119 (0%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
            GY   TLHG K+QEQRE SL   R  + N+LVATD+AGRGID+ DV+ V+N++MP +IE
Sbjct: 565 WGYSTVTLHGSKTQEQREASLASVRNGQANILVATDLAGRGIDVADVSLVVNFNMPSSIE 624

Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSN-SPVPPELAKHEASKFKP 118
            YTHRIGRTGRAGK+GVA TFL   D+DV YDLKQ++ +S+ S VP EL +HEA++ KP
Sbjct: 625 AYTHRIGRTGRAGKSGVAITFLGNEDSDVMYDLKQIISKSSISKVPEELRRHEAAQSKP 683

ATP-dependent RNA helicase involved in mRNA splicing. May destabilize the U1/5'-splice site duplex to permit an effective competition for the 5'-splice site by the U6 snRNA, resulting in the switch between U1 and U6 at the 5'-splice site. May also act to unwind the U4/U6 base-pairing interaction in the U4/U6/U5 snRNP, facilitating the first covalent step of splicing.

Chaetomium globosum (strain ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970) (taxid: 306901)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q2UH00|PRP28_ASPOR Pre-mRNA-splicing ATP-dependent RNA helicase prp28 OS=Aspergillus oryzae (strain ATCC 42149 / RIB 40) GN=prp28 PE=3 SV=1

 Score =  152 bits (384), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 74/119 (62%), Positives = 92/119 (77%), Gaps = 1/119 (0%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
            G+   TLHG K+QEQRE +L   R  + +VLVATD+AGRGID+PDV+ VIN++M   IE
Sbjct: 665 WGFSSVTLHGSKTQEQREAALASVRNGQTDVLVATDLAGRGIDVPDVSLVINFNMATTIE 724

Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSN-SPVPPELAKHEASKFKP 118
            YTHRIGRTGRAGK+GVA TFL   DTDV YDLKQM+++S+ S +P EL KHEA++ KP
Sbjct: 725 SYTHRIGRTGRAGKSGVAITFLGNEDTDVMYDLKQMIMKSSISRLPEELRKHEAAQSKP 783

ATP-dependent RNA helicase involved in mRNA splicing. May destabilize the U1/5'-splice site duplex to permit an effective competition for the 5'-splice site by the U6 snRNA, resulting in the switch between U1 and U6 at the 5'-splice site. May also act to unwind the U4/U6 base-pairing interaction in the U4/U6/U5 snRNP, facilitating the first covalent step of splicing.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A1CX72|PRP28_NEOFI Pre-mRNA-splicing ATP-dependent RNA helicase prp28 OS=Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) GN=prp28 PE=3 SV=1

 Score =  152 bits (383), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 74/119 (62%), Positives = 91/119 (76%), Gaps = 1/119 (0%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
           +G+   TLHG K+QEQRE +L   R    +VLVATD+AGRGID+PDV+ V+N++M  +IE
Sbjct: 657 MGFSSVTLHGSKTQEQREAALASVRNGSTDVLVATDLAGRGIDVPDVSLVVNFNMANSIE 716

Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSN-SPVPPELAKHEASKFKP 118
            YTHRIGRTGRAGK+GVA TFL   D DV YDLKQML++S  S VP EL KHEA++ KP
Sbjct: 717 SYTHRIGRTGRAGKSGVAITFLGNEDADVMYDLKQMLMKSPISRVPEELRKHEAAQSKP 775

ATP-dependent RNA helicase involved in mRNA splicing. May destabilize the U1/5'-splice site duplex to permit an effective competition for the 5'-splice site by the U6 snRNA, resulting in the switch between U1 and U6 at the 5'-splice site. May also act to unwind the U4/U6 base-pairing interaction in the U4/U6/U5 snRNP, facilitating the first covalent step of splicing.

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|Q5BCU6|PRP28_EMENI Pre-mRNA-splicing ATP-dependent RNA helicase prp28 OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) GN=prp28 PE=3 SV=2

 Score =  152 bits (383), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 76/119 (63%), Positives = 90/119 (75%), Gaps = 1/119 (0%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
            G+   TLHG K+QEQRE +L   R    +VLVATD+AGRGID+PDV+ VIN++M  +IE
Sbjct: 644 WGFSSVTLHGSKTQEQREAALASVRNGSTDVLVATDLAGRGIDVPDVSLVINFNMATSIE 703

Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSN-SPVPPELAKHEASKFKP 118
            YTHRIGRTGRAGK+GVA TFL   D DV YDLKQMLI+S  S VP EL KHEA++ KP
Sbjct: 704 SYTHRIGRTGRAGKSGVAITFLGNEDADVMYDLKQMLIKSPISRVPEELRKHEAAQSKP 762

ATP-dependent RNA helicase involved in mRNA splicing. May destabilize the U1/5'-splice site duplex to permit an effective competition for the 5'-splice site by the U6 snRNA, resulting in the switch between U1 and U6 at the 5'-splice site. May also act to unwind the U4/U6 base-pairing interaction in the U4/U6/U5 snRNP, facilitating the first covalent step of splicing.

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

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	135
356565647	706	PREDICTED: DEAD-box ATP-dependent RNA he	0.992	0.189	0.977	5e-74
225443496	709	PREDICTED: DEAD-box ATP-dependent RNA he	0.992	0.188	0.970	8e-74
147774689	661	hypothetical protein VITISV_005473 [Viti	0.992	0.202	0.970	1e-73
359475106	712	PREDICTED: DEAD-box ATP-dependent RNA he	0.992	0.188	0.962	2e-73
356522085	701	PREDICTED: DEAD-box ATP-dependent RNA he	0.992	0.191	0.970	2e-73
224135589	710	predicted protein [Populus trichocarpa]	0.992	0.188	0.962	4e-72
297735665	688	unnamed protein product [Vitis vinifera]	0.985	0.193	0.954	2e-71
358347102	781	DEAD-box ATP-dependent RNA helicase [Med	0.985	0.170	0.954	3e-71
449455778	715	PREDICTED: DEAD-box ATP-dependent RNA he	0.992	0.187	0.932	5e-71
449484526	715	PREDICTED: LOW QUALITY PROTEIN: DEAD-box	0.992	0.187	0.932	5e-71

>gi|356565647|ref|XP_003551050.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 21-like isoform 1 [Glycine max] gi|356565649|ref|XP_003551051.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 21-like isoform 2 [Glycine max]

 Score =  281 bits (720), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 131/134 (97%), Positives = 133/134 (99%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM
Sbjct: 573 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 632

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTI 121
           YTHRIGRTGRAGKTGVATTFLT HD+DVFYDLKQMLIQSNSPVPPELA+HEASKFKPGTI
Sbjct: 633 YTHRIGRTGRAGKTGVATTFLTLHDSDVFYDLKQMLIQSNSPVPPELARHEASKFKPGTI 692

Query: 122 PDRPPRRNDTVFAH 135
           PDRPPRRNDTVFAH
Sbjct: 693 PDRPPRRNDTVFAH 706

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225443496|ref|XP_002270644.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 21-like [Vitis vinifera]

 Score =  281 bits (718), Expect = 8e-74,   Method: Compositional matrix adjust.
 Identities = 130/134 (97%), Positives = 133/134 (99%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM
Sbjct: 576 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 635

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTI 121
           YTHRIGRTGRAGKTGVATTFLT HD+DVFYDLKQMLIQSNSPVPPELA+HEASKFKPG+I
Sbjct: 636 YTHRIGRTGRAGKTGVATTFLTLHDSDVFYDLKQMLIQSNSPVPPELARHEASKFKPGSI 695

Query: 122 PDRPPRRNDTVFAH 135
           PDRPPRRNDTVFAH
Sbjct: 696 PDRPPRRNDTVFAH 709

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147774689|emb|CAN74342.1| hypothetical protein VITISV_005473 [Vitis vinifera]

 Score =  280 bits (717), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 130/134 (97%), Positives = 133/134 (99%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM
Sbjct: 528 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 587

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTI 121
           YTHRIGRTGRAGKTGVATTFLT HD+DVFYDLKQMLIQSNSPVPPELA+HEASKFKPG+I
Sbjct: 588 YTHRIGRTGRAGKTGVATTFLTLHDSDVFYDLKQMLIQSNSPVPPELARHEASKFKPGSI 647

Query: 122 PDRPPRRNDTVFAH 135
           PDRPPRRNDTVFAH
Sbjct: 648 PDRPPRRNDTVFAH 661

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359475106|ref|XP_003631587.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 21-like [Vitis vinifera]

 Score =  280 bits (715), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 129/134 (96%), Positives = 132/134 (98%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM
Sbjct: 579 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 638

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTI 121
           YTHRIGRTGRAGKTGVATTFLT HD+DVFYDLKQMLIQ+NSPVPPELA+HEASKFKPG I
Sbjct: 639 YTHRIGRTGRAGKTGVATTFLTLHDSDVFYDLKQMLIQNNSPVPPELARHEASKFKPGAI 698

Query: 122 PDRPPRRNDTVFAH 135
           PDRPPRRNDTVFAH
Sbjct: 699 PDRPPRRNDTVFAH 712

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356522085|ref|XP_003529680.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 21-like [Glycine max]

 Score =  279 bits (714), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 130/134 (97%), Positives = 132/134 (98%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM
Sbjct: 568 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 627

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTI 121
           YTHRIGRTGRAGKTGVATTFLT  D+DVFYDLKQMLIQSNSPVPPELA+HEASKFKPGTI
Sbjct: 628 YTHRIGRTGRAGKTGVATTFLTLQDSDVFYDLKQMLIQSNSPVPPELARHEASKFKPGTI 687

Query: 122 PDRPPRRNDTVFAH 135
           PDRPPRRNDTVFAH
Sbjct: 688 PDRPPRRNDTVFAH 701

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224135589|ref|XP_002322111.1| predicted protein [Populus trichocarpa] gi|222869107|gb|EEF06238.1| predicted protein [Populus trichocarpa]

 Score =  275 bits (703), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 129/134 (96%), Positives = 131/134 (97%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM
Sbjct: 577 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 636

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTI 121
           YTHRIGRTGRAGKTGVA+TFLT  DTDVFYDLKQMLIQSNS VPPELA+HEASKFKPGTI
Sbjct: 637 YTHRIGRTGRAGKTGVASTFLTLGDTDVFYDLKQMLIQSNSSVPPELARHEASKFKPGTI 696

Query: 122 PDRPPRRNDTVFAH 135
           PDRPPRRNDTVFAH
Sbjct: 697 PDRPPRRNDTVFAH 710

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297735665|emb|CBI18352.3| unnamed protein product [Vitis vinifera]

 Score =  273 bits (698), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 127/133 (95%), Positives = 130/133 (97%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM
Sbjct: 497 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 556

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTI 121
           YTHRIGRTGRAGKTGVATTFLT HD+DVFYDLKQMLIQSNSPVPPELA+HEASKFKPG+I
Sbjct: 557 YTHRIGRTGRAGKTGVATTFLTLHDSDVFYDLKQMLIQSNSPVPPELARHEASKFKPGSI 616

Query: 122 PDRPPRRNDTVFA 134
           PDRPPRRNDT F 
Sbjct: 617 PDRPPRRNDTYFC 629

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358347102|ref|XP_003637601.1| DEAD-box ATP-dependent RNA helicase [Medicago truncatula] gi|355503536|gb|AES84739.1| DEAD-box ATP-dependent RNA helicase [Medicago truncatula]

 Score =  272 bits (696), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 127/133 (95%), Positives = 131/133 (98%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           GYRVTTLHGGKSQ+QREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM
Sbjct: 573 GYRVTTLHGGKSQDQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 632

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTI 121
           YTHRIGRTGRAGKTGVATTFLT  DTDVFY+LKQMLIQSNSPVPPELA+HEASKFKPG+I
Sbjct: 633 YTHRIGRTGRAGKTGVATTFLTLQDTDVFYELKQMLIQSNSPVPPELARHEASKFKPGSI 692

Query: 122 PDRPPRRNDTVFA 134
           PDRPPRRNDTVFA
Sbjct: 693 PDRPPRRNDTVFA 705

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449455778|ref|XP_004145628.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 21-like [Cucumis sativus]

 Score =  271 bits (694), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 125/134 (93%), Positives = 131/134 (97%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMP NIEM
Sbjct: 582 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPSNIEM 641

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTI 121
           YTHRIGRTGRAGKTGVATTFLT  D++VFYDLKQMLIQSNSPVPPELA+HEASKFKPG+I
Sbjct: 642 YTHRIGRTGRAGKTGVATTFLTLQDSEVFYDLKQMLIQSNSPVPPELARHEASKFKPGSI 701

Query: 122 PDRPPRRNDTVFAH 135
           PDRPPRRN+T+FAH
Sbjct: 702 PDRPPRRNETLFAH 715

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449484526|ref|XP_004156907.1| PREDICTED: LOW QUALITY PROTEIN: DEAD-box ATP-dependent RNA helicase 21-like [Cucumis sativus]

 Score =  271 bits (694), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 125/134 (93%), Positives = 131/134 (97%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMP NIEM
Sbjct: 582 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPSNIEM 641

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTI 121
           YTHRIGRTGRAGKTGVATTFLT  D++VFYDLKQMLIQSNSPVPPELA+HEASKFKPG+I
Sbjct: 642 YTHRIGRTGRAGKTGVATTFLTLQDSEVFYDLKQMLIQSNSPVPPELARHEASKFKPGSI 701

Query: 122 PDRPPRRNDTVFAH 135
           PDRPPRRN+T+FAH
Sbjct: 702 PDRPPRRNETLFAH 715

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	135
TAIR|locus:2057640	733	AT2G33730 [Arabidopsis thalian	0.977	0.180	0.878	1.6e-61
ZFIN|ZDB-GENE-030131-6215	807	ddx23 "DEAD (Asp-Glu-Ala-Asp)	0.985	0.164	0.607	5.4e-37
RGD|1308685	819	Ddx23 "DEAD (Asp-Glu-Ala-Asp)	0.985	0.162	0.6	2e-36
UNIPROTKB|A6QLB2	820	DDX23 "Uncharacterized protein	0.985	0.162	0.6	2e-36
UNIPROTKB|E2RTL6	820	DDX23 "Uncharacterized protein	0.985	0.162	0.6	2e-36
UNIPROTKB|Q9BUQ8	820	DDX23 "Probable ATP-dependent	0.985	0.162	0.6	2e-36
GENEDB_PFALCIPARUM|PFE0925c	1123	PFE0925c "snrnp protein, putat	0.962	0.115	0.572	7.9e-35
UNIPROTKB|Q8I0W7	1123	PFE0925c "Snrnp protein, putat	0.962	0.115	0.572	7.9e-35
WB|WBGene00017162	730	ddx-23 [Caenorhabditis elegans	0.977	0.180	0.559	1.2e-33
FB|FBgn0032690	822	CG10333 [Drosophila melanogast	0.970	0.159	0.583	1.3e-33

TAIR|locus:2057640 AT2G33730 [Arabidopsis thaliana (taxid:3702)]

 Score = 629 (226.5 bits), Expect = 1.6e-61, P = 1.6e-61
 Identities = 116/132 (87%), Positives = 126/132 (95%)

Query:     2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
             GYRVTTLHGGKSQEQREISLEGFR KRYNVLVATDV GRGIDIPDVAHVINYDMP +IEM
Sbjct:   600 GYRVTTLHGGKSQEQREISLEGFRAKRYNVLVATDVVGRGIDIPDVAHVINYDMPKHIEM 659

Query:    62 YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTI 121
             YTHRIGRTGRAGK+GVAT+FLT HDT+VFYDLKQML+QSNS VPPELA+HEAS+FKPGT+
Sbjct:   660 YTHRIGRTGRAGKSGVATSFLTLHDTEVFYDLKQMLVQSNSAVPPELARHEASRFKPGTV 719

Query:   122 PDRPPRRNDTVF 133
             PDRPPR +DTV+
Sbjct:   720 PDRPPRHSDTVY 731

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0005737 "cytoplasm" evidence=IDA

GO:0006486 "protein glycosylation" evidence=RCA

ZFIN|ZDB-GENE-030131-6215 ddx23 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 23" [Danio rerio (taxid:7955)]

 Score = 406 (148.0 bits), Expect = 5.4e-37, P = 5.4e-37
 Identities = 82/135 (60%), Positives = 99/135 (73%)

Query:     1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
             +GY   TLHGGK QEQRE +L   +    ++LVATDVAGRGIDI DV+ V+NYDM  NIE
Sbjct:   674 MGYNACTLHGGKGQEQREFALSNLKAGAKDILVATDVAGRGIDIQDVSMVLNYDMAKNIE 733

Query:    61 MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSN-SPVPPELAKHEASKFKPG 119
              Y HRIGRTGRAGK+GVA TFLT  D+ VFYDLKQ +++S  S  PPELA H  ++ KPG
Sbjct:   734 DYIHRIGRTGRAGKSGVAMTFLTKEDSSVFYDLKQAILESPVSTCPPELANHPDAQHKPG 793

Query:   120 TIPDRPPRRNDTVFA 134
             TI  +  RR +T+FA
Sbjct:   794 TILTKK-RREETIFA 807

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0004386 "helicase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

RGD|1308685 Ddx23 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 23" [Rattus norvegicus (taxid:10116)]

 Score = 401 (146.2 bits), Expect = 2.0e-36, P = 2.0e-36
 Identities = 81/135 (60%), Positives = 99/135 (73%)

Query:     1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
             +GY   TLHGGK QEQRE +L   +    ++LVATDVAGRGIDI DV+ V+NYDM  NIE
Sbjct:   686 MGYNACTLHGGKGQEQREFALSNLKAGAKDILVATDVAGRGIDIQDVSMVVNYDMAKNIE 745

Query:    61 MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSN-SPVPPELAKHEASKFKPG 119
              Y HRIGRTGRAGK+GVA TFLT  D+ VFY+LKQ +++S  S  PPELA H  ++ KPG
Sbjct:   746 DYIHRIGRTGRAGKSGVAITFLTKEDSAVFYELKQAILESPVSSCPPELANHPDAQHKPG 805

Query:   120 TIPDRPPRRNDTVFA 134
             TI  +  RR +T+FA
Sbjct:   806 TILTKK-RREETIFA 819

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005682 "U5 snRNP" evidence=IEA;ISO

GO:0005739 "mitochondrion" evidence=IEA;ISO

GO:0005886 "plasma membrane" evidence=IEA;ISO

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

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

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|A6QLB2 DDX23 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 401 (146.2 bits), Expect = 2.0e-36, P = 2.0e-36
 Identities = 81/135 (60%), Positives = 99/135 (73%)

Query:     1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
             +GY   TLHGGK QEQRE +L   +    ++LVATDVAGRGIDI DV+ V+NYDM  NIE
Sbjct:   687 MGYNACTLHGGKGQEQREFALSNLKAGAKDILVATDVAGRGIDIQDVSMVVNYDMAKNIE 746

Query:    61 MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSN-SPVPPELAKHEASKFKPG 119
              Y HRIGRTGRAGK+GVA TFLT  D+ VFY+LKQ +++S  S  PPELA H  ++ KPG
Sbjct:   747 DYIHRIGRTGRAGKSGVAITFLTKEDSAVFYELKQAILESPVSSCPPELANHPDAQHKPG 806

Query:   120 TIPDRPPRRNDTVFA 134
             TI  +  RR +T+FA
Sbjct:   807 TILTKK-RREETIFA 820

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

GO:0005886 "plasma membrane" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005682 "U5 snRNP" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|E2RTL6 DDX23 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 401 (146.2 bits), Expect = 2.0e-36, P = 2.0e-36
 Identities = 81/135 (60%), Positives = 99/135 (73%)

Query:     1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
             +GY   TLHGGK QEQRE +L   +    ++LVATDVAGRGIDI DV+ V+NYDM  NIE
Sbjct:   687 MGYNACTLHGGKGQEQREFALSNLKAGAKDILVATDVAGRGIDIQDVSMVVNYDMAKNIE 746

Query:    61 MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSN-SPVPPELAKHEASKFKPG 119
              Y HRIGRTGRAGK+GVA TFLT  D+ VFY+LKQ +++S  S  PPELA H  ++ KPG
Sbjct:   747 DYIHRIGRTGRAGKSGVAITFLTKEDSAVFYELKQAILESPVSSCPPELANHPDAQHKPG 806

Query:   120 TIPDRPPRRNDTVFA 134
             TI  +  RR +T+FA
Sbjct:   807 TILTKK-RREETIFA 820

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

GO:0005886 "plasma membrane" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005682 "U5 snRNP" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q9BUQ8 DDX23 "Probable ATP-dependent RNA helicase DDX23" [Homo sapiens (taxid:9606)]

 Score = 401 (146.2 bits), Expect = 2.0e-36, P = 2.0e-36
 Identities = 81/135 (60%), Positives = 99/135 (73%)

Query:     1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
             +GY   TLHGGK QEQRE +L   +    ++LVATDVAGRGIDI DV+ V+NYDM  NIE
Sbjct:   687 MGYNACTLHGGKGQEQREFALSNLKAGAKDILVATDVAGRGIDIQDVSMVVNYDMAKNIE 746

Query:    61 MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSN-SPVPPELAKHEASKFKPG 119
              Y HRIGRTGRAGK+GVA TFLT  D+ VFY+LKQ +++S  S  PPELA H  ++ KPG
Sbjct:   747 DYIHRIGRTGRAGKSGVAITFLTKEDSAVFYELKQAILESPVSSCPPELANHPDAQHKPG 806

Query:   120 TIPDRPPRRNDTVFA 134
             TI  +  RR +T+FA
Sbjct:   807 TILTKK-RREETIFA 820

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0000375 "RNA splicing, via transesterification reactions" evidence=TAS

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

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

GO:0005515 "protein binding" evidence=IPI

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

GO:0000354 "cis assembly of pre-catalytic spliceosome" evidence=IC

GO:0005682 "U5 snRNP" evidence=IDA

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GENEDB_PFALCIPARUM|PFE0925c PFE0925c "snrnp protein, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 389 (142.0 bits), Expect = 7.9e-35, P = 7.9e-35
 Identities = 75/131 (57%), Positives = 98/131 (74%)

Query:     3 YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMY 62
             Y+   LHGGK+QE RE +L  F+   +++LVATDVAGRGID+  V  VIN+DMP +IE Y
Sbjct:   992 YKAVALHGGKAQEIREQTLSAFKNAEFDILVATDVAGRGIDVHGVKLVINFDMPKDIESY 1051

Query:    63 THRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTIP 122
             THRIGRTGRAG  G+A +F+T HD+ +FYDLKQ LI SN+ VP ELA + ASK KPGT+ 
Sbjct:  1052 THRIGRTGRAGMKGLAISFITEHDSHLFYDLKQFLISSNNIVPLELANNPASKVKPGTVM 1111

Query:   123 DRPPRRNDTVF 133
              + P++N  ++
Sbjct:  1112 -QTPKKNQILY 1121

GO:0020011 "apicoplast" evidence=RCA

UNIPROTKB|Q8I0W7 PFE0925c "Snrnp protein, putative" [Plasmodium falciparum 3D7 (taxid:36329)]

 Score = 389 (142.0 bits), Expect = 7.9e-35, P = 7.9e-35
 Identities = 75/131 (57%), Positives = 98/131 (74%)

Query:     3 YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMY 62
             Y+   LHGGK+QE RE +L  F+   +++LVATDVAGRGID+  V  VIN+DMP +IE Y
Sbjct:   992 YKAVALHGGKAQEIREQTLSAFKNAEFDILVATDVAGRGIDVHGVKLVINFDMPKDIESY 1051

Query:    63 THRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTIP 122
             THRIGRTGRAG  G+A +F+T HD+ +FYDLKQ LI SN+ VP ELA + ASK KPGT+ 
Sbjct:  1052 THRIGRTGRAGMKGLAISFITEHDSHLFYDLKQFLISSNNIVPLELANNPASKVKPGTVM 1111

Query:   123 DRPPRRNDTVF 133
              + P++N  ++
Sbjct:  1112 -QTPKKNQILY 1121

GO:0020011 "apicoplast" evidence=RCA

WB|WBGene00017162 ddx-23 [Caenorhabditis elegans (taxid:6239)]

 Score = 374 (136.7 bits), Expect = 1.2e-33, P = 1.2e-33
 Identities = 75/134 (55%), Positives = 99/134 (73%)

Query:     1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
             LG++ T LHGGK Q+QRE +L+  +    ++LVATDVAGRGID+ DV+ V+NYDM  +IE
Sbjct:   596 LGFKPTVLHGGKGQDQREYALQALKEGTSDILVATDVAGRGIDVKDVSLVLNYDMAKSIE 655

Query:    61 MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSN-SPVPPELAKHEASKFKPG 119
              YTHRIGRTGRAGK G A TFLT  DT V++DLKQ+L++S  S  PPELA H  ++ KPG
Sbjct:   656 DYTHRIGRTGRAGKHGKAITFLTPDDTAVYFDLKQVLVESPVSSCPPELANHPDAQSKPG 715

Query:   120 TIPDRPPRRNDTVF 133
                 +  R+++T+F
Sbjct:   716 VFTSKK-RQDETLF 728

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0004386 "helicase activity" evidence=IEA

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

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

GO:0040011 "locomotion" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

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

GO:0040020 "regulation of meiosis" evidence=IMP

GO:0010172 "embryonic body morphogenesis" evidence=IMP

GO:0048589 "developmental growth" evidence=IMP

GO:0007281 "germ cell development" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

GO:0040021 "hermaphrodite germ-line sex determination" evidence=IMP

FB|FBgn0032690 CG10333 [Drosophila melanogaster (taxid:7227)]

 Score = 375 (137.1 bits), Expect = 1.3e-33, P = 1.3e-33
 Identities = 80/137 (58%), Positives = 97/137 (70%)

Query:     1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
             LGY   TLHGGK QEQRE +L   ++   ++LVATDVAGRGIDI DV+ VINYDM   IE
Sbjct:   689 LGYNSCTLHGGKGQEQREYALAALKSGAKDILVATDVAGRGIDIKDVSLVINYDMAKTIE 748

Query:    61 MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPV---PPELAKHEASKFK 117
              YTHRIGRTGRAGKTG A +F+T  D+ +FYDLKQ +  S SPV   PPEL  H  ++ K
Sbjct:   749 DYTHRIGRTGRAGKTGCAISFVTKDDSALFYDLKQCV--SASPVSTCPPELMNHPEAQHK 806

Query:   118 PGTIPDRPPRRNDTVFA 134
             PGT+  +  RR + +FA
Sbjct:   807 PGTVVTKK-RREEKIFA 822

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

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

GO:0005681 "spliceosomal complex" evidence=ISS

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

GO:0005682 "U5 snRNP" evidence=ISS

GO:0005524 "ATP binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0071011 "precatalytic spliceosome" evidence=IDA

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

GO:0022008 "neurogenesis" 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)
P93008	RH21_ARATH	3, ., 6, ., 4, ., 1, 3	0.8787	0.9777	0.1800	yes	no
Q53RK8	RH21_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.8195	0.9851	0.1807	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00029727001 SubName- Full=Chromosome chr9 scaffold_49, whole genome shotgun sequence; (406 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	135
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	7e-39
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	3e-35
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	1e-34
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	5e-34
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	4e-32
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	2e-30
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	4e-26
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	4e-25
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	9e-24
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	2e-23
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	8e-23
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	2e-22
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	1e-20
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	2e-18
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	5e-16
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	2e-15
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	2e-12
COG1111	542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	2e-12
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	8e-12
PRK11057	607	PRK11057, PRK11057, ATP-dependent DNA helicase Rec	4e-10
PLN03137	1195	PLN03137, PLN03137, ATP-dependent DNA helicase; Q4	1e-08
TIGR00580	926	TIGR00580, mfd, transcription-repair coupling fact	8e-07
COG1205	851	COG1205, COG1205, Distinct helicase family with a	2e-06
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	2e-06
COG1197	1139	COG1197, Mfd, Transcription-repair coupling factor	2e-05
PRK09200	790	PRK09200, PRK09200, preprotein translocase subunit	3e-05
TIGR03714	762	TIGR03714, secA2, accessory Sec system translocase	1e-04
COG1200	677	COG1200, RecG, RecG-like helicase [DNA replication	7e-04
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	8e-04
TIGR00643	630	TIGR00643, recG, ATP-dependent DNA helicase RecG	0.001
PRK12899	970	PRK12899, secA, preprotein translocase subunit Sec	0.001
PRK01172	674	PRK01172, PRK01172, ski2-like helicase; Provisiona	0.003

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

 Score =  136 bits (344), Expect = 7e-39
 Identities = 53/128 (41%), Positives = 75/128 (58%), Gaps = 4/128 (3%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
            G++V  LHG   QE+R+ +LE F+     VLVATDVA RG+DIPDV+HVINYD+P + E
Sbjct: 296 RGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPE 355

Query: 61  MYTHRIGRTGRAGKTGVATTFLTFH-DTDVFYDLKQML---IQSNSPVPPELAKHEASKF 116
            Y HRIGRTGRAG+ GVA +F+T   +      +++ L   + S   +P +  +      
Sbjct: 356 DYVHRIGRTGRAGRKGVAISFVTEEEEVKKLKRIEKRLERKLPSAVLLPLDEPEDAKLLK 415

Query: 117 KPGTIPDR 124
                 + 
Sbjct: 416 TTRPGLEE 423

Length = 513

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

 Score =  127 bits (320), Expect = 3e-35
 Identities = 53/109 (48%), Positives = 71/109 (65%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G+    +HG K QE+R   L  F+T +  +++ATDVA RG+D+ DV +VIN+D P  IE 
Sbjct: 401 GWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIED 460

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAK 110
           Y HRIGRTGRAG  G + TFLT     +  DL ++L ++  PVPPEL K
Sbjct: 461 YVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELEK 509

Length = 545

>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 =  116 bits (293), Expect = 1e-34
 Identities = 43/81 (53%), Positives = 52/81 (64%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
            G +V  LHG  SQE+RE  L+ FR     VLVATDV  RGID+P+V+ VINYD+P +  
Sbjct: 51  PGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPS 110

Query: 61  MYTHRIGRTGRAGKTGVATTF 81
            Y  RIGR GRAG+ G A   
Sbjct: 111 SYLQRIGRAGRAGQKGTAILL 131

Length = 131

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

 Score =  113 bits (284), Expect = 5e-34
 Identities = 47/73 (64%), Positives = 52/73 (71%)

Query: 1  LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
           G +V  LHGG SQE+RE  LE FR  +  VLVATDVAGRGID+PDV  VINYD+P N  
Sbjct: 6  PGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLPWNPA 65

Query: 61 MYTHRIGRTGRAG 73
           Y  RIGR GRAG
Sbjct: 66 SYIQRIGRAGRAG 78

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|197757 smart00490, HELICc, helicase superfamily c-terminal domain

 Score =  108 bits (272), Expect = 4e-32
 Identities = 41/73 (56%), Positives = 49/73 (67%)

Query: 1  LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
          LG +V  LHGG SQE+RE  L+ F   +  VLVATDVA RG+D+P V  VI YD+P +  
Sbjct: 10 LGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPA 69

Query: 61 MYTHRIGRTGRAG 73
           Y  RIGR GRAG
Sbjct: 70 SYIQRIGRAGRAG 82

Length = 82

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

 Score =  112 bits (283), Expect = 2e-30
 Identities = 44/85 (51%), Positives = 55/85 (64%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G     L G   Q +R  +++     R NVLVATDVA RGIDI DV+HVIN+DMP + + 
Sbjct: 269 GINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADT 328

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHD 86
           Y HRIGRTGRAG+ G A + +  HD
Sbjct: 329 YLHRIGRTGRAGRKGTAISLVEAHD 353

Length = 434

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

 Score =  100 bits (252), Expect = 4e-26
 Identities = 41/80 (51%), Positives = 53/80 (66%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G+RV  L G  +Q++R   LE F     ++LVATDVA RG+ IP V HV NYD+P + E 
Sbjct: 279 GHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCED 338

Query: 62  YTHRIGRTGRAGKTGVATTF 81
           Y HRIGRTGRAG +G + + 
Sbjct: 339 YVHRIGRTGRAGASGHSISL 358

Length = 423

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

 Score = 98.3 bits (246), Expect = 4e-25
 Identities = 37/80 (46%), Positives = 50/80 (62%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G+    LHG   Q  R+  L  F  +  +VLVATDVA RG+DI  +  VINY++  + E+
Sbjct: 266 GFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARDPEV 325

Query: 62  YTHRIGRTGRAGKTGVATTF 81
           + HRIGRTGRAG  G+A + 
Sbjct: 326 HVHRIGRTGRAGSKGLALSL 345

Length = 460

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

 Score = 94.6 bits (235), Expect = 9e-24
 Identities = 44/90 (48%), Positives = 57/90 (63%), Gaps = 2/90 (2%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G     L G   Q +R  +LEGFR  +  VLVATDVAGRGI I  ++HVIN+ +P + + 
Sbjct: 359 GINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDD 418

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFY 91
           Y HRIGRTGRAG +GV+ +F    + D F 
Sbjct: 419 YVHRIGRTGRAGASGVSISFAG--EDDAFQ 446

Length = 475

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

 Score = 93.4 bits (232), Expect = 2e-23
 Identities = 38/93 (40%), Positives = 60/93 (64%)

Query: 3   YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMY 62
           + V+ +HG   Q+ R++ +  FR+    VL+ TD+  RGID+  V+ VINYD+P + E Y
Sbjct: 292 FTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENY 351

Query: 63  THRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQ 95
            HRIGR+GR G+ GVA  F+T  D +   ++++
Sbjct: 352 IHRIGRSGRFGRKGVAINFVTPDDIEQLKEIER 384

Length = 401

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

 Score = 92.2 bits (229), Expect = 8e-23
 Identities = 45/129 (34%), Positives = 68/129 (52%), Gaps = 4/129 (3%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G +  ++HG KS ++R   ++ F      V+VAT V GRG+D+  V  VI +DMP  I+ 
Sbjct: 392 GLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKE 451

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTI 121
           Y H+IGR  R G+ G A  F+   D ++F +L  +L  S + +P ELA         G+ 
Sbjct: 452 YIHQIGRASRMGEKGTAIVFVNEEDRNLFPELVALLKSSGAAIPRELANSRYL----GSG 507

Query: 122 PDRPPRRND 130
             R  +R  
Sbjct: 508 RKRKKKRRY 516

Length = 518

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

 Score = 90.6 bits (225), Expect = 2e-22
 Identities = 42/96 (43%), Positives = 61/96 (63%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G R   +HG KSQ  R  +L  F++    VLVATD+A RG+DI ++ HV+NY++P   E 
Sbjct: 269 GIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPED 328

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQML 97
           Y HRIGRTGRA  TG A + +   +  +  D++++L
Sbjct: 329 YVHRIGRTGRAAATGEALSLVCVDEHKLLRDIEKLL 364

Length = 456

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

 Score = 86.4 bits (214), Expect = 1e-20
 Identities = 39/81 (48%), Positives = 55/81 (67%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           GY    L+G  +Q  RE +LE  +  R ++L+ATDVA RG+D+  ++ V+NYD+P + E 
Sbjct: 269 GYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSES 328

Query: 62  YTHRIGRTGRAGKTGVATTFL 82
           Y HRIGRTGRAG+ G A  F+
Sbjct: 329 YVHRIGRTGRAGRAGRALLFV 349

Length = 629

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

 Score = 79.6 bits (196), Expect = 2e-18
 Identities = 40/80 (50%), Positives = 51/80 (63%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           GYRV  L G   Q++RE  L  F+  +  +LVATDVA RG+ I  V +V NYD+P + E 
Sbjct: 281 GYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAED 340

Query: 62  YTHRIGRTGRAGKTGVATTF 81
           Y HRIGRT R G+ G A +F
Sbjct: 341 YVHRIGRTARLGEEGDAISF 360

Length = 572

>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication, recombination, and repair]

 Score = 72.7 bits (179), Expect = 5e-16
 Identities = 40/115 (34%), Positives = 53/115 (46%), Gaps = 5/115 (4%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G      H G S E+RE   + F      V+VAT+  G GID PDV  VI+YD+PG+IE 
Sbjct: 254 GISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIES 313

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKF 116
           Y    GR GR G    A    +  D       + ++ QS      E  + E +K 
Sbjct: 314 YYQETGRAGRDGLPAEAILLYSPEDIRW---QRYLIEQSKP--DEEQKQIELAKL 363

Length = 590

>gnl|CDD|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ

 Score = 71.3 bits (175), Expect = 2e-15
 Identities = 38/102 (37%), Positives = 50/102 (49%), Gaps = 3/102 (2%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G      H G S + R  + E F      V+VAT+  G GID P+V  VI+YDMPGN+E 
Sbjct: 248 GISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLES 307

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSP 103
           Y    GR GR G    A    +  D  +   LK+ + QS + 
Sbjct: 308 YYQEAGRAGRDGLPAEAILLYSPADIAL---LKRRIEQSEAD 346

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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 591

>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family

 Score = 62.5 bits (152), Expect = 2e-12
 Identities = 31/101 (30%), Positives = 44/101 (43%), Gaps = 3/101 (2%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
           LG      H G     R+     F+     V+VAT   G GI+ PDV  VI+Y +P ++E
Sbjct: 249 LGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSME 308

Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSN 101
            Y    GR GR G       F    D      L+++L++  
Sbjct: 309 SYYQESGRAGRDGLPSECHLFYAPAD---INRLRRLLMEEP 346

All proteins in this family for which functions are known are 3'-5' DNA-DNA helicases. These proteins are used for recombination, recombinational repair, and possibly maintenance of chromosome stability. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 470

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

 Score = 62.7 bits (153), Expect = 2e-12
 Identities = 33/63 (52%), Positives = 40/63 (63%), Gaps = 4/63 (6%)

Query: 11  GKSQ-EQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYD-MPGNIEMYTHRIGR 68
           G SQ EQ+EI ++ FR   YNVLVAT V   G+DIP+V  VI Y+ +P  I     R GR
Sbjct: 408 GMSQKEQKEI-IDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRS-IQRKGR 465

Query: 69  TGR 71
           TGR
Sbjct: 466 TGR 468

Length = 542

>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional

 Score = 60.7 bits (148), Expect = 8e-12
 Identities = 33/66 (50%), Positives = 40/66 (60%), Gaps = 4/66 (6%)

Query: 11  GKSQ-EQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYD-MPGNIEMYTHRIGR 68
           G SQ EQ EI L+ FR   +NVLV+T VA  G+DIP V  VI Y+ +P  I     R GR
Sbjct: 406 GMSQKEQIEI-LDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRS-IQRKGR 463

Query: 69  TGRAGK 74
           TGR  +
Sbjct: 464 TGRQEE 469

Length = 773

>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional

 Score = 55.9 bits (135), Expect = 4e-10
 Identities = 29/85 (34%), Positives = 43/85 (50%), Gaps = 3/85 (3%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G      H G   + R    E F+     ++VAT   G GI+ P+V  V+++D+P NIE 
Sbjct: 260 GISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIES 319

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHD 86
           Y      TGRAG+ G+    + F+D
Sbjct: 320 YYQ---ETGRAGRDGLPAEAMLFYD 341

Length = 607

>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like; Provisional

 Score = 51.8 bits (124), Expect = 1e-08
 Identities = 29/98 (29%), Positives = 47/98 (47%), Gaps = 3/98 (3%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G++    HG     QR    + +     N++ AT   G GI+ PDV  VI++ +P +IE 
Sbjct: 704 GHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEG 763

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQ 99
           Y    GR GR G+      + ++ D   +  +K M+ Q
Sbjct: 764 YHQECGRAGRDGQRSSCVLYYSYSD---YIRVKHMISQ 798

Length = 1195

>gnl|CDD|233032 TIGR00580, mfd, transcription-repair coupling factor (mfd)

 Score = 46.6 bits (111), Expect = 8e-07
 Identities = 27/85 (31%), Positives = 39/85 (45%), Gaps = 4/85 (4%)

Query: 4   RVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVI--NYDMPGNIEM 61
           R+   HG  ++ + E  +  F    + VLV T +   GIDIP+   +I    D  G  ++
Sbjct: 688 RIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQL 747

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHD 86
           Y  R GR GR+ K   A   L  H 
Sbjct: 748 YQLR-GRVGRSKKKAYA-YLLYPHQ 770

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 transcribed 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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 926

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

 Score = 45.5 bits (108), Expect = 2e-06
 Identities = 24/77 (31%), Positives = 35/77 (45%), Gaps = 1/77 (1%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
           L   V+T   G  +E+R      F+      ++AT+    GIDI  +  VI Y  PG   
Sbjct: 337 LLDAVSTYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSV 396

Query: 61  M-YTHRIGRTGRAGKTG 76
           + +  R GR GR G+  
Sbjct: 397 LSFRQRAGRAGRRGQES 413

Length = 851

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

 Score = 45.5 bits (108), Expect = 2e-06
 Identities = 24/64 (37%), Positives = 33/64 (51%)

Query: 5   VTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTH 64
           V  + G   +E+RE  LE FRT    VLV   V   G+DIPD   +I     G+  ++  
Sbjct: 309 VEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQ 368

Query: 65  RIGR 68
           R+GR
Sbjct: 369 RLGR 372

Length = 442

>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 26/78 (33%), Positives = 37/78 (47%), Gaps = 3/78 (3%)

Query: 3   YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVI--NYDMPGNIE 60
            R+   HG   + + E  +  F    Y+VLV T +   GIDIP+   +I    D  G  +
Sbjct: 830 ARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTIIIERADKFGLAQ 889

Query: 61  MYTHRIGRTGRAGKTGVA 78
           +Y  R GR GR+ K   A
Sbjct: 890 LYQLR-GRVGRSNKQAYA 906

Length = 1139

>gnl|CDD|236408 PRK09200, PRK09200, preprotein translocase subunit SecA; Reviewed

 Score = 41.8 bits (99), Expect = 3e-05
 Identities = 28/91 (30%), Positives = 43/91 (47%), Gaps = 22/91 (24%)

Query: 13  SQEQREISLEGFRTKRYNVLVATDVAGRGIDI---PDVA-----HVINYDMPGNIEMYTH 64
           ++E + I+  G   ++  V VAT++AGRG DI     V       VI     G   M + 
Sbjct: 464 AKEAQIIAEAG---QKGAVTVATNMAGRGTDIKLGEGVHELGGLAVI-----GTERMESR 515

Query: 65  RI-----GRTGRAGKTGVATTFLTFHDTDVF 90
           R+     GR+GR G  G +  F++  D D+ 
Sbjct: 516 RVDLQLRGRSGRQGDPGSSQFFISLED-DLL 545

Length = 790

>gnl|CDD|163426 TIGR03714, secA2, accessory Sec system translocase SecA2

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 35/112 (31%), Positives = 48/112 (42%), Gaps = 25/112 (22%)

Query: 31  VLVATDVAGRGIDI---PDVAHVINYDMPGNIEMYTHRI-----GRTGRAGKTGVATTFL 82
           V VAT +AGRG DI     VA +    + G   M   R+     GR+GR G  G +  F+
Sbjct: 475 VTVATSMAGRGTDIKLGKGVAELGGLAVIGTERMENSRVDLQLRGRSGRQGDPGSSQFFV 534

Query: 83  TFHDTDVFYDLKQMLIQSNSPVPPELAKH------EASKFKPGTIPDRPPRR 128
           +  D          LI+  S  P  L K+      + SK KP  +  R  R+
Sbjct: 535 SLEDD---------LIKRWS--PSWLKKYYKKYSVKDSKLKPSALFKRRFRK 575

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 [Protein fate, Protein and peptide secretion and trafficking]. Length = 762

>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination, and repair / Transcription]

 Score = 38.0 bits (89), Expect = 7e-04
 Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 2/46 (4%)

Query: 2   GYRVTTLHG-GKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPD 46
             +V  +HG  K  E+  + +E F+    ++LVAT V   G+D+P+
Sbjct: 507 ELKVGLVHGRMKPAEKDAV-MEAFKEGEIDILVATTVIEVGVDVPN 551

Length = 677

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

 Score = 37.6 bits (88), Expect = 8e-04
 Identities = 22/63 (34%), Positives = 29/63 (46%)

Query: 9   HGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGR 68
           HG  S+E R    E  +      +VAT     GIDI D+  VI    P ++  +  RIGR
Sbjct: 285 HGSLSRELRLEVEERLKEGELKAVVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGR 344

Query: 69  TGR 71
            G 
Sbjct: 345 AGH 347

Length = 814

>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 19/45 (42%), Positives = 27/45 (60%), Gaps = 2/45 (4%)

Query: 3   YRVTTLHG-GKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPD 46
           Y V  LHG  KS E+  + +E FR    ++LVAT V   G+D+P+
Sbjct: 483 YNVGLLHGRMKSDEKEAV-MEEFREGEVDILVATTVIEVGVDVPN 526

[DNA metabolism, DNA replication, recombination, and repair]. Length = 630

>gnl|CDD|237254 PRK12899, secA, preprotein translocase subunit SecA; Reviewed

 Score = 37.1 bits (86), Expect = 0.001
 Identities = 29/89 (32%), Positives = 38/89 (42%), Gaps = 10/89 (11%)

Query: 6   TTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDI---PDVAHVINYDMPGNIEMY 62
           T L+     ++ EI       K   V VAT++AGRG DI    +   V    + G     
Sbjct: 596 TVLNAKNHAQEAEIIAGA--GKLGAVTVATNMAGRGTDIKLDEEAVAVGGLYVIGTSRHQ 653

Query: 63  THRI-----GRTGRAGKTGVATTFLTFHD 86
           + RI     GR  R G  G A  FL+F D
Sbjct: 654 SRRIDRQLRGRCARLGDPGAAKFFLSFED 682

Length = 970

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

 Score = 36.0 bits (83), Expect = 0.003
 Identities = 26/74 (35%), Positives = 34/74 (45%), Gaps = 10/74 (13%)

Query: 9   HGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPD----VAHVINYDMPG-----NI 59
           H G S EQR    E FR +   V+VAT     G+++P     V  +  Y   G     N+
Sbjct: 292 HAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIVRDITRYGNGGIRYLSNM 351

Query: 60  EMYTHRIGRTGRAG 73
           E+    IGR GR G
Sbjct: 352 EI-KQMIGRAGRPG 364

Length = 674

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	135
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	99.95
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	99.95
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	99.94
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.94
PTZ00110	545	helicase; Provisional	99.94
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.93
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	99.93
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.92
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	99.92
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	99.92
PTZ00424	401	helicase 45; Provisional	99.92
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.91
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	99.91
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.91
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.91
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	99.91
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.91
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.91
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	99.91
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	99.9
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.9
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.9
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.9
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	99.9
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.89
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.89
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.88
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.87
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.87
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	99.87
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	99.87
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	99.86
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	99.85
KOG0327	397	consensus Translation initiation factor 4F, helica	99.85
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.84
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.84
KOG0343	758	consensus RNA Helicase [RNA processing and modific	99.83
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.83
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.81
PRK04914	956	ATP-dependent helicase HepA; Validated	99.81
KOG0347	731	consensus RNA helicase [RNA processing and modific	99.81
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	99.8
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.8
PRK13767	876	ATP-dependent helicase; Provisional	99.79
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.79
PRK02362	737	ski2-like helicase; Provisional	99.78
PRK10689	1147	transcription-repair coupling factor; Provisional	99.78
PRK05298	652	excinuclease ABC subunit B; Provisional	99.77
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.76
KOG0334	997	consensus RNA helicase [RNA processing and modific	99.76
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.76
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.75
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.73
KOG4284	980	consensus DEAD box protein [Transcription]	99.73
KOG0346	569	consensus RNA helicase [RNA processing and modific	99.73
PRK00254	720	ski2-like helicase; Provisional	99.72
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	99.72
PRK01172	674	ski2-like helicase; Provisional	99.71
PHA02653	675	RNA helicase NPH-II; Provisional	99.7
KOG0354	746	consensus DEAD-box like helicase [General function	99.69
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.69
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.68
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.68
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.68
PRK13766	773	Hef nuclease; Provisional	99.67
PHA02558	501	uvsW UvsW helicase; Provisional	99.66
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.65
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.64
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	99.63
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	99.61
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.6
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.6
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.58
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.54
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.54
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.51
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	99.51
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.5
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.49
COG1204	766	Superfamily II helicase [General function predicti	99.49
PRK05580	679	primosome assembly protein PriA; Validated	99.48
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.47
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.42
COG1202	830	Superfamily II helicase, archaea-specific [General	99.41
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	99.4
KOG0353	695	consensus ATP-dependent DNA helicase [General func	99.37
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.36
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.34
PRK09401	1176	reverse gyrase; Reviewed	99.33
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.33
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	99.33
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	99.33
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.3
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.24
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.24
PRK09694	878	helicase Cas3; Provisional	99.24
PRK14701	1638	reverse gyrase; Provisional	99.23
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.2
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	99.16
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	99.16
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.15
COG1205	851	Distinct helicase family with a unique C-terminal	99.14
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.1
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.06
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	99.04
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	99.02
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.01
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.01
PRK12904	830	preprotein translocase subunit SecA; Reviewed	98.97
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	98.95
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	98.95
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	98.94
PRK13107	908	preprotein translocase subunit SecA; Reviewed	98.93
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	98.92
COG1198	730	PriA Primosomal protein N' (replication factor Y)	98.86
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	98.86
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	98.81
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	98.62
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	98.43
KOG0387	923	consensus Transcription-coupled repair protein CSB	98.35
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	98.29
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	98.12
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.11
PRK12326	764	preprotein translocase subunit SecA; Reviewed	98.04
KOG1123	776	consensus RNA polymerase II transcription initiati	98.02
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	98.01
COG4889	1518	Predicted helicase [General function prediction on	98.0
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	97.91
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.91
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	97.87
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	97.84
PF13871	278	Helicase_C_4: Helicase_C-like	97.71
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	97.67
KOG4439	901	consensus RNA polymerase II transcription terminat	97.64
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	97.63
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	97.63
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	97.6
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	97.56
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	97.55
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	97.41
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	97.34
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	97.22
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	97.06
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	97.05
KOG1015	1567	consensus Transcription regulator XNP/ATRX, DEAD-b	97.04
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	97.04
CHL00122	870	secA preprotein translocase subunit SecA; Validate	96.95
COG4096	875	HsdR Type I site-specific restriction-modification	96.91
PF10593	239	Z1: Z1 domain; InterPro: IPR018310 This entry repr	96.78
PRK14873	665	primosome assembly protein PriA; Provisional	96.77
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	96.77
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	96.68
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	96.64
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	96.63
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	96.48
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	96.48
KOG0701	1606	consensus dsRNA-specific nuclease Dicer and relate	96.36
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	96.07
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	95.58
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	95.58
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	95.5
PRK14873	665	primosome assembly protein PriA; Provisional	95.43
PRK05580	679	primosome assembly protein PriA; Validated	95.28
KOG1016	1387	consensus Predicted DNA helicase, DEAD-box superfa	95.19
TIGR00595	505	priA primosomal protein N'. All proteins in this f	95.16
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	95.1
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	95.08
COG1198	730	PriA Primosomal protein N' (replication factor Y)	94.97
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	94.89
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	94.87
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	94.85
KOG1513	1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	94.82
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	94.73
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	93.7
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	92.74
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	92.69
PRK10689	1147	transcription-repair coupling factor; Provisional	92.57
PRK14701	1638	reverse gyrase; Provisional	88.95
KOG1001	674	consensus Helicase-like transcription factor HLTF/	88.36
PRK15483	986	type III restriction-modification system StyLTI en	88.21
COG0610	962	Type I site-specific restriction-modification syst	88.2
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	87.15
COG3587	985	Restriction endonuclease [Defense mechanisms]	85.72
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	85.25
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	84.63
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	84.62
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	83.37
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	82.92

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

Probab=99.95  E-value=6e-28  Score=183.77  Aligned_cols=133  Identities=64%  Similarity=0.952  Sum_probs=124.9

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      .|+.+..+||+-++++|+.+++.|++|..+||||||++++|+|+|+|++|||||++++..+|.||+||+||.|+.|.+++
T Consensus       540 ~g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTDvAgRGIDIpnVSlVinydmaksieDYtHRIGRTgRAGk~GtaiS  619 (673)
T KOG0333|consen  540 AGYKVTTLHGGKSQEQRENALADFREGTGDILVATDVAGRGIDIPNVSLVINYDMAKSIEDYTHRIGRTGRAGKSGTAIS  619 (673)
T ss_pred             ccceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEecccccCCCCCccceeeecchhhhHHHHHHHhccccccccCceeEE
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHHHHHHHHHh-hCCCCCChHHHHHHHhhCCCCCCCCCCCCCCCcccc
Q 037139           81 FLTFHDTDVFYDLKQMLI-QSNSPVPPELAKHEASKFKPGTIPDRPPRRNDTVFA  134 (135)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  134 (135)
                      |+++.+...++.|+..+. ....-.|..+..+....+++..+.... +.++.||+
T Consensus       620 flt~~dt~v~ydLkq~l~es~~s~~P~Ela~h~~a~~K~~~~~~k~-~~~e~i~~  673 (673)
T KOG0333|consen  620 FLTPADTAVFYDLKQALRESVKSHCPPELANHPDAQFKPGTIKAKK-REPETIRY  673 (673)
T ss_pred             EeccchhHHHHHHHHHHHHhhhccCChhhccChhhccccccccccc-cCcccccC
Confidence            999999999988888776 678889999999999999999999888 66777763

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

Probab=99.95  E-value=2.9e-27  Score=169.21  Aligned_cols=109  Identities=39%  Similarity=0.725  Sum_probs=105.2

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      +|.|.+.||+|++++|.+++..|++|+.+||++||+.++|+|+|.|++|||||+|.+.+.|+||+||+||.|+.|.++.|
T Consensus       290 nftVssmHGDm~qkERd~im~dFRsg~SrvLitTDVwaRGiDv~qVslviNYDLP~nre~YIHRIGRSGRFGRkGvainF  369 (400)
T KOG0328|consen  290 NFTVSSMHGDMEQKERDKIMNDFRSGKSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAINF  369 (400)
T ss_pred             CceeeeccCCcchhHHHHHHHHhhcCCceEEEEechhhccCCcceeEEEEecCCCccHHHHhhhhccccccCCcceEEEE
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCCCCCChHHHH
Q 037139           82 LTFHDTDVFYDLKQMLIQSNSPVPPELAK  110 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  110 (135)
                      +...+...++.++++++....++|-.+.+
T Consensus       370 Vk~~d~~~lrdieq~yst~i~emp~nvad  398 (400)
T KOG0328|consen  370 VKSDDLRILRDIEQYYSTQIDEMPMNVAD  398 (400)
T ss_pred             ecHHHHHHHHHHHHHHhhhcccccchhhh
Confidence            99999999999999999999999887654

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

Probab=99.94  E-value=8.5e-27  Score=179.32  Aligned_cols=114  Identities=49%  Similarity=0.821  Sum_probs=108.9

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+.+|||+.++.+|+.+++.|++|+..||||||++++|+|+|+|++|||||+|.++++|+||+||+||.|+.|.+++|
T Consensus       365 ~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdVAaRGLDi~dV~lVInydfP~~vEdYVHRiGRTGRa~~~G~A~tf  444 (519)
T KOG0331|consen  365 GWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDVAARGLDVPDVDLVINYDFPNNVEDYVHRIGRTGRAGKKGTAITF  444 (519)
T ss_pred             CcceeeecccccHHHHHHHHHhcccCCcceEEEcccccccCCCccccEEEeCCCCCCHHHHHhhcCccccCCCCceEEEE
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCCCCCChHHHHHHHhh
Q 037139           82 LTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASK  115 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  115 (135)
                      +...+......+.+.+....+.+|+.+.......
T Consensus       445 ft~~~~~~a~~l~~~l~e~~q~v~~~l~~~~~~~  478 (519)
T KOG0331|consen  445 FTSDNAKLARELIKVLREAGQTVPPDLLEYARVS  478 (519)
T ss_pred             EeHHHHHHHHHHHHHHHHccCCCChHHHHHHhhc
Confidence            9999999999999999999999999998765443

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

Probab=99.94  E-value=1.2e-26  Score=181.69  Aligned_cols=111  Identities=38%  Similarity=0.662  Sum_probs=106.6

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++++|..++++|++|+++|||||+++++|+|+|++++||+||+|.+..+|+||+||+||.|..|.+++|
T Consensus       392 g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTdvl~rGiDip~v~~VI~~d~P~s~~~yihRiGRaGR~g~~G~ai~f  471 (518)
T PLN00206        392 GLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVF  471 (518)
T ss_pred             CcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEecHhhccCCcccCCEEEEeCCCCCHHHHHHhccccccCCCCeEEEEE
Confidence            67889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCCCCCChHHHHHH
Q 037139           82 LTFHDTDVFYDLKQMLIQSNSPVPPELAKHE  112 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  112 (135)
                      +...+...+..+.+.++.....+|++|...-
T Consensus       472 ~~~~~~~~~~~l~~~l~~~~~~vp~~l~~~~  502 (518)
T PLN00206        472 VNEEDRNLFPELVALLKSSGAAIPRELANSR  502 (518)
T ss_pred             EchhHHHHHHHHHHHHHHcCCCCCHHHHhCh
Confidence            9999999999999999999999999998643

>PTZ00110 helicase; Provisional

Probab=99.94  E-value=2.6e-26  Score=180.71  Aligned_cols=114  Identities=46%  Similarity=0.770  Sum_probs=109.3

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++++|..++++|++|+++|||||+++++|+|+|+|++||+||+|.+..+|+||+||+||.|..|.+++|
T Consensus       401 g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTdv~~rGIDi~~v~~VI~~d~P~s~~~yvqRiGRtGR~G~~G~ai~~  480 (545)
T PTZ00110        401 GWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTF  480 (545)
T ss_pred             CCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcchhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEE
Confidence            67889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCCCCCChHHHHHHHhh
Q 037139           82 LTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASK  115 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  115 (135)
                      +++.+......+.+.+....+++|++|.++....
T Consensus       481 ~~~~~~~~~~~l~~~l~~~~q~vp~~l~~~~~~~  514 (545)
T PTZ00110        481 LTPDKYRLARDLVKVLREAKQPVPPELEKLSNER  514 (545)
T ss_pred             ECcchHHHHHHHHHHHHHccCCCCHHHHHHHHHh
Confidence            9999999999999999999999999999875443

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.93  E-value=5.3e-26  Score=174.31  Aligned_cols=103  Identities=41%  Similarity=0.596  Sum_probs=96.8

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++++|..++++|++|+++|||||+++++|+|+|++++||+||+|.+...|+||+||+||.|+.|.+++|
T Consensus       279 g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTdv~~rGiDip~v~~VI~~d~P~s~~~yiqR~GR~gR~G~~G~ai~~  358 (423)
T PRK04837        279 GHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISL  358 (423)
T ss_pred             CCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEechhhcCCCccccCEEEEeCCCCchhheEeccccccCCCCCeeEEEE
Confidence            78899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCCCCC
Q 037139           82 LTFHDTDVFYDLKQMLIQSNSPV  104 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~  104 (135)
                      +.+.+...+..+++++.....+.
T Consensus       359 ~~~~~~~~~~~i~~~~~~~~~~~  381 (423)
T PRK04837        359 ACEEYALNLPAIETYIGHSIPVS  381 (423)
T ss_pred             eCHHHHHHHHHHHHHhCCCCCCc
Confidence            99988888888888887765443

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

Probab=99.93  E-value=1.1e-25  Score=166.52  Aligned_cols=106  Identities=41%  Similarity=0.658  Sum_probs=100.4

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      +|+.+..+||.|++..|..++++|++|..+||+|||++++|+|+|.|++|||||.|.+..+|+||+||++|.|.+|.++.
T Consensus       323 lg~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~TDVaSRGLDip~Vd~VVNyDiP~~skDYIHRvGRtaRaGrsG~~It  402 (476)
T KOG0330|consen  323 LGFQAIPLHGQMSQSKRLGALNKFKAGARSILVCTDVASRGLDIPHVDVVVNYDIPTHSKDYIHRVGRTARAGRSGKAIT  402 (476)
T ss_pred             cCcceecccchhhHHHHHHHHHHHhccCCcEEEecchhcccCCCCCceEEEecCCCCcHHHHHHHcccccccCCCcceEE
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHHHHHHHHHhhCCCC--CCh
Q 037139           81 FLTFHDTDVFYDLKQMLIQSNSP--VPP  106 (135)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~--~~~  106 (135)
                      +++..|.+.+..++..+.+...+  +++
T Consensus       403 lVtqyDve~~qrIE~~~gkkl~~~~~~~  430 (476)
T KOG0330|consen  403 LVTQYDVELVQRIEHALGKKLPEYKVDK  430 (476)
T ss_pred             EEehhhhHHHHHHHHHHhcCCCccCcch
Confidence            99999999999999998887654  444

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

Probab=99.92  E-value=2.3e-25  Score=174.28  Aligned_cols=100  Identities=51%  Similarity=0.840  Sum_probs=95.3

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      +|+++..+||+|++++|.++++.|++|+.+||||||++++|+|+|++++|||||+|.+.+.|+||+||+||.|..|.+++
T Consensus       296 ~g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTDvaaRGiDi~~v~~VinyD~p~~~e~yvHRiGRTgRaG~~G~ai~  375 (513)
T COG0513         296 RGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAIS  375 (513)
T ss_pred             CCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEechhhccCCccccceeEEccCCCCHHHheeccCccccCCCCCeEEE
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecC-ChhHHHHHHHHHhhC
Q 037139           81 FLTFH-DTDVFYDLKQMLIQS  100 (135)
Q Consensus        81 ~~~~~-~~~~~~~~~~~~~~~  100 (135)
                      |+.+. +...+..+++.+...
T Consensus       376 fv~~~~e~~~l~~ie~~~~~~  396 (513)
T COG0513         376 FVTEEEEVKKLKRIEKRLERK  396 (513)
T ss_pred             EeCcHHHHHHHHHHHHHHhcc
Confidence            99986 888888888887665

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

Probab=99.92  E-value=6e-25  Score=167.13  Aligned_cols=113  Identities=46%  Similarity=0.783  Sum_probs=108.5

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      .|+++..+||..++.+|.+.++.|++|++.+||||+++++|+|+|+|.+||+||+|.+..+|+||+||+||.|+.|.+..
T Consensus       360 ~~~~~~sIhg~~tq~er~~al~~Fr~g~~pvlVaT~VaaRGlDi~~V~hVInyDmP~d~d~YvHRIGRTGR~Gn~G~ats  439 (482)
T KOG0335|consen  360 NGYPAKSIHGDRTQIEREQALNDFRNGKAPVLVATNVAARGLDIPNVKHVINYDMPADIDDYVHRIGRTGRVGNGGRATS  439 (482)
T ss_pred             CCCCceeecchhhhhHHHHHHHHhhcCCcceEEEehhhhcCCCCCCCceeEEeecCcchhhHHHhccccccCCCCceeEE
Confidence            36788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHHHHHHHHHhhCCCCCChHHHHHHH
Q 037139           81 FLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEA  113 (135)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  113 (135)
                      |++..+.+..+.|.+.+....+++|+||.....
T Consensus       440 f~n~~~~~i~~~L~~~l~ea~q~vP~wl~~~~~  472 (482)
T KOG0335|consen  440 FFNEKNQNIAKALVEILTEANQEVPQWLSELSR  472 (482)
T ss_pred             EeccccchhHHHHHHHHHHhcccCcHHHHhhhh
Confidence            999999999999999999999999999998433

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

Probab=99.92  E-value=7.6e-25  Score=163.44  Aligned_cols=110  Identities=48%  Similarity=0.840  Sum_probs=107.0

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+.++||+-++.+|+..+++|++|+++|||+||++++|+|+|++.+|+|||.|.+++.|+||+||+||.|+.|..++|
T Consensus       489 gi~~q~lHG~r~Q~DrE~al~~~ksG~vrILvaTDlaSRGlDv~DiTHV~NyDFP~nIeeYVHRvGrtGRaGr~G~sis~  568 (629)
T KOG0336|consen  489 GISSQSLHGNREQSDREMALEDFKSGEVRILVATDLASRGLDVPDITHVYNYDFPRNIEEYVHRVGRTGRAGRTGTSISF  568 (629)
T ss_pred             ccchhhccCChhhhhHHHHHHhhhcCceEEEEEechhhcCCCchhcceeeccCCCccHHHHHHHhcccccCCCCcceEEE
Confidence            67888999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCCCCCChHHHHH
Q 037139           82 LTFHDTDVFYDLKQMLIQSNSPVPPELAKH  111 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  111 (135)
                      ++..+......+.+.++...+++|+.|..+
T Consensus       569 lt~~D~~~a~eLI~ILe~aeQevPdeL~~m  598 (629)
T KOG0336|consen  569 LTRNDWSMAEELIQILERAEQEVPDELVRM  598 (629)
T ss_pred             EehhhHHHHHHHHHHHHHhhhhCcHHHHHH
Confidence            999999999999999999999999998764

>PTZ00424 helicase 45; Provisional

Probab=99.92  E-value=8.9e-25  Score=166.10  Aligned_cols=107  Identities=37%  Similarity=0.691  Sum_probs=100.3

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++++|..++++|++|+++|||||+++++|+|+|++++||++|+|.+...|+||+||+||.|..|.++++
T Consensus       291 ~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~~l~~GiDip~v~~VI~~~~p~s~~~y~qr~GRagR~g~~G~~i~l  370 (401)
T PTZ00424        291 DFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINF  370 (401)
T ss_pred             CCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcccccCCcCcccCCEEEEECCCCCHHHEeecccccccCCCCceEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCCCCCChHH
Q 037139           82 LTFHDTDVFYDLKQMLIQSNSPVPPEL  108 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~l  108 (135)
                      +.+.+...+..+++.+.....+.+...
T Consensus       371 ~~~~~~~~~~~~e~~~~~~~~~~~~~~  397 (401)
T PTZ00424        371 VTPDDIEQLKEIERHYNTQIEEMPMEV  397 (401)
T ss_pred             EcHHHHHHHHHHHHHHCCcccccCcch
Confidence            999999999999988888777666543

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.91  E-value=2e-24  Score=167.06  Aligned_cols=100  Identities=42%  Similarity=0.733  Sum_probs=95.2

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++++|.+++++|++|+++|||||+++++|+|+|++++||+||+|.+..+|+||+||+||.|..|.++++
T Consensus       269 g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yvqR~GRaGR~g~~G~ai~l  348 (456)
T PRK10590        269 GIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSL  348 (456)
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEccHHhcCCCcccCCEEEEeCCCCCHHHhhhhccccccCCCCeeEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCC
Q 037139           82 LTFHDTDVFYDLKQMLIQSN  101 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~  101 (135)
                      +...+...++.+++.+....
T Consensus       349 ~~~~d~~~~~~ie~~l~~~~  368 (456)
T PRK10590        349 VCVDEHKLLRDIEKLLKKEI  368 (456)
T ss_pred             ecHHHHHHHHHHHHHhcCCC
Confidence            99999888898988876654

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

Probab=99.91  E-value=3.1e-25  Score=161.14  Aligned_cols=110  Identities=41%  Similarity=0.684  Sum_probs=106.6

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      +|+++.++|+.|.++.|..++..|++|.++.|||||.+.+|+|++.+++|||||.|++.++|+||+||+||.|..|.++.
T Consensus       345 lGyscyyiHakM~Q~hRNrVFHdFr~G~crnLVctDL~TRGIDiqavNvVINFDfpk~aEtYLHRIGRsGRFGhlGlAIn  424 (459)
T KOG0326|consen  345 LGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLVCTDLFTRGIDIQAVNVVINFDFPKNAETYLHRIGRSGRFGHLGLAIN  424 (459)
T ss_pred             ccchhhHHHHHHHHhhhhhhhhhhhccccceeeehhhhhcccccceeeEEEecCCCCCHHHHHHHccCCccCCCcceEEE
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHHHHHHHHHhhCCCCCChHHHH
Q 037139           81 FLTFHDTDVFYDLKQMLIQSNSPVPPELAK  110 (135)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  110 (135)
                      +++..+...+..+++.+..+..++|+.++.
T Consensus       425 Lityedrf~L~~IE~eLGtEI~pip~~iDk  454 (459)
T KOG0326|consen  425 LITYEDRFNLYRIEQELGTEIKPIPSNIDK  454 (459)
T ss_pred             EEehhhhhhHHHHHHHhccccccCCCcCCc
Confidence            999999999999999999999999987764

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.91  E-value=2.6e-24  Score=166.47  Aligned_cols=100  Identities=38%  Similarity=0.607  Sum_probs=94.5

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++++|+.++++|++|+++|||||+++++|+|+|++++||+||+|.+...|+||+||+||.|..|.++++
T Consensus       266 ~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTdv~~rGiDi~~v~~VI~~d~p~~~~~yiqR~GRtGR~g~~G~ai~l  345 (460)
T PRK11776        266 GFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSL  345 (460)
T ss_pred             CCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEecccccccchhcCCeEEEecCCCCHhHhhhhcccccCCCCcceEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCC
Q 037139           82 LTFHDTDVFYDLKQMLIQSN  101 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~  101 (135)
                      +.+.+...+..+++.+....
T Consensus       346 ~~~~e~~~~~~i~~~~~~~~  365 (460)
T PRK11776        346 VAPEEMQRANAIEDYLGRKL  365 (460)
T ss_pred             EchhHHHHHHHHHHHhCCCC
Confidence            99988888888888776543

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.91  E-value=4.1e-24  Score=166.03  Aligned_cols=105  Identities=44%  Similarity=0.735  Sum_probs=97.3

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++++|.++++.|++|+++|||||+++++|+|+|++++||++|+|.+..+|+||+||+||.|..|.++++
T Consensus       359 ~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~~l~~GIDi~~v~~VI~~~~P~s~~~y~Qr~GRaGR~g~~g~~i~~  438 (475)
T PRK01297        359 GINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISF  438 (475)
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEccccccCCcccCCCEEEEeCCCCCHHHHHHhhCccCCCCCCceEEEE
Confidence            67889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCC-CCCCh
Q 037139           82 LTFHDTDVFYDLKQMLIQSN-SPVPP  106 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~-~~~~~  106 (135)
                      +...|...+..+++++.... .++|+
T Consensus       439 ~~~~d~~~~~~~~~~~~~~~~~~~~~  464 (475)
T PRK01297        439 AGEDDAFQLPEIEELLGRKISCEMPP  464 (475)
T ss_pred             ecHHHHHHHHHHHHHhCCCCcccCCc
Confidence            99888888889988887774 44443

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

Probab=99.91  E-value=2e-24  Score=158.33  Aligned_cols=107  Identities=36%  Similarity=0.602  Sum_probs=100.8

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      +++++.++|+.|++++|...+.+|+++.++||||||++++|+|+|.|++|+|+|.|.++.+|+||+||+.|.|+.|.+++
T Consensus       277 le~r~~~lHs~m~Q~eR~~aLsrFrs~~~~iliaTDVAsRGLDIP~V~LVvN~diPr~P~~yiHRvGRtARAGR~G~aiS  356 (442)
T KOG0340|consen  277 LEVRVVSLHSQMPQKERLAALSRFRSNAARILIATDVASRGLDIPTVELVVNHDIPRDPKDYIHRVGRTARAGRKGMAIS  356 (442)
T ss_pred             hceeeeehhhcchHHHHHHHHHHHhhcCccEEEEechhhcCCCCCceeEEEecCCCCCHHHHHHhhcchhcccCCcceEE
Confidence            46889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHHHHHHHHHhhCCCCCChH
Q 037139           81 FLTFHDTDVFYDLKQMLIQSNSPVPPE  107 (135)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~  107 (135)
                      ++...|.+.+..+++...+...+.+..
T Consensus       357 ivt~rDv~l~~aiE~~igkKl~e~~~~  383 (442)
T KOG0340|consen  357 IVTQRDVELLQAIEEEIGKKLTEYNKV  383 (442)
T ss_pred             EechhhHHHHHHHHHHHhccccccccc
Confidence            999999999999999888877665443

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.91  E-value=4.7e-24  Score=163.95  Aligned_cols=100  Identities=44%  Similarity=0.703  Sum_probs=94.6

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++.+|..++++|++|+++|||||+++++|+|+|++++||+||+|.+...|+||+||+||.|..|.++++
T Consensus       269 ~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd~~~~GiDip~v~~VI~~d~p~s~~~yiqr~GR~gR~g~~g~ai~l  348 (434)
T PRK11192        269 GINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISL  348 (434)
T ss_pred             CCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEccccccCccCCCCCEEEEECCCCCHHHHhhcccccccCCCCceEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCC
Q 037139           82 LTFHDTDVFYDLKQMLIQSN  101 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~  101 (135)
                      +...+...+..+++++....
T Consensus       349 ~~~~d~~~~~~i~~~~~~~~  368 (434)
T PRK11192        349 VEAHDHLLLGKIERYIEEPL  368 (434)
T ss_pred             ecHHHHHHHHHHHHHHhccc
Confidence            99988888888888776543

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.91  E-value=6e-24  Score=168.10  Aligned_cols=100  Identities=42%  Similarity=0.612  Sum_probs=94.3

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++.+|+.++++|++|+++|||||+++++|+|+|++++||+||+|.+...|+||+||+||.|..|.+++|
T Consensus       281 g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv~arGIDip~V~~VInyd~P~s~~~yvqRiGRaGR~G~~G~ai~~  360 (572)
T PRK04537        281 GYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISF  360 (572)
T ss_pred             CCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehhhhcCCCccCCCEEEEcCCCCCHHHHhhhhcccccCCCCceEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCC
Q 037139           82 LTFHDTDVFYDLKQMLIQSN  101 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~  101 (135)
                      +.+.+...+..+++.+....
T Consensus       361 ~~~~~~~~l~~i~~~~~~~~  380 (572)
T PRK04537        361 ACERYAMSLPDIEAYIEQKI  380 (572)
T ss_pred             ecHHHHHHHHHHHHHHcCCC
Confidence            99888888888888776654

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

Probab=99.91  E-value=4.8e-24  Score=158.38  Aligned_cols=111  Identities=54%  Similarity=0.934  Sum_probs=104.9

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+.++++|...++.|+.|+-+|||+||+++.|+|||++.+|||||+|..+++|+||+||+||.|+.|.+.+|
T Consensus       445 GVEavaIHGGKDQedR~~ai~afr~gkKDVLVATDVASKGLDFp~iqHVINyDMP~eIENYVHRIGRTGRsg~~GiATTf  524 (610)
T KOG0341|consen  445 GVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATDVASKGLDFPDIQHVINYDMPEEIENYVHRIGRTGRSGKTGIATTF  524 (610)
T ss_pred             cceeEEeecCcchhHHHHHHHHHhcCCCceEEEecchhccCCCccchhhccCCChHHHHHHHHHhcccCCCCCcceeeee
Confidence            78899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecC-ChhHHHHHHHHHhhCCCCCChHHHHHH
Q 037139           82 LTFH-DTDVFYDLKQMLIQSNSPVPPELAKHE  112 (135)
Q Consensus        82 ~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~~  112 (135)
                      ++.. +...+..++.++....+++|+.|+.+.
T Consensus       525 INK~~~esvLlDLK~LL~EakQ~vP~~L~~L~  556 (610)
T KOG0341|consen  525 INKNQEESVLLDLKHLLQEAKQEVPPVLAELA  556 (610)
T ss_pred             ecccchHHHHHHHHHHHHHhhccCCHHHHHhC
Confidence            9865 566778899999999999999998653

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

Probab=99.90  E-value=1.4e-23  Score=161.36  Aligned_cols=111  Identities=41%  Similarity=0.644  Sum_probs=107.0

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      ++.+.++||+.++.+|.+++++|+.|++.+||||+++++|+|+.++++|||||.|.+..+|+||+||+||.|+.|.+++|
T Consensus       412 ~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicTdll~RGiDf~gvn~VInyD~p~s~~syihrIGRtgRag~~g~Aitf  491 (593)
T KOG0344|consen  412 NINVDVIHGERSQKQRDETMERFRIGKIWVLICTDLLARGIDFKGVNLVINYDFPQSDLSYIHRIGRTGRAGRSGKAITF  491 (593)
T ss_pred             CcceeeEecccchhHHHHHHHHHhccCeeEEEehhhhhccccccCcceEEecCCCchhHHHHHHhhccCCCCCCcceEEE
Confidence            56799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCCCCCChHHHHHH
Q 037139           82 LTFHDTDVFYDLKQMLIQSNSPVPPELAKHE  112 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  112 (135)
                      +...+....+.+.+.+.....++|+++..+-
T Consensus       492 ytd~d~~~ir~iae~~~~sG~evpe~~m~~~  522 (593)
T KOG0344|consen  492 YTDQDMPRIRSIAEVMEQSGCEVPEKIMGIK  522 (593)
T ss_pred             eccccchhhhhHHHHHHHcCCcchHHHHhhh
Confidence            9999999999999999999999999987653

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.90  E-value=1.3e-23  Score=163.11  Aligned_cols=93  Identities=32%  Similarity=0.503  Sum_probs=86.7

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      .|+.+..+||+|++++|..++++|++|+++|||||+++++|+|+|+|++||++|+|.+...|+||+||+||.|.+|.+++
T Consensus       249 ~g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~GID~p~V~~VI~~~~P~s~~~y~Qr~GRaGR~G~~~~~~~  328 (470)
T TIGR00614       249 LGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHL  328 (470)
T ss_pred             cCCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhccCCcccceEEEEeCCCCCHHHHHhhhcCcCCCCCCceEEE
Confidence            37889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHHHHH
Q 037139           81 FLTFHDTDVFYDL   93 (135)
Q Consensus        81 ~~~~~~~~~~~~~   93 (135)
                      ++.+.+...++.+
T Consensus       329 ~~~~~d~~~~~~~  341 (470)
T TIGR00614       329 FYAPADINRLRRL  341 (470)
T ss_pred             EechhHHHHHHHH
Confidence            9988776554433

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

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.90  E-value=2e-23  Score=166.44  Aligned_cols=100  Identities=39%  Similarity=0.711  Sum_probs=92.9

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      .|+.+..+||+|++.+|+.++++|++|+++|||||+++++|+|+|+|++||+||+|.+...|+||+||+||.|+.|.+++
T Consensus       268 ~g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATdv~arGIDip~V~~VI~~d~P~~~e~yvqRiGRtGRaGr~G~ai~  347 (629)
T PRK11634        268 NGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALL  347 (629)
T ss_pred             CCCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcchHhcCCCcccCCEEEEeCCCCCHHHHHHHhccccCCCCcceEEE
Confidence            37889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHHHHHHHHHhhC
Q 037139           81 FLTFHDTDVFYDLKQMLIQS  100 (135)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~  100 (135)
                      ++.+.+...++.+++.++..
T Consensus       348 ~v~~~e~~~l~~ie~~~~~~  367 (629)
T PRK11634        348 FVENRERRLLRNIERTMKLT  367 (629)
T ss_pred             EechHHHHHHHHHHHHhCCC
Confidence            99988777777777765544

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

Probab=99.90  E-value=1.5e-23  Score=172.44  Aligned_cols=90  Identities=29%  Similarity=0.506  Sum_probs=84.8

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      .|+++..|||+|++++|..++++|..|+++|||||+++++|||+|+|++||+||+|.+++.|+||+|||||.|.++.|++
T Consensus       703 ~Gika~~YHAGLs~eeR~~vqe~F~~Gei~VLVATdAFGMGIDkPDVR~VIHydlPkSiEsYyQriGRAGRDG~~g~cIL  782 (1195)
T PLN03137        703 FGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVL  782 (1195)
T ss_pred             CCCCeeeeeCCCCHHHHHHHHHHHhcCCCcEEEEechhhcCCCccCCcEEEEcCCCCCHHHHHhhhcccCCCCCCceEEE
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHH
Q 037139           81 FLTFHDTDVF   90 (135)
Q Consensus        81 ~~~~~~~~~~   90 (135)
                      ++...+....
T Consensus       783 lys~~D~~~~  792 (1195)
T PLN03137        783 YYSYSDYIRV  792 (1195)
T ss_pred             EecHHHHHHH
Confidence            9987655433

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

Probab=99.90  E-value=5.5e-23  Score=151.70  Aligned_cols=110  Identities=36%  Similarity=0.629  Sum_probs=97.3

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCC------CHHHHHHHhhhcCCCCCC
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPG------NIEMYTHRIGRTGRAGKT   75 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~------~~~~~~qr~GR~gR~~~~   75 (135)
                      |+.|.++||+|+-.+|..+++.|+.|+.+|||+|++++||+|++.|++|||||+|.      +.+.|+||+||+||.|+.
T Consensus       354 Gh~V~~l~G~l~~~~R~~ii~~Fr~g~~kVLitTnV~ARGiDv~qVs~VvNydlP~~~~~~pD~etYlHRiGRtGRFGkk  433 (477)
T KOG0332|consen  354 GHQVSLLHGDLTVEQRAAIIDRFREGKEKVLITTNVCARGIDVAQVSVVVNYDLPVKYTGEPDYETYLHRIGRTGRFGKK  433 (477)
T ss_pred             CceeEEeeccchhHHHHHHHHHHhcCcceEEEEechhhcccccceEEEEEecCCccccCCCCCHHHHHHHhccccccccc
Confidence            78999999999999999999999999999999999999999999999999999996      689999999999999999


Q ss_pred             ceEEEEeecC-ChhHHHHHHHHHhhCC-CCCChHHHHH
Q 037139           76 GVATTFLTFH-DTDVFYDLKQMLIQSN-SPVPPELAKH  111 (135)
Q Consensus        76 g~~~~~~~~~-~~~~~~~~~~~~~~~~-~~~~~~l~~~  111 (135)
                      |.++.++... ....++.++++++... ...|..+.+.
T Consensus       434 G~a~n~v~~~~s~~~mn~iq~~F~~~i~~~~~~d~~E~  471 (477)
T KOG0332|consen  434 GLAINLVDDKDSMNIMNKIQKHFNMKIKRLDPDDLDEL  471 (477)
T ss_pred             ceEEEeecccCcHHHHHHHHHHHhhcceecCCccHHHH
Confidence            9999999876 4566789999986554 3444445443

>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=99.89  E-value=4.7e-23  Score=123.51  Aligned_cols=73  Identities=48%  Similarity=0.804  Sum_probs=71.0

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCC
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAG   73 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~   73 (135)
                      .|+.+..+||++++++|..+++.|++++.+|||||+++++|+|+|.+++||++++|++...|.|++||++|.|
T Consensus         6 ~~~~~~~i~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gid~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~g   78 (78)
T PF00271_consen    6 KGIKVAIIHGDMSQKERQEILKKFNSGEIRVLIATDILGEGIDLPDASHVIFYDPPWSPEEYIQRIGRAGRIG   78 (78)
T ss_dssp             TTSSEEEESTTSHHHHHHHHHHHHHTTSSSEEEESCGGTTSSTSTTESEEEESSSESSHHHHHHHHTTSSTTT
T ss_pred             CCCcEEEEECCCCHHHHHHHHHHhhccCceEEEeeccccccccccccccccccccCCCHHHHHHHhhcCCCCC
Confidence            4789999999999999999999999999999999999999999999999999999999999999999999975

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 ....

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.89  E-value=7.2e-23  Score=163.07  Aligned_cols=90  Identities=32%  Similarity=0.526  Sum_probs=84.9

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      .|+.+..+||+|++++|.++++.|+.|+++|||||+++++|+|+|+|++||+||+|.+.+.|+||+||+||.|.+|.+++
T Consensus       259 ~g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GIDip~V~~VI~~d~P~s~~~y~Qr~GRaGR~G~~~~~il  338 (607)
T PRK11057        259 RGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAML  338 (607)
T ss_pred             CCCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccCCCCCcCEEEEeCCCCCHHHHHHHhhhccCCCCCceEEE
Confidence            36789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHH
Q 037139           81 FLTFHDTDVF   90 (135)
Q Consensus        81 ~~~~~~~~~~   90 (135)
                      ++++.+...+
T Consensus       339 l~~~~d~~~~  348 (607)
T PRK11057        339 FYDPADMAWL  348 (607)
T ss_pred             EeCHHHHHHH
Confidence            9988765443

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

Probab=99.88  E-value=1.4e-22  Score=164.23  Aligned_cols=99  Identities=20%  Similarity=0.270  Sum_probs=88.0

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      +.++..+||+|++++|.+++++|++|++++||||+++++|+|+|++++||++|.|.+..+|+||+||+||.|..|.++++
T Consensus       303 ~~~v~~~hgg~~~~eR~~ie~~f~~G~i~vLVaTd~lerGIDI~~vd~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v  382 (742)
T TIGR03817       303 AERVAAYRAGYLPEDRRELERALRDGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLV  382 (742)
T ss_pred             ccchhheecCCCHHHHHHHHHHHHcCCceEEEECchHhccCCcccccEEEEeCCCCCHHHHHHhccccCCCCCCcEEEEE
Confidence            46788999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             eecC--ChhHHHHHHHHHhhC
Q 037139           82 LTFH--DTDVFYDLKQMLIQS  100 (135)
Q Consensus        82 ~~~~--~~~~~~~~~~~~~~~  100 (135)
                      ....  +...+...+++++..
T Consensus       383 ~~~~~~d~~~~~~~~~~~~~~  403 (742)
T TIGR03817       383 ARDDPLDTYLVHHPEALFDRP  403 (742)
T ss_pred             eCCChHHHHHHhCHHHHhcCC
Confidence            8643  444455566666554

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.

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.87  E-value=4.1e-22  Score=158.41  Aligned_cols=89  Identities=38%  Similarity=0.586  Sum_probs=83.5

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      .|+.+..+||+|++++|+.++++|.+|+++|||||+++++|+|+|++++||++|+|.+.+.|.|++||+||.|.++.+++
T Consensus       247 ~g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~a~~~GID~p~v~~VI~~~~p~s~~~y~Q~~GRaGR~G~~~~~il  326 (591)
T TIGR01389       247 QGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAIL  326 (591)
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEechhhccCcCCCCCEEEEcCCCCCHHHHhhhhccccCCCCCceEEE
Confidence            36789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhH
Q 037139           81 FLTFHDTDV   89 (135)
Q Consensus        81 ~~~~~~~~~   89 (135)
                      ++.+.+...
T Consensus       327 ~~~~~d~~~  335 (591)
T TIGR01389       327 LYSPADIAL  335 (591)
T ss_pred             ecCHHHHHH
Confidence            988765433

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.

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

Probab=99.87  E-value=9.2e-22  Score=153.91  Aligned_cols=94  Identities=38%  Similarity=0.569  Sum_probs=88.3

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..|||||+.++|+.+.++|..++++|+|||.++++|||-|+|++|||||+|.+++.|.|-+|||||.|.++.++++
T Consensus       254 g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfViH~~lP~s~EsYyQE~GRAGRDG~~a~aill  333 (590)
T COG0514         254 GISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILL  333 (590)
T ss_pred             CCceEEecCCCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCceEEEEecCCCCHHHHHHHHhhccCCCCcceEEEe
Confidence            78899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHH
Q 037139           82 LTFHDTDVFYDLKQ   95 (135)
Q Consensus        82 ~~~~~~~~~~~~~~   95 (135)
                      +.+.|....+.+.+
T Consensus       334 ~~~~D~~~~~~~i~  347 (590)
T COG0514         334 YSPEDIRWQRYLIE  347 (590)
T ss_pred             eccccHHHHHHHHH
Confidence            99988765544433

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

Probab=99.87  E-value=2.3e-22  Score=153.29  Aligned_cols=96  Identities=47%  Similarity=0.746  Sum_probs=91.2

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      +|++++-+||++++.+|.+.+++|+.+++++|||||++++|+|++.|..||||++|.+...|+||+||+.|.|+.|.+++
T Consensus       449 lgl~agElHGsLtQ~QRlesL~kFk~~eidvLiaTDvAsRGLDI~gV~tVINy~mP~t~e~Y~HRVGRTARAGRaGrsVt  528 (691)
T KOG0338|consen  449 LGLKAGELHGSLTQEQRLESLEKFKKEEIDVLIATDVASRGLDIEGVQTVINYAMPKTIEHYLHRVGRTARAGRAGRSVT  528 (691)
T ss_pred             hhchhhhhcccccHHHHHHHHHHHHhccCCEEEEechhhccCCccceeEEEeccCchhHHHHHHHhhhhhhcccCcceEE
Confidence            58899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHHHHHHHH
Q 037139           81 FLTFHDTDVFYDLKQM   96 (135)
Q Consensus        81 ~~~~~~~~~~~~~~~~   96 (135)
                      |+...+...++.+-+-
T Consensus       529 lvgE~dRkllK~iik~  544 (691)
T KOG0338|consen  529 LVGESDRKLLKEIIKS  544 (691)
T ss_pred             EeccccHHHHHHHHhh
Confidence            9999988777666654

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

Probab=99.87  E-value=2.5e-22  Score=152.13  Aligned_cols=95  Identities=40%  Similarity=0.644  Sum_probs=91.3

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      .+.|..+||++++..|..+...|++.+.-||+|||+.+||+|+|+|++||+||+|.++++|+||+||+||.|..|.++++
T Consensus       354 dlpv~eiHgk~~Q~kRT~~~~~F~kaesgIL~cTDVaARGlD~P~V~~VvQ~~~P~d~~~YIHRvGRTaR~gk~G~alL~  433 (543)
T KOG0342|consen  354 DLPVLEIHGKQKQNKRTSTFFEFCKAESGILVCTDVAARGLDIPDVDWVVQYDPPSDPEQYIHRVGRTAREGKEGKALLL  433 (543)
T ss_pred             CCchhhhhcCCcccccchHHHHHhhcccceEEecchhhccCCCCCceEEEEeCCCCCHHHHHHHhccccccCCCceEEEE
Confidence            56788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHH
Q 037139           82 LTFHDTDVFYDLKQM   96 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~   96 (135)
                      +.+.+..+++.+++.
T Consensus       434 l~p~El~Flr~LK~l  448 (543)
T KOG0342|consen  434 LAPWELGFLRYLKKL  448 (543)
T ss_pred             eChhHHHHHHHHhhC
Confidence            999999999999854

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

Probab=99.86  E-value=8.1e-22  Score=148.88  Aligned_cols=90  Identities=39%  Similarity=0.622  Sum_probs=84.3

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      +..+..+||.|++..|..+++.|+...-.+|+|||++++|+|+|++++||+||+|.+++.|+||+||++|.|+.|.+++|
T Consensus       281 ~~~i~~iHGK~~q~~R~k~~~~F~~~~~~vl~~TDVaARGlDip~iD~VvQ~DpP~~~~~FvHR~GRTaR~gr~G~Aivf  360 (567)
T KOG0345|consen  281 KREIFSIHGKMSQKARAKVLEAFRKLSNGVLFCTDVAARGLDIPGIDLVVQFDPPKDPSSFVHRCGRTARAGREGNAIVF  360 (567)
T ss_pred             CCcEEEecchhcchhHHHHHHHHHhccCceEEeehhhhccCCCCCceEEEecCCCCChhHHHhhcchhhhccCccceEEE
Confidence            45788999999999999999999998888999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHH
Q 037139           82 LTFHDTDVFY   91 (135)
Q Consensus        82 ~~~~~~~~~~   91 (135)
                      +.+.+..+.+
T Consensus       361 l~p~E~aYve  370 (567)
T KOG0345|consen  361 LNPREEAYVE  370 (567)
T ss_pred             ecccHHHHHH
Confidence            9997665543

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

Probab=99.85  E-value=2.6e-21  Score=148.13  Aligned_cols=96  Identities=40%  Similarity=0.613  Sum_probs=89.8

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      +.++.-+||+|++++|..+++.|....-.||+|||++++|+|+|+|.+||+||+|.+..+|+||+||+.|.|..|.+++|
T Consensus       471 ~~k~~rLHGsm~QeeRts~f~~Fs~~~~~VLLcTDVAaRGLDlP~V~~vVQYd~P~s~adylHRvGRTARaG~kG~alLf  550 (708)
T KOG0348|consen  471 DLKFYRLHGSMEQEERTSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQYDPPFSTADYLHRVGRTARAGEKGEALLF  550 (708)
T ss_pred             cceEEEecCchhHHHHHHHHHhhccccceEEEehhhhhccCCCCCcCeEEEeCCCCCHHHHHHHhhhhhhccCCCceEEE
Confidence            45678899999999999999999998888999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHH
Q 037139           82 LTFHDTDVFYDLKQML   97 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~   97 (135)
                      +.+.+.++++.++..-
T Consensus       551 L~P~Eaey~~~l~~~~  566 (708)
T KOG0348|consen  551 LLPSEAEYVNYLKKHH  566 (708)
T ss_pred             ecccHHHHHHHHHhhc
Confidence            9999998877776643

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

Probab=99.85  E-value=3.1e-21  Score=142.49  Aligned_cols=110  Identities=37%  Similarity=0.687  Sum_probs=105.7

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      +|+.+.++||+|.+.+|..+++.|+.|..+|||+|+.+++|+|+..+++|+|||+|....+|++|+||+||.|.+|.++.
T Consensus       286 ~~~~~s~~~~d~~q~~R~~~~~ef~~gssrvlIttdl~argidv~~~slvinydlP~~~~~yihR~gr~gr~grkg~~in  365 (397)
T KOG0327|consen  286 HGFTVSAIHGDMEQNERDTLMREFRSGSSRVLITTDLLARGIDVQQVSLVVNYDLPARKENYIHRIGRAGRFGRKGVAIN  365 (397)
T ss_pred             CCceEEEeecccchhhhhHHHHHhhcCCceEEeeccccccccchhhcceeeeeccccchhhhhhhcccccccCCCceeee
Confidence            47889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHHHHHHHHHhhCCCCCChHHHH
Q 037139           81 FLTFHDTDVFYDLKQMLIQSNSPVPPELAK  110 (135)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  110 (135)
                      ++...+...++.+++++.....++|.....
T Consensus       366 ~v~~~d~~~lk~ie~~y~~~i~e~p~~~~~  395 (397)
T KOG0327|consen  366 FVTEEDVRDLKDIEKFYNTPIEELPSNFAD  395 (397)
T ss_pred             eehHhhHHHHHhHHHhcCCcceecccchhh
Confidence            999999999999999999999999987653

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

Probab=99.84  E-value=6.3e-21  Score=145.01  Aligned_cols=98  Identities=39%  Similarity=0.615  Sum_probs=89.4

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      ++++.++.|+++.+.|.+.++.|+.|++++|||||+++||+|+.+++.|||||+|.+...|+||+||++|.|+.|.++.+
T Consensus       457 ~~~~s~~t~~l~~k~r~k~l~~f~~g~i~vLIcSD~laRGiDv~~v~~VINYd~P~~~ktyVHR~GRTARAgq~G~a~tl  536 (620)
T KOG0350|consen  457 NFKVSEFTGQLNGKRRYKMLEKFAKGDINVLICSDALARGIDVNDVDNVINYDPPASDKTYVHRAGRTARAGQDGYAITL  536 (620)
T ss_pred             cchhhhhhhhhhHHHHHHHHHHHhcCCceEEEehhhhhcCCcccccceEeecCCCchhhHHHHhhcccccccCCceEEEe
Confidence            35567789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhh
Q 037139           82 LTFHDTDVFYDLKQMLIQ   99 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~   99 (135)
                      +...+...|.++.+....
T Consensus       537 l~~~~~r~F~klL~~~~~  554 (620)
T KOG0350|consen  537 LDKHEKRLFSKLLKKTNL  554 (620)
T ss_pred             eccccchHHHHHHHHhcc
Confidence            999888777666554433

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.84  E-value=5.3e-20  Score=147.23  Aligned_cols=82  Identities=27%  Similarity=0.455  Sum_probs=78.3

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCC-CHHHHHHHhhhcCCCCCCceEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPG-NIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~-~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      ++.+..+||+|++++|.+++++|++|+++|||||+++++|+|+|++++||++|.|. +...|.||+||+||.|..|.|++
T Consensus       482 ~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GvDiP~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~il  561 (630)
T TIGR00643       482 KYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLL  561 (630)
T ss_pred             CCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECceeecCcccCCCcEEEEeCCCcCCHHHHHHHhhhcccCCCCcEEEE
Confidence            56799999999999999999999999999999999999999999999999999986 68899999999999999999999


Q ss_pred             Eee
Q 037139           81 FLT   83 (135)
Q Consensus        81 ~~~   83 (135)
                      ++.
T Consensus       562 ~~~  564 (630)
T TIGR00643       562 VYK  564 (630)
T ss_pred             EEC
Confidence            984

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=99.83  E-value=1.8e-20  Score=144.06  Aligned_cols=94  Identities=38%  Similarity=0.592  Sum_probs=87.0

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+++.++||.|++..|.+++++|.....-||+|||++++|+|||.|++||++|.|.++.+|+||+||+.|.+..|.++++
T Consensus       339 g~~l~~L~G~~~Q~~R~ev~~~F~~~~~~vLF~TDv~aRGLDFpaVdwViQ~DCPedv~tYIHRvGRtAR~~~~G~sll~  418 (758)
T KOG0343|consen  339 GIPLLALHGTMSQKKRIEVYKKFVRKRAVVLFCTDVAARGLDFPAVDWVIQVDCPEDVDTYIHRVGRTARYKERGESLLM  418 (758)
T ss_pred             CCceeeeccchhHHHHHHHHHHHHHhcceEEEeehhhhccCCCcccceEEEecCchhHHHHHHHhhhhhcccCCCceEEE
Confidence            78899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCC-hhHHHHHHH
Q 037139           82 LTFHD-TDVFYDLKQ   95 (135)
Q Consensus        82 ~~~~~-~~~~~~~~~   95 (135)
                      +.+.+ ..+...+++
T Consensus       419 L~psEeE~~l~~Lq~  433 (758)
T KOG0343|consen  419 LTPSEEEAMLKKLQK  433 (758)
T ss_pred             EcchhHHHHHHHHHH
Confidence            99987 444444443

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.83  E-value=7.3e-20  Score=147.49  Aligned_cols=83  Identities=22%  Similarity=0.390  Sum_probs=78.6

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCC-CHHHHHHHhhhcCCCCCCceEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPG-NIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~-~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      ++++..+||+|++++|.+++++|++|+++|||||+++++|+|+|++++||++|.|. ....|.||+||+||.|..|.|++
T Consensus       505 ~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GiDip~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~il  584 (681)
T PRK10917        505 ELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVL  584 (681)
T ss_pred             CCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECcceeeCcccCCCcEEEEeCCCCCCHHHHHHHhhcccCCCCceEEEE
Confidence            36799999999999999999999999999999999999999999999999999987 58899999999999999999999


Q ss_pred             Eeec
Q 037139           81 FLTF   84 (135)
Q Consensus        81 ~~~~   84 (135)
                      ++..
T Consensus       585 l~~~  588 (681)
T PRK10917        585 LYKD  588 (681)
T ss_pred             EECC
Confidence            9953

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.81  E-value=4.5e-19  Score=146.01  Aligned_cols=84  Identities=25%  Similarity=0.374  Sum_probs=79.1

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCC-CHHHHHHHhhhcCCCCCCceEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPG-NIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~-~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      ++++..+||+|++++|++++++|++|+++|||||+++++|+|+|++++||+++.|. +..+|.||+||+||.|..|.|++
T Consensus       686 ~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~iie~GIDIp~v~~VIi~~a~~~gls~l~Qr~GRvGR~g~~g~ail  765 (926)
T TIGR00580       686 EARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYL  765 (926)
T ss_pred             CCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcccccccCCEEEEecCCCCCHHHHHHHhcCCCCCCCCeEEEE
Confidence            57899999999999999999999999999999999999999999999999999875 68899999999999999999999


Q ss_pred             EeecC
Q 037139           81 FLTFH   85 (135)
Q Consensus        81 ~~~~~   85 (135)
                      ++...
T Consensus       766 l~~~~  770 (926)
T TIGR00580       766 LYPHQ  770 (926)
T ss_pred             EECCc
Confidence            98654

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.

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.81  E-value=2.4e-19  Score=147.53  Aligned_cols=98  Identities=21%  Similarity=0.372  Sum_probs=86.1

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcC--CCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTK--RYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVAT   79 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g--~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~   79 (135)
                      |+++..+||+|++.+|.++++.|+++  ..+|||||+++++|+|++.+++||+||+|+++..|.||+||++|.|+.+.+.
T Consensus       518 Gi~~~~ihG~~s~~eR~~~~~~F~~~~~~~~VLIsTdvgseGlNlq~a~~VInfDlP~nP~~~eQRIGR~~RiGQ~~~V~  597 (956)
T PRK04914        518 GIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLLCSEIGSEGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQKHDIQ  597 (956)
T ss_pred             CeeEEEEECCCCHHHHHHHHHHHhcCCCCccEEEechhhccCCCcccccEEEEecCCCCHHHHHHHhcccccCCCCceEE
Confidence            78999999999999999999999984  5999999999999999999999999999999999999999999999988777


Q ss_pred             EEeecCChhHHHHHHHHHhh
Q 037139           80 TFLTFHDTDVFYDLKQMLIQ   99 (135)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~   99 (135)
                      +++........+.+.+.+..
T Consensus       598 i~~~~~~~t~~e~i~~~~~~  617 (956)
T PRK04914        598 IHVPYLEGTAQERLFRWYHE  617 (956)
T ss_pred             EEEccCCCCHHHHHHHHHhh
Confidence            76665555455555555554

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=99.81  E-value=3.3e-20  Score=142.59  Aligned_cols=101  Identities=40%  Similarity=0.590  Sum_probs=94.8

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      +++....+|+.|.++.|.+.+++|++..--||||||++++|+|+|.|.+||+|-.|.+.+.|+||.||+.|.+..|..++
T Consensus       486 L~i~p~~LHA~M~QKqRLknLEkF~~~~~~VLiaTDVAARGLDIp~V~HVIHYqVPrtseiYVHRSGRTARA~~~Gvsvm  565 (731)
T KOG0347|consen  486 LDIPPLPLHASMIQKQRLKNLEKFKQSPSGVLIATDVAARGLDIPGVQHVIHYQVPRTSEIYVHRSGRTARANSEGVSVM  565 (731)
T ss_pred             cCCCCchhhHHHHHHHHHHhHHHHhcCCCeEEEeehhhhccCCCCCcceEEEeecCCccceeEecccccccccCCCeEEE
Confidence            46677889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHHHHHHHHHhhCC
Q 037139           81 FLTFHDTDVFYDLKQMLIQSN  101 (135)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~  101 (135)
                      ++.+.+...+.++.+.++...
T Consensus       566 l~~P~e~~~~~KL~ktL~k~~  586 (731)
T KOG0347|consen  566 LCGPQEVGPLKKLCKTLKKKE  586 (731)
T ss_pred             EeChHHhHHHHHHHHHHhhcc
Confidence            999999988888888876643

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

Probab=99.80  E-value=2.5e-19  Score=136.85  Aligned_cols=121  Identities=45%  Similarity=0.682  Sum_probs=112.4

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      .||.|..+||+|.+.+|.+++.+|+.+...||++||+.++|+|+|.+..|||||.-.+++.|.||+||+||.|..|.+++
T Consensus       491 k~~~v~llhgdkdqa~rn~~ls~fKkk~~~VlvatDvaargldI~~ikTVvnyD~ardIdththrigrtgRag~kGvayT  570 (731)
T KOG0339|consen  491 KGFNVSLLHGDKDQAERNEVLSKFKKKRKPVLVATDVAARGLDIPSIKTVVNYDFARDIDTHTHRIGRTGRAGEKGVAYT  570 (731)
T ss_pred             ccceeeeecCchhhHHHHHHHHHHhhcCCceEEEeeHhhcCCCccccceeecccccchhHHHHHHhhhcccccccceeeE
Confidence            37899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHHHHHHHHHhhCCCCCChHHHHHH--HhhCCCCCC
Q 037139           81 FLTFHDTDVFYDLKQMLIQSNSPVPPELAKHE--ASKFKPGTI  121 (135)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~~~~~~~~  121 (135)
                      ++++.+..+.-.|.+-|+...+.+|+.|.++.  .++|+...+
T Consensus       571 lvTeKDa~fAG~LVnnLe~agQnVP~~l~dlamk~s~fr~~r~  613 (731)
T KOG0339|consen  571 LVTEKDAEFAGHLVNNLEGAGQNVPDELMDLAMKSSWFRSSRF  613 (731)
T ss_pred             EechhhHHHhhHHHHHHhhccccCChHHHHHHhhhhhhhhhhc
Confidence            99999999999999999999999999998764  455554433

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.80  E-value=3e-19  Score=106.89  Aligned_cols=72  Identities=57%  Similarity=0.875  Sum_probs=69.6

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCC
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAG   73 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~   73 (135)
                      ++.+..+||+|++++|..+++.|+.++..||++|+++++|+|+|.++.||.+++|++...|.|++||++|.|
T Consensus        11 ~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gi~~~~~~~vi~~~~~~~~~~~~Q~~gR~~R~g   82 (82)
T smart00490       11 GIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG   82 (82)
T ss_pred             CCeEEEEECCCCHHHHHHHHHHHHcCCCeEEEECChhhCCcChhcCCEEEEeCCCCCHHHHHHhhcccccCC
Confidence            678999999999999999999999999999999999999999999999999999999999999999999975

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.79  E-value=5.3e-19  Score=145.70  Aligned_cols=82  Identities=23%  Similarity=0.325  Sum_probs=73.4

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCC-CCCceEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRA-GKTGVATT   80 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~-~~~g~~~~   80 (135)
                      +..+.++||+|++++|..++++|++|+++|||||+++++|+|+|++++||+++.|.+...|+||+||+||. |..+.+++
T Consensus       314 ~~~i~~hHg~ls~~~R~~ve~~fk~G~i~vLVaTs~Le~GIDip~Vd~VI~~~~P~sv~~ylQRiGRaGR~~g~~~~g~i  393 (876)
T PRK13767        314 EDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAGHRLGEVSKGRI  393 (876)
T ss_pred             ccceeeeeCCCCHHHHHHHHHHHHcCCCeEEEECChHHhcCCCCCCcEEEEeCCCCCHHHHHHhcccCCCCCCCCCcEEE
Confidence            35789999999999999999999999999999999999999999999999999999999999999999986 33344444


Q ss_pred             Eee
Q 037139           81 FLT   83 (135)
Q Consensus        81 ~~~   83 (135)
                      +..
T Consensus       394 i~~  396 (876)
T PRK13767        394 IVV  396 (876)
T ss_pred             EEc
Confidence            443

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

Probab=99.79  E-value=6.7e-19  Score=134.27  Aligned_cols=78  Identities=38%  Similarity=0.549  Sum_probs=73.3

Q ss_pred             CCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEEeecCChh
Q 037139           10 GGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDTD   88 (135)
Q Consensus        10 g~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~~~~~~~~   88 (135)
                      .||+++++.+++++|++|+++|||||++.++|+|+|.++.||.|++-.|...++||.||+||. +.|.+++++..+..+
T Consensus       407 ~GMsQkeQ~eiI~~Fr~Ge~nVLVaTSVgEEGLDIp~vDlVifYEpvpSeIR~IQR~GRTGR~-r~Grv~vLvt~gtrd  484 (542)
T COG1111         407 KGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRK-RKGRVVVLVTEGTRD  484 (542)
T ss_pred             cccCHHHHHHHHHHHhcCCceEEEEcccccccCCCCcccEEEEecCCcHHHHHHHhhCccccC-CCCeEEEEEecCchH
Confidence            579999999999999999999999999999999999999999999999999999999999998 688999998877443

>PRK02362 ski2-like helicase; Provisional

Probab=99.78  E-value=8.6e-19  Score=142.47  Aligned_cols=83  Identities=29%  Similarity=0.463  Sum_probs=76.1

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEE----ec-----CCCCHHHHHHHhhhcCCCC
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVIN----YD-----MPGNIEMYTHRIGRTGRAG   73 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~----~d-----~p~~~~~~~qr~GR~gR~~   73 (135)
                      ..|++|||+|++.+|..+++.|++|.++|||||+++++|+|+|.+.+||+    ||     .|.+..+|.||+|||||.|
T Consensus       304 ~gva~hHagl~~~eR~~ve~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~g  383 (737)
T PRK02362        304 KGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPG  383 (737)
T ss_pred             hCEEeecCCCCHHHHHHHHHHHHcCCCeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCCC
Confidence            46899999999999999999999999999999999999999999999996    76     6889999999999999987


Q ss_pred             CC--ceEEEEeecC
Q 037139           74 KT--GVATTFLTFH   85 (135)
Q Consensus        74 ~~--g~~~~~~~~~   85 (135)
                      .+  |.+++++...
T Consensus       384 ~d~~G~~ii~~~~~  397 (737)
T PRK02362        384 LDPYGEAVLLAKSY  397 (737)
T ss_pred             CCCCceEEEEecCc
Confidence            54  8888888654

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.78  E-value=4.9e-18  Score=142.44  Aligned_cols=84  Identities=26%  Similarity=0.369  Sum_probs=76.2

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCC-CCHHHHHHHhhhcCCCCCCceEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMP-GNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p-~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      ++++.++||+|++++|++++.+|++|+++|||||+++++|+|+|++++||..+.. .+..+|+||+||+||.+..|.|++
T Consensus       835 ~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdIierGIDIP~v~~VIi~~ad~fglaq~~Qr~GRvGR~g~~g~a~l  914 (1147)
T PRK10689        835 EARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWL  914 (1147)
T ss_pred             CCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECchhhcccccccCCEEEEecCCCCCHHHHHHHhhccCCCCCceEEEE
Confidence            5689999999999999999999999999999999999999999999999965543 467789999999999999999998


Q ss_pred             EeecC
Q 037139           81 FLTFH   85 (135)
Q Consensus        81 ~~~~~   85 (135)
                      ++...
T Consensus       915 l~~~~  919 (1147)
T PRK10689        915 LTPHP  919 (1147)
T ss_pred             EeCCC
Confidence            88643

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.77  E-value=4.8e-18  Score=136.36  Aligned_cols=115  Identities=22%  Similarity=0.334  Sum_probs=101.2

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecC-----CCCHHHHHHHhhhcCCCCCC
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDM-----PGNIEMYTHRIGRTGRAGKT   75 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~-----p~~~~~~~qr~GR~gR~~~~   75 (135)
                      .|+++..+||++++.+|..+++.|+.|++.|+|||+.+++|+|+|.+++|+++|.     |.+...|+||+||+||. ..
T Consensus       469 ~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~rGfdlp~v~lVii~d~eifG~~~~~~~yiqr~GR~gR~-~~  547 (652)
T PRK05298        469 LGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VN  547 (652)
T ss_pred             cceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHhCCccccCCcEEEEeCCcccccCCCHHHHHHHhccccCC-CC
Confidence            3788999999999999999999999999999999999999999999999999885     78999999999999996 68


Q ss_pred             ceEEEEeec---------CChhHHHHHHHHHhhCCCCCChHHHHHHHhhC
Q 037139           76 GVATTFLTF---------HDTDVFYDLKQMLIQSNSPVPPELAKHEASKF  116 (135)
Q Consensus        76 g~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  116 (135)
                      |.+++++..         .+....+.++..++.....+|+.+.+.....+
T Consensus       548 G~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~  597 (652)
T PRK05298        548 GKVILYADKITDSMQKAIDETERRREIQIAYNEEHGITPKTIKKKIRDIL  597 (652)
T ss_pred             CEEEEEecCCCHHHHHHHHHHHHHHHHHHHhhhccCCCChhHHHHHHHHH
Confidence            999999984         35556677778889999999999876655544

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.76  E-value=3.1e-18  Score=145.32  Aligned_cols=78  Identities=31%  Similarity=0.428  Sum_probs=70.9

Q ss_pred             EEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCC-CCCceEEEEe
Q 037139            5 VTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRA-GKTGVATTFL   82 (135)
Q Consensus         5 v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~-~~~g~~~~~~   82 (135)
                      +.+|||+|++++|..++++|++|++++||||+.+++|||++++++||+++.|.++.+|+||+||+||. +..+.++++.
T Consensus       304 a~~HHGsLSkeeR~~IE~~fK~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~~gg~s~gli~p  382 (1490)
T PRK09751        304 ARSHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQVGGVSKGLFFP  382 (1490)
T ss_pred             eeeccccCCHHHHHHHHHHHHhCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCCCCCccEEEEEe
Confidence            67899999999999999999999999999999999999999999999999999999999999999996 3344555433

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=99.76  E-value=2.5e-18  Score=139.47  Aligned_cols=111  Identities=43%  Similarity=0.710  Sum_probs=104.3

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+.++.+|..+++.|+++.+++||||+++++|+|++.+.+|||||.|.....|+||+||+||.|..|.+++|
T Consensus       637 g~~~~slHGgv~q~dR~sti~dfK~~~~~LLvaTsvvarGLdv~~l~Lvvnyd~pnh~edyvhR~gRTgragrkg~AvtF  716 (997)
T KOG0334|consen  637 GYNCDSLHGGVDQHDRSSTIEDFKNGVVNLLVATSVVARGLDVKELILVVNYDFPNHYEDYVHRVGRTGRAGRKGAAVTF  716 (997)
T ss_pred             CcchhhhcCCCchHHHHhHHHHHhccCceEEEehhhhhcccccccceEEEEcccchhHHHHHHHhcccccCCccceeEEE
Confidence            66777899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCCCCCChHHHHHH
Q 037139           82 LTFHDTDVFYDLKQMLIQSNSPVPPELAKHE  112 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  112 (135)
                      +.+.+......|.+.+.....++|..|..+.
T Consensus       717 i~p~q~~~a~dl~~al~~~~~~~P~~l~~l~  747 (997)
T KOG0334|consen  717 ITPDQLKYAGDLCKALELSKQPVPKLLQALS  747 (997)
T ss_pred             eChHHhhhHHHHHHHHHhccCCCchHHHHHH
Confidence            9998888888899999999999998877654

>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=99.76  E-value=3.9e-18  Score=110.46  Aligned_cols=79  Identities=54%  Similarity=0.844  Sum_probs=74.9

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      +..+.++||++++.+|..+++.|+++...||++|+++++|+|+|.+++||.+++|++...|.|++||++|.|+.|.+++
T Consensus        52 ~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~  130 (131)
T cd00079          52 GIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAIL  130 (131)
T ss_pred             CCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcChhhcCcChhhCCEEEEeCCCCCHHHheecccccccCCCCceEEe
Confidence            5678899999999999999999999999999999999999999999999999999999999999999999998877664

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.75  E-value=1.5e-17  Score=133.26  Aligned_cols=110  Identities=20%  Similarity=0.310  Sum_probs=92.7

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEec-----CCCCHHHHHHHhhhcCCCCCCc
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYD-----MPGNIEMYTHRIGRTGRAGKTG   76 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d-----~p~~~~~~~qr~GR~gR~~~~g   76 (135)
                      |+.+..+||++++.+|.++++.|+.|++.|||||+.+++|+|+|++++|+++|     .|.+..+|+||+||+||. ..|
T Consensus       466 gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~L~rGfDiP~v~lVvi~DadifG~p~~~~~~iqriGRagR~-~~G  544 (655)
T TIGR00631       466 GIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNG  544 (655)
T ss_pred             ccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcChhcCCeeeCCCcEEEEeCcccccCCCCHHHHHHHhcCCCCC-CCC
Confidence            78899999999999999999999999999999999999999999999999998     799999999999999998 589


Q ss_pred             eEEEEeecCChhHHHHHH---------HHHhhCCCCCChHHHHHH
Q 037139           77 VATTFLTFHDTDVFYDLK---------QMLIQSNSPVPPELAKHE  112 (135)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~l~~~~  112 (135)
                      .+++++...+......+.         ..++......|+.+.+..
T Consensus       545 ~vi~~~~~~~~~~~~ai~~~~~~~~iq~~~~~~~~~~p~~~~~~~  589 (655)
T TIGR00631       545 KVIMYADKITDSMQKAIEETERRRKIQMAYNEEHGITPQTIRKPI  589 (655)
T ss_pred             EEEEEEcCCCHHHHHHHHHHHhHHHHHhhhhhhcCCCCcccCcch
Confidence            999999876554433333         344455566666665443

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

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.73  E-value=3.6e-18  Score=139.39  Aligned_cols=84  Identities=23%  Similarity=0.313  Sum_probs=77.2

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCC------------------CHHHHH
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPG------------------NIEMYT   63 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~------------------~~~~~~   63 (135)
                      ++.+..+||+|++++|.++++.|++|+.+|||||+++++|+|+|+|++||+++.|.                  |..+|.
T Consensus       236 ~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATnIAErgItIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~  315 (819)
T TIGR01970       236 DVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQASAT  315 (819)
T ss_pred             CcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecchHhhcccccCceEEEEcCcccccccccccCCceeeEEEECHHHHH
Confidence            57899999999999999999999999999999999999999999999999999875                  245689


Q ss_pred             HHhhhcCCCCCCceEEEEeecCC
Q 037139           64 HRIGRTGRAGKTGVATTFLTFHD   86 (135)
Q Consensus        64 qr~GR~gR~~~~g~~~~~~~~~~   86 (135)
                      ||+||+||. .+|.|+.+++..+
T Consensus       316 QR~GRAGR~-~~G~cyrL~t~~~  337 (819)
T TIGR01970       316 QRAGRAGRL-EPGVCYRLWSEEQ  337 (819)
T ss_pred             hhhhhcCCC-CCCEEEEeCCHHH
Confidence            999999999 7999999998654

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.

>KOG4284 consensus DEAD box protein [Transcription]

Probab=99.73  E-value=1.4e-17  Score=130.35  Aligned_cols=87  Identities=41%  Similarity=0.645  Sum_probs=83.4

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      .|+.|.++.|.|++.+|..++++++.-..+|||+||+.++|+|-+++++|||.|+|.+-.+|.||+|||||.|..|.+++
T Consensus       295 sG~d~~~ISgaM~Q~~Rl~a~~~lr~f~~rILVsTDLtaRGIDa~~vNLVVNiD~p~d~eTY~HRIGRAgRFG~~G~aVT  374 (980)
T KOG4284|consen  295 SGLDVTFISGAMSQKDRLLAVDQLRAFRVRILVSTDLTARGIDADNVNLVVNIDAPADEETYFHRIGRAGRFGAHGAAVT  374 (980)
T ss_pred             cCCCeEEeccccchhHHHHHHHHhhhceEEEEEecchhhccCCccccceEEecCCCcchHHHHHHhhhcccccccceeEE
Confidence            38999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCCh
Q 037139           81 FLTFHDT   87 (135)
Q Consensus        81 ~~~~~~~   87 (135)
                      ++.....
T Consensus       375 ~~~~~~e  381 (980)
T KOG4284|consen  375 LLEDERE  381 (980)
T ss_pred             Eeccchh
Confidence            9987644

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=99.73  E-value=6.3e-18  Score=127.31  Aligned_cols=100  Identities=30%  Similarity=0.532  Sum_probs=90.2

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCC-----------------------------------Cccccccc
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDV-----------------------------------AGRGIDIP   45 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~-----------------------------------~~~G~d~~   45 (135)
                      +|++..+++|.|+...|.-++++|+.|-++|+||||.                                   .++|+||.
T Consensus       291 FGiksciLNseLP~NSR~Hii~QFNkG~YdivIAtD~s~~~~~~eee~kgk~~e~~~kndkkskkK~D~E~GVsRGIDF~  370 (569)
T KOG0346|consen  291 FGIKSCILNSELPANSRCHIIEQFNKGLYDIVIATDDSADGDKLEEEVKGKSDEKNPKNDKKSKKKLDKESGVSRGIDFH  370 (569)
T ss_pred             hCcHhhhhcccccccchhhHHHHhhCcceeEEEEccCccchhhhhccccccccccCCCCccccccccCchhchhccccch
Confidence            4788889999999999999999999999999999992                                   23899999


Q ss_pred             CCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEEeecCChhHHHHHHHHHhhC
Q 037139           46 DVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQS  100 (135)
Q Consensus        46 ~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~~~~~~~~~~~~~~~~~~~~  100 (135)
                      +|.+|+|||+|.+...|+||+||++|.+++|.+++|+.+.+..-...++..+...
T Consensus       371 ~V~~VlNFD~P~t~~sYIHRvGRTaRg~n~GtalSfv~P~e~~g~~~le~~~~d~  425 (569)
T KOG0346|consen  371 HVSNVLNFDFPETVTSYIHRVGRTARGNNKGTALSFVSPKEEFGKESLESILKDE  425 (569)
T ss_pred             heeeeeecCCCCchHHHHHhccccccCCCCCceEEEecchHHhhhhHHHHHHhhH
Confidence            9999999999999999999999999999999999999998887666666666543

>PRK00254 ski2-like helicase; Provisional

Probab=99.72  E-value=1.5e-17  Score=134.99  Aligned_cols=84  Identities=24%  Similarity=0.371  Sum_probs=73.7

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEE-------ecCCC-CHHHHHHHhhhcCCCC-
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVIN-------YDMPG-NIEMYTHRIGRTGRAG-   73 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~-------~d~p~-~~~~~~qr~GR~gR~~-   73 (135)
                      ..|.+|||+|++++|..+++.|++|.++|||||+++++|+|+|.+++||.       ++.|. +..+|.||+|||||.| 
T Consensus       296 ~gv~~hHagl~~~eR~~ve~~F~~G~i~VLvaT~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR~~~  375 (720)
T PRK00254        296 GGVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGRPKY  375 (720)
T ss_pred             hCEEEeCCCCCHHHHHHHHHHHHCCCCeEEEeCcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhhccCCCCc
Confidence            46899999999999999999999999999999999999999999999983       44443 5779999999999965 


Q ss_pred             -CCceEEEEeecCC
Q 037139           74 -KTGVATTFLTFHD   86 (135)
Q Consensus        74 -~~g~~~~~~~~~~   86 (135)
                       ..|.+++++...+
T Consensus       376 d~~G~~ii~~~~~~  389 (720)
T PRK00254        376 DEVGEAIIVATTEE  389 (720)
T ss_pred             CCCceEEEEecCcc
Confidence             5689999987654

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

Probab=99.72  E-value=1.2e-17  Score=136.91  Aligned_cols=89  Identities=31%  Similarity=0.537  Sum_probs=84.3

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+++..||+||++.+|..+.++|..++++|++||=++++|+|.|+|+.||+|.+|++.+.|.|-+|||||.|....|++|
T Consensus       509 ~~~a~~YHAGl~~~~R~~Vq~~w~~~~~~VivATVAFGMGIdK~DVR~ViH~~lPks~E~YYQE~GRAGRDG~~s~C~l~  588 (941)
T KOG0351|consen  509 GKSAAFYHAGLPPKERETVQKAWMSDKIRVIVATVAFGMGIDKPDVRFVIHYSLPKSFEGYYQEAGRAGRDGLPSSCVLL  588 (941)
T ss_pred             chhhHhhhcCCCHHHHHHHHHHHhcCCCeEEEEEeeccCCCCCCceeEEEECCCchhHHHHHHhccccCcCCCcceeEEe
Confidence            56788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHH
Q 037139           82 LTFHDTDVF   90 (135)
Q Consensus        82 ~~~~~~~~~   90 (135)
                      +...+...+
T Consensus       589 y~~~D~~~l  597 (941)
T KOG0351|consen  589 YGYADISEL  597 (941)
T ss_pred             cchhHHHHH
Confidence            998865444

>PRK01172 ski2-like helicase; Provisional

Probab=99.71  E-value=3.8e-17  Score=131.79  Aligned_cols=96  Identities=27%  Similarity=0.337  Sum_probs=76.0

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEec---------CCCCHHHHHHHhhhcCCCC
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYD---------MPGNIEMYTHRIGRTGRAG   73 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d---------~p~~~~~~~qr~GR~gR~~   73 (135)
                      ..+.++||+|++++|..+++.|++|.++|||||+++++|+|+|...+|| .|         .|.+..+|.||+|||||.|
T Consensus       286 ~gv~~~hagl~~~eR~~ve~~f~~g~i~VLvaT~~la~Gvnipa~~VII-~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g  364 (674)
T PRK01172        286 HGVAFHHAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIV-RDITRYGNGGIRYLSNMEIKQMIGRAGRPG  364 (674)
T ss_pred             cCEEEecCCCCHHHHHHHHHHHHcCCCeEEEecchhhccCCCcceEEEE-cCceEeCCCCceeCCHHHHHHHhhcCCCCC
Confidence            3588999999999999999999999999999999999999999865444 33         3568899999999999987


Q ss_pred             C--CceEEEEeecCChhHHHHHHHHHhhCC
Q 037139           74 K--TGVATTFLTFHDTDVFYDLKQMLIQSN  101 (135)
Q Consensus        74 ~--~g~~~~~~~~~~~~~~~~~~~~~~~~~  101 (135)
                      .  .|.+++++...+  .....++++....
T Consensus       365 ~d~~g~~~i~~~~~~--~~~~~~~~l~~~~  392 (674)
T PRK01172        365 YDQYGIGYIYAASPA--SYDAAKKYLSGEP  392 (674)
T ss_pred             CCCcceEEEEecCcc--cHHHHHHHHcCCC
Confidence            4  566777765432  2234556664443

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.70  E-value=4.2e-17  Score=130.78  Aligned_cols=83  Identities=24%  Similarity=0.370  Sum_probs=74.2

Q ss_pred             CceEEEecCCCCHHHHHHHHHHH-hcCCCcEEEecCCCcccccccCCcEEEEec---CCC---------CHHHHHHHhhh
Q 037139            2 GYRVTTLHGGKSQEQREISLEGF-RTKRYNVLVATDVAGRGIDIPDVAHVINYD---MPG---------NIEMYTHRIGR   68 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f-~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d---~p~---------~~~~~~qr~GR   68 (135)
                      |+.+.++||+|++.  ++++++| ++|+.+|||||+++++|+|+|+|++||++|   .|.         |.++|.||+||
T Consensus       421 ~~~v~~LHG~Lsq~--eq~l~~ff~~gk~kILVATdIAERGIDIp~V~~VID~G~~k~p~~~~g~~~~iSkasa~QRaGR  498 (675)
T PHA02653        421 IYDFYIIHGKVPNI--DEILEKVYSSKNPSIIISTPYLESSVTIRNATHVYDTGRVYVPEPFGGKEMFISKSMRTQRKGR  498 (675)
T ss_pred             CceEEeccCCcCHH--HHHHHHHhccCceeEEeccChhhccccccCeeEEEECCCccCCCcccCcccccCHHHHHHhccC
Confidence            57899999999985  5677777 789999999999999999999999999998   565         88899999999


Q ss_pred             cCCCCCCceEEEEeecCCh
Q 037139           69 TGRAGKTGVATTFLTFHDT   87 (135)
Q Consensus        69 ~gR~~~~g~~~~~~~~~~~   87 (135)
                      +||. ++|.|+.+++..+.
T Consensus       499 AGR~-~~G~c~rLyt~~~~  516 (675)
T PHA02653        499 VGRV-SPGTYVYFYDLDLL  516 (675)
T ss_pred             cCCC-CCCeEEEEECHHHh
Confidence            9999 78999999987653

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

Probab=99.69  E-value=1.2e-16  Score=127.28  Aligned_cols=76  Identities=37%  Similarity=0.484  Sum_probs=69.2

Q ss_pred             CCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEEeecCCh
Q 037139           10 GGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDT   87 (135)
Q Consensus        10 g~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~~~~~~~   87 (135)
                      .+|+++++++++++|++|+++|||||+++++|+|++.|++||.||.-.++...+||.|| ||.. .|.++++++..+.
T Consensus       456 ~gmtqk~Q~evl~~Fr~G~~NvLVATSV~EEGLDI~ec~lVIcYd~~snpIrmIQrrGR-gRa~-ns~~vll~t~~~~  531 (746)
T KOG0354|consen  456 TGMTQKEQKEVLDKFRDGEINVLVATSVAEEGLDIGECNLVICYDYSSNPIRMVQRRGR-GRAR-NSKCVLLTTGSEV  531 (746)
T ss_pred             cccCHHHHHHHHHHHhCCCccEEEEecchhccCCcccccEEEEecCCccHHHHHHHhcc-cccc-CCeEEEEEcchhH
Confidence            47999999999999999999999999999999999999999999999999999999999 8874 5677777774433

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.69  E-value=9e-17  Score=130.12  Aligned_cols=85  Identities=29%  Similarity=0.417  Sum_probs=78.1

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccc---cCCc-----EEEEecCCCCHHHHHHHhhhcCCC
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDI---PDVA-----HVINYDMPGNIEMYTHRIGRTGRA   72 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~---~~v~-----~vi~~d~p~~~~~~~qr~GR~gR~   72 (135)
                      .|+++..+||++.++++..+..+++.|  +|+|||++++||+|+   |.|.     +||++|+|.+...|.||+||+||.
T Consensus       451 ~gi~~~~L~~~~~~~e~~~i~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~GGL~VI~~d~p~s~r~y~qr~GRtGR~  528 (790)
T PRK09200        451 AGIPHNLLNAKNAAKEAQIIAEAGQKG--AVTVATNMAGRGTDIKLGEGVHELGGLAVIGTERMESRRVDLQLRGRSGRQ  528 (790)
T ss_pred             CCCCEEEecCCccHHHHHHHHHcCCCC--eEEEEccchhcCcCCCcccccccccCcEEEeccCCCCHHHHHHhhccccCC
Confidence            378999999999999988888888776  799999999999999   6898     999999999999999999999999


Q ss_pred             CCCceEEEEeecCCh
Q 037139           73 GKTGVATTFLTFHDT   87 (135)
Q Consensus        73 ~~~g~~~~~~~~~~~   87 (135)
                      |.+|.++.+++..+.
T Consensus       529 G~~G~s~~~is~eD~  543 (790)
T PRK09200        529 GDPGSSQFFISLEDD  543 (790)
T ss_pred             CCCeeEEEEEcchHH
Confidence            999999999987554

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

Probab=99.68  E-value=3e-16  Score=123.70  Aligned_cols=99  Identities=18%  Similarity=0.326  Sum_probs=85.1

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCC-CHHHHHHHhhhcCCCCCCceEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPG-NIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~-~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      ++++..+||.|+++++.+++++|++|+++|||||.+++.|+|+|+.+++|..|.-. ..+++.|..||+||.+..++|++
T Consensus       507 ~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILVaTTVIEVGVdVPnATvMVIe~AERFGLaQLHQLRGRVGRG~~qSyC~L  586 (677)
T COG1200         507 ELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGDLQSYCVL  586 (677)
T ss_pred             cceeEEEecCCChHHHHHHHHHHHcCCCcEEEEeeEEEecccCCCCeEEEEechhhhhHHHHHHhccccCCCCcceEEEE
Confidence            46799999999999999999999999999999999999999999999999888654 78999999999999999999999


Q ss_pred             EeecCChhHHHHHHHHHhhC
Q 037139           81 FLTFHDTDVFYDLKQMLIQS  100 (135)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~  100 (135)
                      ++.+.....-+.--+.+...
T Consensus       587 l~~~~~~~~a~~RL~im~~t  606 (677)
T COG1200         587 LYKPPLSEVAKQRLKIMRET  606 (677)
T ss_pred             EeCCCCChhHHHHHHHHHhc
Confidence            99987743333333334443

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.68  E-value=4e-17  Score=133.37  Aligned_cols=85  Identities=20%  Similarity=0.319  Sum_probs=76.8

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCC------------------CHHHHH
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPG------------------NIEMYT   63 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~------------------~~~~~~   63 (135)
                      ++.+..+||+|++++|.++++.|++|+.+|||||+++++|+|+|+|++||+++.+.                  |..+|.
T Consensus       239 ~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~  318 (812)
T PRK11664        239 DVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMT  318 (812)
T ss_pred             CceEEEeeCCCCHHHHHHHhccccCCCeEEEEecchHHhcccccCceEEEECCCcccccccccCCcceeEEEeechhhhh
Confidence            56789999999999999999999999999999999999999999999999988764                  346899


Q ss_pred             HHhhhcCCCCCCceEEEEeecCCh
Q 037139           64 HRIGRTGRAGKTGVATTFLTFHDT   87 (135)
Q Consensus        64 qr~GR~gR~~~~g~~~~~~~~~~~   87 (135)
                      ||+||+||. .+|.|+.+++..+.
T Consensus       319 QR~GRaGR~-~~G~cyrL~t~~~~  341 (812)
T PRK11664        319 QRAGRAGRL-EPGICLHLYSKEQA  341 (812)
T ss_pred             hhccccCCC-CCcEEEEecCHHHH
Confidence            999999999 69999999986533

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.68  E-value=1.8e-16  Score=126.13  Aligned_cols=85  Identities=32%  Similarity=0.457  Sum_probs=73.4

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCccccccc---CCc-----EEEEecCCCCHHHHHHHhhhcCCC
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIP---DVA-----HVINYDMPGNIEMYTHRIGRTGRA   72 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~---~v~-----~vi~~d~p~~~~~~~qr~GR~gR~   72 (135)
                      .|+++..+||+++.+  +..+..|+.++.+|+|||+++++|+|++   +|.     +||++|.|.+...|.||+||+||.
T Consensus       496 ~gi~~~~Lhg~~~~r--E~~ii~~ag~~g~VlVATdmAgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~y~hr~GRTGRq  573 (656)
T PRK12898        496 AGLPHQVLNAKQDAE--EAAIVARAGQRGRITVATNMAGRGTDIKLEPGVAARGGLHVILTERHDSARIDRQLAGRCGRQ  573 (656)
T ss_pred             CCCCEEEeeCCcHHH--HHHHHHHcCCCCcEEEEccchhcccCcCCccchhhcCCCEEEEcCCCCCHHHHHHhcccccCC
Confidence            378999999997644  4555556666668999999999999999   665     999999999999999999999999


Q ss_pred             CCCceEEEEeecCCh
Q 037139           73 GKTGVATTFLTFHDT   87 (135)
Q Consensus        73 ~~~g~~~~~~~~~~~   87 (135)
                      |.+|.++.+++..|.
T Consensus       574 G~~G~s~~~is~eD~  588 (656)
T PRK12898        574 GDPGSYEAILSLEDD  588 (656)
T ss_pred             CCCeEEEEEechhHH
Confidence            999999999987554

>PRK13766 Hef nuclease; Provisional

Probab=99.67  E-value=8e-16  Score=125.74  Aligned_cols=84  Identities=35%  Similarity=0.485  Sum_probs=75.9

Q ss_pred             CceEEEecCC--------CCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCC
Q 037139            2 GYRVTTLHGG--------KSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAG   73 (135)
Q Consensus         2 g~~v~~~hg~--------~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~   73 (135)
                      |+.+..+||.        |++.+|..++++|++|++++||||+++++|+|+|.+++||+||+|++...|+||+||+||.+
T Consensus       389 ~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~g~~~vLvaT~~~~eGldi~~~~~VI~yd~~~s~~r~iQR~GR~gR~~  468 (773)
T PRK13766        389 GIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGRQE  468 (773)
T ss_pred             CCceEEEEccccccccCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccCcCC
Confidence            5667777775        99999999999999999999999999999999999999999999999999999999999986


Q ss_pred             CCceEEEEeecCC
Q 037139           74 KTGVATTFLTFHD   86 (135)
Q Consensus        74 ~~g~~~~~~~~~~   86 (135)
                       +|.++.++....
T Consensus       469 -~~~v~~l~~~~t  480 (773)
T PRK13766        469 -EGRVVVLIAKGT  480 (773)
T ss_pred             -CCEEEEEEeCCC
Confidence             477888877553

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.66  E-value=4.3e-16  Score=122.01  Aligned_cols=74  Identities=23%  Similarity=0.196  Sum_probs=70.0

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEec-CCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCC
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVAT-DVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKT   75 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T-~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~   75 (135)
                      |.++..+||+|+.++|..+++.|++|+..||||| +++++|+|+|++++||+++++.+...|+||+||++|.+..
T Consensus       368 g~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLvaT~~~l~eG~Dip~ld~vIl~~p~~s~~~~~QriGR~~R~~~~  442 (501)
T PHA02558        368 YDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYGVFSTGISIKNLHHVIFAHPSKSKIIVLQSIGRVLRKHGS  442 (501)
T ss_pred             CCCEEEEeCCCCHHHHHHHHHHHhCCCCeEEEEEcceeccccccccccEEEEecCCcchhhhhhhhhccccCCCC
Confidence            6789999999999999999999999999999998 8999999999999999999999999999999999997644

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.65  E-value=2.7e-16  Score=118.21  Aligned_cols=81  Identities=25%  Similarity=0.312  Sum_probs=68.2

Q ss_pred             eEEEecCCCCHHHHHH----HHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCC----
Q 037139            4 RVTTLHGGKSQEQREI----SLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKT----   75 (135)
Q Consensus         4 ~v~~~hg~~~~~~r~~----~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~----   75 (135)
                      .+..+||+|++.+|.+    +++.|++|+..|||||+++++|+|++ ++++|+++.|  .++|+||+||+||.|..    
T Consensus       250 ~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~~~~~GiDi~-~~~vi~~~~~--~~~~iqr~GR~gR~g~~~~~~  326 (358)
T TIGR01587       250 EIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDIS-ADVMITELAP--IDSLIQRLGRLHRYGRKNGEN  326 (358)
T ss_pred             eEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECcchhceeccC-CCEEEEcCCC--HHHHHHHhccccCCCCCCCCC
Confidence            5889999999999976    48999999999999999999999996 7888888766  78999999999998743    


Q ss_pred             ceEEEEeecCCh
Q 037139           76 GVATTFLTFHDT   87 (135)
Q Consensus        76 g~~~~~~~~~~~   87 (135)
                      |.++++....+.
T Consensus       327 ~~~~v~~~~~~~  338 (358)
T TIGR01587       327 FEVYIITIAPEG  338 (358)
T ss_pred             CeEEEEeecCCC
Confidence            366666654433

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.

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.64  E-value=1.8e-15  Score=121.76  Aligned_cols=85  Identities=22%  Similarity=0.358  Sum_probs=74.5

Q ss_pred             EEEecCCCCHHHHHHHHHHHhcC-CCcEEEecCCCcccccccCCcEEEEecCC-CCHHHHHHHhhhcCCCCCCc------
Q 037139            5 VTTLHGGKSQEQREISLEGFRTK-RYNVLVATDVAGRGIDIPDVAHVINYDMP-GNIEMYTHRIGRTGRAGKTG------   76 (135)
Q Consensus         5 v~~~hg~~~~~~r~~~~~~f~~g-~~~ilv~T~~~~~G~d~~~v~~vi~~d~p-~~~~~~~qr~GR~gR~~~~g------   76 (135)
                      +..+||++++.+|++++++|+.| ++++||+|+++.+|+|+|++++||+++.| .+...|+||+||++|.+..+      
T Consensus       518 ~~~I~G~ts~~ER~~il~~Fr~~~~i~vLv~SkVgdeGIDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~~  597 (732)
T TIGR00603       518 KPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYN  597 (732)
T ss_pred             CceEECCCCHHHHHHHHHHHHhCCCccEEEEecccccccCCCCCCEEEEeCCCCCCHHHHHHHhcccccCCCCCcccccc
Confidence            46789999999999999999875 88999999999999999999999999998 49999999999999976443      


Q ss_pred             -eEEEEeecCChhH
Q 037139           77 -VATTFLTFHDTDV   89 (135)
Q Consensus        77 -~~~~~~~~~~~~~   89 (135)
                       ..+.+++.+..+.
T Consensus       598 A~fY~lVs~dT~E~  611 (732)
T TIGR00603       598 AFFYSLVSKDTQEM  611 (732)
T ss_pred             ceEEEEecCCchHH
Confidence             4488888765544

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).

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

Probab=99.63  E-value=6.4e-16  Score=116.55  Aligned_cols=92  Identities=27%  Similarity=0.429  Sum_probs=86.5

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      .|+.+..+|+|+...+|.++.++|.++++.|+++|..+++|+|-|+|++||++|+|.+..-|.|-.|||||.|.+++|-+
T Consensus       278 ~Gi~A~AYHAGLK~~ERTeVQe~WM~~~~PvI~AT~SFGMGVDKp~VRFViHW~~~qn~AgYYQESGRAGRDGk~SyCRL  357 (641)
T KOG0352|consen  278 AGIPAMAYHAGLKKKERTEVQEKWMNNEIPVIAATVSFGMGVDKPDVRFVIHWSPSQNLAGYYQESGRAGRDGKRSYCRL  357 (641)
T ss_pred             cCcchHHHhcccccchhHHHHHHHhcCCCCEEEEEeccccccCCcceeEEEecCchhhhHHHHHhccccccCCCccceee
Confidence            37788889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHHHH
Q 037139           81 FLTFHDTDVFYD   92 (135)
Q Consensus        81 ~~~~~~~~~~~~   92 (135)
                      ++...+.+.++-
T Consensus       358 YYsR~D~~~i~F  369 (641)
T KOG0352|consen  358 YYSRQDKNALNF  369 (641)
T ss_pred             eecccchHHHHH
Confidence            999887765543

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

Probab=99.61  E-value=1.2e-15  Score=115.45  Aligned_cols=83  Identities=37%  Similarity=0.702  Sum_probs=77.8

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      .+++.|+||+..|.+|++.++.|+.++++.|||||++++|+|+..+.++||.-+|.+..+|++|+||+||..+-|.+|++
T Consensus       532 ~~scvclhgDrkP~Erk~nle~Fkk~dvkflictdvaargldi~g~p~~invtlpd~k~nyvhrigrvgraermglaisl  611 (725)
T KOG0349|consen  532 HYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITGLPFMINVTLPDDKTNYVHRIGRVGRAERMGLAISL  611 (725)
T ss_pred             cceeEEEecCCChhHHHHHHHhhhhcCeEEEEEehhhhccccccCCceEEEEecCcccchhhhhhhccchhhhcceeEEE
Confidence            47899999999999999999999999999999999999999999999999999999999999999999998777778777


Q ss_pred             eec
Q 037139           82 LTF   84 (135)
Q Consensus        82 ~~~   84 (135)
                      +..
T Consensus       612 vat  614 (725)
T KOG0349|consen  612 VAT  614 (725)
T ss_pred             eec
Confidence            653

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

Probab=99.60  E-value=5.5e-15  Score=119.75  Aligned_cols=82  Identities=28%  Similarity=0.380  Sum_probs=75.5

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCC-CCCCceEEEE
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGR-AGKTGVATTF   81 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR-~~~~g~~~~~   81 (135)
                      ..+..|||+++.+.|..+.++|++|+++.+|||+.++.|+|+.++++||+++.|.++..+.||+||+|+ .+....++++
T Consensus       279 ~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TSSLELGIDiG~vdlVIq~~SP~sV~r~lQRiGRsgHr~~~~Skg~ii  358 (814)
T COG1201         279 DIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKGIII  358 (814)
T ss_pred             CceeeecccccHHHHHHHHHHHhcCCceEEEEccchhhccccCCceEEEEeCCcHHHHHHhHhccccccccCCcccEEEE
Confidence            568899999999999999999999999999999999999999999999999999999999999999996 5555677776


Q ss_pred             eec
Q 037139           82 LTF   84 (135)
Q Consensus        82 ~~~   84 (135)
                      ...
T Consensus       359 ~~~  361 (814)
T COG1201         359 AED  361 (814)
T ss_pred             ecC
Confidence            665

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.60  E-value=3.3e-15  Score=120.44  Aligned_cols=84  Identities=29%  Similarity=0.377  Sum_probs=75.8

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCccccccc---------CCcEEEEecCCCCHHHHHHHhhhcCC
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIP---------DVAHVINYDMPGNIEMYTHRIGRTGR   71 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~---------~v~~vi~~d~p~~~~~~~qr~GR~gR   71 (135)
                      .|+++..+||.+.++++..+.++++.|  .|+|||++++||+|++         .+.+|+++++|..... .||+||+||
T Consensus       447 ~gi~~~~L~a~~~~~E~~ii~~ag~~g--~VlIATdmAgRGtDI~l~~~v~~~GGL~vIit~~~ps~rid-~qr~GRtGR  523 (762)
T TIGR03714       447 EGIPHNLLNAQNAAKEAQIIAEAGQKG--AVTVATSMAGRGTDIKLGKGVAELGGLAVIGTERMENSRVD-LQLRGRSGR  523 (762)
T ss_pred             CCCCEEEecCCChHHHHHHHHHcCCCC--eEEEEccccccccCCCCCccccccCCeEEEEecCCCCcHHH-HHhhhcccC
Confidence            378899999999999988888877777  7999999999999999         8899999999988766 999999999


Q ss_pred             CCCCceEEEEeecCCh
Q 037139           72 AGKTGVATTFLTFHDT   87 (135)
Q Consensus        72 ~~~~g~~~~~~~~~~~   87 (135)
                      .|.+|.++.+++..+.
T Consensus       524 qG~~G~s~~~is~eD~  539 (762)
T TIGR03714       524 QGDPGSSQFFVSLEDD  539 (762)
T ss_pred             CCCceeEEEEEccchh
Confidence            9999999999987654

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.

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.58  E-value=1.1e-14  Score=117.08  Aligned_cols=85  Identities=28%  Similarity=0.397  Sum_probs=79.2

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccC-------CcEEEEecCCCCHHHHHHHhhhcCCCC
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPD-------VAHVINYDMPGNIEMYTHRIGRTGRAG   73 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~-------v~~vi~~d~p~~~~~~~qr~GR~gR~~   73 (135)
                      .|++...+|++  +.+|+..+.+|+.+..+|+|||++++||+|++.       .-+||+++.|.+...|.|+.||+||.|
T Consensus       428 ~gi~~~~Lna~--q~~rEa~ii~~ag~~g~VtIATnmAgRGtDI~l~~V~~~GGl~VI~t~~p~s~ri~~q~~GRtGRqG  505 (745)
T TIGR00963       428 RGIPHNVLNAK--NHEREAEIIAQAGRKGAVTIATNMAGRGTDIKLEEVKELGGLYVIGTERHESRRIDNQLRGRSGRQG  505 (745)
T ss_pred             cCCCeEEeeCC--hHHHHHHHHHhcCCCceEEEEeccccCCcCCCccchhhcCCcEEEecCCCCcHHHHHHHhccccCCC
Confidence            37888999998  889999999999999999999999999999998       459999999999999999999999999


Q ss_pred             CCceEEEEeecCCh
Q 037139           74 KTGVATTFLTFHDT   87 (135)
Q Consensus        74 ~~g~~~~~~~~~~~   87 (135)
                      .+|.+..+++..+.
T Consensus       506 ~~G~s~~~ls~eD~  519 (745)
T TIGR00963       506 DPGSSRFFLSLEDN  519 (745)
T ss_pred             CCcceEEEEeccHH
Confidence            99999999988755

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.

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.54  E-value=6.9e-15  Score=123.69  Aligned_cols=80  Identities=21%  Similarity=0.369  Sum_probs=71.1

Q ss_pred             eEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEec---------------CC---CCHHHHHHH
Q 037139            4 RVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYD---------------MP---GNIEMYTHR   65 (135)
Q Consensus         4 ~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d---------------~p---~~~~~~~qr   65 (135)
                      .+..+||+|++++|..+++.  .|..+|||||+++++|+|+|+|++||+++               +|   .|..+|.||
T Consensus       315 ~VlpLhg~Ls~~eQ~~Vf~~--~g~rkIIVATNIAEtSITIpgI~yVID~Gl~k~~~Yd~~~~~~~Lp~~~iSkasa~QR  392 (1294)
T PRK11131        315 EILPLYARLSNSEQNRVFQS--HSGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLPIEPISQASANQR  392 (1294)
T ss_pred             eEeecccCCCHHHHHHHhcc--cCCeeEEEeccHHhhccccCcceEEEECCCccccccccccCcccCCeeecCHhhHhhh
Confidence            47789999999999999986  57899999999999999999999999986               33   466899999


Q ss_pred             hhhcCCCCCCceEEEEeecCC
Q 037139           66 IGRTGRAGKTGVATTFLTFHD   86 (135)
Q Consensus        66 ~GR~gR~~~~g~~~~~~~~~~   86 (135)
                      +||+||. .+|.|+.+++..+
T Consensus       393 aGRAGR~-~~G~c~rLyte~d  412 (1294)
T PRK11131        393 KGRCGRV-SEGICIRLYSEDD  412 (1294)
T ss_pred             ccccCCC-CCcEEEEeCCHHH
Confidence            9999999 6899999998654

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.54  E-value=2.3e-14  Score=115.94  Aligned_cols=85  Identities=28%  Similarity=0.440  Sum_probs=77.6

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCccccccc---CCc-----EEEEecCCCCHHHHHHHhhhcCCC
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIP---DVA-----HVINYDMPGNIEMYTHRIGRTGRA   72 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~---~v~-----~vi~~d~p~~~~~~~qr~GR~gR~   72 (135)
                      .|+++..+|+++..+++..+.++++.|.  |+|||++++||+|++   +|.     +||+++.|.+...|.|+.||+||.
T Consensus       463 ~gi~~~~Lna~~~~~Ea~ii~~ag~~g~--VtIATnmAGRGtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~GRtGRq  540 (796)
T PRK12906        463 AGIPHAVLNAKNHAKEAEIIMNAGQRGA--VTIATNMAGRGTDIKLGPGVKELGGLAVIGTERHESRRIDNQLRGRSGRQ  540 (796)
T ss_pred             CCCCeeEecCCcHHHHHHHHHhcCCCce--EEEEeccccCCCCCCCCcchhhhCCcEEEeeecCCcHHHHHHHhhhhccC
Confidence            3788999999999888888888888876  999999999999994   788     999999999999999999999999


Q ss_pred             CCCceEEEEeecCCh
Q 037139           73 GKTGVATTFLTFHDT   87 (135)
Q Consensus        73 ~~~g~~~~~~~~~~~   87 (135)
                      |.+|.+..+++..|.
T Consensus       541 G~~G~s~~~~sleD~  555 (796)
T PRK12906        541 GDPGSSRFYLSLEDD  555 (796)
T ss_pred             CCCcceEEEEeccch
Confidence            999999999987754

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.51  E-value=2e-14  Score=121.17  Aligned_cols=83  Identities=19%  Similarity=0.297  Sum_probs=71.5

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCC------------------CCHHHHH
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMP------------------GNIEMYT   63 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p------------------~~~~~~~   63 (135)
                      ++.+..+||+|++++|.++++.+  +..+|+|||++++.|+++|+|.+||+++.+                  .|..+|.
T Consensus       306 ~~~VlpLhg~Ls~~eQ~~vf~~~--~~rkIVLATNIAEtSLTIpgV~yVIDsGl~r~~~yd~~~~~~~L~~~~ISkasa~  383 (1283)
T TIGR01967       306 HTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASAN  383 (1283)
T ss_pred             CcEEEeccCCCCHHHHHHHhCCC--CCceEEEeccHHHhccccCCeeEEEeCCCccccccccccCccccCCccCCHHHHH
Confidence            35688999999999999997654  346899999999999999999999998843                  3668999


Q ss_pred             HHhhhcCCCCCCceEEEEeecCCh
Q 037139           64 HRIGRTGRAGKTGVATTFLTFHDT   87 (135)
Q Consensus        64 qr~GR~gR~~~~g~~~~~~~~~~~   87 (135)
                      ||+||+||.+ +|.|+.+++..+.
T Consensus       384 QRaGRAGR~~-~G~cyRLyte~~~  406 (1283)
T TIGR01967       384 QRKGRCGRVA-PGICIRLYSEEDF  406 (1283)
T ss_pred             HHhhhhCCCC-CceEEEecCHHHH
Confidence            9999999997 9999999986543

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.

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

Probab=99.51  E-value=5.1e-15  Score=111.25  Aligned_cols=100  Identities=38%  Similarity=0.623  Sum_probs=93.3

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..++|.|++..|...+.+|+.++..+||.|+++++|+|+|-.+.|||||.|.+...|++|+||+.|.|+.|++|.+
T Consensus       285 g~~~s~iysslD~~aRk~~~~~F~~~k~~~lvvTdvaaRG~diplldnvinyd~p~~~klFvhRVgr~aragrtg~aYs~  364 (529)
T KOG0337|consen  285 GGEGSDIYSSLDQEARKINGRDFRGRKTSILVVTDVAARGLDIPLLDNVINYDFPPDDKLFVHRVGRVARAGRTGRAYSL  364 (529)
T ss_pred             CCCccccccccChHhhhhccccccCCccceEEEehhhhccCCCccccccccccCCCCCceEEEEecchhhccccceEEEE
Confidence            67788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCC
Q 037139           82 LTFHDTDVFYDLKQMLIQSN  101 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~  101 (135)
                      +.+.+...+-.+..++....
T Consensus       365 V~~~~~~yl~DL~lflgr~~  384 (529)
T KOG0337|consen  365 VASTDDPYLLDLQLFLGRPL  384 (529)
T ss_pred             EecccchhhhhhhhhcCCce
Confidence            99998888877777766543

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

Probab=99.50  E-value=1.3e-13  Score=114.07  Aligned_cols=83  Identities=27%  Similarity=0.368  Sum_probs=76.0

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCC-CCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMP-GNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p-~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      .++.+.||.|+..+-+.++..|.+|+.+|||||.+++.|+|+|+++.+|.-+.. ...+++.|..||+||.+..++|+.+
T Consensus       830 arI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TTIIEtGIDIPnANTiIIe~AD~fGLsQLyQLRGRVGRS~~~AYAYfl  909 (1139)
T COG1197         830 ARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSNKQAYAYFL  909 (1139)
T ss_pred             eEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEeeeeecCcCCCCCceEEEeccccccHHHHHHhccccCCccceEEEEEe
Confidence            468999999999999999999999999999999999999999999998865544 3689999999999999999999999


Q ss_pred             eecC
Q 037139           82 LTFH   85 (135)
Q Consensus        82 ~~~~   85 (135)
                      +.+.
T Consensus       910 ~p~~  913 (1139)
T COG1197         910 YPPQ  913 (1139)
T ss_pred             ecCc
Confidence            9864

>TIGR00595 priA primosomal protein N'

Probab=99.49  E-value=1.5e-13  Score=107.79  Aligned_cols=84  Identities=24%  Similarity=0.414  Sum_probs=70.5

Q ss_pred             CceEEEecCCCCHHHH--HHHHHHHhcCCCcEEEecCCCcccccccCCcEEE--EecC----CC------CHHHHHHHhh
Q 037139            2 GYRVTTLHGGKSQEQR--EISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVI--NYDM----PG------NIEMYTHRIG   67 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r--~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi--~~d~----p~------~~~~~~qr~G   67 (135)
                      +.++..+|++++...+  ++++++|++|+.+|||+|+++++|+|+|+|++|+  ++|.    |.      ....|.|++|
T Consensus       284 ~~~v~~~d~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~i~kG~d~~~v~lV~vl~aD~~l~~pd~ra~E~~~~ll~q~~G  363 (505)
T TIGR00595       284 GARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAG  363 (505)
T ss_pred             CCcEEEEecccccCccHHHHHHHHHhcCCCCEEEeCcccccCCCCCcccEEEEEcCcccccCcccchHHHHHHHHHHHHh
Confidence            4678899999887766  8999999999999999999999999999999885  5553    32      2567899999


Q ss_pred             hcCCCCCCceEEEEeecC
Q 037139           68 RTGRAGKTGVATTFLTFH   85 (135)
Q Consensus        68 R~gR~~~~g~~~~~~~~~   85 (135)
                      |+||.+..|.+++.....
T Consensus       364 RagR~~~~g~viiqt~~p  381 (505)
T TIGR00595       364 RAGRAEDPGQVIIQTYNP  381 (505)
T ss_pred             ccCCCCCCCEEEEEeCCC
Confidence            999998899888665433

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).

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.49  E-value=7.5e-14  Score=113.53  Aligned_cols=80  Identities=30%  Similarity=0.475  Sum_probs=69.7

Q ss_pred             eEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEE----Eec-----CCCCHHHHHHHhhhcCCCCC
Q 037139            4 RVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVI----NYD-----MPGNIEMYTHRIGRTGRAGK   74 (135)
Q Consensus         4 ~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi----~~d-----~p~~~~~~~qr~GR~gR~~~   74 (135)
                      .+++||++|+.++|..+.+.|+.|.++||+||.++++|+|+|.-..||    .||     .+.+.-++.||.|||||.|-
T Consensus       316 GvafHhAGL~~~~R~~vE~~Fr~g~ikVlv~TpTLA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~dv~QM~GRAGRPg~  395 (766)
T COG1204         316 GVAFHHAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPGY  395 (766)
T ss_pred             CccccccCCCHHHHHHHHHHHhcCCceEEEechHHhhhcCCcceEEEEeeeEEEcCCCCeEECchhhHhhccCcCCCCCc
Confidence            478999999999999999999999999999999999999999977776    566     55678999999999999874


Q ss_pred             --CceEEEEee
Q 037139           75 --TGVATTFLT   83 (135)
Q Consensus        75 --~g~~~~~~~   83 (135)
                        .|.++++..
T Consensus       396 d~~G~~~i~~~  406 (766)
T COG1204         396 DDYGEAIILAT  406 (766)
T ss_pred             CCCCcEEEEec
Confidence              456666653

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.48  E-value=2e-13  Score=110.31  Aligned_cols=85  Identities=24%  Similarity=0.313  Sum_probs=72.0

Q ss_pred             CceEEEecCCCC--HHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEE--ecCCCC----------HHHHHHHhh
Q 037139            2 GYRVTTLHGGKS--QEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVIN--YDMPGN----------IEMYTHRIG   67 (135)
Q Consensus         2 g~~v~~~hg~~~--~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~--~d~p~~----------~~~~~qr~G   67 (135)
                      +.++..+|++++  ++++++++++|++|+++|||+|+++++|+|+|++++|+.  .|.+.+          ...|.|++|
T Consensus       452 ~~~v~~~~~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~iakG~d~p~v~lV~il~aD~~l~~pdfra~Er~~~~l~q~~G  531 (679)
T PRK05580        452 EARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDFRASERTFQLLTQVAG  531 (679)
T ss_pred             CCcEEEEeccccccchhHHHHHHHHhcCCCCEEEEChhhccCCCCCCcCEEEEEcCchhccCCccchHHHHHHHHHHHHh
Confidence            567889999986  467999999999999999999999999999999999864  454433          367899999


Q ss_pred             hcCCCCCCceEEEEeecCC
Q 037139           68 RTGRAGKTGVATTFLTFHD   86 (135)
Q Consensus        68 R~gR~~~~g~~~~~~~~~~   86 (135)
                      |+||.+..|.+++.....+
T Consensus       532 RagR~~~~g~viiqT~~p~  550 (679)
T PRK05580        532 RAGRAEKPGEVLIQTYHPE  550 (679)
T ss_pred             hccCCCCCCEEEEEeCCCC
Confidence            9999998999997765443

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

Probab=99.47  E-value=1.4e-13  Score=112.12  Aligned_cols=74  Identities=23%  Similarity=0.342  Sum_probs=62.7

Q ss_pred             EEecCCCCHHHHH-----HHHHHHhc----CC-------CcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhc
Q 037139            6 TTLHGGKSQEQRE-----ISLEGFRT----KR-------YNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRT   69 (135)
Q Consensus         6 ~~~hg~~~~~~r~-----~~~~~f~~----g~-------~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~   69 (135)
                      ..+||+|++.+|.     .++++|++    |+       ..|||||+++++|+|++. ++||++..|  .+.|+||+||+
T Consensus       298 ~lLHG~m~q~dR~~~~~~~il~~Fk~~~~~g~~~~~~~g~~ILVATdVaerGLDId~-d~VI~d~aP--~esyIQRiGRt  374 (844)
T TIGR02621       298 ELLTGTLRGAERDDLVKKEIFNRFLPQMLSGSRARPQQGTVYLVCTSAGEVGVNISA-DHLVCDLAP--FESMQQRFGRV  374 (844)
T ss_pred             eEeeCCCCHHHHhhHHHHHHHHHHhccccccccccccccceEEeccchhhhcccCCc-ceEEECCCC--HHHHHHHhccc
Confidence            7899999999999     88999987    54       689999999999999987 888887766  58999999999


Q ss_pred             CCCCCC-ceEEEEe
Q 037139           70 GRAGKT-GVATTFL   82 (135)
Q Consensus        70 gR~~~~-g~~~~~~   82 (135)
                      ||.|.. +..+.++
T Consensus       375 gR~G~~~~~~i~vv  388 (844)
T TIGR02621       375 NRFGELQACQIAVV  388 (844)
T ss_pred             CCCCCCCCceEEEE
Confidence            999874 3334444

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.

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.42  E-value=3.2e-13  Score=110.76  Aligned_cols=84  Identities=25%  Similarity=0.404  Sum_probs=76.0

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCccccccc---CCc-----EEEEecCCCCHHHHHHHhhhcCCCC
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIP---DVA-----HVINYDMPGNIEMYTHRIGRTGRAG   73 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~---~v~-----~vi~~d~p~~~~~~~qr~GR~gR~~   73 (135)
                      |+++..+|+  .+.+|+..+.+|+.+...|+|||++++||+|++   .|.     +||.++.|.+...|.|+.||+||.|
T Consensus       622 gI~h~vLna--kq~~REa~Iia~AG~~g~VtIATNMAGRGtDIkl~~~V~~vGGL~VIgterhes~Rid~Ql~GRtGRqG  699 (1025)
T PRK12900        622 RIAHNVLNA--KQHDREAEIVAEAGQKGAVTIATNMAGRGTDIKLGEGVRELGGLFILGSERHESRRIDRQLRGRAGRQG  699 (1025)
T ss_pred             CCCceeecC--CHHHhHHHHHHhcCCCCeEEEeccCcCCCCCcCCccchhhhCCceeeCCCCCchHHHHHHHhhhhhcCC
Confidence            778889997  588999999999999999999999999999999   453     4588999999999999999999999


Q ss_pred             CCceEEEEeecCCh
Q 037139           74 KTGVATTFLTFHDT   87 (135)
Q Consensus        74 ~~g~~~~~~~~~~~   87 (135)
                      .+|.++.|++..+.
T Consensus       700 dpGsS~ffvSleD~  713 (1025)
T PRK12900        700 DPGESVFYVSLEDE  713 (1025)
T ss_pred             CCcceEEEechhHH
Confidence            99999999987655

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

Probab=99.41  E-value=1.9e-13  Score=106.44  Aligned_cols=85  Identities=18%  Similarity=0.363  Sum_probs=74.6

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEE---EecCC-CCHHHHHHHhhhcCCCC--C
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVI---NYDMP-GNIEMYTHRIGRTGRAG--K   74 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi---~~d~p-~~~~~~~qr~GR~gR~~--~   74 (135)
                      .|+++.+||+||+..+|+.+..+|.++++.++|+|-+++.|+|||.-.+|+   -.+.- .++.+|.||.|||||.+  .
T Consensus       463 kG~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVTTAAL~AGVDFPASQVIFEsLaMG~~WLs~~EF~QM~GRAGRp~yHd  542 (830)
T COG1202         463 KGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAGVDFPASQVIFESLAMGIEWLSVREFQQMLGRAGRPDYHD  542 (830)
T ss_pred             CCcccccccCCCcHHHHHHHHHHHhcCCcceEeehhhhhcCCCCchHHHHHHHHHcccccCCHHHHHHHhcccCCCCccc
Confidence            478999999999999999999999999999999999999999999876554   23333 48999999999999976  4


Q ss_pred             CceEEEEeecC
Q 037139           75 TGVATTFLTFH   85 (135)
Q Consensus        75 ~g~~~~~~~~~   85 (135)
                      .|.+++++.+.
T Consensus       543 rGkVyllvepg  553 (830)
T COG1202         543 RGKVYLLVEPG  553 (830)
T ss_pred             CceEEEEecCC
Confidence            69999999865

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

Probab=99.40  E-value=9.6e-14  Score=99.05  Aligned_cols=78  Identities=40%  Similarity=0.694  Sum_probs=70.6

Q ss_pred             EEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEEeecC-ChhHHHHHHHHHhhCCCCCChHHH
Q 037139           32 LVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFH-DTDVFYDLKQMLIQSNSPVPPELA  109 (135)
Q Consensus        32 lv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~  109 (135)
                      +|+|+++++|+|+..+++++|||+|.+..+|.+|+|||||.|..|.++.|++.. +...+..+.+.+.....++|+.+.
T Consensus       302 ~vat~lfgrgmdiervNi~~NYdmp~~~DtYlHrv~rAgrfGtkglaitfvs~e~da~iLn~vqdRf~v~i~eLpdeid  380 (387)
T KOG0329|consen  302 LVATDLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNPVQDRFEVNIKELPDEID  380 (387)
T ss_pred             hHHhhhhccccCcccceeeeccCCCCCchHHHHHhhhhhccccccceeehhcchhhHHHhchhhHhhhccHhhcCcccc
Confidence            899999999999999999999999999999999999999999999999999865 556678888888888888888754

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

Probab=99.37  E-value=3.2e-13  Score=101.16  Aligned_cols=87  Identities=31%  Similarity=0.474  Sum_probs=81.7

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHH----------------
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTH----------------   64 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~q----------------   64 (135)
                      +|+.+..+|+.|.|+++.-+-+.|-.|+++|+|+|-++++|+|-|+|++||+-.+|.+.++|.|                
T Consensus       340 ~gi~a~~yha~lep~dks~~hq~w~a~eiqvivatvafgmgidkpdvrfvihhsl~ksienyyqasarillrmtkqknks  419 (695)
T KOG0353|consen  340 HGIHAGAYHANLEPEDKSGAHQGWIAGEIQVIVATVAFGMGIDKPDVRFVIHHSLPKSIENYYQASARILLRMTKQKNKS  419 (695)
T ss_pred             cCccccccccccCccccccccccccccceEEEEEEeeecccCCCCCeeEEEecccchhHHHHHHHHHHHHHHHhhhcccc
Confidence            4788899999999999999999999999999999999999999999999999999999999999                


Q ss_pred             ---------------------------HhhhcCCCCCCceEEEEeecCCh
Q 037139           65 ---------------------------RIGRTGRAGKTGVATTFLTFHDT   87 (135)
Q Consensus        65 ---------------------------r~GR~gR~~~~g~~~~~~~~~~~   87 (135)
                                                 -.||+||.+.+..|++++.-.+.
T Consensus       420 dtggstqinilevctnfkiffavfsekesgragrd~~~a~cilyy~~~di  469 (695)
T KOG0353|consen  420 DTGGSTQINILEVCTNFKIFFAVFSEKESGRAGRDDMKADCILYYGFADI  469 (695)
T ss_pred             cCCCcceeehhhhhccceeeeeeecchhccccccCCCcccEEEEechHHH
Confidence                                       67999999999999999876544

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

Probab=99.36  E-value=7.3e-12  Score=96.90  Aligned_cols=116  Identities=20%  Similarity=0.316  Sum_probs=94.8

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEec-----CCCCHHHHHHHhhhcCCCCCC
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYD-----MPGNIEMYTHRIGRTGRAGKT   75 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d-----~p~~~~~~~qr~GR~gR~~~~   75 (135)
                      +|+++..+|++...-+|.+++++++.|+++|||+-+.+-+|+|+|.|++|..+|     ...|..+++|-+|||.|.- .
T Consensus       469 ~gikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLLREGLDiPEVsLVAIlDADKeGFLRse~SLIQtIGRAARN~-~  547 (663)
T COG0556         469 LGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNV-N  547 (663)
T ss_pred             cCceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhhhccCCCcceeEEEEeecCccccccccchHHHHHHHHhhcc-C
Confidence            589999999999999999999999999999999999999999999999998877     4458999999999999974 6


Q ss_pred             ceEEEEeecCChhH---------HHHHHHHHhhCCCCCChHHHHHHHhhCC
Q 037139           76 GVATTFLTFHDTDV---------FYDLKQMLIQSNSPVPPELAKHEASKFK  117 (135)
Q Consensus        76 g~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~l~~~~~~~~~  117 (135)
                      |.++++...-..+.         -+.+...++......|+.+.+...+...
T Consensus       548 GkvIlYAD~iT~sM~~Ai~ET~RRR~iQ~~yN~~hgItP~ti~K~i~d~l~  598 (663)
T COG0556         548 GKVILYADKITDSMQKAIDETERRREIQMAYNEEHGITPQTIKKKIRDILD  598 (663)
T ss_pred             CeEEEEchhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCchhhhhhhhHhhh
Confidence            88999887654433         3344445666777777777665544433

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

Probab=99.34  E-value=8.6e-12  Score=96.56  Aligned_cols=67  Identities=37%  Similarity=0.595  Sum_probs=65.2

Q ss_pred             EEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCC
Q 037139            5 VTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGR   71 (135)
Q Consensus         5 v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR   71 (135)
                      +..+.|+.++.+|.++++.|+.|++++|+++.++.+|+|+|+++++|...+..|...|.||+||.-|
T Consensus       309 ~~~it~~t~~~eR~~il~~fr~g~~~~lv~~~vl~EGvDiP~~~~~i~~~~t~S~~~~~Q~lGR~LR  375 (442)
T COG1061         309 VEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRLGRGLR  375 (442)
T ss_pred             eEEEECCCCHHHHHHHHHHHHcCCCCEEEEeeeccceecCCCCcEEEEeCCCCcHHHHHHHhhhhcc
Confidence            5689999999999999999999999999999999999999999999999999999999999999999

>PRK09401 reverse gyrase; Reviewed

Probab=99.33  E-value=4.8e-12  Score=107.05  Aligned_cols=52  Identities=35%  Similarity=0.523  Sum_probs=47.3

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEe----cCCCcccccccC-CcEEEEecCCC
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVA----TDVAGRGIDIPD-VAHVINYDMPG   57 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~----T~~~~~G~d~~~-v~~vi~~d~p~   57 (135)
                      .|+++..+||+|     ++.+++|++|+++||||    |++++||+|+|+ +++|||||+|.
T Consensus       354 ~gi~v~~~hg~l-----~~~l~~F~~G~~~VLVatas~tdv~aRGIDiP~~IryVI~y~vP~  410 (1176)
T PRK09401        354 LGINAELAISGF-----ERKFEKFEEGEVDVLVGVASYYGVLVRGIDLPERIRYAIFYGVPK  410 (1176)
T ss_pred             CCCcEEEEeCcH-----HHHHHHHHCCCCCEEEEecCCCCceeecCCCCcceeEEEEeCCCC
Confidence            488999999999     23459999999999999    699999999999 89999999997

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.33  E-value=1.6e-11  Score=102.45  Aligned_cols=85  Identities=26%  Similarity=0.395  Sum_probs=73.7

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCC---CcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCc-
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKR---YNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTG-   76 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~---~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g-   76 (135)
                      .|+....++|+++..+|..+++.|+...   .-+|++|.+++.|+|+..+++||+||++|++....|+.||+.|.|+.. 
T Consensus       510 ~g~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLSTrAGGlGINLt~Ad~VIiyD~dWNP~~d~QAidRaHRIGQkk~  589 (1033)
T PLN03142        510 RGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKE  589 (1033)
T ss_pred             cCCcEEEECCCCCHHHHHHHHHHhccccCCceEEEEeccccccCCchhhCCEEEEeCCCCChHHHHHHHHHhhhcCCCce
Confidence            3678889999999999999999997643   346899999999999999999999999999999999999999999764 


Q ss_pred             -eEEEEeecC
Q 037139           77 -VATTFLTFH   85 (135)
Q Consensus        77 -~~~~~~~~~   85 (135)
                       .++.++...
T Consensus       590 V~VyRLIt~g  599 (1033)
T PLN03142        590 VQVFRFCTEY  599 (1033)
T ss_pred             EEEEEEEeCC
Confidence             445555554

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

Probab=99.33  E-value=4.7e-12  Score=98.24  Aligned_cols=96  Identities=26%  Similarity=0.435  Sum_probs=74.8

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhc--CCCcEEEecCCCcccccccCCcEEEEecC---------CCCHHHHHHHhhhcCC
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRT--KRYNVLVATDVAGRGIDIPDVAHVINYDM---------PGNIEMYTHRIGRTGR   71 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~--g~~~ilv~T~~~~~G~d~~~v~~vi~~d~---------p~~~~~~~qr~GR~gR   71 (135)
                      .++++|+|+++|+.|.+-...|++  ++.+||||||++++|+|+ +++-||.+++         |.+..+..|-+|||||
T Consensus       382 ~k~aVIYGsLPPeTr~aQA~~FNd~~~e~dvlVAsDAIGMGLNL-~IrRiiF~sl~Kysg~e~~~it~sqikQIAGRAGR  460 (700)
T KOG0953|consen  382 HKCAVIYGSLPPETRLAQAALFNDPSNECDVLVASDAIGMGLNL-NIRRIIFYSLIKYSGRETEDITVSQIKQIAGRAGR  460 (700)
T ss_pred             cceEEEecCCCCchhHHHHHHhCCCCCccceEEeeccccccccc-ceeEEEEeecccCCcccceeccHHHHHHHhhcccc
Confidence            458999999999999999999987  899999999999999998 5666776663         3467889999999999


Q ss_pred             CCC---CceEEEEeecCChhHHHHHHHHHhhCCCC
Q 037139           72 AGK---TGVATTFLTFHDTDVFYDLKQMLIQSNSP  103 (135)
Q Consensus        72 ~~~---~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  103 (135)
                      .|.   .|.+.++.    ...+..+.+.++.+..+
T Consensus       461 f~s~~~~G~vTtl~----~eDL~~L~~~l~~p~ep  491 (700)
T KOG0953|consen  461 FGSKYPQGEVTTLH----SEDLKLLKRILKRPVEP  491 (700)
T ss_pred             cccCCcCceEEEee----HhhHHHHHHHHhCCchH
Confidence            864   35555443    34455666666655444

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

Probab=99.33  E-value=3.7e-12  Score=103.47  Aligned_cols=103  Identities=26%  Similarity=0.370  Sum_probs=84.1

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEE---ec-CCCCHHHHHHHhhhcCCCCC--Cc
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVIN---YD-MPGNIEMYTHRIGRTGRAGK--TG   76 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~---~d-~p~~~~~~~qr~GR~gR~~~--~g   76 (135)
                      +.+++||+|++.++|+.+...|++|.+.|++||+.++.|+|+|..++++-   +. .+.+..+|.||+|||||.|.  .|
T Consensus       523 ~GvAyHhaGLT~eER~~iE~afr~g~i~vl~aTSTlaaGVNLPArRVIiraP~~g~~~l~~~~YkQM~GRAGR~gidT~G  602 (1008)
T KOG0950|consen  523 YGVAYHHAGLTSEEREIIEAAFREGNIFVLVATSTLAAGVNLPARRVIIRAPYVGREFLTRLEYKQMVGRAGRTGIDTLG  602 (1008)
T ss_pred             ccceecccccccchHHHHHHHHHhcCeEEEEecchhhccCcCCcceeEEeCCccccchhhhhhHHhhhhhhhhcccccCc
Confidence            46889999999999999999999999999999999999999999998884   33 33478899999999999874  58


Q ss_pred             eEEEEeecCChhHHHHHHHHHhhCCCCCChHH
Q 037139           77 VATTFLTFHDTDVFYDLKQMLIQSNSPVPPEL  108 (135)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  108 (135)
                      .+++++...+...+.   +++.....++..-+
T Consensus       603 dsiLI~k~~e~~~~~---~lv~~~~~~~~S~l  631 (1008)
T KOG0950|consen  603 DSILIIKSSEKKRVR---ELVNSPLKPLNSCL  631 (1008)
T ss_pred             ceEEEeeccchhHHH---HHHhcccccccccc
Confidence            899999888876655   44455544444443

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.30  E-value=4.7e-12  Score=95.62  Aligned_cols=60  Identities=22%  Similarity=0.484  Sum_probs=52.1

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcC
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTG   70 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~g   70 (135)
                      ++.+..+||.+++.+|.++      ++.+|||||+++++|+|+|.+ +|| ++ |.+.+.|+||+||+|
T Consensus       298 ~~~~~~l~g~~~~~~R~~~------~~~~iLVaTdv~~rGiDi~~~-~vi-~~-p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       298 GDDIGRITGFAPKKDRERA------MQFDILLGTSTVDVGVDFKRD-WLI-FS-ARDAAAFWQRLGRLG  357 (357)
T ss_pred             CceEEeeecCCCHHHHHHh------ccCCEEEEecHHhcccCCCCc-eEE-EC-CCCHHHHhhhcccCC
Confidence            3578889999999998754      478999999999999999987 555 55 899999999999987

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.

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

Probab=99.24  E-value=2e-11  Score=99.45  Aligned_cols=82  Identities=27%  Similarity=0.314  Sum_probs=68.5

Q ss_pred             eEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEE----ec----CCCCHHHHHHHhhhcCCCCC-
Q 037139            4 RVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVIN----YD----MPGNIEMYTHRIGRTGRAGK-   74 (135)
Q Consensus         4 ~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~----~d----~p~~~~~~~qr~GR~gR~~~-   74 (135)
                      .+++||||+-|=-++-+.-.|..|-++||+||.++++|+|.|.-.+|+.    .|    .-..+.+|.||+|||||.|- 
T Consensus       632 GiaVHH~GlLPivKE~VE~LFqrGlVKVLFATETFAMGVNMPARtvVF~Sl~KhDG~efR~L~PGEytQMAGRAGRRGlD  711 (1248)
T KOG0947|consen  632 GIAVHHGGLLPIVKEVVELLFQRGLVKVLFATETFAMGVNMPARTVVFSSLRKHDGNEFRELLPGEYTQMAGRAGRRGLD  711 (1248)
T ss_pred             cchhhcccchHHHHHHHHHHHhcCceEEEeehhhhhhhcCCCceeEEeeehhhccCcceeecCChhHHhhhccccccccC
Confidence            3567999999999999999999999999999999999999998766652    11    12357899999999999874 


Q ss_pred             -CceEEEEeecC
Q 037139           75 -TGVATTFLTFH   85 (135)
Q Consensus        75 -~g~~~~~~~~~   85 (135)
                       .|.+++++...
T Consensus       712 ~tGTVii~~~~~  723 (1248)
T KOG0947|consen  712 ETGTVIIMCKDS  723 (1248)
T ss_pred             cCceEEEEecCC
Confidence             58888877654

>TIGR01054 rgy reverse gyrase

Probab=99.24  E-value=2.5e-11  Score=102.78  Aligned_cols=53  Identities=25%  Similarity=0.442  Sum_probs=48.3

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEe----cCCCcccccccC-CcEEEEecCCC
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVA----TDVAGRGIDIPD-VAHVINYDMPG   57 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~----T~~~~~G~d~~~-v~~vi~~d~p~   57 (135)
                      .|+++..+||+|+    +.++++|++|+++||||    |++++||+|+|+ |++||+||+|.
T Consensus       352 ~g~~a~~lhg~~~----~~~l~~Fr~G~~~vLVata~~tdv~aRGIDip~~V~~vI~~~~P~  409 (1171)
T TIGR01054       352 HGVKAVAYHATKP----KEDYEKFAEGEIDVLIGVASYYGTLVRGLDLPERVRYAVFLGVPK  409 (1171)
T ss_pred             CCceEEEEeCCCC----HHHHHHHHcCCCCEEEEeccccCcccccCCCCccccEEEEECCCC
Confidence            3789999999997    37899999999999999    599999999999 89999999884

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.

>PRK09694 helicase Cas3; Provisional

Probab=99.24  E-value=2.4e-10  Score=94.41  Aligned_cols=69  Identities=25%  Similarity=0.461  Sum_probs=59.5

Q ss_pred             ceEEEecCCCCHHHH----HHHHHHH-hcCC---CcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCC
Q 037139            3 YRVTTLHGGKSQEQR----EISLEGF-RTKR---YNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGK   74 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r----~~~~~~f-~~g~---~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~   74 (135)
                      ..+..+||.+++.+|    +++++.| ++|+   ..|||||+++++|+|+ +++++|....|  .+.++||+||++|.+.
T Consensus       588 ~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaTQViE~GLDI-d~DvlItdlaP--idsLiQRaGR~~R~~~  664 (878)
T PRK09694        588 VDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILVATQVVEQSLDL-DFDWLITQLCP--VDLLFQRLGRLHRHHR  664 (878)
T ss_pred             ceEEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEECcchhheeec-CCCeEEECCCC--HHHHHHHHhccCCCCC
Confidence            578999999999999    4677788 6666   4799999999999999 57989988777  6799999999999764

>PRK14701 reverse gyrase; Provisional

Probab=99.23  E-value=6.6e-12  Score=108.61  Aligned_cols=74  Identities=15%  Similarity=0.358  Sum_probs=64.9

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEec----CCCcccccccC-CcEEEEecCCC---CHHHHHHHh------
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVAT----DVAGRGIDIPD-VAHVINYDMPG---NIEMYTHRI------   66 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T----~~~~~G~d~~~-v~~vi~~d~p~---~~~~~~qr~------   66 (135)
                      .|+++..+||+     |..++++|++|+++|||||    ++++||+|+|+ |++||+||+|.   +.+.|.|-.      
T Consensus       356 ~Gi~a~~~h~~-----R~~~l~~F~~G~~~VLVaT~s~~gvaaRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~~~~~~~~  430 (1638)
T PRK14701        356 DGFKIELVSAK-----NKKGFDLFEEGEIDYLIGVATYYGTLVRGLDLPERIRFAVFYGVPKFRFRVDLEDPTIYRILGL  430 (1638)
T ss_pred             CCCeEEEecch-----HHHHHHHHHcCCCCEEEEecCCCCeeEecCccCCccCEEEEeCCCCCCcchhhcccchhhhhcc
Confidence            48899999995     8999999999999999999    58999999999 99999999999   777665544      


Q ss_pred             -------hhcCCCCCCceEE
Q 037139           67 -------GRTGRAGKTGVAT   79 (135)
Q Consensus        67 -------GR~gR~~~~g~~~   79 (135)
                             ||+||.|.++.++
T Consensus       431 ~~~~~~~~~a~~~g~~~~~~  450 (1638)
T PRK14701        431 LSEILKIEEELKEGIPIEGV  450 (1638)
T ss_pred             hHHHHHhhhhcccCCcchhH
Confidence                   9999998776555

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

Probab=99.20  E-value=4.5e-11  Score=99.56  Aligned_cols=83  Identities=24%  Similarity=0.353  Sum_probs=69.8

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEE----EecC------CCCHHHHHHHhhhcCC
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVI----NYDM------PGNIEMYTHRIGRTGR   71 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi----~~d~------p~~~~~~~qr~GR~gR   71 (135)
                      .+.+++||+||+..+|..+.+.|+.|.+++|++|-.+++|+|+|.-.++|    .||+      +.++.+..||.|||||
T Consensus       607 pygfaIHhAGl~R~dR~~~EdLf~~g~iqvlvstatlawgvnlpahtViikgtqvy~pekg~w~elsp~dv~qmlgragr  686 (1674)
T KOG0951|consen  607 PYGFAIHHAGLNRKDRELVEDLFADGHIQVLVSTATLAWGVNLPAHTVIIKGTQVYDPEKGRWTELSPLDVMQMLGRAGR  686 (1674)
T ss_pred             hccceeeccCCCcchHHHHHHHHhcCceeEEEeehhhhhhcCCCcceEEecCccccCcccCccccCCHHHHHHHHhhcCC
Confidence            45688999999999999999999999999999999999999999988887    4663      3478999999999999


Q ss_pred             CCC--CceEEEEeec
Q 037139           72 AGK--TGVATTFLTF   84 (135)
Q Consensus        72 ~~~--~g~~~~~~~~   84 (135)
                      .+.  .|..++....
T Consensus       687 p~~D~~gegiiit~~  701 (1674)
T KOG0951|consen  687 PQYDTCGEGIIITDH  701 (1674)
T ss_pred             CccCcCCceeeccCc
Confidence            754  3555544433

>KOG4150 consensus Predicted ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.16  E-value=7.3e-11  Score=92.40  Aligned_cols=119  Identities=19%  Similarity=0.256  Sum_probs=92.8

Q ss_pred             EEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEEeecC
Q 037139            6 TTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFH   85 (135)
Q Consensus         6 ~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~~~~~   85 (135)
                      ..+.||.+.++|.++...+--|+..-+|+|++++.|+|+...+.|++.+.|.|..++.|..|||||.++++.++.+....
T Consensus       561 ~SYRGGY~A~DRRKIE~~~F~G~L~giIaTNALELGIDIG~LDAVl~~GFP~S~aNl~QQ~GRAGRRNk~SLavyva~~~  640 (1034)
T KOG4150|consen  561 TSYRGGYIAEDRRKIESDLFGGKLCGIIATNALELGIDIGHLDAVLHLGFPGSIANLWQQAGRAGRRNKPSLAVYVAFLG  640 (1034)
T ss_pred             HhhcCccchhhHHHHHHHhhCCeeeEEEecchhhhccccccceeEEEccCchhHHHHHHHhccccccCCCceEEEEEecc
Confidence            34679999999999999999999999999999999999999999999999999999999999999999887766655543


Q ss_pred             --ChhHHHHHHHHHhhCCCCCChHHHHH--HHhhCCCCCCCCC
Q 037139           86 --DTDVFYDLKQMLIQSNSPVPPELAKH--EASKFKPGTIPDR  124 (135)
Q Consensus        86 --~~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~~~~~  124 (135)
                        +...+.....++..++.++.-++.+.  .++.++...+..+
T Consensus       641 PVDQ~Y~~HP~~l~~~pN~EL~LD~~N~~iL~~HlQCAA~ELP  683 (1034)
T KOG4150|consen  641 PVDQYYMSHPDKLFGSPNEELHLDSQNKHVLMQHLQCAALELP  683 (1034)
T ss_pred             chhhHhhcCcHHHhCCCcceeEEecccHHHHHHHHhHHhhcCc
Confidence              44445555666667766655554432  3344444444433

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

Probab=99.16  E-value=1.8e-11  Score=97.86  Aligned_cols=103  Identities=23%  Similarity=0.296  Sum_probs=78.4

Q ss_pred             eEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEE----EecCC----CCHHHHHHHhhhcCCCCC-
Q 037139            4 RVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVI----NYDMP----GNIEMYTHRIGRTGRAGK-   74 (135)
Q Consensus         4 ~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi----~~d~p----~~~~~~~qr~GR~gR~~~-   74 (135)
                      .+++||+|+-|--++.+.-.|+.|-+++|+||.+++.|+|.|.-.+|+    -||.-    .+.-+|+||.|||||.|. 
T Consensus       448 GIGIHHsGLLPIlKE~IEILFqEGLvKvLFATETFsiGLNMPAkTVvFT~~rKfDG~~fRwissGEYIQMSGRAGRRG~D  527 (1041)
T KOG0948|consen  448 GIGIHHSGLLPILKEVIEILFQEGLVKVLFATETFSIGLNMPAKTVVFTAVRKFDGKKFRWISSGEYIQMSGRAGRRGID  527 (1041)
T ss_pred             ccccccccchHHHHHHHHHHHhccHHHHHHhhhhhhhccCCcceeEEEeeccccCCcceeeecccceEEecccccccCCC
Confidence            356799999999999999999999999999999999999999977665    24422    267899999999999885 


Q ss_pred             -CceEEEEeecCChhHHHHHHHHHhhCCCCCChHH
Q 037139           75 -TGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPEL  108 (135)
Q Consensus        75 -~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  108 (135)
                       .|.+|++++..-..  ...+.+++....++..++
T Consensus       528 drGivIlmiDekm~~--~~ak~m~kG~aD~LnSaF  560 (1041)
T KOG0948|consen  528 DRGIVILMIDEKMEP--QVAKDMLKGSADPLNSAF  560 (1041)
T ss_pred             CCceEEEEecCcCCH--HHHHHHhcCCCcchhhhh
Confidence             58888888754221  223344444444444443

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

Probab=99.15  E-value=3.4e-10  Score=83.86  Aligned_cols=89  Identities=21%  Similarity=0.319  Sum_probs=68.4

Q ss_pred             eEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEE-ec-CCCCHHHHHHHhhhcCCCCC--CceEE
Q 037139            4 RVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVIN-YD-MPGNIEMYTHRIGRTGRAGK--TGVAT   79 (135)
Q Consensus         4 ~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~-~d-~p~~~~~~~qr~GR~gR~~~--~g~~~   79 (135)
                      .++++|+.  .+.|.+..++|++|++++||+|.++++|+.+|+|++.+. .. .-.+.+.++|.+||+||.-.  .|.++
T Consensus       333 ~i~~Vhs~--d~~R~EkV~~fR~G~~~lLiTTTILERGVTfp~vdV~Vlgaeh~vfTesaLVQIaGRvGRs~~~PtGdv~  410 (441)
T COG4098         333 TIASVHSE--DQHRKEKVEAFRDGKITLLITTTILERGVTFPNVDVFVLGAEHRVFTESALVQIAGRVGRSLERPTGDVL  410 (441)
T ss_pred             ceeeeecc--CccHHHHHHHHHcCceEEEEEeehhhcccccccceEEEecCCcccccHHHHHHHhhhccCCCcCCCCcEE
Confidence            35677866  678899999999999999999999999999999997653 32 23578899999999999543  36666


Q ss_pred             EEeecCChhHHHHHH
Q 037139           80 TFLTFHDTDVFYDLK   94 (135)
Q Consensus        80 ~~~~~~~~~~~~~~~   94 (135)
                      .|-...........+
T Consensus       411 FFH~G~skaM~~A~k  425 (441)
T COG4098         411 FFHYGKSKAMKQARK  425 (441)
T ss_pred             EEeccchHHHHHHHH
Confidence            665555555544443

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

Probab=99.14  E-value=8.5e-11  Score=96.97  Aligned_cols=81  Identities=30%  Similarity=0.483  Sum_probs=75.2

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCC-CHHHHHHHhhhcCCCCCCceEEEE
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPG-NIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~-~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      ..+..++|+|.+.+|.++...|+.|++.++++|.+++-|+|+..++.||.+..|. +..++.||.||+||.++.+..+..
T Consensus       339 ~~v~~~~~~~~~~er~~ie~~~~~g~~~~~~st~AlelgidiG~ldavi~~g~P~~s~~~~~Q~~GRaGR~~~~~l~~~v  418 (851)
T COG1205         339 DAVSTYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVV  418 (851)
T ss_pred             hheeeccccCCHHHHHHHHHHHhcCCccEEecchhhhhceeehhhhhHhhcCCCCchHHHHHHhhhhccCCCCCceEEEE
Confidence            4578899999999999999999999999999999999999999999999999999 899999999999999877666666


Q ss_pred             ee
Q 037139           82 LT   83 (135)
Q Consensus        82 ~~   83 (135)
                      ..
T Consensus       419 ~~  420 (851)
T COG1205         419 LR  420 (851)
T ss_pred             eC
Confidence            65

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

Probab=99.10  E-value=2.4e-10  Score=94.01  Aligned_cols=111  Identities=22%  Similarity=0.364  Sum_probs=81.4

Q ss_pred             eEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEE----EecCCC------CHHHHHHHhhhcCCC-
Q 037139            4 RVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVI----NYDMPG------NIEMYTHRIGRTGRA-   72 (135)
Q Consensus         4 ~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi----~~d~p~------~~~~~~qr~GR~gR~-   72 (135)
                      ..+++|+||...+|..+.+.|..|.++||+||..+++|+|+|+--.+|    .||.-.      +.-+.+|..|||||. 
T Consensus       398 g~~iHhAGm~r~DR~l~E~~F~~G~i~vL~cTaTLAwGVNLPA~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPq  477 (1230)
T KOG0952|consen  398 GMGIHHAGMLRSDRQLVEKEFKEGHIKVLCCTATLAWGVNLPAYAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQ  477 (1230)
T ss_pred             hhhhcccccchhhHHHHHHHHhcCCceEEEecceeeeccCCcceEEEecCCcccccccCceeeehHHHHHHHHhccCCCC
Confidence            356799999999999999999999999999999999999999866666    355443      456779999999995 


Q ss_pred             -CCCceEEEEeecCChhHHHHHHHHHhhCCCCCChHHHHHHHhhCCC
Q 037139           73 -GKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKP  118 (135)
Q Consensus        73 -~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  118 (135)
                       +..|.++++.+.+-.+.+..+    -....++...+-....+.+..
T Consensus       478 Fd~~G~giIiTt~dkl~~Y~sL----l~~~~piES~~~~~L~dnLnA  520 (1230)
T KOG0952|consen  478 FDSSGEGIIITTRDKLDHYESL----LTGQNPIESQLLPCLIDNLNA  520 (1230)
T ss_pred             CCCCceEEEEecccHHHHHHHH----HcCCChhHHHHHHHHHHhhhh
Confidence             466888888776544443332    233444444544444444443

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

Probab=99.06  E-value=8.2e-10  Score=93.38  Aligned_cols=67  Identities=22%  Similarity=0.477  Sum_probs=60.8

Q ss_pred             eEEEecCCCCHHHHHHHHHHHhcCCC-cEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCC
Q 037139            4 RVTTLHGGKSQEQREISLEGFRTKRY-NVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRA   72 (135)
Q Consensus         4 ~v~~~hg~~~~~~r~~~~~~f~~g~~-~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~   72 (135)
                      .+..+||+++  ++..++++|++++. +|+|+++++.+|+|+|.|.+||.++++.|...|+||+||+.|.
T Consensus       733 ~v~~itg~~~--~~~~li~~Fk~~~~p~IlVsvdmL~TG~DvP~v~~vVf~rpvkS~~lf~QmIGRgtR~  800 (1123)
T PRK11448        733 AVIKITGSID--KPDQLIRRFKNERLPNIVVTVDLLTTGIDVPSICNLVFLRRVRSRILYEQMLGRATRL  800 (1123)
T ss_pred             ceEEEeCCcc--chHHHHHHHhCCCCCeEEEEecccccCCCcccccEEEEecCCCCHHHHHHHHhhhccC
Confidence            4566888875  46789999999987 6899999999999999999999999999999999999999995

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

Probab=99.04  E-value=8.7e-10  Score=90.39  Aligned_cols=80  Identities=26%  Similarity=0.319  Sum_probs=66.7

Q ss_pred             EEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEec-CCCCHHHHHHHhhhcCCCCCC--ceEEEE
Q 037139            5 VTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYD-MPGNIEMYTHRIGRTGRAGKT--GVATTF   81 (135)
Q Consensus         5 v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d-~p~~~~~~~qr~GR~gR~~~~--g~~~~~   81 (135)
                      ++++|++|....|..+.=.||.|...||++|.+++-|+|.|--.+|+--| +-.++-.|.|++|||||.|-+  |.++.+
T Consensus       965 iG~HHaglNr~yR~~VEvLFR~g~L~VlfaT~TLsLGiNMPCrTVvF~gDsLQL~plny~QmaGRAGRRGFD~lGnV~Fm 1044 (1330)
T KOG0949|consen  965 IGVHHAGLNRKYRSLVEVLFRQGHLQVLFATETLSLGINMPCRTVVFAGDSLQLDPLNYKQMAGRAGRRGFDTLGNVVFM 1044 (1330)
T ss_pred             ccccccccchHHHHHHHHHhhcCceEEEEEeeehhcccCCCceeEEEeccccccCchhHHhhhccccccccccccceEEE
Confidence            56799999999999999999999999999999999999999766555444 335788999999999998753  666555


Q ss_pred             eec
Q 037139           82 LTF   84 (135)
Q Consensus        82 ~~~   84 (135)
                      -.+
T Consensus      1045 giP 1047 (1330)
T KOG0949|consen 1045 GIP 1047 (1330)
T ss_pred             eCc
Confidence            443

>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]

Probab=99.02  E-value=1.5e-10  Score=91.40  Aligned_cols=82  Identities=22%  Similarity=0.387  Sum_probs=73.0

Q ss_pred             EEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEE--------ec----------CCCCHHHHHHHh
Q 037139            5 VTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVIN--------YD----------MPGNIEMYTHRI   66 (135)
Q Consensus         5 v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~--------~d----------~p~~~~~~~qr~   66 (135)
                      +.++||.|+.+++.++++.--.|.-+|+++|++++..+.+|.+.+||+        |+          .|-|..+-.||.
T Consensus       293 ~lply~aL~~e~Q~rvF~p~p~g~RKvIlsTNIAETSlTI~GI~YVVDsG~vK~~~y~p~~g~~~L~v~~ISkasA~QRa  372 (674)
T KOG0922|consen  293 ILPLYGALPSEEQSRVFDPAPPGKRKVILSTNIAETSLTIDGIRYVVDSGFVKQKKYNPRTGLDSLIVVPISKASANQRA  372 (674)
T ss_pred             eeeecccCCHHHhhccccCCCCCcceEEEEcceeeeeEEecceEEEEcCCceEEEeeccccCccceeEEechHHHHhhhc
Confidence            467999999999999999999999999999999999999999999984        33          355788899999


Q ss_pred             hhcCCCCCCceEEEEeecCCh
Q 037139           67 GRTGRAGKTGVATTFLTFHDT   87 (135)
Q Consensus        67 GR~gR~~~~g~~~~~~~~~~~   87 (135)
                      |||||.+ +|.|+-++...+.
T Consensus       373 GRAGRt~-pGkcyRLYte~~~  392 (674)
T KOG0922|consen  373 GRAGRTG-PGKCYRLYTESAY  392 (674)
T ss_pred             ccCCCCC-CceEEEeeeHHHH
Confidence            9999986 8999999987654

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

Probab=99.01  E-value=7.1e-10  Score=92.05  Aligned_cols=100  Identities=22%  Similarity=0.292  Sum_probs=75.5

Q ss_pred             EEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEE----Eec----CCCCHHHHHHHhhhcCCCCCC-
Q 037139            5 VTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVI----NYD----MPGNIEMYTHRIGRTGRAGKT-   75 (135)
Q Consensus         5 v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi----~~d----~p~~~~~~~qr~GR~gR~~~~-   75 (135)
                      +++||++|-|..+..+...|..|.++|+++|.+++.|+|.|.-.+|+    .+|    .+.++.+|.|+.|||||.|.+ 
T Consensus       447 iavHH~GlLP~~K~~vE~Lfq~GLvkvvFaTeT~s~GiNmPartvv~~~l~K~dG~~~r~L~~gEy~QmsGRAGRRGlD~  526 (1041)
T COG4581         447 IAVHHAGLLPAIKELVEELFQEGLVKVVFATETFAIGINMPARTVVFTSLSKFDGNGHRWLSPGEYTQMSGRAGRRGLDV  526 (1041)
T ss_pred             hhhhccccchHHHHHHHHHHhccceeEEeehhhhhhhcCCcccceeeeeeEEecCCceeecChhHHHHhhhhhccccccc
Confidence            44799999999999999999999999999999999999999877765    333    445799999999999998864 


Q ss_pred             -ceEEEEeecCChhHHHHHHHHHhhCCCCCC
Q 037139           76 -GVATTFLTFHDTDVFYDLKQMLIQSNSPVP  105 (135)
Q Consensus        76 -g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  105 (135)
                       |.+++...+...+ ......+.......+.
T Consensus       527 ~G~vI~~~~~~~~~-~~e~~~l~~~~~~~L~  556 (1041)
T COG4581         527 LGTVIVIEPPFESE-PSEAAGLASGKLDPLR  556 (1041)
T ss_pred             cceEEEecCCCCCC-hHHHHHhhcCCCccch
Confidence             6666664443332 3333344444433333

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

Probab=99.01  E-value=2.9e-10  Score=93.20  Aligned_cols=82  Identities=26%  Similarity=0.385  Sum_probs=72.4

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEec------------------CCCCHHHHHH
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYD------------------MPGNIEMYTH   64 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d------------------~p~~~~~~~q   64 (135)
                      +.+.++||.|+.+++.++++--..|+-+|+++|++++.++.+|+|.+||.-+                  .|.|..+..|
T Consensus       288 ~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATNIAETSLTI~gIr~VIDsG~ak~~~y~~~~g~~~L~~~~ISqAsA~Q  367 (845)
T COG1643         288 LEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYVIDSGLAKEKRYDPRTGLTRLETEPISKASADQ  367 (845)
T ss_pred             cEEeeccccCCHHHHHhhcCCCCCCcceEEEEccccccceeeCCeEEEecCCcccccccccccCceeeeEEEechhhhhh
Confidence            6789999999999999999888888778999999999999999999999443                  3446788899


Q ss_pred             HhhhcCCCCCCceEEEEeecC
Q 037139           65 RIGRTGRAGKTGVATTFLTFH   85 (135)
Q Consensus        65 r~GR~gR~~~~g~~~~~~~~~   85 (135)
                      |.|||||.+ +|.|+-+++..
T Consensus       368 RaGRAGR~~-pGicyRLyse~  387 (845)
T COG1643         368 RAGRAGRTG-PGICYRLYSEE  387 (845)
T ss_pred             hccccccCC-CceEEEecCHH
Confidence            999999985 89999999864

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=98.97  E-value=3.3e-09  Score=86.86  Aligned_cols=85  Identities=28%  Similarity=0.410  Sum_probs=75.7

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCC---------------------------------
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDV---------------------------------   47 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v---------------------------------   47 (135)
                      .|+++..+|+.  +.+|+..+.+|+.+..+|+|||++++||+|++--                                 
T Consensus       453 ~gi~~~vLnak--q~eREa~Iia~Ag~~g~VtIATNmAGRGtDI~LgGn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v  530 (830)
T PRK12904        453 AGIPHNVLNAK--NHEREAEIIAQAGRPGAVTIATNMAGRGTDIKLGGNPEMLAAALLEEETEEQIAKIKAEWQEEHEEV  530 (830)
T ss_pred             CCCceEeccCc--hHHHHHHHHHhcCCCceEEEecccccCCcCccCCCchhhhhhhhhhhhhhHHHHHHHHHHhhhhhhH
Confidence            37889999996  7899999999999999999999999999999753                                 


Q ss_pred             -----cEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEEeecCCh
Q 037139           48 -----AHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDT   87 (135)
Q Consensus        48 -----~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~~~~~~~   87 (135)
                           =+||-...|.|..--.|..||+||.|.+|.+-.+++-.|.
T Consensus       531 ~~~GGLhVigTerhesrRid~QlrGRagRQGdpGss~f~lSleD~  575 (830)
T PRK12904        531 LEAGGLHVIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSLEDD  575 (830)
T ss_pred             HHcCCCEEEecccCchHHHHHHhhcccccCCCCCceeEEEEcCcH
Confidence                 1678888999999999999999999999999988887655

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=98.95  E-value=3.7e-09  Score=86.90  Aligned_cols=85  Identities=26%  Similarity=0.368  Sum_probs=74.9

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCC---------------------------------
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDV---------------------------------   47 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v---------------------------------   47 (135)
                      .|++...+|+.+.+++++.+.++|+.|  .|+|||++++||+|+.=-                                 
T Consensus       467 ~gi~h~vLnak~~q~Ea~iia~Ag~~G--~VtIATNmAGRGtDI~Lggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V  544 (896)
T PRK13104        467 ENIKHQVLNAKFHEKEAQIIAEAGRPG--AVTIATNMAGRGTDIVLGGSLAADLANLPADASEQEKEAVKKEWQKRHDEV  544 (896)
T ss_pred             cCCCeEeecCCCChHHHHHHHhCCCCC--cEEEeccCccCCcceecCCchhhhhhccccchhhHHHHHHHHHhhhhhhHH
Confidence            378899999999999999999999999  499999999999998521                                 


Q ss_pred             -----cEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEEeecCCh
Q 037139           48 -----AHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDT   87 (135)
Q Consensus        48 -----~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~~~~~~~   87 (135)
                           =+||-...+.|..-=.|..||+||.|.+|.+-.|++-.|.
T Consensus       545 ~~~GGL~VIgTerhesrRID~QLrGRaGRQGDPGss~f~lSleD~  589 (896)
T PRK13104        545 IAAGGLRIIGSERHESRRIDNQLRGRAGRQGDPGSSRFYLSLEDN  589 (896)
T ss_pred             HHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEEcCcH
Confidence                 1677788888988889999999999999999888887655

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=98.95  E-value=9.2e-09  Score=83.46  Aligned_cols=87  Identities=23%  Similarity=0.339  Sum_probs=75.0

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCC--cE-EEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCC--
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRY--NV-LVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKT--   75 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~--~i-lv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~--   75 (135)
                      +|+.+..+||.|+..+|+.+++.|++..-  .| |.+|.+.+.|+|+-..+.||.||+.|+++.=.|.++|+.|.|+.  
T Consensus       618 ~g~~~~rLdG~~~~~qRq~~vd~FN~p~~~~~vfLlSsKAgg~GinLiGAsRlil~D~dWNPa~d~QAmaR~~RdGQKk~  697 (776)
T KOG0390|consen  618 RGYEVLRLDGKTSIKQRQKLVDTFNDPESPSFVFLLSSKAGGEGLNLIGASRLILFDPDWNPAVDQQAMARAWRDGQKKP  697 (776)
T ss_pred             cCceEEEEcCCCchHHHHHHHHhccCCCCCceEEEEecccccCceeecccceEEEeCCCCCchhHHHHHHHhccCCCcce
Confidence            47899999999999999999999987543  34 46778999999999999999999999999999999999999975  


Q ss_pred             ceEEEEeecCCh
Q 037139           76 GVATTFLTFHDT   87 (135)
Q Consensus        76 g~~~~~~~~~~~   87 (135)
                      .++|.++..+..
T Consensus       698 v~iYrLlatGti  709 (776)
T KOG0390|consen  698 VYIYRLLATGTI  709 (776)
T ss_pred             EEEEEeecCCCc
Confidence            566667766533

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=98.94  E-value=4.3e-10  Score=89.47  Aligned_cols=83  Identities=22%  Similarity=0.306  Sum_probs=74.9

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEec------------------CCCCHHHHH
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYD------------------MPGNIEMYT   63 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d------------------~p~~~~~~~   63 (135)
                      ++.|.++++.|+.+-+.++++.-..|..+++|+|++++..+.+|++.+||..+                  .|.|..+-.
T Consensus       597 ~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi~gI~yVID~Gy~K~kvyn~~~G~D~L~~~pIS~AnA~  676 (1042)
T KOG0924|consen  597 DLAVLPIYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTIPGIRYVIDTGYCKLKVYNPRIGMDALQIVPISQANAD  676 (1042)
T ss_pred             ceEEEeehhhCchhhhhhhcccCCCCceeEEEeccchhhceeecceEEEEecCceeeeecccccccceeEEEechhccch
Confidence            67899999999999999999999999999999999999999999999999544                  456778889


Q ss_pred             HHhhhcCCCCCCceEEEEeecC
Q 037139           64 HRIGRTGRAGKTGVATTFLTFH   85 (135)
Q Consensus        64 qr~GR~gR~~~~g~~~~~~~~~   85 (135)
                      ||.|||||.| +|.|+-+++..
T Consensus       677 QRaGRAGRt~-pG~cYRlYTe~  697 (1042)
T KOG0924|consen  677 QRAGRAGRTG-PGTCYRLYTED  697 (1042)
T ss_pred             hhccccCCCC-Ccceeeehhhh
Confidence            9999999986 89999998763

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=98.93  E-value=3.6e-09  Score=86.85  Aligned_cols=85  Identities=27%  Similarity=0.376  Sum_probs=75.5

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCC---------------------------------
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDV---------------------------------   47 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v---------------------------------   47 (135)
                      .|+++..+|+.+++.++..+.++|+.|.  |+|||++++||+|+.=-                                 
T Consensus       472 ~gi~~~vLnak~~~~Ea~ii~~Ag~~G~--VtIATnmAGRGTDIkLggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~  549 (908)
T PRK13107        472 EKIPHEVLNAKFHEREAEIVAQAGRTGA--VTIATNMAGRGTDIVLGGNWNMEIEALENPTAEQKAKIKADWQIRHDEVV  549 (908)
T ss_pred             CCCCeEeccCcccHHHHHHHHhCCCCCc--EEEecCCcCCCcceecCCchHHhhhhhcchhhHHHHHHHHHHHhhHHHHH
Confidence            3788899999999999999999999998  99999999999999521                                 


Q ss_pred             ----cEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEEeecCCh
Q 037139           48 ----AHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDT   87 (135)
Q Consensus        48 ----~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~~~~~~~   87 (135)
                          =+||-...+.|..-=.|..||+||.|.+|.+..+++-.|.
T Consensus       550 ~~GGL~VIgTerheSrRID~QLrGRaGRQGDPGss~f~lSlED~  593 (908)
T PRK13107        550 AAGGLHILGTERHESRRIDNQLRGRAGRQGDAGSSRFYLSMEDS  593 (908)
T ss_pred             HcCCCEEEecccCchHHHHhhhhcccccCCCCCceeEEEEeCcH
Confidence                2678888899988889999999999999999988887655

>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=98.92  E-value=1.1e-09  Score=86.96  Aligned_cols=81  Identities=23%  Similarity=0.285  Sum_probs=72.2

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEec------------------CCCCHHHHHH
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYD------------------MPGNIEMYTH   64 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d------------------~p~~~~~~~q   64 (135)
                      +-+.++|++++.+.+.++++---.|..+|++||++++..+.++++.+||.-+                  .|-|..+..|
T Consensus       507 liv~PiYaNLPselQakIFePtP~gaRKVVLATNIAETSlTIdgI~yViDpGf~K~nsynprtGmesL~v~piSKAsA~Q  586 (902)
T KOG0923|consen  507 LIVLPIYANLPSELQAKIFEPTPPGARKVVLATNIAETSLTIDGIKYVIDPGFVKQNSYNPRTGMESLLVTPISKASANQ  586 (902)
T ss_pred             EEEeeccccCChHHHHhhcCCCCCCceeEEEeecchhhceeecCeEEEecCccccccCcCCCcCceeEEEeeechhhhhh
Confidence            4478899999999999999999999999999999999999999999999433                  3456788899


Q ss_pred             HhhhcCCCCCCceEEEEeec
Q 037139           65 RIGRTGRAGKTGVATTFLTF   84 (135)
Q Consensus        65 r~GR~gR~~~~g~~~~~~~~   84 (135)
                      |.|||||.| +|.|+-+++.
T Consensus       587 RaGRAGRtg-PGKCfRLYt~  605 (902)
T KOG0923|consen  587 RAGRAGRTG-PGKCFRLYTA  605 (902)
T ss_pred             hccccCCCC-CCceEEeech
Confidence            999999997 8999999874

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

Probab=98.86  E-value=1.9e-08  Score=81.59  Aligned_cols=85  Identities=25%  Similarity=0.378  Sum_probs=66.0

Q ss_pred             ceEEEecCCCCHH--HHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCC------------CHHHHHHHhhh
Q 037139            3 YRVTTLHGGKSQE--QREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPG------------NIEMYTHRIGR   68 (135)
Q Consensus         3 ~~v~~~hg~~~~~--~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~------------~~~~~~qr~GR   68 (135)
                      .+++.+-++.+..  .-+..++.|.+|+++|||+|+++++|.|+|++.+|...|...            ....+.|-.||
T Consensus       507 ~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRA~Er~fqll~QvaGR  586 (730)
T COG1198         507 ARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRASERTFQLLMQVAGR  586 (730)
T ss_pred             CcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcchHHHHHHHHHHHHhh
Confidence            4566666665443  356889999999999999999999999999999986544222            24556999999


Q ss_pred             cCCCCCCceEEEEeecCCh
Q 037139           69 TGRAGKTGVATTFLTFHDT   87 (135)
Q Consensus        69 ~gR~~~~g~~~~~~~~~~~   87 (135)
                      |||.+.+|.+++-....+.
T Consensus       587 AgR~~~~G~VvIQT~~P~h  605 (730)
T COG1198         587 AGRAGKPGEVVIQTYNPDH  605 (730)
T ss_pred             hccCCCCCeEEEEeCCCCc
Confidence            9999889888877765543

>KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]

Probab=98.86  E-value=3.1e-10  Score=93.17  Aligned_cols=84  Identities=25%  Similarity=0.398  Sum_probs=72.6

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEE--------ecCCC----------CHHHHHH
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVIN--------YDMPG----------NIEMYTH   64 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~--------~d~p~----------~~~~~~q   64 (135)
                      +-+.++|+.|+..+++.++...-.|..+|+++|++++..+.+++|-+||.        ||+-.          +..+-.|
T Consensus       445 ~~ilplHs~~~s~eQ~~VF~~pp~g~RKIIlaTNIAETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~Q  524 (924)
T KOG0920|consen  445 FAILPLHSSIPSEEQQAVFKRPPKGTRKIILATNIAETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQ  524 (924)
T ss_pred             eEEEeccccCChHHHHHhcCCCCCCcchhhhhhhhHhhcccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHH
Confidence            56889999999999999999999999999999999999999999999994        55333          3555699


Q ss_pred             HhhhcCCCCCCceEEEEeecCCh
Q 037139           65 RIGRTGRAGKTGVATTFLTFHDT   87 (135)
Q Consensus        65 r~GR~gR~~~~g~~~~~~~~~~~   87 (135)
                      |.|||||. .+|.|+.++.....
T Consensus       525 R~GRAGRv-~~G~cy~L~~~~~~  546 (924)
T KOG0920|consen  525 RRGRAGRV-RPGICYHLYTRSRY  546 (924)
T ss_pred             hcccccCc-cCCeeEEeechhhh
Confidence            99999998 48999999886533

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.81  E-value=1.3e-09  Score=87.93  Aligned_cols=82  Identities=26%  Similarity=0.333  Sum_probs=70.7

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEE--------ecCCC----------CHHHHHH
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVIN--------YDMPG----------NIEMYTH   64 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~--------~d~p~----------~~~~~~q   64 (135)
                      +.|.++|+-++.+++.++++.--.|..=++|+|++++..+.+|++.+||.        ||.-.          |..+--|
T Consensus       605 LyvLPLYSLLs~~~Q~RVF~~~p~g~RLcVVaTNVAETSLTIPgIkYVVD~Gr~K~R~Yd~~TGV~~FeV~wiSkASadQ  684 (1172)
T KOG0926|consen  605 LYVLPLYSLLSTEKQMRVFDEVPKGERLCVVATNVAETSLTIPGIKYVVDCGRVKERLYDSKTGVSSFEVDWISKASADQ  684 (1172)
T ss_pred             eEEeehhhhcCHHHhhhhccCCCCCceEEEEeccchhcccccCCeeEEEeccchhhhccccccCceeEEEEeeeccccch
Confidence            46889999999999999999999999889999999999999999999995        44333          3344589


Q ss_pred             HhhhcCCCCCCceEEEEeecC
Q 037139           65 RIGRTGRAGKTGVATTFLTFH   85 (135)
Q Consensus        65 r~GR~gR~~~~g~~~~~~~~~   85 (135)
                      |+|||||.| +|+|+.+++..
T Consensus       685 RAGRAGRtg-pGHcYRLYSSA  704 (1172)
T KOG0926|consen  685 RAGRAGRTG-PGHCYRLYSSA  704 (1172)
T ss_pred             hccccCCCC-CCceeehhhhH
Confidence            999999997 89999998753

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=98.62  E-value=1.6e-07  Score=77.10  Aligned_cols=79  Identities=25%  Similarity=0.335  Sum_probs=63.7

Q ss_pred             eEEEecCCCCHHHHHHHHHHHh----cCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCC--CCce
Q 037139            4 RVTTLHGGKSQEQREISLEGFR----TKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAG--KTGV   77 (135)
Q Consensus         4 ~v~~~hg~~~~~~r~~~~~~f~----~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~--~~g~   77 (135)
                      .+..+||.++..+|.+.++.+.    .+...|+|||++++.|+|+. .+++|-=  +..+.+.+||.||+.|.|  ..|.
T Consensus       466 ~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQVIEagvDid-fd~mITe--~aPidSLIQR~GRv~R~g~~~~~~  542 (733)
T COG1203         466 KVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDID-FDVLITE--LAPIDSLIQRAGRVNRHGKKENGK  542 (733)
T ss_pred             CEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEeeEEEEEeccc-cCeeeec--CCCHHHHHHHHHHHhhcccccCCc
Confidence            4789999999999998888665    46788999999999999985 5555432  455778999999999998  5677


Q ss_pred             EEEEeecC
Q 037139           78 ATTFLTFH   85 (135)
Q Consensus        78 ~~~~~~~~   85 (135)
                      ++.+....
T Consensus       543 ~~v~~~~~  550 (733)
T COG1203         543 IYVYNDEE  550 (733)
T ss_pred             eeEeeccc
Confidence            77776644

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]

Probab=98.43  E-value=2e-06  Score=69.69  Aligned_cols=85  Identities=29%  Similarity=0.431  Sum_probs=72.8

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCC---cEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCc-
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRY---NVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTG-   76 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~---~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g-   76 (135)
                      +||...-+-|+++.++|...++.|.....   =.|++|.+.+.|+|+-.+++||.||..|++..=.|..-||-|.|+.. 
T Consensus       510 R~y~ycRiDGSt~~eeR~~aI~~fn~~~s~~FiFlLSTRAGGLGINL~aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~  589 (971)
T KOG0385|consen  510 RGYEYCRLDGSTSHEEREDAIEAFNAPPSEKFIFLLSTRAGGLGINLTAADTVILYDSDWNPQVDLQAMDRAHRIGQKKP  589 (971)
T ss_pred             cCceeEeecCCCCcHHHHHHHHhcCCCCcceEEEEEeccccccccccccccEEEEecCCCCchhhhHHHHHHHhhCCcCc
Confidence            46777889999999999999999987552   25689999999999999999999999999999999999999988754 


Q ss_pred             -eEEEEeecC
Q 037139           77 -VATTFLTFH   85 (135)
Q Consensus        77 -~~~~~~~~~   85 (135)
                       .++.+++..
T Consensus       590 V~V~RLiten  599 (971)
T KOG0385|consen  590 VVVYRLITEN  599 (971)
T ss_pred             eEEEEEeccc
Confidence             455556554

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]

Probab=98.35  E-value=3.1e-06  Score=68.73  Aligned_cols=84  Identities=23%  Similarity=0.321  Sum_probs=72.7

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCc--EEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCc--e
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYN--VLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTG--V   77 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~--ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g--~   77 (135)
                      |+...-+.|..+...|...++.|++++.-  .|++|.+.+.|+|+-.++-||.||+-|+++.=.|..-||.|.|+.-  .
T Consensus       571 ~ysylRmDGtT~~~~R~~lVd~Fne~~s~~VFLLTTrvGGLGlNLTgAnRVIIfDPdWNPStD~QAreRawRiGQkkdV~  650 (923)
T KOG0387|consen  571 GYSYLRMDGTTPAALRQKLVDRFNEDESIFVFLLTTRVGGLGLNLTGANRVIIFDPDWNPSTDNQARERAWRIGQKKDVV  650 (923)
T ss_pred             CceEEEecCCCccchhhHHHHhhcCCCceEEEEEEecccccccccccCceEEEECCCCCCccchHHHHHHHhhcCccceE
Confidence            67788889999999999999999977544  4578999999999999999999999999999999999999999753  4


Q ss_pred             EEEEeecC
Q 037139           78 ATTFLTFH   85 (135)
Q Consensus        78 ~~~~~~~~   85 (135)
                      ++-++...
T Consensus       651 VYRL~t~g  658 (923)
T KOG0387|consen  651 VYRLMTAG  658 (923)
T ss_pred             EEEEecCC
Confidence            55556554

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]

Probab=98.29  E-value=2.9e-06  Score=71.46  Aligned_cols=85  Identities=24%  Similarity=0.327  Sum_probs=74.0

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCC---cEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCc-
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRY---NVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTG-   76 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~---~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g-   76 (135)
                      +||...-+-|++.-+-|+++++.|..-..   =.|+||.+.+.|||+-.++.||.||..|++..=+|...||-|.|+.. 
T Consensus       722 r~ypfQRLDGsvrgelRq~AIDhFnap~SddFvFLLSTRAGGLGINLatADTVIIFDSDWNPQNDLQAqARaHRIGQkk~  801 (1373)
T KOG0384|consen  722 RGYPFQRLDGSVRGELRQQAIDHFNAPDSDDFVFLLSTRAGGLGINLATADTVIIFDSDWNPQNDLQAQARAHRIGQKKH  801 (1373)
T ss_pred             cCCcceeccCCcchHHHHHHHHhccCCCCCceEEEEecccCcccccccccceEEEeCCCCCcchHHHHHHHHHhhcccce
Confidence            36777788899999999999999986543   47899999999999999999999999999999999999999998764 


Q ss_pred             -eEEEEeecC
Q 037139           77 -VATTFLTFH   85 (135)
Q Consensus        77 -~~~~~~~~~   85 (135)
                       .+|-|++..
T Consensus       802 VnVYRLVTk~  811 (1373)
T KOG0384|consen  802 VNVYRLVTKN  811 (1373)
T ss_pred             EEEEEEecCC
Confidence             466677665

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

Probab=98.12  E-value=2.7e-05  Score=64.52  Aligned_cols=84  Identities=20%  Similarity=0.320  Sum_probs=69.8

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcC-CCc-EEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCce--
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTK-RYN-VLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGV--   77 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g-~~~-ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~--   77 (135)
                      ++....++|+++.+.|..+++.|.++ ... +++++.+.+.|+|+-..+.||.+|+.|++....|...|+-|.|+...  
T Consensus       735 ~~~~~~ldG~~~~~~r~~~i~~f~~~~~~~v~lls~kagg~glnLt~a~~vi~~d~~wnp~~~~Qa~dRa~RigQ~~~v~  814 (866)
T COG0553         735 GIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQKRPVK  814 (866)
T ss_pred             CCcEEEEeCCCChhhHHHHHHHhhcCCCCceEEEEecccccceeecccceEEEeccccChHHHHHHHHHHHHhcCcceeE
Confidence            34678899999999999999999986 344 44677899999999999999999999999999999999999887643  


Q ss_pred             EEEEeecC
Q 037139           78 ATTFLTFH   85 (135)
Q Consensus        78 ~~~~~~~~   85 (135)
                      ++.++..+
T Consensus       815 v~r~i~~~  822 (866)
T COG0553         815 VYRLITRG  822 (866)
T ss_pred             EEEeecCC
Confidence            44444443

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=98.11  E-value=1e-05  Score=66.82  Aligned_cols=83  Identities=24%  Similarity=0.390  Sum_probs=61.6

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcC-CCcEEEecCCCcccccccCCc--------EEEEecCCCCHHHHHHHhhhcCCC
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTK-RYNVLVATDVAGRGIDIPDVA--------HVINYDMPGNIEMYTHRIGRTGRA   72 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g-~~~ilv~T~~~~~G~d~~~v~--------~vi~~d~p~~~~~~~qr~GR~gR~   72 (135)
                      |++..++++.....+ ..++.  +.| .-.|.|||++++||.|+.--.        +||....|.|..-=-|..||+||.
T Consensus       450 gi~h~vLNAk~~e~E-A~IIa--~AG~~GaVTIATNMAGRGTDI~Lg~~V~~~GGLhVIgTerheSrRIDnQLrGRaGRQ  526 (925)
T PRK12903        450 NIPHTVLNAKQNARE-AEIIA--KAGQKGAITIATNMAGRGTDIKLSKEVLELGGLYVLGTDKAESRRIDNQLRGRSGRQ  526 (925)
T ss_pred             CCCceeecccchhhH-HHHHH--hCCCCCeEEEecccccCCcCccCchhHHHcCCcEEEecccCchHHHHHHHhcccccC
Confidence            555666666533222 22222  445 356889999999999996432        789999999998889999999999


Q ss_pred             CCCceEEEEeecCCh
Q 037139           73 GKTGVATTFLTFHDT   87 (135)
Q Consensus        73 ~~~g~~~~~~~~~~~   87 (135)
                      |.+|.+-.+++-.|.
T Consensus       527 GDpGss~f~lSLeD~  541 (925)
T PRK12903        527 GDVGESRFFISLDDQ  541 (925)
T ss_pred             CCCCcceEEEecchH
Confidence            999988888876544

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=98.04  E-value=2.6e-05  Score=63.55  Aligned_cols=83  Identities=28%  Similarity=0.400  Sum_probs=62.3

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCC-CcEEEecCCCcccccccCC---------------cEEEEecCCCCHHHHHHH
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKR-YNVLVATDVAGRGIDIPDV---------------AHVINYDMPGNIEMYTHR   65 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~-~~ilv~T~~~~~G~d~~~v---------------~~vi~~d~p~~~~~~~qr   65 (135)
                      |++..++++.-..++ .+++.  +.|. -.|.|||++++||.|+.--               =+||-...+.|...-.|.
T Consensus       451 gI~h~vLNAk~~~~E-A~IIa--~AG~~gaVTIATNMAGRGTDIkLg~~~~~~~~~V~~~GGLhVIgTerheSrRID~QL  527 (764)
T PRK12326        451 GVPAVVLNAKNDAEE-ARIIA--EAGKYGAVTVSTQMAGRGTDIRLGGSDEADRDRVAELGGLHVIGTGRHRSERLDNQL  527 (764)
T ss_pred             CCcceeeccCchHhH-HHHHH--hcCCCCcEEEEecCCCCccCeecCCCcccchHHHHHcCCcEEEeccCCchHHHHHHH
Confidence            566677777644333 23332  2332 3588999999999998622               268889999999999999


Q ss_pred             hhhcCCCCCCceEEEEeecCCh
Q 037139           66 IGRTGRAGKTGVATTFLTFHDT   87 (135)
Q Consensus        66 ~GR~gR~~~~g~~~~~~~~~~~   87 (135)
                      .||+||.|.+|.+-.|++-+|.
T Consensus       528 rGRaGRQGDpGss~f~lSleDd  549 (764)
T PRK12326        528 RGRAGRQGDPGSSVFFVSLEDD  549 (764)
T ss_pred             hcccccCCCCCceeEEEEcchh
Confidence            9999999999999888886654

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

Probab=98.02  E-value=3.6e-05  Score=60.35  Aligned_cols=88  Identities=23%  Similarity=0.396  Sum_probs=70.0

Q ss_pred             EEecCCCCHHHHHHHHHHHhc-CCCcEEEecCCCcccccccCCcEEEEecCCC-CHHHHHHHhhhcCCCC---C---Cce
Q 037139            6 TTLHGGKSQEQREISLEGFRT-KRYNVLVATDVAGRGIDIPDVAHVINYDMPG-NIEMYTHRIGRTGRAG---K---TGV   77 (135)
Q Consensus         6 ~~~hg~~~~~~r~~~~~~f~~-g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~-~~~~~~qr~GR~gR~~---~---~g~   77 (135)
                      .+|+|..++.+|.++++.|+. .+++.++.+.+....+|+|..+++|+..... |..+=.||.||.-|..   .   ...
T Consensus       566 pfIYG~Tsq~ERm~ILqnFq~n~~vNTIFlSKVgDtSiDLPEAnvLIQISSH~GSRRQEAQRLGRILRAKk~~de~fnaf  645 (776)
T KOG1123|consen  566 PFIYGPTSQNERMKILQNFQTNPKVNTIFLSKVGDTSIDLPEANVLIQISSHGGSRRQEAQRLGRILRAKKRNDEEFNAF  645 (776)
T ss_pred             ceEECCCchhHHHHHHHhcccCCccceEEEeeccCccccCCcccEEEEEcccccchHHHHHHHHHHHHHhhcCcccccee
Confidence            368999999999999999975 5799999999999999999999999887664 6777899999987742   1   346


Q ss_pred             EEEEeecCChhHHHHH
Q 037139           78 ATTFLTFHDTDVFYDL   93 (135)
Q Consensus        78 ~~~~~~~~~~~~~~~~   93 (135)
                      .+.+++.+....+..-
T Consensus       646 FYSLVS~DTqEM~YSt  661 (776)
T KOG1123|consen  646 FYSLVSKDTQEMYYST  661 (776)
T ss_pred             eeeeeecchHHHHhhh
Confidence            6777776655554333

>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]

Probab=98.01  E-value=1.8e-05  Score=67.04  Aligned_cols=79  Identities=23%  Similarity=0.320  Sum_probs=68.5

Q ss_pred             EecCCCCHHHHHHHHHHHhcC-CCcEE-EecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCce--EEEEe
Q 037139            7 TLHGGKSQEQREISLEGFRTK-RYNVL-VATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGV--ATTFL   82 (135)
Q Consensus         7 ~~hg~~~~~~r~~~~~~f~~g-~~~il-v~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~--~~~~~   82 (135)
                      -+-|+.++.+|.++.++|+++ .++|| ++|-+.+-|+|+-.++.||.++=.|++..=+|.+-||-|.|+.-.  ++.++
T Consensus      1372 RLDGSVpp~~R~kiV~~FN~DptIDvLlLTThVGGLGLNLTGADTVVFvEHDWNPMrDLQAMDRAHRIGQKrvVNVyRlI 1451 (1549)
T KOG0392|consen 1372 RLDGSVPPGDRQKIVERFNEDPTIDVLLLTTHVGGLGLNLTGADTVVFVEHDWNPMRDLQAMDRAHRIGQKRVVNVYRLI 1451 (1549)
T ss_pred             EecCCCCcHHHHHHHHHhcCCCceeEEEEeeeccccccccCCCceEEEEecCCCchhhHHHHHHHHhhcCceeeeeeeeh
Confidence            567999999999999999998 89988 577899999999999999999999999999999999999987643  44444


Q ss_pred             ecC
Q 037139           83 TFH   85 (135)
Q Consensus        83 ~~~   85 (135)
                      ..+
T Consensus      1452 trG 1454 (1549)
T KOG0392|consen 1452 TRG 1454 (1549)
T ss_pred             hcc
Confidence            443

>COG4889 Predicted helicase [General function prediction only]

Probab=98.00  E-value=1.2e-05  Score=66.53  Aligned_cols=81  Identities=22%  Similarity=0.336  Sum_probs=64.4

Q ss_pred             CceEEEec--CCCCHHHHHHHHHH---HhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCC---
Q 037139            2 GYRVTTLH--GGKSQEQREISLEG---FRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAG---   73 (135)
Q Consensus         2 g~~v~~~h--g~~~~~~r~~~~~~---f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~---   73 (135)
                      ++.+.+=|  |.|...+|...+..   |...+++||-...++.+|+|+|..+.||.+|+-.+.-+.+|.+||+.|..   
T Consensus       497 nL~iSi~HvDGtmNal~R~~l~~l~~~~~~neckIlSNaRcLSEGVDVPaLDsViFf~pr~smVDIVQaVGRVMRKa~gK  576 (1518)
T COG4889         497 NLKISIDHVDGTMNALERLDLLELKNTFEPNECKILSNARCLSEGVDVPALDSVIFFDPRSSMVDIVQAVGRVMRKAKGK  576 (1518)
T ss_pred             CceEEeecccccccHHHHHHHHhccCCCCcchheeeccchhhhcCCCccccceEEEecCchhHHHHHHHHHHHHHhCcCC
Confidence            34455555  88999999655543   35678889988899999999999999999999999999999999999953   


Q ss_pred             CCceEEEEe
Q 037139           74 KTGVATTFL   82 (135)
Q Consensus        74 ~~g~~~~~~   82 (135)
                      ..|+.|+-+
T Consensus       577 ~yGYIILPI  585 (1518)
T COG4889         577 KYGYIILPI  585 (1518)
T ss_pred             ccceEEEEe
Confidence            246666544

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=97.91  E-value=4.6e-05  Score=63.61  Aligned_cols=83  Identities=31%  Similarity=0.380  Sum_probs=60.4

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCC-CcEEEecCCCcccccccC---C-----cEEEEecCCCCHHHHHHHhhhcCCC
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKR-YNVLVATDVAGRGIDIPD---V-----AHVINYDMPGNIEMYTHRIGRTGRA   72 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~-~~ilv~T~~~~~G~d~~~---v-----~~vi~~d~p~~~~~~~qr~GR~gR~   72 (135)
                      |++..++++.-...+-+-+.   +.|. -.|.|||++++||.|+.-   |     =+||-...|.|...-.|..||+||.
T Consensus       592 gi~h~vLNak~~~~Ea~iia---~AG~~g~VTIATNmAGRGTDIkl~~~v~~~GGLhVIgTer~es~Rid~Ql~GRagRQ  668 (970)
T PRK12899        592 RIEHTVLNAKNHAQEAEIIA---GAGKLGAVTVATNMAGRGTDIKLDEEAVAVGGLYVIGTSRHQSRRIDRQLRGRCARL  668 (970)
T ss_pred             CCcceecccchhhhHHHHHH---hcCCCCcEEEeeccccCCcccccCchHHhcCCcEEEeeccCchHHHHHHHhcccccC
Confidence            44555556553322222222   2343 458899999999999942   2     2688899999999999999999999


Q ss_pred             CCCceEEEEeecCCh
Q 037139           73 GKTGVATTFLTFHDT   87 (135)
Q Consensus        73 ~~~g~~~~~~~~~~~   87 (135)
                      |.+|.+..+++-.|.
T Consensus       669 GdpGss~f~lSlEDd  683 (970)
T PRK12899        669 GDPGAAKFFLSFEDR  683 (970)
T ss_pred             CCCCceeEEEEcchH
Confidence            999999988887654

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=97.91  E-value=8.4e-05  Score=58.26  Aligned_cols=86  Identities=19%  Similarity=0.269  Sum_probs=71.9

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcC-CCcEE-EecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCC--Cc
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTK-RYNVL-VATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGK--TG   76 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g-~~~il-v~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~--~g   76 (135)
                      .|+.+.-+-|+|++..|..+++.|.+. +++|+ ++-.+.+..+|+-..+.|+..|+.|++..-.|...|.-|.|+  +-
T Consensus       661 aGfscVkL~GsMs~~ardatik~F~nd~~c~vfLvSLkAGGVALNLteASqVFmmDPWWNpaVe~Qa~DRiHRIGQ~rPv  740 (791)
T KOG1002|consen  661 AGFSCVKLVGSMSPAARDATIKYFKNDIDCRVFLVSLKAGGVALNLTEASQVFMMDPWWNPAVEWQAQDRIHRIGQYRPV  740 (791)
T ss_pred             cCceEEEeccCCChHHHHHHHHHhccCCCeEEEEEEeccCceEeeechhceeEeecccccHHHHhhhhhhHHhhcCccce
Confidence            388999999999999999999999764 67765 556788888999999999999999999998888888877764  55


Q ss_pred             eEEEEeecCC
Q 037139           77 VATTFLTFHD   86 (135)
Q Consensus        77 ~~~~~~~~~~   86 (135)
                      .++.|+.+..
T Consensus       741 kvvrf~iEns  750 (791)
T KOG1002|consen  741 KVVRFCIENS  750 (791)
T ss_pred             eEEEeehhcc
Confidence            6777777653

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

Probab=97.87  E-value=0.00016  Score=59.05  Aligned_cols=54  Identities=22%  Similarity=0.237  Sum_probs=45.6

Q ss_pred             HHHHHHHhc-CCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCC
Q 037139           18 EISLEGFRT-KRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRA   72 (135)
Q Consensus        18 ~~~~~~f~~-g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~   72 (135)
                      ..++++|+. +.++|||+++++..|+|.|.+++++..-+..+ -.++|.+||+.|.
T Consensus       580 ~~~~~~Fk~~~~~~ilIVvdmllTGFDaP~l~tLyldKplk~-h~LlQai~R~nR~  634 (667)
T TIGR00348       580 YKDLERFKKEENPKLLIVVDMLLTGFDAPILNTLYLDKPLKY-HGLLQAIARTNRI  634 (667)
T ss_pred             HHHHHHhcCCCCceEEEEEcccccccCCCccceEEEeccccc-cHHHHHHHHhccc
Confidence            478889976 68999999999999999999998776665554 4589999999993

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

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=97.84  E-value=4.3e-05  Score=64.19  Aligned_cols=59  Identities=31%  Similarity=0.519  Sum_probs=50.4

Q ss_pred             CcEEEecCCCccccccc---CC-----cEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEEeecCCh
Q 037139           29 YNVLVATDVAGRGIDIP---DV-----AHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDT   87 (135)
Q Consensus        29 ~~ilv~T~~~~~G~d~~---~v-----~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~~~~~~~   87 (135)
                      -.|-|||++++||.|+.   .|     =+||-...+.|..--.|..||+||.|.+|.+-.+++-.|.
T Consensus       677 GaVTIATNMAGRGTDIkLg~~V~e~GGL~VIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSLEDd  743 (1112)
T PRK12901        677 GTVTIATNMAGRGTDIKLSPEVKAAGGLAIIGTERHESRRVDRQLRGRAGRQGDPGSSQFYVSLEDN  743 (1112)
T ss_pred             CcEEEeccCcCCCcCcccchhhHHcCCCEEEEccCCCcHHHHHHHhcccccCCCCCcceEEEEcccH
Confidence            35789999999999995   22     3688889999999999999999999999998888886654

>PF13871 Helicase_C_4: Helicase_C-like

Probab=97.71  E-value=0.00044  Score=50.73  Aligned_cols=80  Identities=18%  Similarity=0.268  Sum_probs=59.3

Q ss_pred             HHHHHHHhcCCCcEEEecCCCcccccccC--------CcEEEEecCCCCHHHHHHHhhhcCCCCCC-ceEEEEeecC---
Q 037139           18 EISLEGFRTKRYNVLVATDVAGRGIDIPD--------VAHVINYDMPGNIEMYTHRIGRTGRAGKT-GVATTFLTFH---   85 (135)
Q Consensus        18 ~~~~~~f~~g~~~ilv~T~~~~~G~d~~~--------v~~vi~~d~p~~~~~~~qr~GR~gR~~~~-g~~~~~~~~~---   85 (135)
                      ....+.|.+|+.+|+|.|++.+.|+-+..        -++-|.+.+||+....+|..||+-|.++. ...+.++...   
T Consensus        51 ~~e~~~F~~g~k~v~iis~AgstGiSlHAd~~~~nqr~Rv~i~le~pwsad~aiQ~~GR~hRsnQ~~~P~y~~l~t~~~g  130 (278)
T PF13871_consen   51 IAEKQAFMDGEKDVAIISDAGSTGISLHADRRVKNQRRRVHITLELPWSADKAIQQFGRTHRSNQVSAPEYRFLVTDLPG  130 (278)
T ss_pred             HHHHHHHhCCCceEEEEecccccccchhccccCCCCCceEEEEeeCCCCHHHHHHHhccccccccccCCEEEEeecCCHH
Confidence            35677999999999999999999998853        23457899999999999999999998863 3334444432   


Q ss_pred             ChhHHHHHHHHH
Q 037139           86 DTDVFYDLKQML   97 (135)
Q Consensus        86 ~~~~~~~~~~~~   97 (135)
                      +..+...+.+.+
T Consensus       131 E~Rfas~va~rL  142 (278)
T PF13871_consen  131 ERRFASTVARRL  142 (278)
T ss_pred             HHHHHHHHHHHH
Confidence            444444444444

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]

Probab=97.67  E-value=0.00032  Score=57.17  Aligned_cols=85  Identities=25%  Similarity=0.337  Sum_probs=71.8

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcE-EEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCC--ce
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNV-LVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKT--GV   77 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~i-lv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~--g~   77 (135)
                      +|+.-.-+.|+....+|..++.+|+..++=| |++|.+.+.|+|+..++.||.||..|++..=.|.+.||-|.|+.  -.
T Consensus      1067 r~Y~ylRLDGSsk~~dRrd~vrDwQ~sdiFvFLLSTRAGGLGINLTAADTViFYdSDWNPT~D~QAMDRAHRLGQTrdvt 1146 (1185)
T KOG0388|consen 1067 RGYTYLRLDGSSKASDRRDVVRDWQASDIFVFLLSTRAGGLGINLTAADTVIFYDSDWNPTADQQAMDRAHRLGQTRDVT 1146 (1185)
T ss_pred             hccceEEecCcchhhHHHHHHhhccCCceEEEEEecccCcccccccccceEEEecCCCCcchhhHHHHHHHhccCcccee
Confidence            3566777889999999999999999877654 57999999999999999999999999999999999999998864  34


Q ss_pred             EEEEeecC
Q 037139           78 ATTFLTFH   85 (135)
Q Consensus        78 ~~~~~~~~   85 (135)
                      ++.++..+
T Consensus      1147 vyrl~~rg 1154 (1185)
T KOG0388|consen 1147 VYRLITRG 1154 (1185)
T ss_pred             eeeecccc
Confidence            55555543

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=97.64  E-value=0.00057  Score=55.53  Aligned_cols=80  Identities=19%  Similarity=0.251  Sum_probs=67.8

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhc--CCCcEE-EecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRT--KRYNVL-VATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVA   78 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~--g~~~il-v~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~   78 (135)
                      |+....+||....++|+.+++.|..  |..+|+ +.-.+.+.|+|+-..+++|.+|+.|++.-=.|.+.|..|+|+...+
T Consensus       770 g~~y~si~Gqv~vK~Rq~iv~~FN~~k~~~rVmLlSLtAGGVGLNL~GaNHlilvDlHWNPaLEqQAcDRIYR~GQkK~V  849 (901)
T KOG4439|consen  770 GHIYTSITGQVLVKDRQEIVDEFNQEKGGARVMLLSLTAGGVGLNLIGANHLILVDLHWNPALEQQACDRIYRMGQKKDV  849 (901)
T ss_pred             CeeeeeecCccchhHHHHHHHHHHhccCCceEEEEEEccCcceeeecccceEEEEecccCHHHHHHHHHHHHHhcccCce
Confidence            5667789999999999999999964  556666 4557888999999999999999999999999999999999976555


Q ss_pred             EEE
Q 037139           79 TTF   81 (135)
Q Consensus        79 ~~~   81 (135)
                      ++.
T Consensus       850 ~Ih  852 (901)
T KOG4439|consen  850 FIH  852 (901)
T ss_pred             EEE
Confidence            433

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=97.63  E-value=0.00013  Score=60.69  Aligned_cols=59  Identities=34%  Similarity=0.548  Sum_probs=50.1

Q ss_pred             CcEEEecCCCccccccc--------------------------------CC-----cEEEEecCCCCHHHHHHHhhhcCC
Q 037139           29 YNVLVATDVAGRGIDIP--------------------------------DV-----AHVINYDMPGNIEMYTHRIGRTGR   71 (135)
Q Consensus        29 ~~ilv~T~~~~~G~d~~--------------------------------~v-----~~vi~~d~p~~~~~~~qr~GR~gR   71 (135)
                      -.|.|||++++||.||.                                .|     =+||-...+.|..-=.|..||+||
T Consensus       498 GaVTIATNMAGRGTDIkLg~n~~~~~~~~~~~~~~~~~~~~~~~~~~~e~V~e~GGLhVIgTerheSrRID~QLrGRaGR  577 (913)
T PRK13103        498 GALTIATNMAGRGTDILLGGNWEVEVAALENPTPEQIAQIKADWQKRHQQVIEAGGLHVIASERHESRRIDNQLRGRAGR  577 (913)
T ss_pred             CcEEEeccCCCCCCCEecCCchHHHHHhhhhhhHHHHHHHHHHHHhHHHHHHHcCCCEEEeeccCchHHHHHHhcccccc
Confidence            45889999999999994                                11     268888899999999999999999


Q ss_pred             CCCCceEEEEeecCCh
Q 037139           72 AGKTGVATTFLTFHDT   87 (135)
Q Consensus        72 ~~~~g~~~~~~~~~~~   87 (135)
                      .|.+|.+-.|++-.|.
T Consensus       578 QGDPGsS~f~lSlED~  593 (913)
T PRK13103        578 QGDPGSSRFYLSLEDS  593 (913)
T ss_pred             CCCCCceEEEEEcCcH
Confidence            9999999988887554

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

Probab=97.63  E-value=0.0003  Score=58.97  Aligned_cols=69  Identities=19%  Similarity=0.223  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHhcCCCcEEEecCCCcccccccCCc--EEEEecCCCC------------------------------HHHH
Q 037139           15 EQREISLEGFRTKRYNVLVATDVAGRGIDIPDVA--HVINYDMPGN------------------------------IEMY   62 (135)
Q Consensus        15 ~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~--~vi~~d~p~~------------------------------~~~~   62 (135)
                      .+|.+++++|++++..||+||+.+.+|+|+|+..  +||...+|..                              ...+
T Consensus       712 ~~r~~ll~~F~~~~~~iLlgt~sf~EGVD~~g~~l~~viI~~LPf~~p~dp~~~a~~~~~~~~g~~~f~~~~lP~A~~~l  791 (850)
T TIGR01407       712 GSRAKIKKRFNNGEKAILLGTSSFWEGVDFPGNGLVCLVIPRLPFANPKHPLTKKYWQKLEQEGKNPFYDYVLPMAIIRL  791 (850)
T ss_pred             ccHHHHHHHHHhCCCeEEEEcceeecccccCCCceEEEEEeCCCCCCCCCHHHHHHHHHHHHhcCCchHHhhHHHHHHHH
Confidence            5789999999999999999999999999999876  4555555531                              1224


Q ss_pred             HHHhhhcCCCCCCceEEEEee
Q 037139           63 THRIGRTGRAGKTGVATTFLT   83 (135)
Q Consensus        63 ~qr~GR~gR~~~~g~~~~~~~   83 (135)
                      .|.+||.-|..++.=++++++
T Consensus       792 ~Qa~GRlIRs~~D~G~v~ilD  812 (850)
T TIGR01407       792 RQALGRLIRRENDRGSIVILD  812 (850)
T ss_pred             HHhhccccccCCceEEEEEEc
Confidence            788899988765422333433

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.

>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=97.60  E-value=5.7e-05  Score=58.99  Aligned_cols=78  Identities=24%  Similarity=0.322  Sum_probs=58.5

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhc---C--CCcEEEecCCCcccccccCCcEEEEec------------------CCCCH
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRT---K--RYNVLVATDVAGRGIDIPDVAHVINYD------------------MPGNI   59 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~---g--~~~ilv~T~~~~~G~d~~~v~~vi~~d------------------~p~~~   59 (135)
                      ++|.++|    |.++..+++-...   |  ..+|+|+|++++..+.++.+.+||.-+                  .|.|.
T Consensus       287 l~v~PLy----P~~qq~iFep~p~~~~~~~~RkvVvstniaetsltidgiv~VIDpGf~kqkVYNPRIRvesllv~PISk  362 (699)
T KOG0925|consen  287 LKVVPLY----PAQQQRIFEPAPEKRNGAYGRKVVVSTNIAETSLTIDGIVFVIDPGFSKQKVYNPRIRVESLLVSPISK  362 (699)
T ss_pred             ceEEecC----chhhccccCCCCcccCCCccceEEEEecchheeeeeccEEEEecCchhhhcccCcceeeeeeeeccchH
Confidence            4567777    4444554443321   1  356999999999999999999998544                  56678


Q ss_pred             HHHHHHhhhcCCCCCCceEEEEeecC
Q 037139           60 EMYTHRIGRTGRAGKTGVATTFLTFH   85 (135)
Q Consensus        60 ~~~~qr~GR~gR~~~~g~~~~~~~~~   85 (135)
                      .+..||.||+||. .+|.|+.++.+.
T Consensus       363 asA~qR~gragrt-~pGkcfrLYte~  387 (699)
T KOG0925|consen  363 ASAQQRAGRAGRT-RPGKCFRLYTEE  387 (699)
T ss_pred             hHHHHHhhhccCC-CCCceEEeecHH
Confidence            8899999999987 589999998753

>PF13307 Helicase_C_2: Helicase C-terminal domain; PDB: 4A15_A 2VSF_A 3CRV_A 3CRW_1 2VL7_A

Probab=97.56  E-value=0.00049  Score=46.73  Aligned_cols=70  Identities=26%  Similarity=0.330  Sum_probs=46.8

Q ss_pred             HHHHHHHHHHHhcCCCcEEEecC--CCcccccccC--CcEEEEecCCC----CH--------------------------
Q 037139           14 QEQREISLEGFRTKRYNVLVATD--VAGRGIDIPD--VAHVINYDMPG----NI--------------------------   59 (135)
Q Consensus        14 ~~~r~~~~~~f~~g~~~ilv~T~--~~~~G~d~~~--v~~vi~~d~p~----~~--------------------------   59 (135)
                      ..+....++.|+.++-.||+++.  .+.+|+|+|+  +++||...+|.    ++                          
T Consensus        45 ~~~~~~~l~~~~~~~~~il~~v~~g~~~EGiD~~~~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~a~  124 (167)
T PF13307_consen   45 SKSRDELLEEFKRGEGAILLAVAGGSFSEGIDFPGDLLRAVIIVGLPFPPPSDPLVQAKREYLDKQGKNPFRDWYLPPAI  124 (167)
T ss_dssp             CCHHHHHHHHHCCSSSEEEEEETTSCCGSSS--ECESEEEEEEES-----TTCHHHHHHHHHHHHCCTTCHHHHTHHHHH
T ss_pred             cchHHHHHHHHHhccCeEEEEEecccEEEeecCCCchhheeeecCCCCCCCCCHHHHHHHHHHHHHhccchhhHhhHHHH
Confidence            55788999999999999999998  9999999996  67788888774    21                          


Q ss_pred             HHHHHHhhhcCCCCCCceEEEEee
Q 037139           60 EMYTHRIGRTGRAGKTGVATTFLT   83 (135)
Q Consensus        60 ~~~~qr~GR~gR~~~~g~~~~~~~   83 (135)
                      ....|.+||+-|..++--++.+++
T Consensus       125 ~~l~Qa~GR~iR~~~D~g~i~llD  148 (167)
T PF13307_consen  125 RKLKQAIGRLIRSEDDYGVIILLD  148 (167)
T ss_dssp             HHHHHHHHCC--STT-EEEEEEES
T ss_pred             HHHhhhcCcceeccCCcEEEEEEc
Confidence            113788999988766533333433

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=97.55  E-value=0.0012  Score=43.70  Aligned_cols=50  Identities=26%  Similarity=0.347  Sum_probs=37.9

Q ss_pred             ecCCCCHHHHHHHHHHHhcCC-CcEEEecCCCcccccccC--CcEEEEecCCC
Q 037139            8 LHGGKSQEQREISLEGFRTKR-YNVLVATDVAGRGIDIPD--VAHVINYDMPG   57 (135)
Q Consensus         8 ~hg~~~~~~r~~~~~~f~~g~-~~ilv~T~~~~~G~d~~~--v~~vi~~d~p~   57 (135)
                      +.-+.+..+..++++.|+... ..||+++.-+.+|+|+|+  +.+||...+|.
T Consensus        27 ~~e~~~~~~~~~~l~~f~~~~~~~iL~~~~~~~EGiD~~g~~~r~vii~glPf   79 (141)
T smart00492       27 LVQGEDGKETGKLLEKYVEACENAILLATARFSEGVDFPGDYLRAVIIDGLPF   79 (141)
T ss_pred             EEeCCChhHHHHHHHHHHHcCCCEEEEEccceecceecCCCCeeEEEEEecCC
Confidence            333455656789999998764 379999988999999997  56788777664

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]

Probab=97.41  E-value=0.0011  Score=54.50  Aligned_cols=86  Identities=26%  Similarity=0.320  Sum_probs=71.2

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCC-Cc-EEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCC--c
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKR-YN-VLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKT--G   76 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~-~~-ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~--g   76 (135)
                      +|++..-+-|...-.+|+.+++.|...+ +. .|++|.+.+.|+|+-.++.||.+|...++-.=.|.--||-|.|+.  -
T Consensus       800 l~~~ylRLDGsTqV~~RQ~lId~Fn~d~difVFLLSTKAGG~GINLt~An~VIihD~dFNP~dD~QAEDRcHRvGQtkpV  879 (941)
T KOG0389|consen  800 LGYKYLRLDGSTQVNDRQDLIDEFNTDKDIFVFLLSTKAGGFGINLTCANTVIIHDIDFNPYDDKQAEDRCHRVGQTKPV  879 (941)
T ss_pred             cCceEEeecCCccchHHHHHHHhhccCCceEEEEEeeccCcceecccccceEEEeecCCCCcccchhHHHHHhhCCccee
Confidence            4667777889999999999999997654 44 457999999999999999999999999888888988888888864  4


Q ss_pred             eEEEEeecCC
Q 037139           77 VATTFLTFHD   86 (135)
Q Consensus        77 ~~~~~~~~~~   86 (135)
                      .++.+++...
T Consensus       880 tV~rLItk~T  889 (941)
T KOG0389|consen  880 TVYRLITKST  889 (941)
T ss_pred             EEEEEEecCc
Confidence            5666776653

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=97.34  E-value=0.0019  Score=42.79  Aligned_cols=44  Identities=30%  Similarity=0.358  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHhcCCC---cEEEecCC--CcccccccC--CcEEEEecCCC
Q 037139           14 QEQREISLEGFRTKRY---NVLVATDV--AGRGIDIPD--VAHVINYDMPG   57 (135)
Q Consensus        14 ~~~r~~~~~~f~~g~~---~ilv~T~~--~~~G~d~~~--v~~vi~~d~p~   57 (135)
                      ..+..++++.|++..-   .||+++.-  +.+|+|+|+  +++||...+|.
T Consensus        30 ~~~~~~~l~~f~~~~~~~g~iL~~v~~G~~~EGiD~~g~~~r~vii~glPf   80 (142)
T smart00491       30 SGETEELLEKYSAACEARGALLLAVARGKVSEGIDFPDDLGRAVIIVGIPF   80 (142)
T ss_pred             CchHHHHHHHHHHhcCCCCEEEEEEeCCeeecceecCCCccEEEEEEecCC
Confidence            3345789999987544   68888876  899999997  56788777664

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]

Probab=97.22  E-value=0.0037  Score=53.74  Aligned_cols=84  Identities=27%  Similarity=0.384  Sum_probs=63.9

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCC-Cc-EEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCC--Cce
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKR-YN-VLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGK--TGV   77 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~-~~-ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~--~g~   77 (135)
                      |+...-+-|..+-++|+..+++|+... +- .|++|...+.|||+-..+.||+||..|++.-=.|.--|+-|.|+  +-+
T Consensus      1300 gylY~RLDg~t~vEqRQaLmerFNaD~RIfcfILSTrSggvGiNLtgADTVvFYDsDwNPtMDaQAQDrChRIGqtRDVH 1379 (1958)
T KOG0391|consen 1300 GYLYVRLDGNTSVEQRQALMERFNADRRIFCFILSTRSGGVGINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQTRDVH 1379 (1958)
T ss_pred             ceEEEEecCCccHHHHHHHHHHhcCCCceEEEEEeccCCccccccccCceEEEecCCCCchhhhHHHHHHHhhcCccceE
Confidence            555666788999999999999997654 22 34688899999999999999999999997766665555555443  345


Q ss_pred             EEEEeecC
Q 037139           78 ATTFLTFH   85 (135)
Q Consensus        78 ~~~~~~~~   85 (135)
                      .|.+++..
T Consensus      1380 IYRLISe~ 1387 (1958)
T KOG0391|consen 1380 IYRLISER 1387 (1958)
T ss_pred             EEEeeccc
Confidence            66777654

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]

Probab=97.06  E-value=0.002  Score=50.68  Aligned_cols=75  Identities=17%  Similarity=0.286  Sum_probs=63.6

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcC-CCcEE-EecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCc
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTK-RYNVL-VATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTG   76 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g-~~~il-v~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g   76 (135)
                      ++..+-|-|..++.+|....+.|+.. ++.|- ++-.+++.|+++...+.|+...++|++.-++|.-.|+-|.|+..
T Consensus       516 ~vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvlsItA~gvGLt~tAa~~VVFaEL~wnPgvLlQAEDRaHRiGQks  592 (689)
T KOG1000|consen  516 KVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSITAAGVGLTLTAASVVVFAELHWNPGVLLQAEDRAHRIGQKS  592 (689)
T ss_pred             CCCeEEecCCCCchhHHHHHHHhccccceEEEEEEEeecccceeeeccceEEEEEecCCCceEEechhhhhhccccc
Confidence            55667788999999999999999865 44543 34467899999999999999999999999999999999888754

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=97.05  E-value=0.0028  Score=53.31  Aligned_cols=81  Identities=23%  Similarity=0.290  Sum_probs=68.0

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhcCCCc---EEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEE
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRTKRYN---VLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVAT   79 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~g~~~---ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~   79 (135)
                      ++..-+-|....++|-..++.|...+..   .|..|.+.+.|+|+..++.||.||..|++....|+.-||-|.|+...+-
T Consensus       751 ~kYlRLDG~TK~~eRg~ll~~FN~Pds~yf~FllstragglglNlQtadtviifdsdwnp~~d~qaqdrahrigq~~evR  830 (1157)
T KOG0386|consen  751 YKYLRLDGQTKVEERGDLLEIFNAPDSPYFIFLLSTRAGGLGLNLQTADTVIIFDSDWNPHQDLQAQDRAHRIGQKKEVR  830 (1157)
T ss_pred             hheeeecCCcchhhHHHHHHHhcCCCCceeeeeeeecccccccchhhcceEEEecCCCCchhHHHHHHHHHHhhchhhee
Confidence            4455677889999999999999877644   5679999999999999999999999999999999999999988654444


Q ss_pred             EEee
Q 037139           80 TFLT   83 (135)
Q Consensus        80 ~~~~   83 (135)
                      ++..
T Consensus       831 v~rl  834 (1157)
T KOG0386|consen  831 VLRL  834 (1157)
T ss_pred             eeee
Confidence            4433

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]

Probab=97.04  E-value=0.0019  Score=54.41  Aligned_cols=83  Identities=25%  Similarity=0.287  Sum_probs=68.8

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCC---Cc-EEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCC--
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKR---YN-VLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKT--   75 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~---~~-ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~--   75 (135)
                      |..-.-+-|..+..+|++..+.|++-.   .+ .||.|.+.+.|+|+-.++.||.||..|+++-=.|.+=|+.|+|+.  
T Consensus      1188 GkDyyriDGst~s~~R~k~~~~FNdp~NlRaRl~LISTRAGsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyRfGQtKP 1267 (1567)
T KOG1015|consen 1188 GKDYYRLDGSTTSQSRKKWAEEFNDPTNLRARLFLISTRAGSLGINLVAANRVIIFDASWNPSYDTQSIFRVYRFGQTKP 1267 (1567)
T ss_pred             CCceEEecCcccHHHHHHHHHHhcCcccceeEEEEEeeccCccccceeecceEEEEecccCCccchHHHHHHHhhcCcCc
Confidence            444556789999999999999998642   33 679999999999999999999999999999889999999999975  


Q ss_pred             ceEEEEeec
Q 037139           76 GVATTFLTF   84 (135)
Q Consensus        76 g~~~~~~~~   84 (135)
                      .++|.|+..
T Consensus      1268 vyiYRfiAq 1276 (1567)
T KOG1015|consen 1268 VYIYRFIAQ 1276 (1567)
T ss_pred             eeehhhhhc
Confidence            445555443

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

Probab=97.04  E-value=0.0026  Score=54.01  Aligned_cols=47  Identities=26%  Similarity=0.344  Sum_probs=38.3

Q ss_pred             CCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccC--CcEEEEecCCC
Q 037139           11 GKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPD--VAHVINYDMPG   57 (135)
Q Consensus        11 ~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~--v~~vi~~d~p~   57 (135)
                      +++...|.++++.|+.++-.||++|..+.+|+|+|+  +.+||...+|.
T Consensus       787 g~~~~~r~~l~~~F~~~~~~iLlG~~sFwEGVD~pg~~l~~viI~kLPF  835 (928)
T PRK08074        787 GVSSGSRARLTKQFQQFDKAILLGTSSFWEGIDIPGDELSCLVIVRLPF  835 (928)
T ss_pred             CCCCCCHHHHHHHHHhcCCeEEEecCcccCccccCCCceEEEEEecCCC
Confidence            344456889999999998899999999999999997  46777666554

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=96.95  E-value=0.0055  Score=51.24  Aligned_cols=32  Identities=28%  Similarity=0.505  Sum_probs=24.7

Q ss_pred             CCCHHHHHHHhhhcCCCCCCceEEEEeecCCh
Q 037139           56 PGNIEMYTHRIGRTGRAGKTGVATTFLTFHDT   87 (135)
Q Consensus        56 p~~~~~~~qr~GR~gR~~~~g~~~~~~~~~~~   87 (135)
                      -.|..-=-|..||+||.|.+|..-.|++-+|.
T Consensus       602 heSrRIDnQLrGRaGRQGDPG~s~f~lSLED~  633 (870)
T CHL00122        602 HESRRIDNQLRGRAGRQGDPGSSRFFLSLEDN  633 (870)
T ss_pred             CchHHHHHHHhccccCCCCCCcceEEEEeccH
Confidence            33444448999999999999988888886655

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

Probab=96.91  E-value=0.0022  Score=53.06  Aligned_cols=66  Identities=18%  Similarity=0.369  Sum_probs=51.1

Q ss_pred             EEEecCCCCHHHHHHHHHHHhc--CCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCC
Q 037139            5 VTTLHGGKSQEQREISLEGFRT--KRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRA   72 (135)
Q Consensus         5 v~~~hg~~~~~~r~~~~~~f~~--g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~   72 (135)
                      +..|.|+-.  +-+..++.|..  ..-+|.|+.+++..|+|+|.|.+++.+-.-.|...|.||+||+-|.
T Consensus       458 a~~IT~d~~--~~q~~Id~f~~ke~~P~IaitvdlL~TGiDvpev~nlVF~r~VrSktkF~QMvGRGTRl  525 (875)
T COG4096         458 AMKITGDAE--QAQALIDNFIDKEKYPRIAITVDLLTTGVDVPEVVNLVFDRKVRSKTKFKQMVGRGTRL  525 (875)
T ss_pred             EEEEeccch--hhHHHHHHHHhcCCCCceEEehhhhhcCCCchheeeeeehhhhhhHHHHHHHhcCcccc
Confidence            445555532  22444555543  3456889999999999999999999999999999999999999883

>PF10593 Z1: Z1 domain; InterPro: IPR018310 This entry represents the Z1 domain of unknown function that is found in a group of putative endonucleases

Probab=96.78  E-value=0.0056  Score=44.10  Aligned_cols=110  Identities=13%  Similarity=0.222  Sum_probs=74.9

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCC----CcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcC-CCCCCc
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKR----YNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTG-RAGKTG   76 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~----~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~g-R~~~~g   76 (135)
                      |+.+..++++.+.+.     -.+..+.    ..|+|+=+.++||+.+++..+......+...+++.||.-..| |.|-..
T Consensus       110 ~~~v~~vNS~~~~~~-----ldy~~~~~~~~~~I~VGGn~LsRGlTleGL~vsYf~R~s~~~DTL~QmgRwFGYR~gY~d  184 (239)
T PF10593_consen  110 GIEVVVVNSGSSDDS-----LDYDDGENLGLNVIAVGGNKLSRGLTLEGLTVSYFLRNSKQYDTLMQMGRWFGYRPGYED  184 (239)
T ss_pred             CceEEEEeCCCcccc-----ccccccccCCceEEEECCccccCceeECCcEEEEecCCCchHHHHHHHhhcccCCccccc
Confidence            477888887765544     4455554    789999999999999999999999999999999999965566 555566


Q ss_pred             eEEEEeecCChhHHHHHHHHHhhCCCCCChHHHHHHHhhCCCCC
Q 037139           77 VATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGT  120 (135)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  120 (135)
                      .|-++..+.-...+..+.+    ...++.+++.........|..
T Consensus       185 l~Ri~~~~~l~~~f~~i~~----~~e~lr~~i~~~~~~~~tp~~  224 (239)
T PF10593_consen  185 LCRIYMPEELYDWFRHIAE----AEEELREEIKEMANNGLTPKD  224 (239)
T ss_pred             ceEEecCHHHHHHHHHHHH----HHHHHHHHHHHHHhcCCCHHH
Confidence            7777776654444444333    333344455554444444433

This domain is found associated with a helicase domain of superfamily type II [].

>PRK14873 primosome assembly protein PriA; Provisional

Probab=96.77  E-value=0.0089  Score=49.03  Aligned_cols=61  Identities=8%  Similarity=0.029  Sum_probs=44.7

Q ss_pred             HHHHHHhcCCCcEEEecC----CCcccccccCCcEEEEecC------CC------CHHHHHHHhhhcCCCCCCceEEEEe
Q 037139           19 ISLEGFRTKRYNVLVATD----VAGRGIDIPDVAHVINYDM------PG------NIEMYTHRIGRTGRAGKTGVATTFL   82 (135)
Q Consensus        19 ~~~~~f~~g~~~ilv~T~----~~~~G~d~~~v~~vi~~d~------p~------~~~~~~qr~GR~gR~~~~g~~~~~~   82 (135)
                      .+++.|. ++.+|||+|.    ++.     +++.+|+.+|.      |.      ....+.|-+||+||.+..|.+++..
T Consensus       463 ~~l~~~~-~~~~IlVGTqgaepm~~-----g~~~lV~ildaD~~L~~pDfRA~Er~~qll~qvagragr~~~~G~V~iq~  536 (665)
T PRK14873        463 QVVDTVD-AGPALVVATPGAEPRVE-----GGYGAALLLDAWALLGRQDLRAAEDTLRRWMAAAALVRPRADGGQVVVVA  536 (665)
T ss_pred             HHHHhhc-cCCCEEEECCCCccccc-----CCceEEEEEcchhhhcCCCcChHHHHHHHHHHHHHhhcCCCCCCEEEEEe
Confidence            4788896 5999999998    555     35677665552      21      2455689999999988889988875


Q ss_pred             ecC
Q 037139           83 TFH   85 (135)
Q Consensus        83 ~~~   85 (135)
                      .++
T Consensus       537 ~p~  539 (665)
T PRK14873        537 ESS  539 (665)
T ss_pred             CCC
Confidence            444

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

Probab=96.77  E-value=0.002  Score=54.45  Aligned_cols=52  Identities=31%  Similarity=0.564  Sum_probs=44.9

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEec----CCCcccccccC-CcEEEEecCCC
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVAT----DVAGRGIDIPD-VAHVINYDMPG   57 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T----~~~~~G~d~~~-v~~vi~~d~p~   57 (135)
                      .|+++..+|++     .++.++.|..|++++||+.    .++-+|+|+|. +.++|.++.|.
T Consensus       361 ~Gi~a~~~~a~-----~~~~le~F~~GeidvLVGvAsyYG~lVRGlDLP~rirYaIF~GvPk  417 (1187)
T COG1110         361 HGINAELIHAE-----KEEALEDFEEGEVDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVPK  417 (1187)
T ss_pred             cCceEEEeecc-----chhhhhhhccCceeEEEEecccccceeecCCchhheeEEEEecCCc
Confidence            47888889984     3889999999999999875    47889999997 78999999994

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=96.68  E-value=0.0049  Score=52.51  Aligned_cols=68  Identities=18%  Similarity=0.193  Sum_probs=50.7

Q ss_pred             eEEEecCCCCHHHHHHHHHHH----------------------hc----CCCcEEEecCCCcccccccCCcEEEEecCCC
Q 037139            4 RVTTLHGGKSQEQREISLEGF----------------------RT----KRYNVLVATDVAGRGIDIPDVAHVINYDMPG   57 (135)
Q Consensus         4 ~v~~~hg~~~~~~r~~~~~~f----------------------~~----g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~   57 (135)
                      .+.+||+..+...|..+.+.+                      .+    +..-|+|+|++++.|+|+. .+.+|  --|.
T Consensus       788 ~~~~yHSr~~l~~Rs~~E~~Ld~~L~R~~~~~~~~~~~i~~~l~~~~~~~~~~i~v~Tqv~E~g~D~d-fd~~~--~~~~  864 (1110)
T TIGR02562       788 HLCCYHAQDPLLLRSYIERRLDQLLTRHKPEQLFQDDEIIDLMQNSPALNHLFIVLATPVEEVGRDHD-YDWAI--ADPS  864 (1110)
T ss_pred             eEEEecccChHHHHHHHHHHHHHHhcccChhhhhchHHHHHHHhcccccCCCeEEEEeeeEEEEeccc-CCeee--eccC
Confidence            467899998888877766553                      12    3567999999999999983 34333  2366


Q ss_pred             CHHHHHHHhhhcCCCCC
Q 037139           58 NIEMYTHRIGRTGRAGK   74 (135)
Q Consensus        58 ~~~~~~qr~GR~gR~~~   74 (135)
                      +..+.+|++||+.|.+.
T Consensus       865 ~~~sliQ~aGR~~R~~~  881 (1110)
T TIGR02562       865 SMRSIIQLAGRVNRHRL  881 (1110)
T ss_pred             cHHHHHHHhhccccccc
Confidence            78899999999998654

The helicase in many CRISPR-associated (cas) gene clusters is designated Cas3, and most Cas3 proteins are described by model TIGR01587. Members of this family are considerably larger, show a number of motifs in common with TIGR01587 sequences, and replace Cas3 in some CRISPR/cas loci in a number of Proteobacteria, including Yersinia pestis, Chromobacterium violaceum, Erwinia carotovora subsp. atroseptica SCRI1043, Photorhabdus luminescens subsp. laumondii TTO1, Legionella pneumophila, etc.

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

Probab=96.64  E-value=0.0079  Score=49.06  Aligned_cols=67  Identities=25%  Similarity=0.368  Sum_probs=48.7

Q ss_pred             HHHHHHHHHHHhcCCC-cEEEecCCCcccccccC--CcEEEEecCCCC------------------------------HH
Q 037139           14 QEQREISLEGFRTKRY-NVLVATDVAGRGIDIPD--VAHVINYDMPGN------------------------------IE   60 (135)
Q Consensus        14 ~~~r~~~~~~f~~g~~-~ilv~T~~~~~G~d~~~--v~~vi~~d~p~~------------------------------~~   60 (135)
                      ...+.+.++.|+.+.- -++|+|..+.+|+|+|+  ..+||...+|.-                              ..
T Consensus       513 ~~~~~~~l~~f~~~~~~~~lv~~gsf~EGVD~~g~~l~~vvI~~lPfp~p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~  592 (654)
T COG1199         513 EDEREELLEKFKASGEGLILVGGGSFWEGVDFPGDALRLVVIVGLPFPNPDDPLLKARLEFLKRLGGDPFEEFYLPPAVI  592 (654)
T ss_pred             CCcHHHHHHHHHHhcCCeEEEeeccccCcccCCCCCeeEEEEEecCCCCCCCHHHHHHHHHHHHhcCCCceEeehHHHHH
Confidence            3344588888877655 89999999999999987  467777776642                              23


Q ss_pred             HHHHHhhhcCCCCCC-ceEEE
Q 037139           61 MYTHRIGRTGRAGKT-GVATT   80 (135)
Q Consensus        61 ~~~qr~GR~gR~~~~-g~~~~   80 (135)
                      ...|.+||+-|.-++ |.+++
T Consensus       593 ~l~QavGRlIR~~~D~G~ivl  613 (654)
T COG1199         593 KLRQAVGRLIRSEDDRGVIVL  613 (654)
T ss_pred             HHHHhhccccccCCCceEEEE
Confidence            458999999986544 44333

>PF06862 DUF1253: Protein of unknown function (DUF1253); InterPro: IPR010678 This family is defined by a C-terminal region of approximately 500 residues, Digestive organ expansion factor (DEF) is thought to Regulate the p53 pathway to control the expansion growth of digestive organs and is required for the expansion growth of intestine, liver and exocrine pancreas, but not endocrine pancreas [, ]

Probab=96.63  E-value=0.032  Score=43.66  Aligned_cols=92  Identities=17%  Similarity=0.175  Sum_probs=71.6

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecC--CCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCC-----
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATD--VAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGK-----   74 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~--~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~-----   74 (135)
                      ++....+|--.++.+-..+-..|..|+.+||+.|.  -.-+=..+.++..||.|.+|..+.=|...++..+....     
T Consensus       324 ~~sF~~i~EYts~~~isRAR~~F~~G~~~iLL~TER~HFfrRy~irGi~~viFY~~P~~p~fY~El~n~~~~~~~~~~~~  403 (442)
T PF06862_consen  324 NISFVQISEYTSNSDISRARSQFFHGRKPILLYTERFHFFRRYRIRGIRHVIFYGPPENPQFYSELLNMLDESSGGEVDA  403 (442)
T ss_pred             CCeEEEecccCCHHHHHHHHHHHHcCCceEEEEEhHHhhhhhceecCCcEEEEECCCCChhHHHHHHhhhcccccccccc
Confidence            45677888889999999999999999999999997  33445667889999999999999888887765554332     


Q ss_pred             -CceEEEEeecCChhHHHHH
Q 037139           75 -TGVATTFLTFHDTDVFYDL   93 (135)
Q Consensus        75 -~g~~~~~~~~~~~~~~~~~   93 (135)
                       ...|.++++.-|.-.++.+
T Consensus       404 ~~~~~~~lysk~D~~~LErI  423 (442)
T PF06862_consen  404 ADATVTVLYSKYDALRLERI  423 (442)
T ss_pred             cCceEEEEecHhHHHHHHHH
Confidence             4678888877666544433

; GO: 0005634 nucleus

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

Probab=96.48  E-value=0.016  Score=48.73  Aligned_cols=67  Identities=18%  Similarity=0.146  Sum_probs=47.3

Q ss_pred             HHHHHHHHhcCCCcEEEecCCCcccccccC--CcEEEEecCCC----C--------------------------HHHHHH
Q 037139           17 REISLEGFRTKRYNVLVATDVAGRGIDIPD--VAHVINYDMPG----N--------------------------IEMYTH   64 (135)
Q Consensus        17 r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~--v~~vi~~d~p~----~--------------------------~~~~~q   64 (135)
                      +.+++++|++++-.||++|+.+-+|+|+|.  ..+||...+|.    +                          ...+.|
T Consensus       683 ~~~l~~~F~~~~~~vLlG~~sFwEGVD~p~~~~~~viI~kLPF~~P~dP~~~a~~~~~~~~g~~~F~~~~lP~A~iklkQ  762 (820)
T PRK07246        683 AYNIKKRFDRGEQQILLGLGSFWEGVDFVQADRMIEVITRLPFDNPEDPFVKKMNQYLLQEGKNPFYDYFLPMTILRLKQ  762 (820)
T ss_pred             HHHHHHHHHcCCCeEEEecchhhCCCCCCCCCeEEEEEecCCCCCCCCHHHHHHHHHHHHhCCCchhheeHHHHHHHHHH
Confidence            466899999998899999999999999974  44555555442    2                          122488


Q ss_pred             HhhhcCCCCC-CceEEEEeec
Q 037139           65 RIGRTGRAGK-TGVATTFLTF   84 (135)
Q Consensus        65 r~GR~gR~~~-~g~~~~~~~~   84 (135)
                      -+||.=|... .|. +++++.
T Consensus       763 g~GRLIRs~~D~Gv-v~ilD~  782 (820)
T PRK07246        763 AIGRTMRREDQKSA-VLILDR  782 (820)
T ss_pred             HhcccccCCCCcEE-EEEECC
Confidence            8899988764 454 344443

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=96.48  E-value=0.016  Score=47.81  Aligned_cols=42  Identities=26%  Similarity=0.385  Sum_probs=33.4

Q ss_pred             HHHHHHHHHh----cCCCcEEEecCCCcccccccC--CcEEEEecCCC
Q 037139           16 QREISLEGFR----TKRYNVLVATDVAGRGIDIPD--VAHVINYDMPG   57 (135)
Q Consensus        16 ~r~~~~~~f~----~g~~~ilv~T~~~~~G~d~~~--v~~vi~~d~p~   57 (135)
                      .+.++++.|+    .++-.||++|..+.+|+|+|+  +++||...+|.
T Consensus       569 ~~~~ll~~f~~~~~~~~~~VL~g~~sf~EGVD~pGd~l~~vII~kLPF  616 (697)
T PRK11747        569 PRQRLLEKHKKRVDEGEGSVLFGLQSFAEGLDLPGDYLTQVIITKIPF  616 (697)
T ss_pred             hHHHHHHHHHHHhccCCCeEEEEeccccccccCCCCceEEEEEEcCCC
Confidence            4677887776    467789999999999999987  67788766663

>KOG0701 consensus dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification]

Probab=96.36  E-value=0.00098  Score=58.57  Aligned_cols=56  Identities=30%  Similarity=0.532  Sum_probs=53.3

Q ss_pred             HHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCC
Q 037139           17 REISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRA   72 (135)
Q Consensus        17 r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~   72 (135)
                      +++++..|...++++|++|.++.+|+|++.++.++.++.|.....|+|..||+-+.
T Consensus       343 ~~~vl~~~~~~~ln~L~~~~~~~e~~d~~~~~~~~~~~~~~~~~~~vq~~~r~~~~  398 (1606)
T KOG0701|consen  343 QAEVLRRFHFHELNLLIATSVLEEGVDVPKCNLVVLFDAPTYYRSYVQKKGRARAA  398 (1606)
T ss_pred             hHHHHHHHhhhhhhHHHHHHHHHhhcchhhhhhheeccCcchHHHHHHhhcccccc
Confidence            68899999999999999999999999999999999999999999999999999654

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=96.07  E-value=0.014  Score=48.02  Aligned_cols=52  Identities=21%  Similarity=0.344  Sum_probs=45.4

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCC-CcccccccCCcEEEEe
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDV-AGRGIDIPDVAHVINY   53 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~-~~~G~d~~~v~~vi~~   53 (135)
                      |+++..+||+++..+|.++++.+.+|+.+|+|+|.. +...+.+.++.+||.-
T Consensus       338 ~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~v~~~~l~lvVID  390 (681)
T PRK10917        338 GIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIID  390 (681)
T ss_pred             CcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcccchhcccceEEEe
Confidence            688999999999999999999999999999999974 4446788899888743

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

Probab=95.58  E-value=0.03  Score=45.69  Aligned_cols=52  Identities=25%  Similarity=0.356  Sum_probs=46.8

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCc-ccccccCCcEEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAG-RGIDIPDVAHVIN   52 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~-~G~d~~~v~~vi~   52 (135)
                      +|++|..+.|++..+.|++++++..+|+++|+|+|-++- ..+++.+..+||.
T Consensus       338 ~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd~V~F~~LgLVIi  390 (677)
T COG1200         338 LGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQDKVEFHNLGLVII  390 (677)
T ss_pred             cCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhhcceeecceeEEEE
Confidence            478899999999999999999999999999999997654 5799999888874

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=95.58  E-value=0.026  Score=46.11  Aligned_cols=52  Identities=23%  Similarity=0.283  Sum_probs=44.8

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCc-ccccccCCcEEEEe
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAG-RGIDIPDVAHVINY   53 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~-~G~d~~~v~~vi~~   53 (135)
                      |+++..+||+++.++|..+++.+.+|+.+|+|+|..+- ..+.+.++.+||.-
T Consensus       312 gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~~~~~~~l~lvVID  364 (630)
T TIGR00643       312 GIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIID  364 (630)
T ss_pred             CcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhccccccccceEEEe
Confidence            68899999999999999999999999999999997543 45778888888743

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=95.50  E-value=0.092  Score=43.48  Aligned_cols=43  Identities=28%  Similarity=0.370  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHhc----CCCcEEEec--CCCcccccccC--CcEEEEecCCC
Q 037139           15 EQREISLEGFRT----KRYNVLVAT--DVAGRGIDIPD--VAHVINYDMPG   57 (135)
Q Consensus        15 ~~r~~~~~~f~~----g~~~ilv~T--~~~~~G~d~~~--v~~vi~~d~p~   57 (135)
                      .++.++++.|+.    +.-.||+|+  ..+.+|+|+++  +++||..++|.
T Consensus       565 ~~~~~~l~~f~~~~~~~~gavL~av~gGk~sEGIDf~~~~~r~ViivGlPf  615 (705)
T TIGR00604       565 QETSDALERYKQAVSEGRGAVLLSVAGGKVSEGIDFCDDLGRAVIMVGIPY  615 (705)
T ss_pred             chHHHHHHHHHHHHhcCCceEEEEecCCcccCccccCCCCCcEEEEEccCC
Confidence            577889999964    455699998  88999999987  67888888876

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).

>PRK14873 primosome assembly protein PriA; Provisional

Probab=95.43  E-value=0.057  Score=44.44  Aligned_cols=51  Identities=20%  Similarity=0.137  Sum_probs=42.9

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEec
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYD   54 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d   54 (135)
                      ..+..+|+++++.+|.+.+.+..+|+.+|+|+|.. +.=..+++..+||..+
T Consensus       215 ~~v~~lhS~l~~~~R~~~w~~~~~G~~~IViGtRS-AvFaP~~~LgLIIvdE  265 (665)
T PRK14873        215 GDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRS-AVFAPVEDLGLVAIWD  265 (665)
T ss_pred             CcEEEECCCCCHHHHHHHHHHHhCCCCcEEEEcce-eEEeccCCCCEEEEEc
Confidence            56889999999999999999999999999999975 3345667788887554

>PRK05580 primosome assembly protein PriA; Validated

Probab=95.28  E-value=0.058  Score=44.52  Aligned_cols=52  Identities=19%  Similarity=0.208  Sum_probs=42.9

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEec
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYD   54 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d   54 (135)
                      |..+..+||+++..+|.+.+.++..|+.+|+|+|.... -..+.++.+||..+
T Consensus       215 g~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal-~~p~~~l~liVvDE  266 (679)
T PRK05580        215 GAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSAL-FLPFKNLGLIIVDE  266 (679)
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHh-cccccCCCEEEEEC
Confidence            56789999999999999999999999999999997432 25567788887544

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]

Probab=95.19  E-value=0.054  Score=45.27  Aligned_cols=81  Identities=21%  Similarity=0.269  Sum_probs=65.3

Q ss_pred             ecCCCCHHHHHHHHHHHhcC---CCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEEeec
Q 037139            8 LHGGKSQEQREISLEGFRTK---RYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTF   84 (135)
Q Consensus         8 ~hg~~~~~~r~~~~~~f~~g---~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~~~~   84 (135)
                      +.|..+..+|++.+++|++-   .+-+++.|.....|+|+-..+-++.+|.-|++.--.|.+-|+-|.|+...|+++-.-
T Consensus       767 ldG~t~a~~rekLinqfN~e~~lsWlfllstrag~lGinLIsanr~~ifda~wnpchdaqavcRvyrYGQ~KpcfvYRlV  846 (1387)
T KOG1016|consen  767 LDGTTSAADREKLINQFNSEPGLSWLFLLSTRAGSLGINLISANRCIIFDACWNPCHDAQAVCRVYRYGQQKPCFVYRLV  846 (1387)
T ss_pred             ccCCcccchHHHHHHhccCCCCceeeeeehhccccccceeeccceEEEEEeecCccccchhhhhhhhhcCcCceeEEeeh
Confidence            45778889999999999753   346788999999999999999999999999998889999999999876555554433


Q ss_pred             CChh
Q 037139           85 HDTD   88 (135)
Q Consensus        85 ~~~~   88 (135)
                      .+..
T Consensus       847 mD~~  850 (1387)
T KOG1016|consen  847 MDNS  850 (1387)
T ss_pred             hhhh
Confidence            3333

>TIGR00595 priA primosomal protein N'

Probab=95.16  E-value=0.052  Score=43.27  Aligned_cols=52  Identities=19%  Similarity=0.267  Sum_probs=42.4

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEec
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYD   54 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d   54 (135)
                      |..+..+||++++.+|.+.+.+..+|+.+|+|+|..... ..+.++++||.-+
T Consensus        50 ~~~v~vlhs~~~~~er~~~~~~~~~g~~~IVVGTrsalf-~p~~~l~lIIVDE  101 (505)
T TIGR00595        50 GSQVAVLHSGLSDSEKLQAWRKVKNGEILVVIGTRSALF-LPFKNLGLIIVDE  101 (505)
T ss_pred             CCcEEEEECCCCHHHHHHHHHHHHcCCCCEEECChHHHc-CcccCCCEEEEEC
Confidence            567889999999999999999999999999999974322 4567788877443

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).

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

Probab=95.10  E-value=0.026  Score=48.04  Aligned_cols=31  Identities=19%  Similarity=0.412  Sum_probs=29.5

Q ss_pred             ecCCCCHHHHHHHHHHHhcCCCcEEEecCCC
Q 037139            8 LHGGKSQEQREISLEGFRTKRYNVLVATDVA   38 (135)
Q Consensus         8 ~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~   38 (135)
                      +||.|+.+++++++++|.+|+.+|||+|+.+
T Consensus       161 yh~~l~~~ekee~le~i~~gdfdIlitTs~F  191 (1187)
T COG1110         161 YHSALPTKEKEEALERIESGDFDILITTSQF  191 (1187)
T ss_pred             eccccchHHHHHHHHHHhcCCccEEEEeHHH
Confidence            9999999999999999999999999999854

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=95.08  E-value=0.12  Score=43.79  Aligned_cols=25  Identities=36%  Similarity=0.683  Sum_probs=21.2

Q ss_pred             HHHhhhcCCCCCCceEEEEeecCCh
Q 037139           63 THRIGRTGRAGKTGVATTFLTFHDT   87 (135)
Q Consensus        63 ~qr~GR~gR~~~~g~~~~~~~~~~~   87 (135)
                      -|..||+||.|.+|..-.|++-.|.
T Consensus       666 NQLRGRaGRQGDPGsSrFflSLEDd  690 (939)
T PRK12902        666 NQLRGRAGRQGDPGSTRFFLSLEDN  690 (939)
T ss_pred             HHhhcccccCCCCCcceEEEEechH
Confidence            7888999999999988888876554

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

Probab=94.97  E-value=0.034  Score=46.03  Aligned_cols=50  Identities=22%  Similarity=0.289  Sum_probs=42.5

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVI   51 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi   51 (135)
                      +|.++..+|+++++.+|...+.+.++|+.+|+|+|-. +--..+++..+||
T Consensus       269 Fg~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRS-AlF~Pf~~LGLII  318 (730)
T COG1198         269 FGAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRS-ALFLPFKNLGLII  318 (730)
T ss_pred             hCCChhhhcccCChHHHHHHHHHHhcCCceEEEEech-hhcCchhhccEEE
Confidence            3678899999999999999999999999999999964 2345667788777

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=94.89  E-value=0.14  Score=43.08  Aligned_cols=50  Identities=18%  Similarity=-0.019  Sum_probs=36.7

Q ss_pred             EecCCCcccccccC----------------------C----------cEEEEecCCCCHHHHHH--HhhhcCCCCCCceE
Q 037139           33 VATDVAGRGIDIPD----------------------V----------AHVINYDMPGNIEMYTH--RIGRTGRAGKTGVA   78 (135)
Q Consensus        33 v~T~~~~~G~d~~~----------------------v----------~~vi~~d~p~~~~~~~q--r~GR~gR~~~~g~~   78 (135)
                      ++|+...+|+|+|.                      +          ++||.|++-.+...-+|  |.||.||   ++.+
T Consensus       431 ~~~~~~~e~~d~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~L~e~~P~~VImYEP~~sfIR~IEvyra~r~~r---~~rV  507 (814)
T TIGR00596       431 FEIIDEENDIDIYSGAEFDNLPQHITHFLWGERDEYVLRCSLEELMPRYVIMYEPDISFIRQLEVYKASRPLR---PLRV  507 (814)
T ss_pred             ccccccccccccchhhccccccceeeeecccccchhhHHHHHhhhCCCEEEEECCChHHHHHHHHHHccCCCC---CcEE
Confidence            67888889999997                      5          89999997776655566  5555554   5677


Q ss_pred             EEEeecC
Q 037139           79 TTFLTFH   85 (135)
Q Consensus        79 ~~~~~~~   85 (135)
                      +.++..+
T Consensus       508 yfL~y~~  514 (814)
T TIGR00596       508 YFLYYGG  514 (814)
T ss_pred             EEEEECC
Confidence            7777655

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

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

Probab=94.87  E-value=0.076  Score=46.36  Aligned_cols=77  Identities=19%  Similarity=0.210  Sum_probs=59.8

Q ss_pred             cCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEE----Eec------CCCCHHHHHHHhhhcCCCCCCceE
Q 037139            9 HGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVI----NYD------MPGNIEMYTHRIGRTGRAGKTGVA   78 (135)
Q Consensus         9 hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi----~~d------~p~~~~~~~qr~GR~gR~~~~g~~   78 (135)
                      |-+|+..++.-+-..|..|.++++|...- ..|+-...--+|+    .||      .+.+.....|++|+|.|   .|.|
T Consensus      1412 ~e~~s~~d~~iv~~l~e~g~i~v~v~s~~-~~~~~~~~~lVvvmgt~~ydg~e~~~~~y~i~~ll~m~G~a~~---~~k~ 1487 (1674)
T KOG0951|consen 1412 HEGLSSNDQEIVQQLFEAGAIQVCVMSRD-CYGTKLKAHLVVVMGTQYYDGKEHSYEDYPIAELLQMVGLASG---AGKC 1487 (1674)
T ss_pred             ccccCcchHHHHHHHHhcCcEEEEEEEcc-cccccccceEEEEecceeecccccccccCchhHHHHHhhhhcC---CccE
Confidence            88999999999999999999999998766 7777765433333    455      34467889999999988   5578


Q ss_pred             EEEeecCChhH
Q 037139           79 TTFLTFHDTDV   89 (135)
Q Consensus        79 ~~~~~~~~~~~   89 (135)
                      ++++.......
T Consensus      1488 vi~~~~~~k~y 1498 (1674)
T KOG0951|consen 1488 VIMCHTPKKEY 1498 (1674)
T ss_pred             EEEecCchHHH
Confidence            88887765543

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

Probab=94.85  E-value=0.32  Score=39.96  Aligned_cols=67  Identities=22%  Similarity=0.226  Sum_probs=47.4

Q ss_pred             EecCCCCHHHHHHHHHHHhc----CCCcEEEecCCCcccccc--------c--CCcEEEEecCCCC--------------
Q 037139            7 TLHGGKSQEQREISLEGFRT----KRYNVLVATDVAGRGIDI--------P--DVAHVINYDMPGN--------------   58 (135)
Q Consensus         7 ~~hg~~~~~~r~~~~~~f~~----g~~~ilv~T~~~~~G~d~--------~--~v~~vi~~d~p~~--------------   58 (135)
                      .+.|+.+  .+...+++|+.    |.-.||++|+.+-+|+|+        |  .+++||...+|..              
T Consensus       499 l~qg~~~--~~~~l~~~f~~~~~~~~~~vL~gt~sfweGvDv~~~~~~p~~G~~Ls~ViI~kLPF~~~dp~a~~~~~~~~  576 (636)
T TIGR03117       499 VIQSEKN--RLASAEQQFLALYANGIQPVLIAAGGAWTGIDLTHKPVSPDKDNLLTDLIITCAPFGLNRSLSMLKRIRKT  576 (636)
T ss_pred             EEeCCCc--cHHHHHHHHHHhhcCCCCcEEEeCCccccccccCCccCCCCCCCcccEEEEEeCCCCcCChHHHHHHHHhc
Confidence            4455443  34668888887    478999999999999999        2  3788887776632              


Q ss_pred             -----------HHHHHHHhhhcCCCCCC
Q 037139           59 -----------IEMYTHRIGRTGRAGKT   75 (135)
Q Consensus        59 -----------~~~~~qr~GR~gR~~~~   75 (135)
                                 .-.+.|-+||.=|...+
T Consensus       577 g~~~f~~~p~a~i~lkQg~GRLIR~~~D  604 (636)
T TIGR03117       577 SVRPWEIINESLMMLRQGLGRLVRHPDM  604 (636)
T ss_pred             CCChHhhhHHHHHHHHHhcCceeecCCC
Confidence                       12247888888786543

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.

>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]

Probab=94.82  E-value=0.09  Score=44.10  Aligned_cols=79  Identities=16%  Similarity=0.199  Sum_probs=57.3

Q ss_pred             HHHHhcCCCcEEEecCCCcccccccCCcEE--------EEecCCCCHHHHHHHhhhcCCCCC---CceEEEEee-cCChh
Q 037139           21 LEGFRTKRYNVLVATDVAGRGIDIPDVAHV--------INYDMPGNIEMYTHRIGRTGRAGK---TGVATTFLT-FHDTD   88 (135)
Q Consensus        21 ~~~f~~g~~~ilv~T~~~~~G~d~~~v~~v--------i~~d~p~~~~~~~qr~GR~gR~~~---~g~~~~~~~-~~~~~   88 (135)
                      -++|..|+-.|-|-+.+++-|+-+..-..|        |-+.+|||....+|..||+-|.++   +.+++++.. ..+..
T Consensus       850 KqrFM~GeK~vAIISEAaSSGiSLQsDrRv~NqRRRvHiTLELPWSADrAIQQFGRTHRSNQVsaPEYvFlIseLAGErR  929 (1300)
T KOG1513|consen  850 KQRFMDGEKLVAIISEAASSGISLQSDRRVQNQRRRVHITLELPWSADRAIQQFGRTHRSNQVSAPEYVFLISELAGERR  929 (1300)
T ss_pred             HhhhccccceeeeeehhhccCceeecchhhhhhhheEEEEEECCcchhHHHHHhcccccccccCCCeEEEEehhhccchH
Confidence            367999999999999999999998754433        568899999999999999999765   333333332 23555


Q ss_pred             HHHHHHHHHhh
Q 037139           89 VFYDLKQMLIQ   99 (135)
Q Consensus        89 ~~~~~~~~~~~   99 (135)
                      +...+.+.++.
T Consensus       930 FAS~VAKRLES  940 (1300)
T KOG1513|consen  930 FASIVAKRLES  940 (1300)
T ss_pred             HHHHHHHHHHh
Confidence            55555555543

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=94.73  E-value=0.0059  Score=51.20  Aligned_cols=80  Identities=23%  Similarity=0.362  Sum_probs=63.4

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEec------------------CCCCHHHHHH
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYD------------------MPGNIEMYTH   64 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d------------------~p~~~~~~~q   64 (135)
                      +.+...|+-+...++.++.+-...|..++++.|.+....+.+.++..|+..+                  .-.+..+..|
T Consensus       675 y~ilp~Hsq~~~~eqrkvf~~~p~gv~kii~stniaetsiTidd~v~vid~cka~~~~~~s~nn~~~~Atvw~sktn~eq  754 (1282)
T KOG0921|consen  675 YEILPLHSQLTSQEQRKVFEPVPEGVTKIILSTNIAETSITIDDVVYVIDSCKAKEKLFTSHNNMTHYATVWASKTNLEQ  754 (1282)
T ss_pred             cccccchhhcccHhhhhccCcccccccccccccceeeEeeeecceeEEEeeeeeeeeeeccccceeeeeeecccccchHh
Confidence            3466789999999999999999999999999999999888888877666433                  1224566799


Q ss_pred             HhhhcCCCCCCceEEEEee
Q 037139           65 RIGRTGRAGKTGVATTFLT   83 (135)
Q Consensus        65 r~GR~gR~~~~g~~~~~~~   83 (135)
                      |.||+||. ++|.|..+++
T Consensus       755 r~gr~grv-R~G~~f~lcs  772 (1282)
T KOG0921|consen  755 RKGRAGRV-RPGFCFHLCS  772 (1282)
T ss_pred             hcccCcee-cccccccccH
Confidence            99999986 4677777765

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=93.70  E-value=0.13  Score=43.91  Aligned_cols=51  Identities=14%  Similarity=0.266  Sum_probs=43.6

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecC-CCcccccccCCcEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATD-VAGRGIDIPDVAHVIN   52 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~-~~~~G~d~~~v~~vi~   52 (135)
                      ++++..++|..+.+++.++++.+++|+++|+|+|. .+...+.+.++.++|.
T Consensus       528 ~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll~~~v~f~~L~llVI  579 (926)
T TIGR00580       528 PVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLII  579 (926)
T ss_pred             CcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHhhCCCCcccCCEEEe
Confidence            56788899999999999999999999999999996 4445678888888774

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.

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

Probab=92.74  E-value=0.29  Score=42.48  Aligned_cols=50  Identities=16%  Similarity=0.359  Sum_probs=44.5

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEec-CCCcccccccCCcEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVAT-DVAGRGIDIPDVAHVI   51 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T-~~~~~G~d~~~v~~vi   51 (135)
                      +++|..+..=.+.+++.++++.+++|+++|+|+| .++..++-|.+..++|
T Consensus       671 PV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL~kdv~FkdLGLlI  721 (1139)
T COG1197         671 PVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVKFKDLGLLI  721 (1139)
T ss_pred             CeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHhhCCCcEEecCCeEE
Confidence            4567777777899999999999999999999999 5788899999999987

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=92.69  E-value=0.14  Score=42.94  Aligned_cols=56  Identities=34%  Similarity=0.529  Sum_probs=39.6

Q ss_pred             cEEEecCCCcccccccCCc-----------EEEEecCCCCHHHHHHHhhhcCCCCCCceEEEEeecC
Q 037139           30 NVLVATDVAGRGIDIPDVA-----------HVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFH   85 (135)
Q Consensus        30 ~ilv~T~~~~~G~d~~~v~-----------~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~~~~~   85 (135)
                      .|-|||+++++|.|+.--.           +||=...-.|..-=-|..||+||.|.+|..-.+++-.
T Consensus       479 aVTiATNMAGRGTDIkLg~~~~~V~~lGGL~VIgTERhESRRIDnQLRGRsGRQGDpG~S~F~lSle  545 (822)
T COG0653         479 AVTIATNMAGRGTDIKLGGNPEFVMELGGLHVIGTERHESRRIDNQLRGRAGRQGDPGSSRFYLSLE  545 (822)
T ss_pred             ccccccccccCCcccccCCCHHHHHHhCCcEEEecccchhhHHHHHhhcccccCCCcchhhhhhhhH
Confidence            4679999999999984222           3444444445544569999999999888777666543

>PRK10689 transcription-repair coupling factor; Provisional

Probab=92.57  E-value=0.24  Score=43.34  Aligned_cols=51  Identities=16%  Similarity=0.221  Sum_probs=42.7

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecC-CCcccccccCCcEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATD-VAGRGIDIPDVAHVIN   52 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~-~~~~G~d~~~v~~vi~   52 (135)
                      ++++.+++|..+.+++.++++.+.+|.++|+|+|. .+...+.+.++.++|.
T Consensus       677 ~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~~~v~~~~L~lLVI  728 (1147)
T PRK10689        677 PVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIV  728 (1147)
T ss_pred             CceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHhCCCCHhhCCEEEE
Confidence            46788899999999999999999999999999996 4444577778888773

>PRK14701 reverse gyrase; Provisional

Probab=88.95  E-value=0.85  Score=41.47  Aligned_cols=36  Identities=22%  Similarity=0.367  Sum_probs=32.8

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCC
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDV   37 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~   37 (135)
                      ++.+..+||+++.+++.++++.+.+|+.+|||+|.-
T Consensus       152 ~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPg  187 (1638)
T PRK14701        152 DVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQ  187 (1638)
T ss_pred             ceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCc
Confidence            456789999999999999999999999999999974

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=88.36  E-value=0.045  Score=45.06  Aligned_cols=76  Identities=21%  Similarity=0.268  Sum_probs=63.4

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcC-CCcEE-EecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCce
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTK-RYNVL-VATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGV   77 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g-~~~il-v~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~   77 (135)
                      |+....+-|.|+...|.+.+..|..+ ..+++ ++..+...|+|+-.+.+|+..|+-|++..--|.+-|+-|-|+.-.
T Consensus       563 ~~~~~~~~g~~~~~~r~~s~~~~~~~~~~~vll~Slkag~~glnlt~a~~v~~~d~~wnp~~eeQaidR~hrigq~k~  640 (674)
T KOG1001|consen  563 GFVFLRYDGEMLMKIRTKSFTDFPCDPLVTALLMSLKAGKVGLNLTAASHVLLMDPWWNPAVEEQAIDRAHRIGQTKP  640 (674)
T ss_pred             ccccchhhhhhHHHHHHhhhcccccCccHHHHHHHHHHhhhhhchhhhhHHHhhchhcChHHHHHHHHHHHHhcccce
Confidence            44555667899999999999999754 34455 577889999999999999999999999999999999999886543

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

Probab=88.21  E-value=2.1  Score=36.95  Aligned_cols=73  Identities=16%  Similarity=0.226  Sum_probs=56.0

Q ss_pred             CCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCC-----CC----Cce-EEEEeecCChhHHHHHHHHH
Q 037139           28 RYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRA-----GK----TGV-ATTFLTFHDTDVFYDLKQML   97 (135)
Q Consensus        28 ~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~-----~~----~g~-~~~~~~~~~~~~~~~~~~~~   97 (135)
                      .++.+++-+++.+|.|.|++-.+..+.-..|...-.|.+||..|.     |.    ... ..++++....++...|.+-.
T Consensus       501 ~~~fifs~~al~egwd~~~~~~~~~l~~~~s~~~~~q~~gr~lr~~vnq~G~R~~~~~~~LTvianesy~dFa~~LQ~EI  580 (986)
T PRK15483        501 TRRFLFSKWTLREGWDNPNVFQIAKLRSSGSETSKLQEVGRGLRLPVDENGHRVSQEEFRLNYLIDYDEKDFASKLVGEI  580 (986)
T ss_pred             CeEEEEEhHHhhhcCCCCCeEEEEEeccCCchHHHHHHhccceeccccccCccccCccEEEEEEeCccHHHHHHHHHHHH
Confidence            578999999999999999998888888888888889999999883     21    112 22344556677788888777


Q ss_pred             hhC
Q 037139           98 IQS  100 (135)
Q Consensus        98 ~~~  100 (135)
                      +..
T Consensus       581 ~~~  583 (986)
T PRK15483        581 NSD  583 (986)
T ss_pred             Hhh
Confidence            654

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

Probab=88.20  E-value=2.5  Score=36.60  Aligned_cols=65  Identities=23%  Similarity=0.373  Sum_probs=47.9

Q ss_pred             HHHHHH--HhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCC--C--CCceEEEEee
Q 037139           18 EISLEG--FRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRA--G--KTGVATTFLT   83 (135)
Q Consensus        18 ~~~~~~--f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~--~--~~g~~~~~~~   83 (135)
                      ......  ......++||.++++-.|.|-|.+. .+.+|-|.-.-..+|.+.|+.|.  +  ..|.++.+..
T Consensus       581 ~~~~~r~~~~~d~~kilIV~dmlLTGFDaP~L~-TmYvDK~Lk~H~L~QAisRtNR~~~~~K~~G~IVDf~g  651 (962)
T COG0610         581 KDLIKRFKLKDDPLDLLIVVDMLLTGFDAPCLN-TLYVDKPLKYHNLIQAISRTNRVFPGKKKFGLIVDFRG  651 (962)
T ss_pred             hhhhhhhcCcCCCCCEEEEEccccccCCccccc-eEEeccccccchHHHHHHHhccCCCCCCCCcEEEECcc
Confidence            344444  3556799999999999999999876 55667777777889999999994  2  2355555554

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

Probab=87.15  E-value=3.8  Score=33.13  Aligned_cols=47  Identities=26%  Similarity=0.398  Sum_probs=37.8

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecC------CCcccccccCCcEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATD------VAGRGIDIPDVAHVIN   52 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~------~~~~G~d~~~v~~vi~   52 (135)
                      |+.+.++||+++..++...++    -...|+|||.      +--.++|+..+++++.
T Consensus       324 gl~~v~~ygGgsk~eQ~k~Lk----~g~EivVaTPgRlid~VkmKatn~~rvS~LV~  376 (731)
T KOG0339|consen  324 GLRVVAVYGGGSKWEQSKELK----EGAEIVVATPGRLIDMVKMKATNLSRVSYLVL  376 (731)
T ss_pred             cceEEEeecCCcHHHHHHhhh----cCCeEEEechHHHHHHHHhhcccceeeeEEEE
Confidence            788999999999999888777    4468999997      2235789999988763

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=85.72  E-value=2  Score=36.53  Aligned_cols=72  Identities=17%  Similarity=0.216  Sum_probs=55.9

Q ss_pred             CCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCC--CCCc-----------eEEEEeecCChhHHHHHH
Q 037139           28 RYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRA--GKTG-----------VATTFLTFHDTDVFYDLK   94 (135)
Q Consensus        28 ~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~--~~~g-----------~~~~~~~~~~~~~~~~~~   94 (135)
                      ..+.+++-.++.+|.|-|+|=.+.-+....|..+=.|-+||.-|.  +..|           ...+++...+..+...+.
T Consensus       483 plRFIFS~waLrEGWDNPNVFtIckL~~S~SeiSK~QeVGRGLRLaVNe~G~RV~~~~~~~n~L~vlv~~sek~Fv~~Lq  562 (985)
T COG3587         483 PLRFIFSKWALREGWDNPNVFTICKLRSSGSEISKLQEVGRGLRLAVNENGERVTKDFDFPNELTVLVNESEKDFVKALQ  562 (985)
T ss_pred             cceeeeehhHHhhcCCCCCeeEEEEecCCCcchHHHHHhccceeeeeccccceecccccccceEEEEecccHHHHHHHHH
Confidence            478899999999999999999888899899999999999999883  1222           234556666777777777


Q ss_pred             HHHhh
Q 037139           95 QMLIQ   99 (135)
Q Consensus        95 ~~~~~   99 (135)
                      +.++.
T Consensus       563 kEI~~  567 (985)
T COG3587         563 KEIND  567 (985)
T ss_pred             HHHHH
Confidence            65543

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

Probab=85.25  E-value=1.7  Score=34.78  Aligned_cols=46  Identities=30%  Similarity=0.532  Sum_probs=36.2

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecC-----CCccc-ccccCCcEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATD-----VAGRG-IDIPDVAHVI   51 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~-----~~~~G-~d~~~v~~vi   51 (135)
                      ++.+.+++|+++...+...++   .| .+|+|+|+     .+.++ +++..+.++|
T Consensus       128 ~~~~~~i~GG~~~~~q~~~l~---~~-~~ivVaTPGRllD~i~~~~l~l~~v~~lV  179 (513)
T COG0513         128 GLRVAVVYGGVSIRKQIEALK---RG-VDIVVATPGRLLDLIKRGKLDLSGVETLV  179 (513)
T ss_pred             CccEEEEECCCCHHHHHHHHh---cC-CCEEEECccHHHHHHHcCCcchhhcCEEE
Confidence            467899999999888775554   46 99999997     45555 8888888877

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=84.63  E-value=12  Score=30.46  Aligned_cols=37  Identities=11%  Similarity=0.090  Sum_probs=33.3

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCC
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDV   37 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~   37 (135)
                      +|+.+..+|++++..++..+++.+..|.++++++|.-
T Consensus        76 ~gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe  112 (591)
T TIGR01389        76 AGVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPE  112 (591)
T ss_pred             cCCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChh
Confidence            3678899999999999999999999999999998853

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=84.62  E-value=1.5  Score=38.76  Aligned_cols=48  Identities=10%  Similarity=0.255  Sum_probs=35.4

Q ss_pred             EEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcc-ccc-cc-CCcEEEE
Q 037139            5 VTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGR-GID-IP-DVAHVIN   52 (135)
Q Consensus         5 v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~-G~d-~~-~v~~vi~   52 (135)
                      +..+||+++..++...++.+.+|..+|+|+|..... .++ +. .++++|.
T Consensus       155 i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l~~~~~~iVv  205 (1171)
T TIGR01054       155 IGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDELGPKFDFIFV  205 (1171)
T ss_pred             eeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHhcCCCCEEEE
Confidence            346899999999999999999999999999974221 111 12 5667664

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.

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

Probab=83.37  E-value=1.7  Score=35.54  Aligned_cols=36  Identities=22%  Similarity=0.363  Sum_probs=33.2

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecC
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATD   36 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~   36 (135)
                      .|+.+.++|+.++.+++..++.++..|.+++|.-++
T Consensus        80 ~Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisP  115 (590)
T COG0514          80 AGIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISP  115 (590)
T ss_pred             cCceeehhhcccCHHHHHHHHHHHhcCceeEEEECc
Confidence            488999999999999999999999999999996664

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=82.92  E-value=7.7  Score=32.51  Aligned_cols=88  Identities=25%  Similarity=0.285  Sum_probs=53.6

Q ss_pred             HHHHHHHh----cCCCcEEEec--CCCcccccccC--CcEEEEecCCCC----H--------------------------
Q 037139           18 EISLEGFR----TKRYNVLVAT--DVAGRGIDIPD--VAHVINYDMPGN----I--------------------------   59 (135)
Q Consensus        18 ~~~~~~f~----~g~~~ilv~T--~~~~~G~d~~~--v~~vi~~d~p~~----~--------------------------   59 (135)
                      +.+++.+.    .|.-.||++.  .-+++|+||.+  +++|+..++|..    +                          
T Consensus       673 ~dvl~~Ya~a~~~g~GaiLlaVVGGKlSEGINF~D~LgRaVvvVGlPyPN~~s~EL~er~k~l~~k~~~~gagke~yEnl  752 (821)
T KOG1133|consen  673 EDVLEGYAEAAERGRGAILLAVVGGKLSEGINFSDDLGRAVVVVGLPYPNIQSVELQERMKHLDGKLPTPGAGKELYENL  752 (821)
T ss_pred             HHHHHHHHHHhhcCCCeEEEEEeccccccccccccccccEEEEeecCCCCCCCHHHHHHHHHhhhccCCCCchHHHHHHH
Confidence            34555554    3444566554  56889999987  788998888753    0                          


Q ss_pred             --HHHHHHhhhcCCCCCCceEEEEeecCChhHHHHHHHHHhhCCCCCChHHHHHHHhh
Q 037139           60 --EMYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASK  115 (135)
Q Consensus        60 --~~~~qr~GR~gR~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  115 (135)
                        ...-|.+|||=|.-++-.++.+++..-.          ......+|.|+.......
T Consensus       753 CMkAVNQsIGRAIRH~~DYA~i~LlD~RY~----------~p~~RKLp~WI~~~v~s~  800 (821)
T KOG1133|consen  753 CMKAVNQSIGRAIRHRKDYASIYLLDKRYA----------RPLSRKLPKWIRKRVHSK  800 (821)
T ss_pred             HHHHHHHHHHHHHhhhccceeEEEehhhhc----------CchhhhccHHHHhHhccc
Confidence              1126889999987666445555543221          112227788886655443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	135
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		5e-29
2jgn_A	185	Ddx3 Helicase Domain Length = 185		6e-26
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		1e-25
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		4e-21
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		4e-21
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		7e-21
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		7e-21
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		7e-21
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		7e-21
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		1e-20
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		3e-19
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		3e-19
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		3e-18
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		6e-17
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		6e-17
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		2e-16
3gfp_A	189	Structure Of The C-Terminal Domain Of The Dead-Box		2e-16
3peu_A	188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		2e-16
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		4e-16
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		2e-15
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		2e-15
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		1e-14
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		2e-14
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		2e-14
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		2e-14
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		2e-13
1t5i_A	172	Crystal Structure Of The C-Terminal Domain Of Uap56		2e-13
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		2e-13
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		2e-13
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		2e-13
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		3e-13
4db4_A	256	Mss116p Dead-Box Helicase Domain 2 Bound To A Chima		4e-12
4db2_C	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		4e-12
4db2_A	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		4e-12
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		7e-12
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		7e-12
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		8e-12
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		1e-11
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		1e-11
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		2e-11
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		2e-11
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		3e-11
3eaq_A	212	Novel Dimerization Motif In The Dead Box Rna Helica		6e-11
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		7e-11
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		6e-08
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		1e-07
2fwr_A	472	Structure Of Archaeoglobus Fulgidis Xpb Length = 47		9e-07
2fzl_A	219	Structure Of C-Terminal Domain Of Archaeoglobus Ful		1e-06
1wp9_A	494	Crystal Structure Of Pyrococcus Furiosus Hef Helica		7e-06
2v1x_A	591	Crystal Structure Of Human Recq-Like Dna Helicase L		3e-05
1gm5_A	780	Structure Of Recg Bound To Three-Way Dna Junction L		5e-05
2va8_A	715	Dna Repair Helicase Hel308 Length = 715		1e-04

>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain Length = 191

Iteration: 1
 Score =  122 bits (307), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 57/108 (52%), Positives = 73/108 (67%), Gaps = 1/108 (0%)
Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G     +HGGK QE+R  ++E FR  + +VLVATDVA +G+D P + HVINYDMP  IE 
Sbjct: 78  GVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIEN 137
Query: 62  YTHRIGRTGRAGKTGVATTFLT-FHDTDVFYDLKQMLIQSNSPVPPEL 108
           Y HRIGRTG +G TG+ATTF+    D  V  DLK +L+++   VPP L
Sbjct: 138 YVHRIGRTGCSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVL 185

>pdb|2JGN|A Chain A, Ddx3 Helicase Domain Length = 185

Iteration: 1
 Score =  112 bits (280), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 51/107 (47%), Positives = 72/107 (67%)
Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           GY  T++HG +SQ  RE +L  FR+ +  +LVAT VA RG+DI +V HVIN+D+P +IE 
Sbjct: 70  GYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEE 129
Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPEL 108
           Y HRIGRTGR G  G+AT+F    + ++  DL  +L+++   VP  L
Sbjct: 130 YVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWL 176

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score =  111 bits (278), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 51/107 (47%), Positives = 72/107 (67%)
Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           GY  T++HG +SQ  RE +L  FR+ +  +LVAT VA RG+DI +V HVIN+D+P +IE 
Sbjct: 300 GYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEE 359
Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPEL 108
           Y HRIGRTGR G  G+AT+F    + ++  DL  +L+++   VP  L
Sbjct: 360 YVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWL 406

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 96.3 bits (238), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 44/107 (41%), Positives = 68/107 (63%)
Query: 3   YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMY 62
           + V+++HG   Q++RE  ++ FR+    VL++TDV  RG+D+P V+ +INYD+P N E+Y
Sbjct: 265 FTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELY 324
Query: 63  THRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELA 109
            HRIGR+GR G+ GVA  F+   D  V  D++Q        +P  +A
Sbjct: 325 IHRIGRSGRYGRKGVAVNFVKNDDIRVLRDIEQYYSTQIDEMPMNVA 371

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 96.3 bits (238), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 44/107 (41%), Positives = 68/107 (63%)
Query: 3   YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMY 62
           + V+++HG   Q++RE  ++ FR+    VL++TDV  RG+D+P V+ +INYD+P N E+Y
Sbjct: 265 FTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELY 324
Query: 63  THRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELA 109
            HRIGR+GR G+ GVA  F+   D  V  D++Q        +P  +A
Sbjct: 325 IHRIGRSGRYGRKGVAVNFVKNDDIRVLRDIEQYYSTQIDEMPMNVA 371

>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 = 95.9 bits (237), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 43/108 (39%), Positives = 68/108 (62%)
Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
            + V+++HG   Q++RE  ++ FR+    VL++TDV  RG+D+P V+ +INYD+P N E+
Sbjct: 301 NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL 360
Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELA 109
           Y HRIGR+GR G+ GVA  F+   D  +  D++Q        +P  +A
Sbjct: 361 YIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVA 408

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 95.9 bits (237), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 43/107 (40%), Positives = 68/107 (63%)
Query: 3   YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMY 62
           + V+++HG   Q++RE  ++ FR+    VL++TDV  RG+D+P V+ +INYD+P N E+Y
Sbjct: 301 FTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELY 360
Query: 63  THRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELA 109
            HRIGR+GR G+ GVA  F+   D  +  D++Q        +P  +A
Sbjct: 361 IHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVA 407

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 95.5 bits (236), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 43/108 (39%), Positives = 68/108 (62%)
Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
            + V+++HG   Q++RE  ++ FR+    VL++TDV  RG+D+P V+ +INYD+P N E+
Sbjct: 279 NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL 338
Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELA 109
           Y HRIGR+GR G+ GVA  F+   D  +  D++Q        +P  +A
Sbjct: 339 YIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVA 386

>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 = 95.5 bits (236), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 43/107 (40%), Positives = 68/107 (63%)
Query: 3   YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMY 62
           + V+++HG   Q++RE  ++ FR+    VL++TDV  RG+D+P V+ +INYD+P N E+Y
Sbjct: 302 FTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELY 361
Query: 63  THRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELA 109
            HRIGR+GR G+ GVA  F+   D  +  D++Q        +P  +A
Sbjct: 362 IHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVA 408

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score = 95.1 bits (235), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 49/104 (47%), Positives = 64/104 (61%), Gaps = 1/104 (0%)
Query: 3   YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMY 62
           +  T++HG + Q QRE +L  F+     VL+AT VA RG+DI ++ HVINYDMP  I+ Y
Sbjct: 325 FPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDY 384
Query: 63  THRIGRTGRAGKTGVATTFLT-FHDTDVFYDLKQMLIQSNSPVP 105
            HRIGRTGR G  G AT+F     D  +  DL ++L  S   VP
Sbjct: 385 VHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKILEGSGQTVP 428

>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The Bacillus Subtilis Yxin Protein Length = 163

Iteration: 1
 Score = 90.5 bits (223), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 45/97 (46%), Positives = 59/97 (60%)
Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
           LGY    +HGG  QE R   +  F+   Y  LVATDVA RGIDI +++ VINYD+P   E
Sbjct: 58  LGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKE 117
Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQML 97
            Y HR GRTGRAG  G A +F+T  +     D+++ +
Sbjct: 118 SYVHRTGRTGRAGNKGKAISFVTAFEKRFLADIEEYI 154

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score = 90.1 bits (222), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 41/83 (49%), Positives = 55/83 (66%)
Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
           +G++   +HG  SQ QRE  +  F+ K+  +L+ATDV  RGID+ D+  VINY +P N E
Sbjct: 261 IGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVXSRGIDVNDLNCVINYHLPQNPE 320
Query: 61  MYTHRIGRTGRAGKTGVATTFLT 83
            Y HRIGRTGRAGK G A + + 
Sbjct: 321 SYXHRIGRTGRAGKKGKAISIIN 343

>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 = 86.7 bits (213), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 42/79 (53%), Positives = 53/79 (67%)
Query: 8   LHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIG 67
           L G   Q +R  +++     R NVLVATDVA RGIDIPDV+HV N+DMP + + Y HRIG
Sbjct: 60  LEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIG 119
Query: 68  RTGRAGKTGVATTFLTFHD 86
           RT RAG+ G A + +  HD
Sbjct: 120 RTARAGRKGTAISLVEAHD 138

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 82.4 bits (202), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 42/95 (44%), Positives = 59/95 (62%), Gaps = 8/95 (8%)
Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMP----- 56
           G+ V+ LHG    ++R+  ++ FR  R  VL+ T+V  RGIDIP V+ V+NYD+P     
Sbjct: 267 GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANG 326
Query: 57  -GNIEMYTHRIGRTGRAGKTGVATTFLTFHDTDVF 90
             +   Y HRIGRTGR G+ GVA +F+  HD + F
Sbjct: 327 QADPATYIHRIGRTGRFGRKGVAISFV--HDKNSF 359

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 82.4 bits (202), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 42/95 (44%), Positives = 59/95 (62%), Gaps = 8/95 (8%)
Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMP----- 56
           G+ V+ LHG    ++R+  ++ FR  R  VL+ T+V  RGIDIP V+ V+NYD+P     
Sbjct: 267 GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANG 326
Query: 57  -GNIEMYTHRIGRTGRAGKTGVATTFLTFHDTDVF 90
             +   Y HRIGRTGR G+ GVA +F+  HD + F
Sbjct: 327 QADPATYIHRIGRTGRFGRKGVAISFV--HDKNSF 359

>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p Length = 187

Iteration: 1
 Score = 80.9 bits (198), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 42/95 (44%), Positives = 59/95 (62%), Gaps = 8/95 (8%)
Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMP----- 56
           G+ V+ LHG    ++R+  ++ FR  R  VL+ T+V  RGIDIP V+ V+NYD+P     
Sbjct: 59  GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANG 118
Query: 57  -GNIEMYTHRIGRTGRAGKTGVATTFLTFHDTDVF 90
             +   Y HRIGRTGR G+ GVA +F+  HD + F
Sbjct: 119 QADPATYIHRIGRTGRFGRKGVAISFV--HDKNSF 151

>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein Dbp5 Length = 189

Iteration: 1
 Score = 80.5 bits (197), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 42/95 (44%), Positives = 59/95 (62%), Gaps = 8/95 (8%)
Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMP----- 56
           G+ V+ LHG    ++R+  ++ FR  R  VL+ T+V  RGIDIP V+ V+NYD+P     
Sbjct: 61  GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANG 120
Query: 57  -GNIEMYTHRIGRTGRAGKTGVATTFLTFHDTDVF 90
             +   Y HRIGRTGR G+ GVA +F+  HD + F
Sbjct: 121 QADPATYIHRIGRTGRFGRKGVAISFV--HDKNSF 153

>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1 H337r And Ip6 Length = 188

Iteration: 1
 Score = 80.5 bits (197), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 42/95 (44%), Positives = 59/95 (62%), Gaps = 8/95 (8%)
Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMP----- 56
           G+ V+ LHG    ++R+  ++ FR  R  VL+ T+V  RGIDIP V+ V+NYD+P     
Sbjct: 60  GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANG 119
Query: 57  -GNIEMYTHRIGRTGRAGKTGVATTFLTFHDTDVF 90
             +   Y HRIGRTGR G+ GVA +F+  HD + F
Sbjct: 120 QADPATYIHRIGRTGRFGRKGVAISFV--HDKNSF 152

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 79.7 bits (195), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 37/75 (49%), Positives = 49/75 (65%)
Query: 8   LHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIG 67
           L G   Q  R  +++ FR   Y++L+ TDVA RG+DIP V  VIN+D P ++  Y HRIG
Sbjct: 246 LRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIG 305
Query: 68  RTGRAGKTGVATTFL 82
           RTGR G+ G A TF+
Sbjct: 306 RTGRMGRKGEAITFI 320

>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 = 77.4 bits (189), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 42/110 (38%), Positives = 54/110 (49%)
Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
           LGY    +H    QE R      FR      LV TD+  RGIDI  V  VIN+D P   E
Sbjct: 67  LGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAE 126
Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAK 110
            Y HRIGR+GR G  G+A   +T+ D      +++ L     P+P  + K
Sbjct: 127 TYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDK 176

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 77.4 bits (189), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 40/110 (36%), Positives = 56/110 (50%)
Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
           LGY     H    Q++R      FR  +   LV +D+  RGIDI  V  VIN+D P   E
Sbjct: 281 LGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAE 340
Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAK 110
            Y HRIGR+GR G  G+A   + ++D    Y ++Q L    + +P  + K
Sbjct: 341 TYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATIDK 390

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 74.7 bits (182), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 41/87 (47%), Positives = 52/87 (59%), Gaps = 6/87 (6%)
Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMP----G 57
           G++V  L G    EQR   +E FR  +  VLV T+V  RGID+  V+ VIN+D+P    G
Sbjct: 357 GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDG 416
Query: 58  NI--EMYTHRIGRTGRAGKTGVATTFL 82
           N   E Y HRIGRTGR GK G+A   +
Sbjct: 417 NPDNETYLHRIGRTGRFGKRGLAVNMV 443

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 74.3 bits (181), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 41/87 (47%), Positives = 52/87 (59%), Gaps = 6/87 (6%)
Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMP----G 57
           G++V  L G    EQR   +E FR  +  VLV T+V  RGID+  V+ VIN+D+P    G
Sbjct: 327 GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDG 386
Query: 58  NI--EMYTHRIGRTGRAGKTGVATTFL 82
           N   E Y HRIGRTGR GK G+A   +
Sbjct: 387 NPDNETYLHRIGRTGRFGKRGLAVNMV 413

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 74.3 bits (181), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 41/87 (47%), Positives = 52/87 (59%), Gaps = 6/87 (6%)
Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMP----G 57
           G++V  L G    EQR   +E FR  +  VLV T+V  RGID+  V+ VIN+D+P    G
Sbjct: 306 GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDG 365
Query: 58  NI--EMYTHRIGRTGRAGKTGVATTFL 82
           N   E Y HRIGRTGR GK G+A   +
Sbjct: 366 NPDNETYLHRIGRTGRFGKRGLAVNMV 392

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 74.3 bits (181), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 41/87 (47%), Positives = 52/87 (59%), Gaps = 6/87 (6%)
Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMP----G 57
           G++V  L G    EQR   +E FR  +  VLV T+V  RGID+  V+ VIN+D+P    G
Sbjct: 290 GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDG 349
Query: 58  NI--EMYTHRIGRTGRAGKTGVATTFL 82
           N   E Y HRIGRTGR GK G+A   +
Sbjct: 350 NPDNETYLHRIGRTGRFGKRGLAVNMV 376

>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56 Length = 172

Iteration: 1
 Score = 70.9 bits (172), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 37/103 (35%), Positives = 59/103 (57%), Gaps = 1/103 (0%)
Query: 7   TLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRI 66
            +H G  QE+R    + F+  +  +LVAT++ GRG+DI  V    NYDMP + + Y HR+
Sbjct: 60  AIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRV 119
Query: 67  GRTGRAGKTGVATTFLT-FHDTDVFYDLKQMLIQSNSPVPPEL 108
            R GR G  G+A TF++  +D  +  D++     + S +P E+
Sbjct: 120 ARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI 162

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 70.9 bits (172), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 37/103 (35%), Positives = 59/103 (57%), Gaps = 1/103 (0%)
Query: 7   TLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRI 66
            +H G  QE+R    + F+  +  +LVAT++ GRG+DI  V    NYDMP + + Y HR+
Sbjct: 279 AIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRV 338
Query: 67  GRTGRAGKTGVATTFLT-FHDTDVFYDLKQMLIQSNSPVPPEL 108
            R GR G  G+A TF++  +D  +  D++     + S +P E+
Sbjct: 339 ARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI 381

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 70.9 bits (172), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 37/103 (35%), Positives = 59/103 (57%), Gaps = 1/103 (0%)
Query: 7   TLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRI 66
            +H G  QE+R    + F+  +  +LVAT++ GRG+DI  V    NYDMP + + Y HR+
Sbjct: 278 AIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRV 337
Query: 67  GRTGRAGKTGVATTFLT-FHDTDVFYDLKQMLIQSNSPVPPEL 108
            R GR G  G+A TF++  +D  +  D++     + S +P E+
Sbjct: 338 ARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI 380

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 70.9 bits (172), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 37/103 (35%), Positives = 59/103 (57%), Gaps = 1/103 (0%)
Query: 7   TLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRI 66
            +H G  QE+R    + F+  +  +LVAT++ GRG+DI  V    NYDMP + + Y HR+
Sbjct: 279 AIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRV 338
Query: 67  GRTGRAGKTGVATTFLT-FHDTDVFYDLKQMLIQSNSPVPPEL 108
            R GR G  G+A TF++  +D  +  D++     + S +P E+
Sbjct: 339 ARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI 381

>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25 Rna Helicase Length = 175

Iteration: 1
 Score = 70.5 bits (171), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 36/83 (43%), Positives = 51/83 (61%), Gaps = 6/83 (7%)
Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPG---- 57
           G++V+ L G  + EQR   ++ FR  +  VL+ T+V  RGID+  V  V+N+D+P     
Sbjct: 58  GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGE 117
Query: 58  --NIEMYTHRIGRTGRAGKTGVA 78
             + E Y HRIGRTGR GK G+A
Sbjct: 118 EPDYETYLHRIGRTGRFGKKGLA 140

>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric Rna-Dna Duplex Length = 256

Iteration: 1
 Score = 66.6 bits (161), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 44/79 (55%)
Query: 5   VTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTH 64
           +   HG  +Q +R   ++ F+     +LV TDV  RG+D P+V  V+   +P  +  Y H
Sbjct: 63  ILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIH 122
Query: 65  RIGRTGRAGKTGVATTFLT 83
           RIGRT R+GK G +  F+ 
Sbjct: 123 RIGRTARSGKEGSSVLFIC 141

>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 66.6 bits (161), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 44/79 (55%)
Query: 5   VTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTH 64
           +   HG  +Q +R   ++ F+     +LV TDV  RG+D P+V  V+   +P  +  Y H
Sbjct: 63  ILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIH 122
Query: 65  RIGRTGRAGKTGVATTFLT 83
           RIGRT R+GK G +  F+ 
Sbjct: 123 RIGRTARSGKEGSSVLFIC 141

>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 66.6 bits (161), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 44/79 (55%)
Query: 5   VTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTH 64
           +   HG  +Q +R   ++ F+     +LV TDV  RG+D P+V  V+   +P  +  Y H
Sbjct: 63  ILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIH 122
Query: 65  RIGRTGRAGKTGVATTFLT 83
           RIGRT R+GK G +  F+ 
Sbjct: 123 RIGRTARSGKEGSSVLFIC 141

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 65.9 bits (159), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 42/107 (39%), Positives = 62/107 (57%)
Query: 3   YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMY 62
           + V+ +HG   Q++R++ +  FR+    VL+ TD+  RGID+  V+ VINYD+P N E Y
Sbjct: 305 FTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENY 364
Query: 63  THRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELA 109
            HRIGR GR G+ GVA   +T  D     D++     S   +P  +A
Sbjct: 365 IHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVA 411

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 65.9 bits (159), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 42/107 (39%), Positives = 62/107 (57%)
Query: 3   YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMY 62
           + V+ +HG   Q++R++ +  FR+    VL+ TD+  RGID+  V+ VINYD+P N E Y
Sbjct: 279 FTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENY 338
Query: 63  THRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELA 109
            HRIGR GR G+ GVA   +T  D     D++     S   +P  +A
Sbjct: 339 IHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVA 385

>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion) Bound To Ssrna And Amp-Pnp Length = 512

Iteration: 1
 Score = 65.5 bits (158), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 29/78 (37%), Positives = 44/78 (56%)
Query: 5   VTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTH 64
           +   HG  +Q +R   ++ F+     +LV TDV  RG+D P+V  V+   +P  +  Y H
Sbjct: 318 ILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIH 377
Query: 65  RIGRTGRAGKTGVATTFL 82
           RIGRT R+GK G +  F+
Sbjct: 378 RIGRTARSGKEGSSVLFI 395

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 65.1 bits (157), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 29/78 (37%), Positives = 44/78 (56%)
Query: 5   VTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTH 64
           +   HG  +Q +R   ++ F+     +LV TDV  RG+D P+V  V+   +P  +  Y H
Sbjct: 318 ILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIH 377
Query: 65  RIGRTGRAGKTGVATTFL 82
           RIGRT R+GK G +  F+
Sbjct: 378 RIGRTARSGKEGSSVLFI 395

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 65.1 bits (157), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 29/78 (37%), Positives = 44/78 (56%)
Query: 5   VTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTH 64
           +   HG  +Q +R   ++ F+     +LV TDV  RG+D P+V  V+   +P  +  Y H
Sbjct: 369 ILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIH 428
Query: 65  RIGRTGRAGKTGVATTFL 82
           RIGRT R+GK G +  F+
Sbjct: 429 RIGRTARSGKEGSSVLFI 446

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 39/107 (36%), Positives = 64/107 (59%)
Query: 3   YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMY 62
           + V+ ++    Q++R+  ++ FR+    +L++TD+  RGID+  V+ VINYD+P N E Y
Sbjct: 285 FTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENY 344
Query: 63  THRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELA 109
            HRIGR GR G+ GVA  F+T  D     +L++        +P ++A
Sbjct: 345 IHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIA 391

>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 39/107 (36%), Positives = 64/107 (59%)
Query: 3   YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMY 62
           + V+ ++    Q++R+  ++ FR+    +L++TD+  RGID+  V+ VINYD+P N E Y
Sbjct: 55  FTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENY 114
Query: 63  THRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELA 109
            HRIGR GR G+ GVA  F+T  D     +L++        +P ++A
Sbjct: 115 IHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIA 161

>pdb|3I32|A Chain A, Dimeric Structure Of A Hera Helicase Fragment Including The C-Terminal Reca Domain, The Dimerization Domain, And The Rna Binding Domain Length = 300

Iteration: 1
 Score = 63.5 bits (153), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 32/64 (50%), Positives = 38/64 (59%)
Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
           LG+    LHG  SQ +RE  +  FR     VLVATDVA RG+DIP V  V++Y MP   E
Sbjct: 51  LGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAE 110
Query: 61  MYTH 64
            Y H
Sbjct: 111 AYQH 114

>pdb|3EAQ|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase Hera Form 2, Complete Dimer, Symmetric Length = 212

Iteration: 1
 Score = 62.8 bits (151), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 32/64 (50%), Positives = 38/64 (59%)
Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
           LG+    LHG  SQ +RE  L  FR     VLVATDVA RG+DIP V  V++Y +P   E
Sbjct: 54  LGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAE 113
Query: 61  MYTH 64
            Y H
Sbjct: 114 AYQH 117

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 62.4 bits (150), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 39/107 (36%), Positives = 63/107 (58%)
Query: 3   YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMY 62
           + V+ ++    Q++R+   + FR+    +L++TD+  RGID+  V+ VINYD+P N E Y
Sbjct: 284 FTVSAIYSDLPQQERDTIXKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENY 343
Query: 63  THRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELA 109
            HRIGR GR G+ GVA  F+T  D     +L++        +P ++A
Sbjct: 344 IHRIGRGGRFGRKGVAINFVTNEDVGAXRELEKFYSTQIEELPSDIA 390

>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S Length = 523

Iteration: 1
 Score = 52.8 bits (125), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 29/85 (34%), Positives = 42/85 (49%), Gaps = 3/85 (3%)
Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G      H G     R    E F+     ++VAT   G GI+ P+V  V+++D+P NIE 
Sbjct: 260 GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIES 319
Query: 62  YTHRIGRTGRAGKTGVATTFLTFHD 86
           Y      TGRAG+ G+    + F+D
Sbjct: 320 YYQ---ETGRAGRDGLPAEAMLFYD 341

>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core Length = 523

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 28/80 (35%), Positives = 37/80 (46%)
Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G      H G     R    E F+     ++VAT   G GI+ P+V  V+++D+P NIE 
Sbjct: 260 GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXGINKPNVRFVVHFDIPRNIES 319
Query: 62  YTHRIGRTGRAGKTGVATTF 81
           Y    GR GR G    A  F
Sbjct: 320 YYQETGRAGRDGLPAEAXLF 339

>pdb|2FWR|A Chain A, Structure Of Archaeoglobus Fulgidis Xpb Length = 472

Iteration: 1
 Score = 48.9 bits (115), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 25/62 (40%), Positives = 35/62 (56%)
Query: 13  SQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRA 72
           S+E+RE  LEGFRT R+  +V++ V   GID+PD    +     G+   Y  R+GR  R 
Sbjct: 379 SREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRP 438
Query: 73  GK 74
            K
Sbjct: 439 SK 440

>pdb|2FZL|A Chain A, Structure Of C-Terminal Domain Of Archaeoglobus Fulgidus Xpb Length = 219

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/62 (40%), Positives = 35/62 (56%)
Query: 13  SQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRA 72
           S+E+RE  LEGFRT R+  +V++ V   GID+PD    +     G+   Y  R+GR  R 
Sbjct: 144 SREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRP 203
Query: 73  GK 74
            K
Sbjct: 204 SK 205

>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase Domain Length = 494

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 26/62 (41%), Positives = 38/62 (61%), Gaps = 2/62 (3%)
Query: 11  GKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYD-MPGNIEMYTHRIGRT 69
           G SQ ++++ L+ F    +NVLVAT V   G+D+P+V  V+ Y+ +P  I     R GRT
Sbjct: 402 GLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRR-GRT 460
Query: 70  GR 71
           GR
Sbjct: 461 GR 462

>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase Length = 591

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 28/101 (27%), Positives = 40/101 (39%), Gaps = 3/101 (2%)
Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
           LG      H     E +      +      V+VAT   G GID PDV  VI++ M  ++E
Sbjct: 290 LGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSME 349
Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSN 101
            Y    GR GR         +  F D    + +  M++  N
Sbjct: 350 NYYQESGRAGRDDMKADCILYYGFGD---IFRISSMVVMEN 387

>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction Length = 780

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 29/86 (33%), Positives = 48/86 (55%), Gaps = 5/86 (5%)
Query: 3   YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIP--DVAHVINYDMPGNIE 60
           +++  +HG  SQE+++  +  F   RY++LV+T V   GID+P  +V  + N +  G  +
Sbjct: 614 FKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQ 673
Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHD 86
           ++  R GR GR G+   A  FL   D
Sbjct: 674 LHQLR-GRVGRGGQE--AYCFLVVGD 696

>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308 Length = 715

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 31/117 (26%), Positives = 50/117 (42%), Gaps = 12/117 (10%)
Query: 9   HGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVI------NYDMPG----- 57
           H G S+  R++  EGFR ++  V+VAT     G+++P    +I      N  + G     
Sbjct: 319 HAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEI 378
Query: 58  NIEMYTHRIGRTGRAGKTGVATTFLTFHDT-DVFYDLKQMLIQSNSPVPPELAKHEA 113
            I  Y    GR GR G   +  + +   D  DV    K+ ++    P+  +L    A
Sbjct: 379 PIMEYKQMSGRAGRPGFDQIGESIVVVRDKEDVDRVFKKYVLSDVEPIESKLGSERA 435

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	135
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	3e-64
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	2e-61
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	1e-60
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	6e-56
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	3e-44
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	4e-44
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	1e-42
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	2e-42
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	2e-42
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	5e-42
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	1e-41
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	3e-41
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	2e-40
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	3e-40
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	3e-40
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	4e-40
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	4e-40
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	2e-39
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	3e-39
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	3e-39
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	5e-39
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	2e-38
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	3e-37
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	2e-36
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	9e-25
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	4e-22
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	6e-16
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	5e-14
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	7e-14
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	1e-13
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	1e-12
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	1e-12
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	2e-12
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	2e-10
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	4e-09
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	5e-09
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	1e-07
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	1e-04
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	4e-04
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	7e-04

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score =  193 bits (492), Expect = 3e-64
 Identities = 57/110 (51%), Positives = 73/110 (66%), Gaps = 1/110 (0%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G     +HGGK QE+R  ++E FR  + +VLVATDVA +G+D P + HVINYDMP  IE 
Sbjct: 78  GVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIEN 137

Query: 62  YTHRIGRTGRAGKTGVATTFLTFH-DTDVFYDLKQMLIQSNSPVPPELAK 110
           Y HRIGRTG +G TG+ATTF+    D  V  DLK +L+++   VPP L  
Sbjct: 138 YVHRIGRTGCSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQV 187

>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 =  185 bits (473), Expect = 2e-61
 Identities = 51/109 (46%), Positives = 72/109 (66%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           GY  T++HG +SQ  RE +L  FR+ +  +LVAT VA RG+DI +V HVIN+D+P +IE 
Sbjct: 70  GYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEE 129

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAK 110
           Y HRIGRTGR G  G+AT+F    + ++  DL  +L+++   VP  L  
Sbjct: 130 YVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLEN 178

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  190 bits (486), Expect = 1e-60
 Identities = 52/118 (44%), Positives = 73/118 (61%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           GY  T++HG +SQ  RE +L  FR+ +  +LVAT VA RG+DI +V HVIN+D+P +IE 
Sbjct: 300 GYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEE 359

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPG 119
           Y HRIGRTGR G  G+AT+F    + ++  DL  +L+++   VP  L          G
Sbjct: 360 YVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAYEHHYKG 417

>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 =  179 bits (456), Expect = 6e-56
 Identities = 50/108 (46%), Positives = 65/108 (60%), Gaps = 1/108 (0%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
            +  T++HG + Q QRE +L  F+     VL+AT VA RG+DI ++ HVINYDMP  I+ 
Sbjct: 324 EFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDD 383

Query: 62  YTHRIGRTGRAGKTGVATTFLTFH-DTDVFYDLKQMLIQSNSPVPPEL 108
           Y HRIGRTGR G  G AT+F     D  +  DL ++L  S   VP  L
Sbjct: 384 YVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKILEGSGQTVPDFL 431

>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 =  142 bits (361), Expect = 3e-44
 Identities = 45/120 (37%), Positives = 58/120 (48%), Gaps = 4/120 (3%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G+    LHG  SQ +RE  L  FR     VLVATDVA RG+DIP V  V++Y +P   E 
Sbjct: 55  GHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEA 114

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDL----KQMLIQSNSPVPPELAKHEASKFK 117
           Y HR GRTGRAG+ G         +      L     +   + N P P E+ + +     
Sbjct: 115 YQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRFKRVNPPTPEEVLEAKWRHLL 174

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score =  141 bits (357), Expect = 4e-44
 Identities = 44/94 (46%), Positives = 57/94 (60%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           GY    +HGG  QE R   +  F+   Y  LVATDVA RGIDI +++ VINYD+P   E 
Sbjct: 59  GYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKES 118

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQ 95
           Y HR GRTGRAG  G A +F+T  +     D+++
Sbjct: 119 YVHRTGRTGRAGNKGKAISFVTAFEKRFLADIEE 152

>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 =  137 bits (348), Expect = 1e-42
 Identities = 46/117 (39%), Positives = 62/117 (52%), Gaps = 8/117 (6%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G     L G   Q +R  +++     R NVLVATDVA RGIDIPDV+HV N+DMP + + 
Sbjct: 54  GINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDT 113

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYD--------LKQMLIQSNSPVPPELAK 110
           Y HRIGRT RAG+ G A + +  HD  +           +K  +I    P     ++
Sbjct: 114 YLHRIGRTARAGRKGTAISLVEAHDHLLLGKVGRYIEEPIKARVIDELRPKTRAPSE 170

>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 =  141 bits (356), Expect = 2e-42
 Identities = 45/120 (37%), Positives = 58/120 (48%), Gaps = 4/120 (3%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G+    LHG  SQ +RE  +  FR     VLVATDVA RG+DIP V  V++Y MP   E 
Sbjct: 52  GHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEA 111

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDL----KQMLIQSNSPVPPELAKHEASKFK 117
           Y HR GRTGRAG+ G         +      L     +   + N P P E+ + +     
Sbjct: 112 YQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRFKRVNPPTPEEVLEAKWRHLL 171

>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 =  142 bits (360), Expect = 2e-42
 Identities = 41/82 (50%), Positives = 54/82 (65%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G++   +HG  SQ QRE  +  F+ K+  +L+ATDV  RGID+ D+  VINY +P N E 
Sbjct: 262 GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPES 321

Query: 62  YTHRIGRTGRAGKTGVATTFLT 83
           Y HRIGRTGRAGK G A + + 
Sbjct: 322 YMHRIGRTGRAGKKGKAISIIN 343

>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 =  141 bits (357), Expect = 1e-41
 Identities = 40/110 (36%), Positives = 56/110 (50%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
           LGY     H    Q++R      FR  +   LV +D+  RGIDI  V  VIN+D P   E
Sbjct: 281 LGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAE 340

Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAK 110
            Y HRIGR+GR G  G+A   + ++D    Y ++Q L    + +P  + K
Sbjct: 341 TYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATIDK 390

>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 =  139 bits (354), Expect = 3e-41
 Identities = 39/110 (35%), Positives = 64/110 (58%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
             + V+ ++    Q++R+  ++ FR+    +L++TD+  RGID+  V+ VINYD+P N E
Sbjct: 282 DKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKE 341

Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAK 110
            Y HRIGR GR G+ GVA  F+T  D     +L++        +P ++A 
Sbjct: 342 NYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIAT 391

>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 =  131 bits (332), Expect = 2e-40
 Identities = 37/109 (33%), Positives = 60/109 (55%), Gaps = 1/109 (0%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
             +    +H G  QE+R    + F+  +  +LVAT++ GRG+DI  V    NYDMP + +
Sbjct: 54  QNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSD 113

Query: 61  MYTHRIGRTGRAGKTGVATTFLTF-HDTDVFYDLKQMLIQSNSPVPPEL 108
            Y HR+ R GR G  G+A TF++  +D  +  D++     + S +P E+
Sbjct: 114 TYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI 162

>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 =  137 bits (348), Expect = 3e-40
 Identities = 43/109 (39%), Positives = 68/109 (62%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
             + V+++HG   Q++RE  ++ FR+    VL++TDV  RG+D+P V+ +INYD+P N E
Sbjct: 299 ANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRE 358

Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELA 109
           +Y HRIGR+GR G+ GVA  F+   D  +  D++Q        +P  +A
Sbjct: 359 LYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVA 407

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score =  131 bits (331), Expect = 3e-40
 Identities = 39/110 (35%), Positives = 64/110 (58%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
            + V+ ++    Q++R+  ++ FR+    +L++TD+  RGID+  V+ VINYD+P N E 
Sbjct: 54  KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKEN 113

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKH 111
           Y HRIGR GR G+ GVA  F+T  D     +L++        +P ++A  
Sbjct: 114 YIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATL 163

>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 =  139 bits (352), Expect = 4e-40
 Identities = 30/105 (28%), Positives = 49/105 (46%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
              +   HG  +Q +R   ++ F+     +LV TDV  RG+D P+V  V+   +P  +  
Sbjct: 366 DLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELAN 425

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPP 106
           Y HRIGRT R+GK G +  F+   +     +L+       +    
Sbjct: 426 YIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEK 470

>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 =  137 bits (347), Expect = 4e-40
 Identities = 42/109 (38%), Positives = 62/109 (56%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
             + V+ +HG   Q++R++ +  FR+    VL+ TD+  RGID+  V+ VINYD+P N E
Sbjct: 303 RDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRE 362

Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELA 109
            Y HRIGR GR G+ GVA   +T  D     D++     S   +P  +A
Sbjct: 363 NYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVA 411

>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 =  129 bits (327), Expect = 2e-39
 Identities = 36/100 (36%), Positives = 54/100 (54%), Gaps = 6/100 (6%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGN--- 58
           G++V+ L G  + EQR   ++ FR  +  VL+ T+V  RGID+  V  V+N+D+P     
Sbjct: 58  GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGE 117

Query: 59  ---IEMYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQ 95
               E Y HRIGRTGR GK G+A   +   +      ++ 
Sbjct: 118 EPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQD 157

>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 =  133 bits (338), Expect = 3e-39
 Identities = 37/82 (45%), Positives = 49/82 (59%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
                 L G   Q  R  +++ FR   Y++L+ TDVA RG+DIP V  VIN+D P ++  
Sbjct: 240 FDNAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRT 299

Query: 62  YTHRIGRTGRAGKTGVATTFLT 83
           Y HRIGRTGR G+ G A TF+ 
Sbjct: 300 YIHRIGRTGRMGRKGEAITFIL 321

>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 =  134 bits (340), Expect = 3e-39
 Identities = 37/108 (34%), Positives = 59/108 (54%), Gaps = 1/108 (0%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
            +    +H G  QE+R    + F+  +  +LVAT++ GRG+DI  V    NYDMP + + 
Sbjct: 274 NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDT 333

Query: 62  YTHRIGRTGRAGKTGVATTFLTFH-DTDVFYDLKQMLIQSNSPVPPEL 108
           Y HR+ R GR G  G+A TF++   D  +  D++     + S +P E+
Sbjct: 334 YLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI 381

>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 =  136 bits (345), Expect = 5e-39
 Identities = 30/105 (28%), Positives = 49/105 (46%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
              +   HG  +Q +R   ++ F+     +LV TDV  RG+D P+V  V+   +P  +  
Sbjct: 315 DLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELAN 374

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPP 106
           Y HRIGRT R+GK G +  F+   +     +L+       +    
Sbjct: 375 YIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEK 419

>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 =  132 bits (334), Expect = 2e-38
 Identities = 39/88 (44%), Positives = 55/88 (62%), Gaps = 6/88 (6%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMP----- 56
           G+ V+ LHG    ++R+  ++ FR  R  VL+ T+V  RGIDIP V+ V+NYD+P     
Sbjct: 267 GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANG 326

Query: 57  -GNIEMYTHRIGRTGRAGKTGVATTFLT 83
             +   Y HRIGRTGR G+ GVA +F+ 
Sbjct: 327 QADPATYIHRIGRTGRFGRKGVAISFVH 354

>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 =  129 bits (328), Expect = 3e-37
 Identities = 39/88 (44%), Positives = 51/88 (57%), Gaps = 6/88 (6%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGN--- 58
           G++V  L G    EQR   +E FR  +  VLV T+V  RGID+  V+ VIN+D+P +   
Sbjct: 290 GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDG 349

Query: 59  ---IEMYTHRIGRTGRAGKTGVATTFLT 83
               E Y HRIGRTGR GK G+A   + 
Sbjct: 350 NPDNETYLHRIGRTGRFGKRGLAVNMVD 377

>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 =  128 bits (324), Expect = 2e-36
 Identities = 39/88 (44%), Positives = 51/88 (57%), Gaps = 6/88 (6%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGN--- 58
           G++V  L G    EQR   +E FR  +  VLV T+V  RGID+  V+ VIN+D+P +   
Sbjct: 357 GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDG 416

Query: 59  ---IEMYTHRIGRTGRAGKTGVATTFLT 83
               E Y HRIGRTGR GK G+A   + 
Sbjct: 417 NPDNETYLHRIGRTGRFGKRGLAVNMVD 444

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 96.3 bits (240), Expect = 9e-25
 Identities = 25/138 (18%), Positives = 50/138 (36%), Gaps = 14/138 (10%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDV----AGRGIDIPD-VAHVINYDMP 56
            + V          + E + E F+  + N+L+          RG+D+P+ + +VI +  P
Sbjct: 276 KFNVGETWS-----EFEKNFEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTP 330

Query: 57  GNIEM--YTHRIGRTGRAGKTGV--ATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHE 112
              ++  Y    GR+ R     +    + +   D ++F  LK  L+        E A+  
Sbjct: 331 SGPDVYTYIQASGRSSRILNGVLVKGVSVIFEEDEEIFESLKTRLLLIAEEEIIEEAEAN 390

Query: 113 ASKFKPGTIPDRPPRRND 130
             +        R     +
Sbjct: 391 WKELVHEVEESRRRSERE 408

>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 = 89.5 bits (221), Expect = 4e-22
 Identities = 28/95 (29%), Positives = 41/95 (43%), Gaps = 1/95 (1%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G        G SQ ++++ L+ F    +NVLVAT V   G+D+P+V  V+ Y+   +   
Sbjct: 393 GQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIR 452

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQM 96
              R GRTGR    G     +     D  Y     
Sbjct: 453 SIQRRGRTGRH-MPGRVIILMAKGTRDEAYYWSSR 486

>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* Length = 523

 Score = 71.8 bits (177), Expect = 6e-16
 Identities = 33/103 (32%), Positives = 48/103 (46%), Gaps = 5/103 (4%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVA-GRGIDIPDVAHVINYDMPGNIE 60
           G      H G     R    E F+     ++VAT VA G GI+ P+V  V+++D+P NIE
Sbjct: 260 GISAAAYHAGLENNVRADVQEKFQRDDLQIVVAT-VAFGMGINKPNVRFVVHFDIPRNIE 318

Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSP 103
            Y    GR GR G    A   L +   D+ + L++ L +    
Sbjct: 319 SYYQETGRAGRDG--LPAEAMLFYDPADMAW-LRRCLEEKPQG 358

>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* Length = 591

 Score = 66.2 bits (162), Expect = 5e-14
 Identities = 29/101 (28%), Positives = 40/101 (39%), Gaps = 5/101 (4%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVA-GRGIDIPDVAHVINYDMPGNIE 60
           G      H     E +      +      V+VAT VA G GID PDV  VI++ M  ++E
Sbjct: 291 GIHAGAYHANLEPEDKTTVHRKWSANEIQVVVAT-VAFGMGIDKPDVRFVIHHSMSKSME 349

Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSN 101
            Y    GR GR         +  F D      +  M++  N
Sbjct: 350 NYYQESGRAGRDDMKADCILYYGFGDIFR---ISSMVVMEN 387

>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} Length = 936

 Score = 66.1 bits (160), Expect = 7e-14
 Identities = 28/135 (20%), Positives = 47/135 (34%), Gaps = 10/135 (7%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYN-VLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
           G        G +   ++  L+ F+T + N +L+AT VA  GIDI     V+ Y+  GN+ 
Sbjct: 667 GRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVT 726

Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFY-------DLKQMLIQSNSPVPPELAKHEA 113
                 GR GRA          +  +            ++    ++       E    + 
Sbjct: 727 KMIQVRGR-GRA-AGSKCILVTSKTEVVENEKCNRYKEEMMNKAVEKIQKWDEETFAKKI 784

Query: 114 SKFKPGTIPDRPPRR 128
              +      R  RR
Sbjct: 785 HNLQMKERVLRDSRR 799

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 65.8 bits (159), Expect = 1e-13
 Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTK-RYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
           G   T  + G +   ++  L+ F+    +N+L+AT VA  GIDI     VI Y+  GN+ 
Sbjct: 434 GRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVI 493

Query: 61  MYTHRIGRTGRAG 73
                 GR    G
Sbjct: 494 KMIQTRGRGRARG 506

>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} Length = 797

 Score = 62.7 bits (151), Expect = 1e-12
 Identities = 27/132 (20%), Positives = 45/132 (34%), Gaps = 12/132 (9%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYN-VLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
           G        G +   ++  L+ F+T + N +L+AT VA  GIDI     V+ Y+  GN+ 
Sbjct: 667 GRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVT 726

Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQML-------IQSNSPVPPELAKHEA 113
                 GR GRA          +  +        +         ++       E    + 
Sbjct: 727 KMIQVRGR-GRA-AGSKCILVTSKTEVVENEKCNRYKEEMMNKAVEKIQKWDEETFAKKI 784

Query: 114 SKF--KPGTIPD 123
                K   + D
Sbjct: 785 HNLQMKERVLRD 796

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 62.6 bits (151), Expect = 1e-12
 Identities = 22/63 (34%), Positives = 30/63 (47%), Gaps = 1/63 (1%)

Query: 10  GGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRT 69
           G     Q+ +      +   N+L+AT VA  GIDI +   VI Y+  GN+       GR 
Sbjct: 434 GMTLPAQKCVLEAFRASGDNNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR- 492

Query: 70  GRA 72
           GRA
Sbjct: 493 GRA 495

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A* Length = 556

 Score = 62.3 bits (150), Expect = 2e-12
 Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 3/64 (4%)

Query: 10  GGKSQEQREISLEGFRTKRYN-VLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGR 68
           G     Q+ + L+ F+T + N +L+AT VA  GIDI     V+ Y+  GN+       GR
Sbjct: 435 GMTLPSQKGV-LDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR 493

Query: 69  TGRA 72
            GRA
Sbjct: 494 -GRA 496

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12} Length = 968

 Score = 56.6 bits (136), Expect = 2e-10
 Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNV--LVATDVAGRGIDIPDVAHVINYDMPGN 58
            G R    H G S  +R+ +   F  +      L+ +++   G +    +H++ +D+P N
Sbjct: 527 EGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFN 586

Query: 59  IEMYTHRIGRTGRAG 73
            ++   RIGR  R G
Sbjct: 587 PDLLEQRIGRLDRIG 601

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A* Length = 472

 Score = 52.5 bits (126), Expect = 4e-09
 Identities = 25/88 (28%), Positives = 38/88 (43%), Gaps = 2/88 (2%)

Query: 3   YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMP-GNIEM 61
           + +  +    S+E+RE  LEGFRT R+  +V++ V   GID+PD    +      G+   
Sbjct: 369 FLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIM-SGSGSARE 427

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDV 89
           Y  R+GR  R  K               
Sbjct: 428 YIQRLGRILRPSKGKKEAVLYELISRGT 455

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Length = 720

 Score = 52.2 bits (125), Expect = 5e-09
 Identities = 25/123 (20%), Positives = 40/123 (32%), Gaps = 12/123 (9%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAH-VI-----NYD 54
           +   V   H G  +++R +  E FR      +VAT     GI+ P  A  VI      Y 
Sbjct: 293 IRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTP--AFRVIIRDIWRYS 350

Query: 55  MPGNIEM----YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAK 110
             G   +        +GR GR     V    +     D    +   +      +  +L+ 
Sbjct: 351 DFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPREVMNHYIFGKPEKLFSQLSN 410

Query: 111 HEA 113
              
Sbjct: 411 ESN 413

>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 = 48.3 bits (115), Expect = 1e-07
 Identities = 24/113 (21%), Positives = 38/113 (33%), Gaps = 11/113 (9%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAH-VI-----NYD 54
           +       H G    QR +  + FR     V+VAT     G+++P  A  VI      +D
Sbjct: 295 VRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLP--ARRVIVRSLYRFD 352

Query: 55  ---MPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPV 104
                  +  Y    GR GR G        +     D    +K+ +      +
Sbjct: 353 GYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDREIAVKRYIFGEPERI 405

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4} Length = 510

 Score = 39.1 bits (90), Expect = 1e-04
 Identities = 18/94 (19%), Positives = 31/94 (32%), Gaps = 1/94 (1%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVAT-DVAGRGIDIPDVAHVINYDMPGNIE 60
             +V  + G    E R I        +  ++VA+  V   GI + ++ HV+      +  
Sbjct: 371 YDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFSTGISVKNLHHVVLAHGVKSKI 430

Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLK 94
           +    IGR  R   +    T     D        
Sbjct: 431 IVLQTIGRVLRKHGSKTIATVWDLIDDAGVKPKS 464

>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 Length = 1151

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 3/70 (4%)

Query: 4   RVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVI--NYDMPGNIEM 61
           R+   HG   + + E  +  F  +R+NVLV T +   GIDIP    +I    D  G  ++
Sbjct: 840 RIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQL 899

Query: 62  YTHRIGRTGR 71
           +  R GR GR
Sbjct: 900 HQLR-GRVGR 908

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 37.4 bits (87), Expect = 7e-04
 Identities = 29/110 (26%), Positives = 45/110 (40%), Gaps = 16/110 (14%)

Query: 9   HGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAH-VI------------NYDM 55
           H G S+  R++  EGFR ++  V+VAT     G+++P  A  VI             Y  
Sbjct: 319 HAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLP--ARTVIIGDIYRFNKKIAGYYD 376

Query: 56  PGNIEMYTHRIGRTGRAGKTGVATTFL-TFHDTDVFYDLKQMLIQSNSPV 104
              I  Y    GR GR G   +  + +      DV    K+ ++    P+
Sbjct: 377 EIPIMEYKQMSGRAGRPGFDQIGESIVVVRDKEDVDRVFKKYVLSDVEPI 426

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	135
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.95
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.95
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.95
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.94
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.94
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.94
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.94
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.94
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.93
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.93
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.85
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.91
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.91
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.91
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.9
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.9
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.89
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.89
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.89
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.88
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.88
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.88
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.87
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.87
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.86
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.84
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.83
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.82
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.81
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.81
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.81
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.81
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.8
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.8
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.79
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.79
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.79
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.79
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.79
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.79
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.78
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.78
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.77
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.77
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.77
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.77
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.76
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.75
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.74
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.74
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.73
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.73
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.72
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.72
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.72
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.71
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.7
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.7
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.7
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.7
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.69
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.69
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.66
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.65
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.64
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.64
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.63
3h1t_A	590	Type I site-specific restriction-modification syst	99.59
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.57
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.18
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	97.8
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	97.42
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	96.77
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	95.15
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	94.56
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	94.42
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	90.15
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	89.97
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	84.09

>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=99.95  E-value=4.7e-28  Score=166.22  Aligned_cols=112  Identities=46%  Similarity=0.792  Sum_probs=93.6

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++.+|..++++|++|+++|||||+++++|+|+|++++||++|+|++...|+||+||+||.|+.|.++++
T Consensus        70 g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R~g~~g~~~~~  149 (185)
T 2jgn_A           70 GYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSF  149 (185)
T ss_dssp             TCCEEEEC--------CHHHHHHHHTSSSEEEEEC------CCCSBSEEEESSCCSSHHHHHHHHTTBCCTTSCEEEEEE
T ss_pred             CCceEEEeCCCCHHHHHHHHHHHHcCCCeEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHccccCCCCCCcEEEEE
Confidence            68899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCCCCCChHHHHHHH
Q 037139           82 LTFHDTDVFYDLKQMLIQSNSPVPPELAKHEA  113 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  113 (135)
                      +.+.+...++.+.+.+.....++|+++..+..
T Consensus       150 ~~~~~~~~~~~l~~~l~~~~~~~~~~l~~~a~  181 (185)
T 2jgn_A          150 FNERNINITKDLLDLLVEAKQEVPSWLENMAY  181 (185)
T ss_dssp             ECGGGGGGHHHHHHHHHHTTCCCCHHHHHHHC
T ss_pred             EchhhHHHHHHHHHHHHhccCCCCHHHHHHHH
Confidence            99999999999999999999999999887643

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.95  E-value=1.4e-27  Score=164.68  Aligned_cols=110  Identities=52%  Similarity=0.886  Sum_probs=101.4

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++++|.++++.|++|+++|||||+++++|+|+|++++||+||+|++...|+||+||+||.|+.|.++++
T Consensus        78 g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~~~~~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~g~~g~~i~l  157 (191)
T 2p6n_A           78 GVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTF  157 (191)
T ss_dssp             TCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECHHHHTTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC---CCEEEEE
T ss_pred             CCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcCchhcCCCcccCCEEEEeCCCCCHHHHHHHhCccccCCCCcEEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecC-ChhHHHHHHHHHhhCCCCCChHHHHH
Q 037139           82 LTFH-DTDVFYDLKQMLIQSNSPVPPELAKH  111 (135)
Q Consensus        82 ~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~  111 (135)
                      +.+. +......+++.+.....++|++|.++
T Consensus       158 ~~~~~~~~~~~~l~~~l~~~~~~~p~~l~~~  188 (191)
T 2p6n_A          158 INKACDESVLMDLKALLLEAKQKVPPVLQVL  188 (191)
T ss_dssp             ECTTSCHHHHHHHHHHHHHTTCCCCHHHHST
T ss_pred             EcCchhHHHHHHHHHHHHHccCcCCHHHHhh
Confidence            9876 67788999999999999999998754

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=99.95  E-value=3.5e-27  Score=158.63  Aligned_cols=103  Identities=44%  Similarity=0.698  Sum_probs=96.8

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      .|+.+..+||+|++.+|..++++|++|+++|||||+++++|+|+|++++||++|+|+++..|+||+||+||.|+.|.+++
T Consensus        58 ~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gld~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~  137 (163)
T 2hjv_A           58 LGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAIS  137 (163)
T ss_dssp             TTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTTTCCCSCCSEEEESSCCSSHHHHHHHTTTSSCTTCCEEEEE
T ss_pred             cCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCCchhcCCEEEEeCCCCCHHHHHHhccccCcCCCCceEEE
Confidence            37889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHHHHHHHHHhhCCCC
Q 037139           81 FLTFHDTDVFYDLKQMLIQSNSP  103 (135)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~  103 (135)
                      ++.+.+...++.+++.+.....+
T Consensus       138 ~~~~~~~~~~~~i~~~~~~~~~~  160 (163)
T 2hjv_A          138 FVTAFEKRFLADIEEYIGFEIQK  160 (163)
T ss_dssp             EECGGGHHHHHHHHHHHTSCCEE
T ss_pred             EecHHHHHHHHHHHHHHCCCcCc
Confidence            99999999999998888765543

>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=99.94  E-value=2.9e-27  Score=160.47  Aligned_cols=109  Identities=34%  Similarity=0.607  Sum_probs=98.2

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++.+|..++++|++|+++|||||+++++|+|+|++++||+||+|++...|+||+||+||.|+.|.++++
T Consensus        55 ~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R~g~~g~~~~~  134 (172)
T 1t5i_A           55 NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITF  134 (172)
T ss_dssp             TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEE
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECCchhcCcchhhCCEEEEECCCCCHHHHHHHhcccccCCCCcEEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecC-ChhHHHHHHHHHhhCCCCCChHHHH
Q 037139           82 LTFH-DTDVFYDLKQMLIQSNSPVPPELAK  110 (135)
Q Consensus        82 ~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~  110 (135)
                      +.+. +...++.+++.+.....++|..+..
T Consensus       135 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~  164 (172)
T 1t5i_A          135 VSDENDAKILNDVQDRFEVNISELPDEIDI  164 (172)
T ss_dssp             ECSHHHHHHHHHHHHHHCCCEEECC-----
T ss_pred             EcChhHHHHHHHHHHHHhcchhhCChhhch
Confidence            9875 4567888999998888888887654

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=99.94  E-value=1.9e-27  Score=160.21  Aligned_cols=108  Identities=36%  Similarity=0.670  Sum_probs=97.0

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++.+|..+++.|++|+++|||||+++++|+|+|++++||++|+|++...|.||+||+||.|+.|.++++
T Consensus        54 ~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G~d~~~~~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~~  133 (165)
T 1fuk_A           54 KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINF  133 (165)
T ss_dssp             TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEE
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCCCCCChHHH
Q 037139           82 LTFHDTDVFYDLKQMLIQSNSPVPPELA  109 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~  109 (135)
                      +.+.+...+..+++.++....++|..+.
T Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (165)
T 1fuk_A          134 VTNEDVGAMRELEKFYSTQIEELPSDIA  161 (165)
T ss_dssp             EETTTHHHHHHHHHHSSCCCEECCSCCT
T ss_pred             EcchHHHHHHHHHHHHccCccccCccHH
Confidence            9999999999999988888877776544

>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=99.94  E-value=1.4e-26  Score=161.94  Aligned_cols=102  Identities=40%  Similarity=0.593  Sum_probs=94.4

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++++|..+++.|++|+++|||||+++++|+|+|++++||++|+|++...|+||+||+||.|+.|.++++
T Consensus        55 ~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~Gidi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~l  134 (212)
T 3eaq_A           55 GHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLL  134 (212)
T ss_dssp             TCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECTTTTCSSSCCCBSEEEESSCCSSHHHHHHHHTTBCCCC--BEEEEE
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecChhhcCCCCccCcEEEECCCCcCHHHHHHHhcccCCCCCCCeEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCCCC
Q 037139           82 LTFHDTDVFYDLKQMLIQSNSP  103 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~  103 (135)
                      +...+...++.+++.++.....
T Consensus       135 ~~~~~~~~~~~i~~~~~~~~~~  156 (212)
T 3eaq_A          135 YGPRERRDVEALERAVGRRFKR  156 (212)
T ss_dssp             ECGGGHHHHHHHHHHHSSCCEE
T ss_pred             EchhHHHHHHHHHHHhcCcCee
Confidence            9999998999998887765433

>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=99.94  E-value=1e-26  Score=157.93  Aligned_cols=104  Identities=36%  Similarity=0.614  Sum_probs=93.0

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCC------CCHHHHHHHhhhcCCCCCC
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMP------GNIEMYTHRIGRTGRAGKT   75 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p------~~~~~~~qr~GR~gR~~~~   75 (135)
                      |+.+..+||+|++.+|..++++|++|+++|||||+++++|+|+|.+++||+||+|      .+...|+||+||+||.|+.
T Consensus        58 ~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~Gid~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR~g~~  137 (175)
T 2rb4_A           58 GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKK  137 (175)
T ss_dssp             TCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECCSCCTTTCCTTEEEEEESSCCC--CCSCCHHHHHHHHCBC----CC
T ss_pred             CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEecchhcCCCcccCCEEEEeCCCCCccccCCHHHHHHHhcccccCCCC
Confidence            6789999999999999999999999999999999999999999999999999999      8999999999999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHHHhhCCCCCC
Q 037139           76 GVATTFLTFHDTDVFYDLKQMLIQSNSPVP  105 (135)
Q Consensus        76 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  105 (135)
                      |.+++++...+...+..+++.++....+++
T Consensus       138 g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  167 (175)
T 2rb4_A          138 GLAFNMIEVDELPSLMKIQDHFNSSIKQLN  167 (175)
T ss_dssp             EEEEEEECGGGHHHHHHHHHHHTCCCEEEC
T ss_pred             ceEEEEEccchHHHHHHHHHHhcCcccccC
Confidence            999999999988888888888876655443

>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=99.94  E-value=1.9e-26  Score=175.87  Aligned_cols=109  Identities=46%  Similarity=0.751  Sum_probs=103.5

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++++|++++++|++|+.+|||||+++++|+|+|++++||+||+|.+..+|+||+||+||.|+.|.+++|
T Consensus       324 ~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v~~rGlDi~~v~~VI~~d~p~~~~~y~qriGR~gR~g~~G~a~~~  403 (434)
T 2db3_A          324 EFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSF  403 (434)
T ss_dssp             TCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECGGGTSSCCCTTCCEEEESSCCSSHHHHHHHHTTSSCTTCCEEEEEE
T ss_pred             CCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEchhhhCCCCcccCCEEEEECCCCCHHHHHHHhcccccCCCCCEEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eec-CChhHHHHHHHHHhhCCCCCChHHHH
Q 037139           82 LTF-HDTDVFYDLKQMLIQSNSPVPPELAK  110 (135)
Q Consensus        82 ~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~  110 (135)
                      +.+ .+......+.+.+....+++|++|.+
T Consensus       404 ~~~~~~~~~~~~l~~~l~~~~~~vp~~l~~  433 (434)
T 2db3_A          404 FDPEKDRAIAADLVKILEGSGQTVPDFLRT  433 (434)
T ss_dssp             ECTTTCGGGHHHHHHHHHHTTCCCCGGGC-
T ss_pred             EeccccHHHHHHHHHHHHHcCCCCCHHHHh
Confidence            995 56778899999999999999999864

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=99.93  E-value=2e-25  Score=163.48  Aligned_cols=102  Identities=41%  Similarity=0.612  Sum_probs=91.5

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      .|+.+..+||+|++.+|..+++.|++|+++|||||+++++|+|+|++++||+||+|++...|+||+||+||.|+.|.+++
T Consensus        51 ~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~va~~Gidi~~v~~VI~~d~p~s~~~y~Qr~GRagR~g~~G~~i~  130 (300)
T 3i32_A           51 LGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVL  130 (300)
T ss_dssp             TTCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECSTTTCSTTCCCCSEEEESSCCSSTTHHHHHHTCCC-----CEEEE
T ss_pred             CCCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEechhhcCccccceeEEEEcCCCCCHHHHHHHccCcCcCCCCceEEE
Confidence            37889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHHHHHHHHHhhCCC
Q 037139           81 FLTFHDTDVFYDLKQMLIQSNS  102 (135)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~  102 (135)
                      ++...+...++.+++.++....
T Consensus       131 l~~~~e~~~~~~ie~~~~~~~~  152 (300)
T 3i32_A          131 LYGPRERRDVEALERAVGRRFK  152 (300)
T ss_dssp             EECSSTHHHHHHHHHHHTCCCE
T ss_pred             EeChHHHHHHHHHHHHhCCcce
Confidence            9999999999988888776543

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.93  E-value=2.8e-25  Score=167.15  Aligned_cols=113  Identities=45%  Similarity=0.786  Sum_probs=106.3

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++++|.++++.|++|+.+|||||+++++|+|+|++++||++|+|.+...|+||+||+||.|+.|.++++
T Consensus       300 ~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~  379 (417)
T 2i4i_A          300 GYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSF  379 (417)
T ss_dssp             TCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECHHHHTTSCCCCEEEEEESSCCSSHHHHHHHHTTBCC--CCEEEEEE
T ss_pred             CCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccCCEEEEEcCCCCHHHHHHhcCccccCCCCceEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCCCCCChHHHHHHHh
Q 037139           82 LTFHDTDVFYDLKQMLIQSNSPVPPELAKHEAS  114 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  114 (135)
                      +.+.+......+.+.+.....++|.++.....+
T Consensus       380 ~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~~  412 (417)
T 2i4i_A          380 FNERNINITKDLLDLLVEAKQEVPSWLENMAYE  412 (417)
T ss_dssp             ECGGGGGGHHHHHHHHHHTTCCCCHHHHHHHTC
T ss_pred             EccccHHHHHHHHHHHHHhcCcCCHHHHHHHHh
Confidence            999999999999999999999999999876544

>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=99.85  E-value=2e-26  Score=155.85  Aligned_cols=100  Identities=43%  Similarity=0.667  Sum_probs=93.4

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++.+|.++++.|++|+++|||||+++++|+|+|++++||++|+|++...|+||+||+||.|+.|.++++
T Consensus        54 ~~~~~~~~g~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gid~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~  133 (170)
T 2yjt_D           54 GINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISL  133 (170)
Confidence            67889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCC
Q 037139           82 LTFHDTDVFYDLKQMLIQSN  101 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~  101 (135)
                      +...+...+..+++.+....
T Consensus       134 ~~~~~~~~~~~~~~~~~~~~  153 (170)
T 2yjt_D          134 VEAHDHLLLGKVGRYIEEPI  153 (170)
Confidence            99888888888877765554

>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=99.91  E-value=2.6e-24  Score=161.26  Aligned_cols=109  Identities=36%  Similarity=0.620  Sum_probs=103.5

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++++|..+++.|++|+.+|||||+++++|+|+|++++||++|+|++...|+||+||+||.|+.|.++++
T Consensus       282 ~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~~~~Gidip~~~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~l  361 (400)
T 1s2m_A          282 GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINL  361 (400)
T ss_dssp             TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEE
T ss_pred             CCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCccccCCCccCCCEEEEeCCCCCHHHHHHhcchhcCCCCCceEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCCCCCChHHHH
Q 037139           82 LTFHDTDVFYDLKQMLIQSNSPVPPELAK  110 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  110 (135)
                      +...+...++.+++.+.....++|.++..
T Consensus       362 ~~~~~~~~~~~i~~~~~~~~~~~~~~~~~  390 (400)
T 1s2m_A          362 INWNDRFNLYKIEQELGTEIAAIPATIDK  390 (400)
T ss_dssp             ECGGGHHHHHHHHHHHTCCCEECCSSCCG
T ss_pred             eccchHHHHHHHHHHhCCCcccccccccc
Confidence            99999999999999999888888877653

>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=99.91  E-value=1.9e-24  Score=162.57  Aligned_cols=107  Identities=39%  Similarity=0.744  Sum_probs=101.8

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++++|.++++.|++|+.+|||||+++++|+|+|++++||++|+|++...|+||+||+||.|+.|.++++
T Consensus       300 ~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~  379 (410)
T 2j0s_A          300 NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINF  379 (410)
T ss_dssp             TCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEE
T ss_pred             CCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECChhhCcCCcccCCEEEEECCCCCHHHHHHhcccccCCCCceEEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCCCCCChHH
Q 037139           82 LTFHDTDVFYDLKQMLIQSNSPVPPEL  108 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~l  108 (135)
                      +...+...++.++++++....++|..+
T Consensus       380 ~~~~~~~~~~~i~~~~~~~~~~~~~~~  406 (410)
T 2j0s_A          380 VKNDDIRILRDIEQYYSTQIDEMPMNV  406 (410)
T ss_dssp             EEGGGHHHHHHHHHHTTCCCEECCSCC
T ss_pred             ecHHHHHHHHHHHHHhCCCceecccch
Confidence            999999999999999998888777543

>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=99.91  E-value=9.3e-25  Score=164.05  Aligned_cols=109  Identities=39%  Similarity=0.681  Sum_probs=87.0

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++++|.++++.|++|+.+|||||+++++|+|+|++++||++|+|.+...|+||+||+||.|+.|.++++
T Consensus       304 ~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~  383 (414)
T 3eiq_A          304 DFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINM  383 (414)
T ss_dssp             TCCCEEC---CHHHHHHHHHHHHSCC---CEEECSSCC--CCGGGCSCEEESSCCSSTHHHHHHSCCC-------CEEEE
T ss_pred             CCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCccccCCCccCCCEEEEeCCCCCHHHhhhhcCcccCCCCCceEEEE
Confidence            67889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCCCCCChHHHH
Q 037139           82 LTFHDTDVFYDLKQMLIQSNSPVPPELAK  110 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  110 (135)
                      +...+...++.++++++....++|..+.+
T Consensus       384 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  412 (414)
T 3eiq_A          384 VTEEDKRTLRDIETFYNTSIEEMPLNVAD  412 (414)
T ss_dssp             ECSTHHHHHHHHHHHTTCCCEECCC----
T ss_pred             EcHHHHHHHHHHHHHHcCCccccChhhhh
Confidence            99999999999999999999888877654

>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=99.90  E-value=3e-23  Score=153.17  Aligned_cols=104  Identities=39%  Similarity=0.656  Sum_probs=98.7

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++++|.++++.|++|+.+|||||+++++|+|+|++++||++|+|++...|.||+||+||.|+.|.++++
T Consensus       262 ~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~  341 (367)
T 1hv8_A          262 GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISI  341 (367)
T ss_dssp             TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEE
T ss_pred             CCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCCCcccCCEEEEecCCCCHHHhhhcccccccCCCccEEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCCCCCC
Q 037139           82 LTFHDTDVFYDLKQMLIQSNSPVP  105 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~  105 (135)
                      +.+.+...++.+++.++....+++
T Consensus       342 ~~~~~~~~~~~i~~~~~~~~~~~~  365 (367)
T 1hv8_A          342 INRREYKKLRYIERAMKLKIKKLK  365 (367)
T ss_dssp             ECTTSHHHHHHHHHHHTCCCCCBC
T ss_pred             EcHHHHHHHHHHHHHhCCCCceec
Confidence            999999999999998888776553

>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=99.90  E-value=2.5e-23  Score=162.50  Aligned_cols=99  Identities=30%  Similarity=0.560  Sum_probs=93.8

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++.+|..+++.|++|+++|||||+++++|+|+|++++||++|+|.+...|+||+||+||.|+.|.++++
T Consensus       366 ~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~  445 (563)
T 3i5x_A          366 DLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLF  445 (563)
T ss_dssp             TSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEE
T ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcchhhcCCCcccCCEEEEECCCCchhhhhhhcCccccCCCCceEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhC
Q 037139           82 LTFHDTDVFYDLKQMLIQS  100 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~  100 (135)
                      +.+.+...++.+++.....
T Consensus       446 ~~~~e~~~~~~l~~~~~~~  464 (563)
T 3i5x_A          446 ICKDELPFVRELEDAKNIV  464 (563)
T ss_dssp             EEGGGHHHHHHHHHHHCCC
T ss_pred             EchhHHHHHHHHHHHhCCC
Confidence            9999988888888776543

>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=99.89  E-value=1.9e-23  Score=155.88  Aligned_cols=108  Identities=34%  Similarity=0.619  Sum_probs=99.3

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++++|.++++.|++|+.+|||||+++++|+|+|++++||++|+|++...|+||+||+||.|+.|.++++
T Consensus       274 ~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~  353 (391)
T 1xti_A          274 NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITF  353 (391)
T ss_dssp             TCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCCCSSCBCCTTEEEEEESSCCSSHHHHHHHHCBCSSSCCCCEEEEE
T ss_pred             CCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHhcccccCCCCceEEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecC-ChhHHHHHHHHHhhCCCCCChHHH
Q 037139           82 LTFH-DTDVFYDLKQMLIQSNSPVPPELA  109 (135)
Q Consensus        82 ~~~~-~~~~~~~~~~~~~~~~~~~~~~l~  109 (135)
                      +.+. +...++.+++.+.....++|..+.
T Consensus       354 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  382 (391)
T 1xti_A          354 VSDENDAKILNDVQDRFEVNISELPDEID  382 (391)
T ss_dssp             ECSHHHHHHHHHHHHHTTCCCEECCSCCC
T ss_pred             EcccchHHHHHHHHHHhcCChhhCCcccc
Confidence            9876 446678888888888888887644

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.89  E-value=6.3e-23  Score=161.22  Aligned_cols=99  Identities=30%  Similarity=0.560  Sum_probs=93.8

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++++|.+++++|++|+.+|||||+++++|+|+|++++||++|+|.+...|+||+||+||.|+.|.++++
T Consensus       315 ~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~  394 (579)
T 3sqw_A          315 DLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLF  394 (579)
T ss_dssp             TSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEE
T ss_pred             CCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcchhhcCCCcccCCEEEEcCCCCCHHHhhhhccccccCCCCceEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhC
Q 037139           82 LTFHDTDVFYDLKQMLIQS  100 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~  100 (135)
                      +.+.+...++.+++.....
T Consensus       395 ~~~~e~~~~~~l~~~~~~~  413 (579)
T 3sqw_A          395 ICKDELPFVRELEDAKNIV  413 (579)
T ss_dssp             EEGGGHHHHHHHHHHHCCC
T ss_pred             EcccHHHHHHHHHHHhCCC
Confidence            9999988888888776443

>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=99.89  E-value=4e-23  Score=154.90  Aligned_cols=106  Identities=37%  Similarity=0.616  Sum_probs=94.8

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCC------CCHHHHHHHhhhcCCCCCC
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMP------GNIEMYTHRIGRTGRAGKT   75 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p------~~~~~~~qr~GR~gR~~~~   75 (135)
                      |+.+..+||+|++++|.++++.|++|+.+|||||+++++|+|+|++++||++|+|      .+...|+||+||+||.|..
T Consensus       290 ~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~  369 (412)
T 3fht_A          290 GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKR  369 (412)
T ss_dssp             TCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTSSCCCTTEEEEEESSCCBCSSSSBCHHHHHHHHTTSSCTTCC
T ss_pred             CCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCccccCCCccCCCEEEEECCCCCCCCCcchheeecccCcccCCCCC
Confidence            6788999999999999999999999999999999999999999999999999999      4678999999999999999


Q ss_pred             ceEEEEeecCC-hhHHHHHHHHHhhCCCCCChH
Q 037139           76 GVATTFLTFHD-TDVFYDLKQMLIQSNSPVPPE  107 (135)
Q Consensus        76 g~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~  107 (135)
                      |.+++++...+ ...++.+++.+.....+++..
T Consensus       370 g~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~  402 (412)
T 3fht_A          370 GLAVNMVDSKHSMNILNRIQEHFNKKIERLDTD  402 (412)
T ss_dssp             EEEEEEECSHHHHHHHHHHHHHHTCCCEEC---
T ss_pred             ceEEEEEcChhhHHHHHHHHHHHCCccccCCCc
Confidence            99999998764 677888888888777666543

>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=99.88  E-value=1.4e-22  Score=157.90  Aligned_cols=89  Identities=33%  Similarity=0.526  Sum_probs=84.2

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++++|.+++++|++|+++|||||+++++|+|+|++++||++|+|.+.+.|.||+||+||.|.+|.++++
T Consensus       260 g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a~~~GiD~p~v~~VI~~~~p~s~~~y~Qr~GRaGR~g~~~~~~l~  339 (523)
T 1oyw_A          260 GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLF  339 (523)
T ss_dssp             TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEE
T ss_pred             CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhCCCCccCccEEEEECCCCCHHHHHHHhccccCCCCCceEEEE
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHH
Q 037139           82 LTFHDTDVF   90 (135)
Q Consensus        82 ~~~~~~~~~   90 (135)
                      +.+.+....
T Consensus       340 ~~~~d~~~~  348 (523)
T 1oyw_A          340 YDPADMAWL  348 (523)
T ss_dssp             ECHHHHHHH
T ss_pred             eCHHHHHHH
Confidence            987655443

>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=99.88  E-value=1.5e-22  Score=159.79  Aligned_cols=90  Identities=29%  Similarity=0.414  Sum_probs=84.4

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      .|+.+..+||+|++++|.+++++|++|+++|||||+++++|+|+|+|++||++|+|.+.+.|+||+||+||.|.+|.+++
T Consensus       290 ~g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~a~~~GID~p~V~~VI~~~~p~s~~~y~Qr~GRaGR~G~~g~~i~  369 (591)
T 2v1x_A          290 LGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCIL  369 (591)
T ss_dssp             TTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTTSCTTCCCSCEEEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEE
T ss_pred             CCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhcCCCcccccEEEEeCCCCCHHHHHHHhccCCcCCCCceEEE
Confidence            37889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHH
Q 037139           81 FLTFHDTDVF   90 (135)
Q Consensus        81 ~~~~~~~~~~   90 (135)
                      ++.+.+....
T Consensus       370 l~~~~D~~~~  379 (591)
T 2v1x_A          370 YYGFGDIFRI  379 (591)
T ss_dssp             EECHHHHHHH
T ss_pred             EEChHHHHHH
Confidence            9987655433

>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=99.88  E-value=1e-22  Score=151.70  Aligned_cols=104  Identities=39%  Similarity=0.707  Sum_probs=91.4

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCC------CHHHHHHHhhhcCCCCCC
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPG------NIEMYTHRIGRTGRAGKT   75 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~------~~~~~~qr~GR~gR~~~~   75 (135)
                      |+.+..+||+|++++|.++++.|++|+.+|||||+++++|+|+|++++||++|+|+      +...|+||+||+||.|+.
T Consensus       267 ~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~  346 (395)
T 3pey_A          267 GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRK  346 (395)
T ss_dssp             TCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGGGSSSCCCTTEEEEEESSCCBCTTSSBCHHHHHHHHTTSSCTTCC
T ss_pred             CCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECChhhcCCCcccCCEEEEcCCCCCCcCCCCHHHhhHhccccccCCCC
Confidence            67889999999999999999999999999999999999999999999999999999      999999999999999999


Q ss_pred             ceEEEEeecC-ChhHHHHHHHHHh-hCCCCCC
Q 037139           76 GVATTFLTFH-DTDVFYDLKQMLI-QSNSPVP  105 (135)
Q Consensus        76 g~~~~~~~~~-~~~~~~~~~~~~~-~~~~~~~  105 (135)
                      |.+++++... +....+.+++.+. .....++
T Consensus       347 g~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~  378 (395)
T 3pey_A          347 GVAISFVHDKNSFNILSAIQKYFGDIEMTRVP  378 (395)
T ss_dssp             EEEEEEECSHHHHHHHHHHHHHTTSCCCEECC
T ss_pred             ceEEEEEechHHHHHHHHHHHHhCCceeecCC
Confidence            9999999864 4455666666665 3333333

>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=99.87  E-value=1.8e-22  Score=147.61  Aligned_cols=94  Identities=40%  Similarity=0.706  Sum_probs=85.4

Q ss_pred             eEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEEee
Q 037139            4 RVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLT   83 (135)
Q Consensus         4 ~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~~~   83 (135)
                      .+..+||+|++.+|.+++++|++|+.+|||||+++++|+|+|++++||++|+|++...|.||+||+||.|+.|.+++++.
T Consensus       242 ~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~gR~g~~g~~~~~~~  321 (337)
T 2z0m_A          242 NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFIL  321 (337)
T ss_dssp             TEEEECTTSCHHHHHHHHHHHHTTSCSEEEECHHHHTTCCCCCBSEEEESSCCSSHHHHHHHHTTBCGGGCCEEEEEEES
T ss_pred             hhhhhcCCCCHHHHHHHHHHHHcCCCcEEEEcCccccCCCccCCCEEEEecCCCCHHHhhHhcCccccCCCCceEEEEEe
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCChhHHHHHHHHHh
Q 037139           84 FHDTDVFYDLKQMLI   98 (135)
Q Consensus        84 ~~~~~~~~~~~~~~~   98 (135)
                       .+....+.+++.+.
T Consensus       322 -~~~~~~~~i~~~~~  335 (337)
T 2z0m_A          322 -NEYWLEKEVKKVSQ  335 (337)
T ss_dssp             -SCHHHHHHHC----
T ss_pred             -CcHHHHHHHHHHhc
Confidence             77777777776654

>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=99.87  E-value=6.2e-24  Score=158.50  Aligned_cols=108  Identities=36%  Similarity=0.670  Sum_probs=0.0

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++++|.++++.|++|+.+|||||+++++|+|+|++++||++|+|++...|+||+||+||.|+.|.++++
T Consensus       283 ~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gldi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~  362 (394)
T 1fuu_A          283 KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINF  362 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCeEEEeeCCCCHHHHHHHHHHHHCCCCcEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHcCcccCCCCCceEEEE
Confidence            56788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCCCCCChHHH
Q 037139           82 LTFHDTDVFYDLKQMLIQSNSPVPPELA  109 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~  109 (135)
                      +.+.+...++.+++++.....++|..+.
T Consensus       363 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~  390 (394)
T 1fuu_A          363 VTNEDVGAMRELEKFYSTQIEELPSDIA  390 (394)
T ss_dssp             ----------------------------
T ss_pred             EchhHHHHHHHHHHHhCCcccccCcchh
Confidence            9999998999999988888887777654

>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=99.86  E-value=1.7e-23  Score=160.81  Aligned_cols=105  Identities=37%  Similarity=0.608  Sum_probs=0.0

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCC------CHHHHHHHhhhcCCCCCC
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPG------NIEMYTHRIGRTGRAGKT   75 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~------~~~~~~qr~GR~gR~~~~   75 (135)
                      |+.+..+||+|++.+|..+++.|++|+++|||||+++++|+|+|++++||+||+|.      +...|+||+||+||.|..
T Consensus       357 ~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~~~~~GlDip~v~~VI~~d~p~~~~~~~s~~~~~Qr~GRagR~g~~  436 (479)
T 3fmp_B          357 GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKR  436 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEccccccCCccccCCEEEEecCCCCCccCCCHHHHHHHhcccccCCCC
Confidence            57789999999999999999999999999999999999999999999999999995      668999999999999999


Q ss_pred             ceEEEEeecCC-hhHHHHHHHHHhhCCCCCCh
Q 037139           76 GVATTFLTFHD-TDVFYDLKQMLIQSNSPVPP  106 (135)
Q Consensus        76 g~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  106 (135)
                      |.+++++...+ ...++.+++.+.....+++.
T Consensus       437 G~~i~~~~~~~~~~~~~~i~~~~~~~~~~l~~  468 (479)
T 3fmp_B          437 GLAVNMVDSKHSMNILNRIQEHFNKKIERLDT  468 (479)
T ss_dssp             --------------------------------
T ss_pred             ceEEEEEcCcchHHHHHHHHHHhCCCceECCC
Confidence            99999998764 66777788877776665554

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=99.83  E-value=3.6e-21  Score=149.22  Aligned_cols=84  Identities=29%  Similarity=0.402  Sum_probs=35.5

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhc-CCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRT-KRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~-g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      |.....+||+|++++|.+++++|++ |+++|||||+++++|+|+|+|++||+||+|+++..|+||+|| ||. ..|.++.
T Consensus       426 g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~  503 (556)
T 4a2p_A          426 GRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCIL  503 (556)
T ss_dssp             ----------------------------CCEEEEEC-----------CEEEEETCCSCHHHHHHC----------CCEEE
T ss_pred             ccCCcccccccCHHHHHHHHHHhcccCceEEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEE
Confidence            4455667889999999999999999 999999999999999999999999999999999999999999 998 7889999


Q ss_pred             EeecCCh
Q 037139           81 FLTFHDT   87 (135)
Q Consensus        81 ~~~~~~~   87 (135)
                      ++...+.
T Consensus       504 l~~~~~~  510 (556)
T 4a2p_A          504 VTSKTEV  510 (556)
T ss_dssp             EESCHHH
T ss_pred             EEeCcch
Confidence            9887654

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.82  E-value=3.3e-21  Score=149.13  Aligned_cols=89  Identities=30%  Similarity=0.364  Sum_probs=58.0

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhc-CCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRT-KRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~-g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      .....+||+|++++|.+++++|++ |+++|||||+++++|+|+|++++||+||+|+++..|+||+|| ||. ..|.++.+
T Consensus       426 ~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~GlDlp~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l  503 (555)
T 3tbk_A          426 RGRTNRATGMTLPAQKCVLEAFRASGDNNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR-GRA-RDSKCFLL  503 (555)
T ss_dssp             --------------------------CCSEEEECCCTTCCEETTSCSEEEEESCCSSCCCEECSSCC-CTT-TSCEEEEE
T ss_pred             cCCcccccccCHHHHHHHHHHHhcCCCeeEEEEcchhhcCCccccCCEEEEeCCCCCHHHHHHhcCc-CcC-CCceEEEE
Confidence            344556779999999999999999 999999999999999999999999999999999999999999 888 78999999


Q ss_pred             eecCChhHHHHH
Q 037139           82 LTFHDTDVFYDL   93 (135)
Q Consensus        82 ~~~~~~~~~~~~   93 (135)
                      +...+......+
T Consensus       504 ~~~~~~~~~~~~  515 (555)
T 3tbk_A          504 TSSADVIEKEKA  515 (555)
T ss_dssp             ESCHHHHHHHHH
T ss_pred             EcCCCHHHHHHH
Confidence            987765544444

>4gl2_A Interferon-induced helicase C domain-containing P; MDA5, dsRNA, anti-viral signaling, RIG-I, MAVS, oligomerizat helicase, ATPase; HET: ANP; 3.56A {Homo sapiens}

Probab=99.81  E-value=9e-20  Score=145.46  Aligned_cols=82  Identities=27%  Similarity=0.369  Sum_probs=67.9

Q ss_pred             CceEEEecCC--------CCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCC
Q 037139            2 GYRVTTLHGG--------KSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAG   73 (135)
Q Consensus         2 g~~v~~~hg~--------~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~   73 (135)
                      |+++..+||+        |++++|.+++++|++|+++|||||+++++|+|+|++++||+||+|+++..|+||+|||||.|
T Consensus       430 g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~~~~~GIDip~v~~VI~~d~p~s~~~~~Qr~GRArr~g  509 (699)
T 4gl2_A          430 GVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARADE  509 (699)
T ss_dssp             ---CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEECSCCTTSCCCSCCCCEEESCCCCHHHHHHHHTTSCSSS
T ss_pred             CcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCccccCCEEEEeCCCCCHHHHHHHcCCCCCCC
Confidence            7889999999        99999999999999999999999999999999999999999999999999999999987654


Q ss_pred             CCceEEEEeecC
Q 037139           74 KTGVATTFLTFH   85 (135)
Q Consensus        74 ~~g~~~~~~~~~   85 (135)
                        +.++++....
T Consensus       510 --~~~~l~~~~~  519 (699)
T 4gl2_A          510 --STYVLVAHSG  519 (699)
T ss_dssp             --CEEEEEEESS
T ss_pred             --ceEEEEEeCC
Confidence              3344444433

>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=99.81  E-value=1.5e-19  Score=144.32  Aligned_cols=92  Identities=24%  Similarity=0.364  Sum_probs=84.5

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecC-----CCCHHHHHHHhhhcCCCCCCc
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDM-----PGNIEMYTHRIGRTGRAGKTG   76 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~-----p~~~~~~~qr~GR~gR~~~~g   76 (135)
                      |+++..+||+|++.+|.+++++|++|+++|||||+++++|+|+|++++||++|.     |.+..+|+||+||+||. ..|
T Consensus       469 gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~GlDip~v~lVi~~d~d~~G~p~s~~~~iQr~GRagR~-~~G  547 (661)
T 2d7d_A          469 GIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-AEG  547 (661)
T ss_dssp             TCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTTCCCTTEEEEEETTTTCCTTTTSHHHHHHHHHTTTTS-TTC
T ss_pred             CCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCCcccCCCCEEEEeCcccccCCCCHHHHHHHhCcccCC-CCC
Confidence            778999999999999999999999999999999999999999999999999997     99999999999999998 689


Q ss_pred             eEEEEeecCChhHHHHHH
Q 037139           77 VATTFLTFHDTDVFYDLK   94 (135)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~   94 (135)
                      .+++++...+....+.++
T Consensus       548 ~~i~~~~~~~~~~~~~i~  565 (661)
T 2d7d_A          548 RVIMYADKITKSMEIAIN  565 (661)
T ss_dssp             EEEEECSSCCHHHHHHHH
T ss_pred             EEEEEEeCCCHHHHHHHH
Confidence            999999887765544433

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=99.81  E-value=4.6e-20  Score=139.67  Aligned_cols=86  Identities=33%  Similarity=0.516  Sum_probs=78.6

Q ss_pred             CceEEEecC--------CCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCC
Q 037139            2 GYRVTTLHG--------GKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAG   73 (135)
Q Consensus         2 g~~v~~~hg--------~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~   73 (135)
                      |+.+..+||        +|++++|.+++++|++|+.+|||||+++++|+|+|.+++||++|+|+++..|.||+||+||.|
T Consensus       385 ~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~~~~vLv~T~~~~~Gldl~~~~~Vi~~d~~~~~~~~~Qr~GR~~R~g  464 (494)
T 1wp9_A          385 GIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHM  464 (494)
T ss_dssp             TCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCC
T ss_pred             CCCcEEEeccccccccccCCHHHHHHHHHHHhcCCceEEEECCccccCCCchhCCEEEEeCCCCCHHHHHHHHhhccCCC
Confidence            678899999        999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCceEEEEeecCChh
Q 037139           74 KTGVATTFLTFHDTD   88 (135)
Q Consensus        74 ~~g~~~~~~~~~~~~   88 (135)
                      + |.++.++...+.+
T Consensus       465 ~-g~~~~l~~~~t~e  478 (494)
T 1wp9_A          465 P-GRVIILMAKGTRD  478 (494)
T ss_dssp             C-SEEEEEEETTSHH
T ss_pred             C-ceEEEEEecCCHH
Confidence            7 9999999887553

>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=99.81  E-value=2.2e-19  Score=143.41  Aligned_cols=93  Identities=23%  Similarity=0.342  Sum_probs=84.7

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecC-----CCCHHHHHHHhhhcCCCCCCc
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDM-----PGNIEMYTHRIGRTGRAGKTG   76 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~-----p~~~~~~~qr~GR~gR~~~~g   76 (135)
                      |+++..+||+|++.+|.+++++|+.|+++|||||+++++|+|+|++++||++|.     |.+..+|+||+||+||.+ .|
T Consensus       463 gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~GlDip~v~lVI~~d~d~~G~p~s~~~~iQr~GRagR~~-~G  541 (664)
T 1c4o_A          463 GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA-RG  541 (664)
T ss_dssp             TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTST-TC
T ss_pred             CCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhcCccCCCCCEEEEeCCcccCCCCCHHHHHHHHCccCcCC-CC
Confidence            678999999999999999999999999999999999999999999999999997     899999999999999985 89


Q ss_pred             eEEEEeecCChhHHHHHHH
Q 037139           77 VATTFLTFHDTDVFYDLKQ   95 (135)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~   95 (135)
                      .+++++...+....+.+.+
T Consensus       542 ~~i~~~~~~~~~~~~~i~~  560 (664)
T 1c4o_A          542 EVWLYADRVSEAMQRAIEE  560 (664)
T ss_dssp             EEEEECSSCCHHHHHHHHH
T ss_pred             EEEEEEcCCCHHHHHHHHH
Confidence            9999998877655444443

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=99.80  E-value=4.9e-20  Score=140.92  Aligned_cols=101  Identities=21%  Similarity=0.274  Sum_probs=80.3

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEE-------------------ecCCCCHHHH
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVIN-------------------YDMPGNIEMY   62 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~-------------------~d~p~~~~~~   62 (135)
                      |+++..+||    ++|.+++++|++|+++|||||+++++|+|+| +++||+                   ++.|.+..+|
T Consensus       201 ~~~v~~lhg----~~R~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI~~g~~~~pv~~~~~~~~vi~~~~p~~~~~~  275 (440)
T 1yks_A          201 GKSVVVLNR----KTFEREYPTIKQKKPDFILATDIAEMGANLC-VERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSA  275 (440)
T ss_dssp             TCCEEECCS----SSCC--------CCCSEEEESSSTTCCTTCC-CSEEEECCEEEEEEEETTTTEEEEEEEEECCHHHH
T ss_pred             CCCEEEecc----hhHHHHHhhhcCCCceEEEECChhheeeccC-ceEEEeCCccceeeecccccceeeccccccCHHHH
Confidence            678999999    4688999999999999999999999999999 999986                   8999999999


Q ss_pred             HHHhhhcCCC-CCCceEEEEe---ecCChhHHHHHHHHHhhCCCCCChH
Q 037139           63 THRIGRTGRA-GKTGVATTFL---TFHDTDVFYDLKQMLIQSNSPVPPE  107 (135)
Q Consensus        63 ~qr~GR~gR~-~~~g~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~  107 (135)
                      +||+||+||. +..|.+++++   .+.+...+..+++.+.....+++..
T Consensus       276 ~Qr~GR~GR~g~~~g~~~~l~~~~~~~~~~~l~~l~~~~~~~~~~l~~~  324 (440)
T 1yks_A          276 AQRRGRIGRNPNRDGDSYYYSEPTSENNAHHVCWLEASMLLDNMEVRGG  324 (440)
T ss_dssp             HHHHTTSSCCTTCCCEEEEECSCCCCCCTTBHHHHHHHHHHTTSCCGGG
T ss_pred             HHhccccCCCCCCCceEEEEeccCChhhhhhhhhhhHHhcccccccccc
Confidence            9999999997 6789999996   5667777888888776666655543

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.80  E-value=3e-19  Score=134.77  Aligned_cols=89  Identities=28%  Similarity=0.528  Sum_probs=80.0

Q ss_pred             CceEE-EecCCCCHHHHHHHHHHHhcCCCcEEEe----cCCCcccccccC-CcEEEEecCC--CCHHHHHHHhhhcCCCC
Q 037139            2 GYRVT-TLHGGKSQEQREISLEGFRTKRYNVLVA----TDVAGRGIDIPD-VAHVINYDMP--GNIEMYTHRIGRTGRAG   73 (135)
Q Consensus         2 g~~v~-~~hg~~~~~~r~~~~~~f~~g~~~ilv~----T~~~~~G~d~~~-v~~vi~~d~p--~~~~~~~qr~GR~gR~~   73 (135)
                      |+.+. .+||.    +|+  +++|++|+++||||    |+++++|+|+|+ +++||++|+|  .+...|+||+||+||.|
T Consensus       276 ~~~~~~~~h~~----~r~--~~~f~~g~~~vLvat~s~T~~~~~GiDip~~v~~VI~~~~p~~~~~~~y~qr~GR~gR~g  349 (414)
T 3oiy_A          276 KFNVGETWSEF----EKN--FEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRIL  349 (414)
T ss_dssp             TCCEEESSSCH----HHH--HHHHHTTSCSEEEEECCTTCCCCCCCCCTTTCCEEEEESCCTTTCHHHHHHHHGGGCCEE
T ss_pred             CCceehhhcCc----chH--HHHHhCCCCeEEEEecCcCchhhccCccccccCEEEEECCCCCCCHHHHHHHhCccccCC
Confidence            67787 88885    344  99999999999999    999999999999 9999999999  99999999999999987


Q ss_pred             ----CCceEEEEeecCChhHHHHHHHHHh
Q 037139           74 ----KTGVATTFLTFHDTDVFYDLKQMLI   98 (135)
Q Consensus        74 ----~~g~~~~~~~~~~~~~~~~~~~~~~   98 (135)
                          ..|.+++++  .+...++.+++.+.
T Consensus       350 ~~~~~~g~~i~~~--~~~~~~~~l~~~~~  376 (414)
T 3oiy_A          350 NGVLVKGVSVIFE--EDEEIFESLKTRLL  376 (414)
T ss_dssp             TTEECCEEEEEEC--CCHHHHHHHHHHHH
T ss_pred             CCCCcceEEEEEE--ccHHHHHHHHHHhc
Confidence                478999988  67778888888887

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=99.79  E-value=2.7e-19  Score=143.70  Aligned_cols=99  Identities=23%  Similarity=0.314  Sum_probs=83.7

Q ss_pred             eEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEE----ec----CCCCHHHHHHHhhhcCCCC--
Q 037139            4 RVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVIN----YD----MPGNIEMYTHRIGRTGRAG--   73 (135)
Q Consensus         4 ~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~----~d----~p~~~~~~~qr~GR~gR~~--   73 (135)
                      .+.++||+|++++|..+++.|++|+++|||||+++++|+|+|++++||+    ||    .|.+..+|.||+|||||.|  
T Consensus       296 ~v~~~h~~l~~~~R~~v~~~f~~g~~~vlvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~g~~  375 (720)
T 2zj8_A          296 GVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYD  375 (720)
T ss_dssp             TEEEECTTSCHHHHHHHHHHHHTTSSCEEEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCTTTC
T ss_pred             CeeeecCCCCHHHHHHHHHHHHCCCCeEEEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCCCCC
Confidence            5899999999999999999999999999999999999999999999998    77    6899999999999999987  


Q ss_pred             CCceEEEEeecCChhHHHHHHHHHhhCCCCC
Q 037139           74 KTGVATTFLTFHDTDVFYDLKQMLIQSNSPV  104 (135)
Q Consensus        74 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~  104 (135)
                      ..|.|++++...+.  ...+++++.....++
T Consensus       376 ~~G~~~~l~~~~~~--~~~~~~~~~~~~~~i  404 (720)
T 2zj8_A          376 EVGEGIIVSTSDDP--REVMNHYIFGKPEKL  404 (720)
T ss_dssp             SEEEEEEECSSSCH--HHHHHHHTTSCCCCC
T ss_pred             CCceEEEEecCccH--HHHHHHHhcCCCCCc
Confidence            46889999887662  223334544443333

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.79  E-value=2.6e-19  Score=143.58  Aligned_cols=84  Identities=29%  Similarity=0.487  Sum_probs=73.6

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEE----ec-------CCCCHHHHHHHhhhcCC
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVIN----YD-------MPGNIEMYTHRIGRTGR   71 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~----~d-------~p~~~~~~~qr~GR~gR   71 (135)
                      ..+.++||+|++++|..+++.|++|+++|||||+++++|+|+|++++||+    ||       .|.+..+|.||+|||||
T Consensus       313 ~~v~~~h~~l~~~~r~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~GRaGR  392 (715)
T 2va8_A          313 KGVAYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGR  392 (715)
T ss_dssp             TTEEEECTTSCHHHHHHHHHHHHTTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHHHHTTBCC
T ss_pred             cCEEEECCCCCHHHHHHHHHHHHcCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHHHhhhcCC
Confidence            35899999999999999999999999999999999999999999999998    99       89999999999999999


Q ss_pred             CC--CCceEEEEeecCC
Q 037139           72 AG--KTGVATTFLTFHD   86 (135)
Q Consensus        72 ~~--~~g~~~~~~~~~~   86 (135)
                      .|  ..|.|+.++...+
T Consensus       393 ~g~~~~G~~~~l~~~~~  409 (715)
T 2va8_A          393 PGFDQIGESIVVVRDKE  409 (715)
T ss_dssp             TTTCSCEEEEEECSCGG
T ss_pred             CCCCCCceEEEEeCCch
Confidence            87  4788999887654

>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=99.79  E-value=2.9e-19  Score=147.54  Aligned_cols=97  Identities=22%  Similarity=0.379  Sum_probs=84.0

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCC--CcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKR--YNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVAT   79 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~--~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~   79 (135)
                      |+++..+||+|++.+|..++++|++|+  ++|||||+++++|+|+|.+++||++|+|+++..|.|++||+||.|+.+.++
T Consensus       528 g~~~~~lhG~~~~~~R~~~l~~F~~g~~~~~vLvaT~v~~~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~Gq~~~v~  607 (968)
T 3dmq_A          528 GIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQ  607 (968)
T ss_dssp             CCCEEEECTTSCTTHHHHHHHHHHSTTSSCEEEECSCCTTCSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCSSSCSCCE
T ss_pred             CCcEEEEeCCCCHHHHHHHHHHHhCCCCcccEEEecchhhcCCCcccCcEEEEecCCCCHHHHHHHhhccccCCCCceEE
Confidence            789999999999999999999999998  999999999999999999999999999999999999999999999887655


Q ss_pred             EEeecCChhHHHHHHHHHh
Q 037139           80 TFLTFHDTDVFYDLKQMLI   98 (135)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~   98 (135)
                      ++....+....+.+.+.+.
T Consensus       608 v~~~~~~~t~ee~i~~~~~  626 (968)
T 3dmq_A          608 IHVPYLEKTAQSVLVRWYH  626 (968)
T ss_dssp             EEEEEETTSHHHHHHHHHH
T ss_pred             EEEecCCChHHHHHHHHHH
Confidence            5544433444444555553

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}

Probab=99.79  E-value=6.8e-20  Score=148.64  Aligned_cols=84  Identities=29%  Similarity=0.402  Sum_probs=41.2

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhc-CCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRT-KRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~-g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      |..+..+||+|++++|.+++++|++ |+++|||||+++++|+|+|+|++||+||+|+++..|+||+|| ||. ..|.++.
T Consensus       667 G~~~~~~hg~~~~~eR~~~l~~F~~~g~~~vLVaT~~~~~GIDlp~v~~VI~yd~p~s~~~~iQr~GR-GR~-~~g~~i~  744 (797)
T 4a2q_A          667 GRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCIL  744 (797)
T ss_dssp             ---------------------------CCSEEEEECC-------CCCSEEEEESCCSCHHHHHTC---------CCCEEE
T ss_pred             ecCCcccCCCCCHHHHHHHHHHhhccCCceEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEE
Confidence            4456677999999999999999999 999999999999999999999999999999999999999999 998 7899999


Q ss_pred             EeecCCh
Q 037139           81 FLTFHDT   87 (135)
Q Consensus        81 ~~~~~~~   87 (135)
                      ++...+.
T Consensus       745 l~~~~~~  751 (797)
T 4a2q_A          745 VTSKTEV  751 (797)
T ss_dssp             EECCHHH
T ss_pred             EEeCCcH
Confidence            9877544

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=99.79  E-value=3.8e-20  Score=149.74  Aligned_cols=93  Identities=24%  Similarity=0.407  Sum_probs=82.1

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCC-CHHHHHHHhhhcCCCCCCceEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPG-NIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~-~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      |+.+..+||+|++++|++++++|++|+++|||||+++++|+|+|++++||++|.|. +...|.||+||+||.|..|.|++
T Consensus       613 ~~~v~~lHG~m~~~eR~~v~~~F~~G~~~ILVaT~vie~GIDiP~v~~VIi~d~~r~~l~~l~Qr~GRaGR~g~~g~~il  692 (780)
T 1gm5_A          613 EFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFL  692 (780)
T ss_dssp             --CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEEC
T ss_pred             CCcEEEEeCCCCHHHHHHHHHHHHCCCCeEEEECCCCCccccCCCCCEEEEeCCCCCCHHHHHHHhcccCcCCCCCEEEE
Confidence            56789999999999999999999999999999999999999999999999999996 78999999999999999999999


Q ss_pred             EeecCChhHHHHHH
Q 037139           81 FLTFHDTDVFYDLK   94 (135)
Q Consensus        81 ~~~~~~~~~~~~~~   94 (135)
                      ++.+.+......++
T Consensus       693 l~~~~~~~~~~rl~  706 (780)
T 1gm5_A          693 VVGDVGEEAMERLR  706 (780)
T ss_dssp             CCCSCCHHHHHHHH
T ss_pred             EECCCChHHHHHHH
Confidence            98854444443333

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.79  E-value=9.3e-21  Score=151.07  Aligned_cols=89  Identities=27%  Similarity=0.369  Sum_probs=46.8

Q ss_pred             ceEEEe--------cCCCCHHHHHHHHHHHhc-CCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCC
Q 037139            3 YRVTTL--------HGGKSQEQREISLEGFRT-KRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAG   73 (135)
Q Consensus         3 ~~v~~~--------hg~~~~~~r~~~~~~f~~-g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~   73 (135)
                      +++..+        ||+|++++|.+++++|++ |+++|||||+++++|+|+|++++||+||+|++...|+||+|| ||. 
T Consensus       427 ~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~~~vLVaT~v~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-GR~-  504 (696)
T 2ykg_A          427 LKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRA-  504 (696)
T ss_dssp             CCEEC-----------------------------CCSCSEEEESSCCC---CCCSEEEEESCC--CCCC-----------
T ss_pred             cceeEEEccCCCccccCCCHHHHHHHHHHHHhcCCccEEEEechhhcCCcCccCCEEEEeCCCCCHHHHHHhhcc-CcC-
Confidence            566666        669999999999999998 999999999999999999999999999999999999999999 998 


Q ss_pred             CCceEEEEeecCChhHHHHH
Q 037139           74 KTGVATTFLTFHDTDVFYDL   93 (135)
Q Consensus        74 ~~g~~~~~~~~~~~~~~~~~   93 (135)
                      +.|.++.++...+......+
T Consensus       505 ~~g~~~~l~~~~~~~~~~~~  524 (696)
T 2ykg_A          505 RGSKCFLLTSNAGVIEKEQI  524 (696)
T ss_dssp             CCCEEEEEESCHHHHHHHHH
T ss_pred             CCceEEEEecCCCHHHHHHH
Confidence            67899999887665444444

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.78  E-value=7.3e-19  Score=145.58  Aligned_cols=98  Identities=21%  Similarity=0.218  Sum_probs=83.8

Q ss_pred             eEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEE----ecC----CCCHHHHHHHhhhcCCCCC-
Q 037139            4 RVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVIN----YDM----PGNIEMYTHRIGRTGRAGK-   74 (135)
Q Consensus         4 ~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~----~d~----p~~~~~~~qr~GR~gR~~~-   74 (135)
                      .+.++||+|++.+|+.+++.|++|.++|||||+++++|+|+|.+++||+    ||.    |.++.+|.||+||+||.|. 
T Consensus       408 gI~~~Hggl~~~eR~~ve~~F~~G~ikVLVAT~~la~GIDiP~~~vVI~~~~kfd~~~~rp~s~~~y~Qr~GRAGR~G~d  487 (1010)
T 2xgj_A          408 GIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLD  487 (1010)
T ss_dssp             TEEEESTTSCHHHHHHHHHHHHTTCCSEEEEEGGGGGSTTCCBSEEEESCSEEECSSCEEECCHHHHHHHHTTBCCTTTC
T ss_pred             CeeEECCCCCHHHHHHHHHHHhcCCCcEEEEehHhhccCCCCCceEEEeCCcccCCcCCccCCHHHHhHhhhhcccCCCC
Confidence            4889999999999999999999999999999999999999999999998    998    8999999999999999986 


Q ss_pred             -CceEEEEeecCChhHHHHHHHHHhhCCCC
Q 037139           75 -TGVATTFLTFHDTDVFYDLKQMLIQSNSP  103 (135)
Q Consensus        75 -~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  103 (135)
                       .|.+++++.+...  ...+.+++.....+
T Consensus       488 ~~G~vi~l~~~~~e--~~~~~~l~~~~~~~  515 (1010)
T 2xgj_A          488 DRGIVIMMIDEKME--PQVAKGMVKGQADR  515 (1010)
T ss_dssp             SSEEEEEEECSCCC--HHHHHHHHSCCCCC
T ss_pred             CceEEEEEECCCCC--HHHHHHHHhCCCcc
Confidence             5999999986522  12344444444443

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=99.78  E-value=2.6e-19  Score=143.42  Aligned_cols=84  Identities=26%  Similarity=0.442  Sum_probs=77.6

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEE----ec---CCCCHHHHHHHhhhcCCCC--
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVIN----YD---MPGNIEMYTHRIGRTGRAG--   73 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~----~d---~p~~~~~~~qr~GR~gR~~--   73 (135)
                      ..+.++||+|++++|..+++.|++|+++|||||+++++|+|+|++++||+    ||   .|.+..+|.||+|||||.|  
T Consensus       297 ~~v~~~h~~l~~~~R~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR~g~~  376 (702)
T 2p6r_A          297 KGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMD  376 (702)
T ss_dssp             TTCCEECTTSCHHHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTC
T ss_pred             cCeEEecCCCCHHHHHHHHHHHHCCCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcCCCCCC
Confidence            35788999999999999999999999999999999999999999999998    76   7899999999999999987  


Q ss_pred             CCceEEEEeecCC
Q 037139           74 KTGVATTFLTFHD   86 (135)
Q Consensus        74 ~~g~~~~~~~~~~   86 (135)
                      ..|.|+.++...+
T Consensus       377 ~~G~~~~l~~~~~  389 (702)
T 2p6r_A          377 ERGEAIIIVGKRD  389 (702)
T ss_dssp             SCEEEEEECCGGG
T ss_pred             CCceEEEEecCcc
Confidence            4788999988765

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=99.77  E-value=8.7e-19  Score=138.93  Aligned_cols=101  Identities=20%  Similarity=0.230  Sum_probs=88.0

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEE--------------------EEecCCCCHHH
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHV--------------------INYDMPGNIEM   61 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~v--------------------i~~d~p~~~~~   61 (135)
                      |+.+..+||+    +|.+++++|++|+.+|||||+++++|+|+| +++|                    +++|.|.+..+
T Consensus       379 g~~v~~lhg~----~R~~~l~~F~~g~~~VLVaTdv~~rGiDi~-v~~VId~g~~~~P~~~~~~~~~~~i~~d~P~s~~~  453 (618)
T 2whx_A          379 GKRVIQLSRK----TFDTEYPKTKLTDWDFVVTTDISEMGANFR-AGRVIDPRRCLKPVILTDGPERVILAGPIPVTPAS  453 (618)
T ss_dssp             TCCEEEECTT----THHHHTTHHHHSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHH
T ss_pred             CCcEEEEChH----HHHHHHHhhcCCCcEEEEECcHHHcCcccC-ceEEEECcceecceecccCCCceEEcccccCCHHH
Confidence            6789999985    688899999999999999999999999998 8887                    78888999999


Q ss_pred             HHHHhhhcCCCCC-CceEEEEee---cCChhHHHHHHHHHhhCCCCCChH
Q 037139           62 YTHRIGRTGRAGK-TGVATTFLT---FHDTDVFYDLKQMLIQSNSPVPPE  107 (135)
Q Consensus        62 ~~qr~GR~gR~~~-~g~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~  107 (135)
                      |+||+||+||.|. .|.+++++.   +.+...+..+++.+......+++.
T Consensus       454 yiQR~GRaGR~g~~~G~ai~l~~~~~~~d~~~l~~le~~i~l~~~~~~~~  503 (618)
T 2whx_A          454 AAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHWTEAKMLLDNIYTPEG  503 (618)
T ss_dssp             HHHHHTTSSCCTTCCCEEEEECSCCCCCCTTCHHHHHHHHHHTTCCCTTC
T ss_pred             HHHhccccCCCCCCCCeEEEEccCCchhhHHHHHHHHhHhccccccCCcc
Confidence            9999999999964 899999997   677777888888777665555554

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.77  E-value=1.9e-18  Score=138.00  Aligned_cols=100  Identities=25%  Similarity=0.404  Sum_probs=82.2

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhc--CCCcEEEecCCCcccccccCCcEEEEecC--------------CCCHHHHHHH
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRT--KRYNVLVATDVAGRGIDIPDVAHVINYDM--------------PGNIEMYTHR   65 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~--g~~~ilv~T~~~~~G~d~~~v~~vi~~d~--------------p~~~~~~~qr   65 (135)
                      |+.+.++||+|++++|.++++.|++  |+++|||||+++++|+|+ ++++||++|.              |.+..+|+||
T Consensus       344 g~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~v~~VI~~~~~k~~~~~~G~~~~~p~s~~~~~QR  422 (677)
T 3rc3_A          344 GLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-SIRRIIFYSLIKPSINEKGERELEPITTSQALQI  422 (677)
T ss_dssp             TCCCEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-CBSEEEESCSBC-----------CBCCHHHHHHH
T ss_pred             CCCeeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-CccEEEECCccccccccCCccccccCCHHHHHHH
Confidence            6789999999999999999999999  889999999999999999 8999999998              7899999999


Q ss_pred             hhhcCCCCCC---ceEEEEeecCChhHHHHHHHHHhhCCCCCCh
Q 037139           66 IGRTGRAGKT---GVATTFLTFHDTDVFYDLKQMLIQSNSPVPP  106 (135)
Q Consensus        66 ~GR~gR~~~~---g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  106 (135)
                      +|||||.|..   |.++.+... +   ...+++++.....++..
T Consensus       423 ~GRAGR~g~~g~~G~v~~l~~~-d---~~~~~~~~~~~~~~i~~  462 (677)
T 3rc3_A          423 AGRAGRFSSRFKEGEVTTMNHE-D---LSLLKEILKRPVDPIRA  462 (677)
T ss_dssp             HTTBTCTTSSCSSEEEEESSTT-H---HHHHHHHHHSCCCCCCC
T ss_pred             hcCCCCCCCCCCCEEEEEEecc-h---HHHHHHHHhcCcchhhh
Confidence            9999999854   666555332 2   22445555555544443

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=99.77  E-value=9.3e-19  Score=146.03  Aligned_cols=102  Identities=20%  Similarity=0.194  Sum_probs=83.0

Q ss_pred             EEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecC--------CCCHHHHHHHhhhcCCCC--C
Q 037139            5 VTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDM--------PGNIEMYTHRIGRTGRAG--K   74 (135)
Q Consensus         5 v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~--------p~~~~~~~qr~GR~gR~~--~   74 (135)
                      +.++||+|++.+|+.+++.|++|+++|||||+++++|+|+|++++||+++.        |.++.+|+||+||+||.|  .
T Consensus       507 V~~~Hg~l~~~~R~~v~~~F~~G~ikVLVAT~vla~GIDiP~v~~VI~~~~~~d~~~~r~iS~~eyiQr~GRAGR~G~d~  586 (1108)
T 3l9o_A          507 IGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDD  586 (1108)
T ss_dssp             EEEECSCSCHHHHHHHHHHHHHTCCCEEEEESCCCSCCCC--CEEEESCSEEESSSCEEECCHHHHHHHHHHSCCSSSCS
T ss_pred             eeeecCCCCHHHHHHHHHHHhCCCCeEEEECcHHhcCCCCCCceEEEecCcccCccccccCCHHHHHHhhcccCCCCCCC
Confidence            889999999999999999999999999999999999999999999996654        347888999999999998  5


Q ss_pred             CceEEEEeecCChhHHHHHHHHHhhCCCCCChHH
Q 037139           75 TGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPEL  108 (135)
Q Consensus        75 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  108 (135)
                      .|.+++++.+...  ...+.+++.....++...+
T Consensus       587 ~G~~ill~~~~~~--~~~~~~l~~~~~~~L~S~f  618 (1108)
T 3l9o_A          587 RGIVIMMIDEKME--PQVAKGMVKGQADRLDSAF  618 (1108)
T ss_dssp             SEEEEEEECCCCC--HHHHHHHHHCCCCCCCCCC
T ss_pred             ceEEEEEecCCcC--HHHHHHHhcCCCccccccc
Confidence            7888888876533  2345666666655555443

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.77  E-value=6.8e-19  Score=127.13  Aligned_cols=84  Identities=20%  Similarity=0.336  Sum_probs=63.5

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcC-CCc-EEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCc--e
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTK-RYN-VLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTG--V   77 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g-~~~-ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g--~   77 (135)
                      |+.+..+||++++++|.+++++|+++ +++ +|++|+++++|+|++.+++||+||+||++..|.|++||++|.|+.+  .
T Consensus       137 g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~st~~~g~Glnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R~Gq~~~v~  216 (271)
T 1z5z_A          137 NTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVI  216 (271)
T ss_dssp             CSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCTTCCCCCCTTCSEEEECSCCSCTTTC--------------CCE
T ss_pred             CCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEEehhhhcCCcCcccCCEEEEECCCCChhHHHHHHHhccccCCCCceE
Confidence            67888999999999999999999999 788 6889999999999999999999999999999999999999998764  4


Q ss_pred             EEEEeecC
Q 037139           78 ATTFLTFH   85 (135)
Q Consensus        78 ~~~~~~~~   85 (135)
                      ++.++...
T Consensus       217 v~~li~~~  224 (271)
T 1z5z_A          217 VHKLISVG  224 (271)
T ss_dssp             EEEEEETT
T ss_pred             EEEEeeCC
Confidence            56666655

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos}

Probab=99.76  E-value=2.7e-19  Score=147.38  Aligned_cols=84  Identities=29%  Similarity=0.402  Sum_probs=41.5

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhc-CCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRT-KRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~-g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      |..+..+||+|++.+|.+++++|++ |+++|||||+++++|+|+|+|++||+||+|+++..|+||+|| ||. ..|.++.
T Consensus       667 G~~~~~~hg~m~~~eR~~il~~Fr~~g~~~VLVaT~~~~eGIDlp~v~~VI~yD~p~s~~~~iQr~GR-GR~-~~g~vi~  744 (936)
T 4a2w_A          667 GRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCIL  744 (936)
T ss_dssp             ---------------------------CCSEEEEECC------CCCCSEEEEESCCSCSHHHHCC---------CCCEEE
T ss_pred             cCCCcccCCCCCHHHHHHHHHHhhccCCeeEEEEeCchhcCCcchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCCEEEE
Confidence            4456677999999999999999999 999999999999999999999999999999999999999999 998 6788998


Q ss_pred             EeecCCh
Q 037139           81 FLTFHDT   87 (135)
Q Consensus        81 ~~~~~~~   87 (135)
                      ++...+.
T Consensus       745 Li~~~t~  751 (936)
T 4a2w_A          745 VTSKTEV  751 (936)
T ss_dssp             EESCHHH
T ss_pred             EEeCCCH
Confidence            8876543

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.75  E-value=1.3e-18  Score=139.05  Aligned_cols=99  Identities=19%  Similarity=0.270  Sum_probs=83.9

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEE--------------------ecCCCCHHH
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVIN--------------------YDMPGNIEM   61 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~--------------------~d~p~~~~~   61 (135)
                      |+.+..+||+    +|.+++++|++|+++|||||+++++|+|+| +++||+                    +|.|.+.++
T Consensus       434 g~~v~~lHg~----eR~~v~~~F~~g~~~VLVaTdv~e~GIDip-v~~VI~~g~~~~p~vi~da~~r~~ll~d~P~s~~~  508 (673)
T 2wv9_A          434 GKRVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFG-ASRVIDCRKSVKPTILDEGEGRVILSVPSAITSAS  508 (673)
T ss_dssp             TCCEEEECSS----SHHHHGGGGGTCCCSEEEECGGGGTTCCCC-CSEEEECCEECCEEEECSTTCEEEECCSEECCHHH
T ss_pred             CCeEEEeChH----HHHHHHHHHHCCCceEEEECchhhcceeeC-CcEEEECCCcccceeeecccccceecccCCCCHHH
Confidence            6789999994    789999999999999999999999999999 999998                    679999999


Q ss_pred             HHHHhhhcCCC-CCCceEEEEe---ecCChhHHHHHHHHHhhCCCCCC
Q 037139           62 YTHRIGRTGRA-GKTGVATTFL---TFHDTDVFYDLKQMLIQSNSPVP  105 (135)
Q Consensus        62 ~~qr~GR~gR~-~~~g~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~  105 (135)
                      |+||+||+||. ++.|.+++++   .+.+...+..++..+.....+++
T Consensus       509 y~Qr~GRaGR~~g~~G~ai~l~~~~~~~d~~~l~~ie~~~~l~~~~~~  556 (673)
T 2wv9_A          509 AAQRRGRVGRNPSQIGDEYHYGGGTSEDDTMLAHWTEAKILLDNIHLP  556 (673)
T ss_dssp             HHHHHTTSSCCSSCCCEEEEECSCCCCCCTTBHHHHHHHHHHHTSCBT
T ss_pred             HHHHhhccCCCCCCCCEEEEEEecCChhHHHHHHHHHHHHhhhhccCC
Confidence            99999999998 7889999996   46666666667666544333333

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=99.74  E-value=6.2e-18  Score=141.59  Aligned_cols=84  Identities=26%  Similarity=0.367  Sum_probs=79.2

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecC-CCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDM-PGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~-p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      ++++..+||+|++++|++++++|++|+++|||||+++++|+|+|++++||+++. +++..+|.||+||+||.|+.|.|++
T Consensus       838 ~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~v~e~GiDip~v~~VIi~~~~~~~l~~l~Qr~GRvgR~g~~g~~~l  917 (1151)
T 2eyq_A          838 EARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWL  917 (1151)
T ss_dssp             TSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEE
T ss_pred             CCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECCcceeeecccCCcEEEEeCCCCCCHHHHHHHHhccCcCCCceEEEE
Confidence            578999999999999999999999999999999999999999999999999988 5799999999999999999999999


Q ss_pred             EeecC
Q 037139           81 FLTFH   85 (135)
Q Consensus        81 ~~~~~   85 (135)
                      ++...
T Consensus       918 l~~~~  922 (1151)
T 2eyq_A          918 LTPHP  922 (1151)
T ss_dssp             EECCG
T ss_pred             EECCc
Confidence            88654

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.74  E-value=1.2e-18  Score=134.60  Aligned_cols=80  Identities=21%  Similarity=0.192  Sum_probs=73.5

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEec-CCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVAT-DVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T-~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      |.++..+||+|++++|++++++|++|+.+||||| +++++|+|+|++++||++++|++...|.|++||+||.|..+..+.
T Consensus       371 ~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~GiDip~v~~vi~~~~~~s~~~~~Q~~GR~gR~g~~~~~v~  450 (510)
T 2oca_A          371 YDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFSTGISVKNLHHVVLAHGVKSKIIVLQTIGRVLRKHGSKTIAT  450 (510)
T ss_dssp             CSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHHSCCCCSEEEEEESSCCCSCCHHHHHHHHHHTTTCCCCCCE
T ss_pred             CCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhcccccccCcEEEEeCCCCCHHHHHHHHhcccccCCCCceEE
Confidence            3478999999999999999999999999999999 999999999999999999999999999999999999887653333


Q ss_pred             E
Q 037139           81 F   81 (135)
Q Consensus        81 ~   81 (135)
                      +
T Consensus       451 i  451 (510)
T 2oca_A          451 V  451 (510)
T ss_dssp             E
T ss_pred             E
Confidence            3

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=99.73  E-value=2.7e-18  Score=131.58  Aligned_cols=81  Identities=32%  Similarity=0.522  Sum_probs=73.4

Q ss_pred             EEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCC---ceEEEE
Q 037139            5 VTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKT---GVATTF   81 (135)
Q Consensus         5 v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~---g~~~~~   81 (135)
                      +..+||+++.++|++++++|++|+++|||||+++++|+|+|++++||++|+|+++..|.||+||+||.|+.   ..++.+
T Consensus       371 ~~~~~g~~~~~~R~~~~~~F~~g~~~vLv~T~~~~~Gldlp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~k~~~~i~~l  450 (472)
T 2fwr_A          371 IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYEL  450 (472)
T ss_dssp             CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEE
T ss_pred             cceeeCCCCHHHHHHHHHHHhCCCCCEEEEcCchhcCcccccCcEEEEECCCCCHHHHHHHHhhccCCCCCCceEEEEEE
Confidence            55799999999999999999999999999999999999999999999999999999999999999998743   355556


Q ss_pred             eecC
Q 037139           82 LTFH   85 (135)
Q Consensus        82 ~~~~   85 (135)
                      +...
T Consensus       451 v~~~  454 (472)
T 2fwr_A          451 ISRG  454 (472)
T ss_dssp             EECS
T ss_pred             EeCC
Confidence            6654

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=99.73  E-value=9.9e-18  Score=128.46  Aligned_cols=78  Identities=22%  Similarity=0.284  Sum_probs=71.1

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEec--------------------CCCCHHH
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYD--------------------MPGNIEM   61 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d--------------------~p~~~~~   61 (135)
                      |+.+..+||++.    .++++.|++|+.+|||||+++++|+|+|+ ++||++|                    .|.+..+
T Consensus       212 g~~~~~lh~~~~----~~~~~~f~~g~~~vLVaT~v~~~GiDip~-~~VI~~~~~~~~~~d~~~~~~l~~~~~~p~s~~~  286 (451)
T 2jlq_A          212 GKRVIQLSRKTF----DTEYPKTKLTDWDFVVTTDISEMGANFRA-GRVIDPRRCLKPVILTDGPERVILAGPIPVTPAS  286 (451)
T ss_dssp             TCCEEEECTTTH----HHHGGGGGSSCCSEEEECGGGGSSCCCCC-SEEEECCEEEEEEEECSSSCEEEEEEEEECCHHH
T ss_pred             CCeEEECCHHHH----HHHHHhhccCCceEEEECCHHHhCcCCCC-CEEEECCCcccccccccccceeeecccccCCHHH
Confidence            678889999864    57999999999999999999999999999 9999998                    9999999


Q ss_pred             HHHHhhhcCCCCC-CceEEEEeec
Q 037139           62 YTHRIGRTGRAGK-TGVATTFLTF   84 (135)
Q Consensus        62 ~~qr~GR~gR~~~-~g~~~~~~~~   84 (135)
                      |+||+||+||.|. .|.++++...
T Consensus       287 y~Qr~GRaGR~g~~~g~~~~~~~~  310 (451)
T 2jlq_A          287 AAQRRGRIGRNPAQEDDQYVFSGD  310 (451)
T ss_dssp             HHHHHTTSSCCTTCCCEEEEECSC
T ss_pred             HHHhccccCCCCCCCccEEEEeCC
Confidence            9999999999997 7888888643

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=99.72  E-value=8.2e-19  Score=142.05  Aligned_cols=83  Identities=22%  Similarity=0.300  Sum_probs=77.9

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHh-----cCCCcEEEecCCCcccccccCCcEEEEecC------------------CCC
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFR-----TKRYNVLVATDVAGRGIDIPDVAHVINYDM------------------PGN   58 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~-----~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~------------------p~~   58 (135)
                      ++.+..+||+|++++|.++++.|+     +|+.+|||||+++++|+|+|++++||+++.                  |.+
T Consensus       338 ~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~iae~GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~S  417 (773)
T 2xau_A          338 PLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPIS  417 (773)
T ss_dssp             CEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECTHHHHTCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEECC
T ss_pred             CeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCcHHHhCcCcCCeEEEEeCCCccceeeccccCccccccccCC
Confidence            567999999999999999999999     999999999999999999999999999777                  899


Q ss_pred             HHHHHHHhhhcCCCCCCceEEEEeecC
Q 037139           59 IEMYTHRIGRTGRAGKTGVATTFLTFH   85 (135)
Q Consensus        59 ~~~~~qr~GR~gR~~~~g~~~~~~~~~   85 (135)
                      ..+|.||+|||||. .+|.|+.++...
T Consensus       418 ~~s~~QR~GRaGR~-~~G~~~~l~~~~  443 (773)
T 2xau_A          418 KASAQQRAGRAGRT-RPGKCFRLYTEE  443 (773)
T ss_dssp             HHHHHHHHHGGGSS-SSEEEEESSCHH
T ss_pred             HHHHHhhccccCCC-CCCEEEEEecHH
Confidence            99999999999999 789999998653

>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase, translocation, secretion, protein transport; 2.18A {Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A 3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A

Probab=99.72  E-value=6.1e-18  Score=136.57  Aligned_cols=85  Identities=26%  Similarity=0.402  Sum_probs=77.2

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCccccccc--------CCcEEEEecCCCCHHHHHHHhhhcCCC
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIP--------DVAHVINYDMPGNIEMYTHRIGRTGRA   72 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~--------~v~~vi~~d~p~~~~~~~qr~GR~gR~   72 (135)
                      .|+++.++||++.++++..+.++|+.|  .|+|||++++||+|++        ++.+||++|.|.+...|.||+||+||.
T Consensus       455 ~gi~~~vLhg~~~~rEr~ii~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr~GRTGRq  532 (844)
T 1tf5_A          455 KGIPHQVLNAKNHEREAQIIEEAGQKG--AVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQ  532 (844)
T ss_dssp             TTCCCEEECSSCHHHHHHHHTTTTSTT--CEEEEETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGG
T ss_pred             CCCCEEEeeCCccHHHHHHHHHcCCCC--eEEEeCCccccCcCccccchhhhcCCcEEEEecCCCCHHHHHhhcCccccC
Confidence            478899999999988888777767665  6999999999999999        788999999999999999999999999


Q ss_pred             CCCceEEEEeecCCh
Q 037139           73 GKTGVATTFLTFHDT   87 (135)
Q Consensus        73 ~~~g~~~~~~~~~~~   87 (135)
                      |.+|.+++|++..+.
T Consensus       533 G~~G~s~~~vs~eD~  547 (844)
T 1tf5_A          533 GDPGITQFYLSMEDE  547 (844)
T ss_dssp             GCCEEEEEEEETTSS
T ss_pred             CCCCeEEEEecHHHH
Confidence            999999999997764

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A

Probab=99.72  E-value=2e-18  Score=132.58  Aligned_cols=79  Identities=19%  Similarity=0.302  Sum_probs=70.5

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEE--------------------ecCCCCHHH
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVIN--------------------YDMPGNIEM   61 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~--------------------~d~p~~~~~   61 (135)
                      |+.+..+||+    +|.++++.|++|+.+|||||+++++|+|+|+ ++||+                    ||.|.+..+
T Consensus       214 g~~v~~lh~~----~R~~~~~~f~~g~~~iLVaT~v~~~GiDip~-~~VI~~G~~~~~~~~~~~~~~~~~~~d~p~s~~~  288 (459)
T 2z83_A          214 GKKVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFGA-SRVIDCRKSVKPTILEEGEGRVILGNPSPITSAS  288 (459)
T ss_dssp             TCCEEEESTT----CCCCCGGGSSSCCCSEEEESSCC---CCCSC-SEEEECCEECCEEEECSSSCEEEECSCEECCHHH
T ss_pred             CCcEEecCHH----HHHHHHhhccCCCceEEEECChHHhCeecCC-CEEEECCcccccccccccccccccccCCCCCHHH
Confidence            6788999985    6889999999999999999999999999999 99998                    779999999


Q ss_pred             HHHHhhhcCCCCC-CceEEEEeecC
Q 037139           62 YTHRIGRTGRAGK-TGVATTFLTFH   85 (135)
Q Consensus        62 ~~qr~GR~gR~~~-~g~~~~~~~~~   85 (135)
                      |+||+||+||.|. +|.+++++...
T Consensus       289 ~~QR~GRaGR~g~~~G~~~~~~~~~  313 (459)
T 2z83_A          289 AAQRRGRVGRNPNQVGDEYHYGGAT  313 (459)
T ss_dssp             HHHHHTTSSCCTTCCCEEEEECSCC
T ss_pred             HHHhccccCCCCCCCCeEEEEEccc
Confidence            9999999999987 89999999875

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.71  E-value=1.1e-17  Score=143.95  Aligned_cols=89  Identities=21%  Similarity=0.249  Sum_probs=78.6

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEE----ec------CCCCHHHHHHHhhhcCCC
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVIN----YD------MPGNIEMYTHRIGRTGRA   72 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~----~d------~p~~~~~~~qr~GR~gR~   72 (135)
                      ..|++|||+|++++|..+++.|++|.++|||||+++++|+|+|...+||.    ||      .|.+..+|.||+|||||.
T Consensus      1214 ~GIa~hHagL~~~~R~~VE~lF~~G~i~VLvaT~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Qm~GRAGR~ 1293 (1724)
T 4f92_B         1214 NGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRP 1293 (1724)
T ss_dssp             TTEEEECTTSCHHHHHHHHHHHHHTSBCEEEEEGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHHHHTTBCCT
T ss_pred             CCEEEECCCCCHHHHHHHHHHHHCCCCeEEEEChHHHcCCCCCccEEEEecCccccCcccccCCCCHHHHHHhhccccCC
Confidence            45889999999999999999999999999999999999999999998882    43      467899999999999998


Q ss_pred             CC--CceEEEEeecCChhHHH
Q 037139           73 GK--TGVATTFLTFHDTDVFY   91 (135)
Q Consensus        73 ~~--~g~~~~~~~~~~~~~~~   91 (135)
                      |.  .|.+++++...+...++
T Consensus      1294 g~d~~G~avll~~~~~~~~~~ 1314 (1724)
T 4f92_B         1294 LQDDEGRCVIMCQGSKKDFFK 1314 (1724)
T ss_dssp             TTCSCEEEEEEEEGGGHHHHH
T ss_pred             CCCCceEEEEEecchHHHHHH
Confidence            75  68999999877665543

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.70  E-value=1.4e-17  Score=143.41  Aligned_cols=92  Identities=22%  Similarity=0.360  Sum_probs=80.4

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEE----ecC------CCCHHHHHHHhhhcCC
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVIN----YDM------PGNIEMYTHRIGRTGR   71 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~----~d~------p~~~~~~~qr~GR~gR   71 (135)
                      ...+++|||+|++++|..+++.|++|.++|||||+++++|+|+|.+++||.    ||+      |.+..+|.||+|||||
T Consensus       378 ~~Gva~HHagL~~~~R~~vE~~F~~G~i~vlvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR  457 (1724)
T 4f92_B          378 PYGFAIHHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGR  457 (1724)
T ss_dssp             TTTEEEECSSSCTHHHHHHHHHHHTTCCCEEEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHHTTBSC
T ss_pred             hcCEEEEcCCCCHHHHHHHHHHHHCCCCeEEEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhhhhccC
Confidence            346889999999999999999999999999999999999999999999984    553      5689999999999999


Q ss_pred             CC--CCceEEEEeecCChhHHHHH
Q 037139           72 AG--KTGVATTFLTFHDTDVFYDL   93 (135)
Q Consensus        72 ~~--~~g~~~~~~~~~~~~~~~~~   93 (135)
                      .|  ..|.+++++...+...+..+
T Consensus       458 ~g~d~~G~~ii~~~~~~~~~~~~l  481 (1724)
T 4f92_B          458 PQYDTKGEGILITSHGELQYYLSL  481 (1724)
T ss_dssp             TTTCSCEEEEEEEESTTCCHHHHH
T ss_pred             CCCCCccEEEEEecchhHHHHHHH
Confidence            76  46899999988877665443

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B*

Probab=99.70  E-value=4.3e-17  Score=135.60  Aligned_cols=92  Identities=21%  Similarity=0.342  Sum_probs=77.9

Q ss_pred             ceEEEecCCCCHHHHHHHHHHHhcCCCcEEEe----cCCCcccccccCC-cEEEEecCC---------------------
Q 037139            3 YRVTTLHGGKSQEQREISLEGFRTKRYNVLVA----TDVAGRGIDIPDV-AHVINYDMP---------------------   56 (135)
Q Consensus         3 ~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~----T~~~~~G~d~~~v-~~vi~~d~p---------------------   56 (135)
                      +.+..+||+|     ..++++|++|+++||||    |+++++|+|+|+| ++||++|+|                     
T Consensus       299 ~~v~~lhg~~-----~~~l~~F~~G~~~VLVaTas~Tdv~~rGIDip~VI~~VI~~~~P~~~~~~~~~~~~~~~~~~~~~  373 (1054)
T 1gku_B          299 FRIGIVTATK-----KGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPSFRVTIEDIDSLSPQMVKLLA  373 (1054)
T ss_dssp             SCEEECTTSS-----SHHHHHHHHTSCSEEEEECC------CCSCCTTTCCEEEEESCCEEEEECSCGGGSCHHHHHHHH
T ss_pred             cCeeEEeccH-----HHHHHHHHcCCCcEEEEecCCCCeeEeccccCCcccEEEEeCCCcccccccccccChHHHHHHHH
Confidence            5788999998     48899999999999999    9999999999996 999999999                     


Q ss_pred             --------------------------------------------------CCHHHHHHHhhhcCCCCCCc--eEEEEeec
Q 037139           57 --------------------------------------------------GNIEMYTHRIGRTGRAGKTG--VATTFLTF   84 (135)
Q Consensus        57 --------------------------------------------------~~~~~~~qr~GR~gR~~~~g--~~~~~~~~   84 (135)
                                                                        .+..+|+||+||+||.|..|  .+++++..
T Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~yiQr~GRagR~g~~g~~~g~~~~~~  453 (1054)
T 1gku_B          374 YLYRNVDEIERLLPAVERHIDEVREILKKVMGKERPQAKDVVVREGEVIFPDLRTYIQGSGRTSRLFAGGLTKGASFLLE  453 (1054)
T ss_dssp             TTTSCHHHHHTTCTTTSSCHHHHHHHHHHHHTTSCCSCSSSEEETTEEEEECHHHHHHHHHTTCCEETTEECCEEEEEEC
T ss_pred             HHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccceeEeecceecCcHHHHhhhhchhhhccCCCCceEEEEEEe
Confidence                                                              78999999999999976665  48888888


Q ss_pred             CChhHHHHHHHHHhh
Q 037139           85 HDTDVFYDLKQMLIQ   99 (135)
Q Consensus        85 ~~~~~~~~~~~~~~~   99 (135)
                      .+...++.+++.++.
T Consensus       454 ~d~~~~~~l~~~l~~  468 (1054)
T 1gku_B          454 DDSELLSAFIERAKL  468 (1054)
T ss_dssp             SCHHHHHHHHHHHHT
T ss_pred             cCHHHHHHHHHHHhh
Confidence            888888999988875

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.70  E-value=4.1e-17  Score=135.09  Aligned_cols=100  Identities=21%  Similarity=0.256  Sum_probs=76.7

Q ss_pred             eEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecC---------CCCHHHHHHHhhhcCCCC-
Q 037139            4 RVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDM---------PGNIEMYTHRIGRTGRAG-   73 (135)
Q Consensus         4 ~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~---------p~~~~~~~qr~GR~gR~~-   73 (135)
                      .+..+||+|++.+|+.+++.|++|+++|||||+++++|+|+|++.+ |+++.         |.+..+|+||+|||||.| 
T Consensus       401 gi~~~H~gl~~~~R~~v~~~F~~G~~kVLvAT~~~a~GIDiP~~~V-Vi~~~~k~dg~~~~~~s~~~y~Qr~GRAGR~G~  479 (997)
T 4a4z_A          401 GIAVHHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPTRTV-IFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGL  479 (997)
T ss_dssp             TEEEECTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCCSEE-EESCSEEEETTEEEECCHHHHHHHHGGGCCTTT
T ss_pred             CeeeecCCCCHHHHHHHHHHHHCCCCcEEEEchHhhCCCCCCCceE-EEeccccccCccCCCCCHHHHhHHhcccccCCC
Confidence            5889999999999999999999999999999999999999999554 44444         449999999999999988 


Q ss_pred             -CCceEEEEeecCChhHHHHHHHHHhhCCCCCC
Q 037139           74 -KTGVATTFLTFHDTDVFYDLKQMLIQSNSPVP  105 (135)
Q Consensus        74 -~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  105 (135)
                       ..|.+++++... ......+++++.....++.
T Consensus       480 ~~~G~vi~l~~~~-~~~~~~~~~~i~~~~~~l~  511 (997)
T 4a4z_A          480 DSTGTVIVMAYNS-PLSIATFKEVTMGVPTRLQ  511 (997)
T ss_dssp             CSSEEEEEECCSS-CCCHHHHHHHHHSCCCCCC
T ss_pred             CcceEEEEecCCC-cchHHHHHHHhcCCCcccc
Confidence             467777777422 2222334444444444433

>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=99.70  E-value=4.5e-17  Score=125.57  Aligned_cols=99  Identities=20%  Similarity=0.283  Sum_probs=76.9

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcC-CCc-EEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCce--
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTK-RYN-VLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGV--   77 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g-~~~-ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~--   77 (135)
                      |+.+..+||++++++|.+++++|+++ +.+ +|++|+++++|+|+|.+++||++|+|+++..|.|++||++|.|+...  
T Consensus       366 ~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~~~~~Glnl~~~~~vi~~d~~~~~~~~~Q~~gR~~R~Gq~~~v~  445 (500)
T 1z63_A          366 NTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVI  445 (500)
T ss_dssp             TCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECCCC-CCCCCTTCSEEEESSCCSCC---CHHHHTTTTTTTTSCEE
T ss_pred             CCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEecccccCCCchhhCCEEEEeCCCCCcchHHHHHHHHHHcCCCCeeE
Confidence            67788999999999999999999998 566 78999999999999999999999999999999999999999987654  


Q ss_pred             EEEEeecCChhHHHHHHHHHhhCCC
Q 037139           78 ATTFLTFHDTDVFYDLKQMLIQSNS  102 (135)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~  102 (135)
                      ++.++.....  -+.+.+.+.....
T Consensus       446 v~~lv~~~ti--ee~i~~~~~~K~~  468 (500)
T 1z63_A          446 VHKLISVGTL--EEKIDQLLAFKRS  468 (500)
T ss_dssp             EEEEEETTSH--HHHTHHHHTTCSS
T ss_pred             EEEEEeCCCH--HHHHHHHHHHHHH
Confidence            4555555432  2344444444443

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.69  E-value=8.7e-17  Score=122.63  Aligned_cols=76  Identities=17%  Similarity=0.280  Sum_probs=66.4

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcE-----------------EEEecCCCCHHHHHH
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAH-----------------VINYDMPGNIEMYTH   64 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~-----------------vi~~d~p~~~~~~~q   64 (135)
                      |+.+..+||+    +|++++++|++|+++|||||+++++|+|+| +..                 ||+++.|.+..+|+|
T Consensus       195 ~~~v~~lhg~----~r~~~~~~f~~g~~~vLVaT~v~e~GiDip-~~~VI~~g~~~~~v~d~~~~vi~~~~p~~~~~~~Q  269 (431)
T 2v6i_A          195 GKKVLYLNRK----TFESEYPKCKSEKWDFVITTDISEMGANFK-ADRVIDPRKTIKPILLDGRVSMQGPIAITPASAAQ  269 (431)
T ss_dssp             TCCEEEESTT----THHHHTTHHHHSCCSEEEECGGGGTSCCCC-CSEEEECCEEEEEEEETTEEEEEEEEECCHHHHHH
T ss_pred             CCeEEEeCCc----cHHHHHHhhcCCCCeEEEECchHHcCcccC-CcEEEecCccccceecccceeecccccCCHHHHHH
Confidence            6789999997    578899999999999999999999999999 544                 678899999999999


Q ss_pred             HhhhcCCCCC-CceEEEEe
Q 037139           65 RIGRTGRAGK-TGVATTFL   82 (135)
Q Consensus        65 r~GR~gR~~~-~g~~~~~~   82 (135)
                      |+||+||.|. .+.++++.
T Consensus       270 r~GR~GR~g~~~~~~~~~~  288 (431)
T 2v6i_A          270 RRGRIGRNPEKLGDIYAYS  288 (431)
T ss_dssp             HHTTSSCCTTCCCCEEEEC
T ss_pred             hhhccCCCCCCCCeEEEEc
Confidence            9999999985 45555554

>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=99.69  E-value=9.5e-17  Score=128.11  Aligned_cols=85  Identities=27%  Similarity=0.380  Sum_probs=75.4

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCccccccc--------CCcEEEEecCCCCHHHHHHHhhhcCCC
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIP--------DVAHVINYDMPGNIEMYTHRIGRTGRA   72 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~--------~v~~vi~~d~p~~~~~~~qr~GR~gR~   72 (135)
                      .|+++.++||++.++++..+.++++.|  .|+|||+++++|+|++        +..+||++++|.+...|.||+||+||.
T Consensus       497 ~Gi~~~vLhgkq~~rE~~ii~~ag~~g--~VtVATdmAgRGtDI~lg~~V~~~GglhVInte~Pes~r~y~qriGRTGRq  574 (822)
T 3jux_A          497 KGIPHQVLNAKYHEKEAEIVAKAGQKG--MVTIATNMAGRGTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQ  574 (822)
T ss_dssp             TTCCCEEECSCHHHHHHHHHHHHHSTT--CEEEEETTTTTTCCCCCCTTTTTTTSCEEEESSCCSSHHHHHHHHTTSSCS
T ss_pred             CCCCEEEeeCCchHHHHHHHHhCCCCC--eEEEEcchhhCCcCccCCcchhhcCCCEEEecCCCCCHHHHHHhhCccccC
Confidence            378899999997777776666677666  6999999999999998        556999999999999999999999999


Q ss_pred             CCCceEEEEeecCCh
Q 037139           73 GKTGVATTFLTFHDT   87 (135)
Q Consensus        73 ~~~g~~~~~~~~~~~   87 (135)
                      |.+|.+++|++..+.
T Consensus       575 G~~G~a~~fvsleD~  589 (822)
T 3jux_A          575 GDPGESIFFLSLEDD  589 (822)
T ss_dssp             SCCCEEEEEEETTSH
T ss_pred             CCCeeEEEEechhHH
Confidence            999999999998875

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.66  E-value=1.5e-16  Score=132.82  Aligned_cols=91  Identities=24%  Similarity=0.429  Sum_probs=77.2

Q ss_pred             CceEE-EecCCCCHHHHHHHHHHHhcCCCcEEEe----cCCCcccccccC-CcEEEEecCCC------------------
Q 037139            2 GYRVT-TLHGGKSQEQREISLEGFRTKRYNVLVA----TDVAGRGIDIPD-VAHVINYDMPG------------------   57 (135)
Q Consensus         2 g~~v~-~~hg~~~~~~r~~~~~~f~~g~~~ilv~----T~~~~~G~d~~~-v~~vi~~d~p~------------------   57 (135)
                      |+.+. .+||.     |.+ +++|++|+++||||    |+++++|+|+|+ |++||+||+|.                  
T Consensus       333 g~~~~~~lhg~-----rr~-l~~F~~G~~~VLVatas~TdvlarGIDip~~V~~VI~~d~P~~~~Sle~~~~~~~~~~~l  406 (1104)
T 4ddu_A          333 KFNVGETWSEF-----EKN-FEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSMRFSLELDKAPRFVLARV  406 (1104)
T ss_dssp             TCCEEESSSSH-----HHH-HHHHHHTSCSEEEEETTTHHHHCCSCCCTTTCCEEEEESCCEEEEECSSSSCCHHHHHHH
T ss_pred             CCCeeeEecCc-----HHH-HHHHHCCCCCEEEEecCCCCeeEecCcCCCCCCEEEEECCCCCCCCcccccCHHHHHHHH
Confidence            67887 89982     555 99999999999999    999999999999 99999999998                  


Q ss_pred             ------------------------------------------------------CHHHHHHHhhhcCCCCCC--ceEEEE
Q 037139           58 ------------------------------------------------------NIEMYTHRIGRTGRAGKT--GVATTF   81 (135)
Q Consensus        58 ------------------------------------------------------~~~~~~qr~GR~gR~~~~--g~~~~~   81 (135)
                                                                            +..+|+||+||+||.+..  +.++++
T Consensus       407 ~~l~~~~~~~~~~~~~~~~e~~~~~l~~~~~~~~i~~~~~~l~~~~~~~~~~~pd~~tYihr~GRtgR~~~gg~~~Glsi  486 (1104)
T 4ddu_A          407 LKEMGLIKAQENPDVEELRKIAKEHLTQKEFVEKVKEMFRGVVVKDEDLELIIPDVYTYIQASGRSSRILNGVLVKGVSV  486 (1104)
T ss_dssp             HHHHSSCSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHCCSSEEETTTTEEEEECHHHHHHHHHTTCCEETTEECCEEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHhhccceEEecCCeeEEEecChhhhhcccCchhcccCCCcccceEE
Confidence                                                                  788999999999996532  234444


Q ss_pred             eecCChhHHHHHHHHHh
Q 037139           82 LTFHDTDVFYDLKQMLI   98 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~   98 (135)
                      +..++...++.+++.++
T Consensus       487 ~~~~d~~~~~~l~~~~~  503 (1104)
T 4ddu_A          487 IFEEDEEIFESLKTRLL  503 (1104)
T ss_dssp             EECCCHHHHHHHHHHHH
T ss_pred             EEEecHHHHHHHHHHHh
Confidence            55578888888888876

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*

Probab=99.65  E-value=1.8e-16  Score=127.99  Aligned_cols=85  Identities=26%  Similarity=0.383  Sum_probs=78.5

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCC---------------------------------
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDV---------------------------------   47 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v---------------------------------   47 (135)
                      .|+++.++||++.++++..+.++|+.|  .|+|||++++||+|++..                                 
T Consensus       464 ~gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~  541 (853)
T 2fsf_A          464 AGIKHNVLNAKFHANEAAIVAQAGYPA--AVTIATNMAGRGTDIVLGGSWQAEVAALENPTAEQIEKIKADWQVRHDAVL  541 (853)
T ss_dssp             TTCCCEECCTTCHHHHHHHHHTTTSTT--CEEEEESCCSSCSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHHHHHHHHHH
T ss_pred             CCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecccccCCcCccCCCchHhhhhhcccchhHHHHHHHHHhhhhhhHHH
Confidence            478899999999999998889999988  699999999999999974                                 


Q ss_pred             ----cEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEEeecCCh
Q 037139           48 ----AHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDT   87 (135)
Q Consensus        48 ----~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~~~~~~~   87 (135)
                          .+||+++.|.+...|.||+||+||.|.+|.++.|++..+.
T Consensus       542 ~~GGl~VI~te~pes~riy~qr~GRTGRqGd~G~s~~fls~eD~  585 (853)
T 2fsf_A          542 EAGGLHIIGTERHESRRIDNQLRGRSGRQGDAGSSRFYLSMEDA  585 (853)
T ss_dssp             HTTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSG
T ss_pred             hcCCcEEEEccCCCCHHHHHhhccccccCCCCeeEEEEecccHH
Confidence                5899999999999999999999999999999999987764

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=99.64  E-value=6.4e-17  Score=128.72  Aligned_cols=79  Identities=29%  Similarity=0.387  Sum_probs=68.9

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEE----------Eec-----------CCCCH
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVI----------NYD-----------MPGNI   59 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi----------~~d-----------~p~~~   59 (135)
                      .|+.+..+||+|++++       |+++..+|||||+++++|+|+| +++||          |||           .|.+.
T Consensus       419 ~g~~v~~lHG~l~q~e-------r~~~~~~VLVATdVaerGIDId-V~~VI~~Gl~~~~ViNyDydP~~gl~~~~~P~s~  490 (666)
T 3o8b_A          419 LGINAVAYYRGLDVSV-------IPTIGDVVVVATDALMTGYTGD-FDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDA  490 (666)
T ss_dssp             TTCCEEEECTTSCGGG-------SCSSSCEEEEECTTHHHHCCCC-BSEEEECCEEEEEEEECCCSSSCEEEEEEEECBH
T ss_pred             CCCcEEEecCCCCHHH-------HHhCCCcEEEECChHHccCCCC-CcEEEecCcccccccccccccccccccccCcCCH
Confidence            3688999999999875       4567779999999999999997 99988          677           89999


Q ss_pred             HHHHHHhhhcCCCCCCceEEEEeecCChhH
Q 037139           60 EMYTHRIGRTGRAGKTGVATTFLTFHDTDV   89 (135)
Q Consensus        60 ~~~~qr~GR~gR~~~~g~~~~~~~~~~~~~   89 (135)
                      ++|+||+||+|| +..|. +.|+.+.+...
T Consensus       491 ~syiQRiGRtGR-g~~G~-i~lvt~~e~~~  518 (666)
T 3o8b_A          491 VSRSQRRGRTGR-GRRGI-YRFVTPGERPS  518 (666)
T ss_dssp             HHHHHHHTTBCS-SSCEE-EEESCCCCBCS
T ss_pred             HHHHHHhccCCC-CCCCE-EEEEecchhhc
Confidence            999999999999 88999 88888776544

>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=99.64  E-value=1.4e-15  Score=121.08  Aligned_cols=84  Identities=18%  Similarity=0.265  Sum_probs=75.9

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCc---EEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCc--
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYN---VLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTG--   76 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~---ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g--   76 (135)
                      |+.+..+||+++.++|.+++++|++++..   +|++|+++++|+|++.+++||+||+||++..+.|++||++|.|+..  
T Consensus       440 g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~v~L~st~a~g~Glnl~~a~~Vi~~d~~wnp~~~~Qa~gR~~R~Gq~~~v  519 (644)
T 1z3i_X          440 RYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTC  519 (644)
T ss_dssp             TCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCE
T ss_pred             CCCEEEEeCCCCHHHHHHHHHHhcCCCCCcEEEEEecccccCCcccccCCEEEEECCCCCccHHHHHHHhhhhcCCCCce
Confidence            67889999999999999999999998764   8899999999999999999999999999999999999999998654  


Q ss_pred             eEEEEeecC
Q 037139           77 VATTFLTFH   85 (135)
Q Consensus        77 ~~~~~~~~~   85 (135)
                      .++.++...
T Consensus       520 ~v~~lv~~~  528 (644)
T 1z3i_X          520 YIYRLLSTG  528 (644)
T ss_dssp             EEEEEEETT
T ss_pred             EEEEEEECC
Confidence            555566655

>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A

Probab=99.63  E-value=1.2e-15  Score=123.70  Aligned_cols=85  Identities=26%  Similarity=0.309  Sum_probs=77.9

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCC---------------------------------
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDV---------------------------------   47 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v---------------------------------   47 (135)
                      .|+++.++||++.++++..+.++|+.|  .|+|||++++||+|++.+                                 
T Consensus       483 ~Gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  560 (922)
T 1nkt_A          483 RRIPHNVLNAKYHEQEATIIAVAGRRG--GVTVATNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSEL  560 (922)
T ss_dssp             TTCCCEEECSSCHHHHHHHHHTTTSTT--CEEEEETTCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHH
T ss_pred             CCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecchhhcCccccCCCCHHHHHHHHHhhccccccccchhhHHHHHHHH
Confidence            478899999999888888888888888  699999999999999975                                 


Q ss_pred             -------------------cEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEEeecCCh
Q 037139           48 -------------------AHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDT   87 (135)
Q Consensus        48 -------------------~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~~~~~~~   87 (135)
                                         .+||+++.|.+...|.||+||+||.|.+|.++.|++..+.
T Consensus       561 ~~~~~~~~~~~~~V~~~GGlhVI~te~pes~riy~qr~GRTGRqGdpG~s~fflSleD~  619 (922)
T 1nkt_A          561 PIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGDE  619 (922)
T ss_dssp             HHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTSH
T ss_pred             HHHHHHHHHhhhHHHhcCCcEEEeccCCCCHHHHHHHhcccccCCCCeeEEEEechhHH
Confidence                               4899999999999999999999999999999999998765

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.59  E-value=2.5e-15  Score=118.21  Aligned_cols=69  Identities=16%  Similarity=0.312  Sum_probs=63.6

Q ss_pred             EEEecCCCCHHHHHHHHHHHhcCCCc---EEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCC
Q 037139            5 VTTLHGGKSQEQREISLEGFRTKRYN---VLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGK   74 (135)
Q Consensus         5 v~~~hg~~~~~~r~~~~~~f~~g~~~---ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~   74 (135)
                      +..+||+++ ++|++++++|++|+.+   |||||+++++|+|+|.+++||++++|++...|+||+||++|.+.
T Consensus       474 ~~~i~g~~~-~~r~~~l~~F~~~~~~~~~ilvtt~~l~~GiDip~v~~Vi~~~~~~s~~~~~Q~iGR~~R~~~  545 (590)
T 3h1t_A          474 VARVTSEEG-KIGKGHLSRFQELETSTPVILTTSQLLTTGVDAPTCKNVVLARVVNSMSEFKQIVGRGTRLRE  545 (590)
T ss_dssp             EEECSSTTH-HHHHHHHHHHHCTTCCCCCEEEESSTTTTTCCCTTEEEEEEESCCCCHHHHHHHHTTSCCCBG
T ss_pred             EEEEeCCCh-HHHHHHHHHHhCCCCCCCEEEEECChhhcCccchheeEEEEEecCCChHHHHHHHhhhcccCc
Confidence            678899875 4799999999998877   88999999999999999999999999999999999999999764

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.57  E-value=6e-15  Score=119.90  Aligned_cols=84  Identities=24%  Similarity=0.372  Sum_probs=75.6

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCc---EEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCC--c
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYN---VLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKT--G   76 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~---ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~--g   76 (135)
                      |+.+..+||+++.++|.+++++|++++..   +|++|.+++.|+|++.+++||+||+|+++..+.|++||+.|.|+.  .
T Consensus       596 g~~~~~i~G~~~~~eR~~~i~~F~~~~~~~~v~LlSt~agg~GlNL~~a~~VI~~D~~wnp~~~~Qa~gR~~RiGQ~k~V  675 (800)
T 3mwy_W          596 GINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHV  675 (800)
T ss_dssp             TCCCEEESTTSCHHHHHHHHHTTSSTTCSCCCEEEEHHHHTTTCCCTTCCEEEESSCCSCSHHHHHHHTTTSCSSCCSCE
T ss_pred             CCCEEEEeCCCCHHHHHHHHHHhhCCCCCceEEEEecccccCCCCccccceEEEecCCCChhhHHHHHHHHHhcCCCceE
Confidence            67889999999999999999999997655   899999999999999999999999999999999999999998865  4


Q ss_pred             eEEEEeecC
Q 037139           77 VATTFLTFH   85 (135)
Q Consensus        77 ~~~~~~~~~   85 (135)
                      .++.++...
T Consensus       676 ~Vyrlv~~~  684 (800)
T 3mwy_W          676 MVYRLVSKD  684 (800)
T ss_dssp             EEEEEEETT
T ss_pred             EEEEEecCC
Confidence            555666655

>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=99.18  E-value=5.2e-11  Score=99.06  Aligned_cols=67  Identities=16%  Similarity=0.183  Sum_probs=59.6

Q ss_pred             HHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCC----ceEEEEee
Q 037139           16 QREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKT----GVATTFLT   83 (135)
Q Consensus        16 ~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~----g~~~~~~~   83 (135)
                      .|..++++|++|+++|||+|+++.+|+|+|.+ .++++|.|.+...|+|++||++|.+..    |.++.|+.
T Consensus       637 ~R~~i~~~Fk~g~i~ILIvvd~lltGfDiP~l-~tlylDkpl~~~~liQaIGRtnR~~~~~K~~G~IVdf~~  707 (1038)
T 2w00_A          637 YYRDLAQRVKNQDIDLLIVVGMFLTGFDAPTL-NTLFVDKNLRYHGLMQAFSRTNRIYDATKTFGNIVTFRD  707 (1038)
T ss_dssp             HHHHHHHHHHTTSSSEEEESSTTSSSCCCTTE-EEEEEESCCCHHHHHHHHHTTCCCCCTTCCSEEEEESSC
T ss_pred             HHHHHHHHHHcCCCeEEEEcchHHhCcCcccc-cEEEEccCCCccceeehhhccCcCCCCCCCcEEEEEccc
Confidence            48899999999999999999999999999999 678999999999999999999997643    66666654

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=97.80  E-value=4.5e-05  Score=59.57  Aligned_cols=48  Identities=15%  Similarity=0.252  Sum_probs=27.4

Q ss_pred             EecCCCCHHHHHHHHHHHhcCCCcEEE--ecCCCcccccccC----CcEEEEecCCC
Q 037139            7 TLHGGKSQEQREISLEGFRTKRYNVLV--ATDVAGRGIDIPD----VAHVINYDMPG   57 (135)
Q Consensus         7 ~~hg~~~~~~r~~~~~~f~~g~~~ilv--~T~~~~~G~d~~~----v~~vi~~d~p~   57 (135)
                      ..+|..  .++.++++.|+.+. .||+  ||..+.+|+|+|+    +++||++++|.
T Consensus       410 ~~q~~~--~~~~~~l~~f~~~~-~il~~V~~~~~~EGiD~~~~~~~~~~Vii~~lPf  463 (540)
T 2vl7_A          410 IEENKK--TRHEEVLELMKTGK-YLVMLVMRAKESEGVEFREKENLFESLVLAGLPY  463 (540)
T ss_dssp             EESTTT--CCHHHHHHHHHTSC-CEEEEEC---------------CEEEEEEESCCC
T ss_pred             EecCCC--CcHHHHHHHHhcCC-eEEEEEecCceecceecCCCcccccEEEEECCCC
Confidence            345543  46889999998864 6777  8899999999997    88999999885

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=97.42  E-value=0.00041  Score=57.27  Aligned_cols=39  Identities=23%  Similarity=0.454  Sum_probs=34.3

Q ss_pred             EEEEecCCCCHHHHHHHhhhcCCCCCCceEEEEeecCCh
Q 037139           49 HVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDT   87 (135)
Q Consensus        49 ~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~~~~~~~   87 (135)
                      +||-...+.|...=.|..||+||.|.+|....+++-.|.
T Consensus       662 hVIGTeRhESrRIDnQLRGRaGRQGDPGsSrF~LSLeDd  700 (997)
T 2ipc_A          662 FIIGTERHESRRIDNQLRGRAGRQGDPGGSRFYVSFDDD  700 (997)
T ss_dssp             CEEESSCCSSHHHHHHHHHTSSCSSCCCEEEEEEESSSH
T ss_pred             EEEeccCCchHHHHHHHhcccccCCCCCCeEEEEECChH
Confidence            688888899999999999999999999998888876654

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=96.77  E-value=0.0065  Score=48.27  Aligned_cols=47  Identities=23%  Similarity=0.359  Sum_probs=31.6

Q ss_pred             CCCCHHHHHHHHHHHhcCCCcEEEecC--CCcccccccC--CcEEEEecCCC
Q 037139           10 GGKSQEQREISLEGFRTKRYNVLVATD--VAGRGIDIPD--VAHVINYDMPG   57 (135)
Q Consensus        10 g~~~~~~r~~~~~~f~~g~~~ilv~T~--~~~~G~d~~~--v~~vi~~d~p~   57 (135)
                      -+++..++.+++++|+ ++-.||+++.  .+.+|+|+|+  ..+||...+|.
T Consensus       477 q~~~~~~~~~ll~~f~-~~~~vL~~v~~gsf~EGiD~~g~~l~~viI~~lPf  527 (620)
T 4a15_A          477 RGIDQKELYSMLKKFR-RDHGTIFAVSGGRLSEGINFPGNELEMIILAGLPF  527 (620)
T ss_dssp             TTCCSHHHHHHHHHHT-TSCCEEEEETTSCC--------CCCCEEEESSCCC
T ss_pred             CCCChhHHHHHHHHhc-cCCcEEEEEecCceeccccCCCCceEEEEEEcCCC
Confidence            3456678999999999 8888999974  8999999986  67888887774

>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=95.15  E-value=0.03  Score=45.68  Aligned_cols=53  Identities=19%  Similarity=0.332  Sum_probs=45.3

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCC-cccccccCCcEEEEec
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVA-GRGIDIPDVAHVINYD   54 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~-~~G~d~~~v~~vi~~d   54 (135)
                      |+++..+||+++..++...++.+.+|+.+|+|+|... ...+++.++++||.-.
T Consensus       445 gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~~~~~~l~lVVIDE  498 (780)
T 1gm5_A          445 NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVIIDE  498 (780)
T ss_dssp             SCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEEEES
T ss_pred             CceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhhhhhccCCceEEecc
Confidence            6889999999999999999999999999999999743 3457788888887544

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=94.56  E-value=0.32  Score=37.84  Aligned_cols=41  Identities=12%  Similarity=0.162  Sum_probs=30.7

Q ss_pred             HHHHHHHHhcCCCcEEEec--CCCccccccc-----CCcEEEEecCCC
Q 037139           17 REISLEGFRTKRYNVLVAT--DVAGRGIDIP-----DVAHVINYDMPG   57 (135)
Q Consensus        17 r~~~~~~f~~g~~~ilv~T--~~~~~G~d~~-----~v~~vi~~d~p~   57 (135)
                      +.+.++.|+...-.||+||  ..+.+|+|+|     .+++||...+|.
T Consensus       426 ~~~~~~~~~~~~~~vl~~v~gg~~~EGiD~~d~~g~~l~~viI~~lPf  473 (551)
T 3crv_A          426 VEDLYSAISANNKVLIGSVGKGKLAEGIELRNNDRSLISDVVIVGIPY  473 (551)
T ss_dssp             HHHHHHHTTSSSSCEEEEESSCCSCCSSCCEETTEESEEEEEEESCCC
T ss_pred             HHHHHHHHHhcCCeEEEEEecceecccccccccCCcceeEEEEEcCCC
Confidence            3557777854444799998  6899999999     367888777664

>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain, chromatin regulator, coiled coil, nucleus, repressor, transcription; 2.20A {Saccharomyces cerevisiae} PDB: 3hgq_A

Probab=94.42  E-value=0.22  Score=36.57  Aligned_cols=81  Identities=6%  Similarity=-0.011  Sum_probs=49.5

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCccccc-----ccCCcEEEEecCCCCHHH-HHHHhhhcCCC---
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGID-----IPDVAHVINYDMPGNIEM-YTHRIGRTGRA---   72 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d-----~~~v~~vi~~d~p~~~~~-~~qr~GR~gR~---   72 (135)
                      |+...-+-|.....+++     -.+....+.+.|...+.|+|     +...+.||.||..|++.. .+|.+-|+.|.   
T Consensus       149 ~~~y~RlDG~~~~~~~k-----~~~~~~~i~Lltsag~~gin~~~~nl~~aD~VI~~DsdwNp~~d~iQa~~r~~R~~~g  223 (328)
T 3hgt_A          149 KVHIKRYDGHSIKSAAA-----ANDFSCTVHLFSSEGINFTKYPIKSKARFDMLICLDTTVDTSQKDIQYLLQYKRERKG  223 (328)
T ss_dssp             SCEEEESSSCCC------------CCSEEEEEEESSCCCTTTSCCCCCSCCSEEEECSTTCCTTSHHHHHHHCCC-----
T ss_pred             CCceEeCCCCchhhhhh-----cccCCceEEEEECCCCCCcCcccccCCCCCEEEEECCCCCCCChHHHHHHHHhhhccC
Confidence            45555566664333211     12455566666777777776     577899999999999877 48877777775   


Q ss_pred             -CCCceEEEEeecCCh
Q 037139           73 -GKTGVATTFLTFHDT   87 (135)
Q Consensus        73 -~~~g~~~~~~~~~~~   87 (135)
                       ++...++.++.....
T Consensus       224 q~k~v~V~RLvt~~Ti  239 (328)
T 3hgt_A          224 LERYAPIVRLVAINSI  239 (328)
T ss_dssp             ----CCEEEEEETTSH
T ss_pred             CCCcceEEEEeCCCCH
Confidence             245678888876544

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=90.15  E-value=0.4  Score=35.46  Aligned_cols=53  Identities=15%  Similarity=0.186  Sum_probs=42.0

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCc----ccccccCCcEEEEec
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAG----RGIDIPDVAHVINYD   54 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~----~G~d~~~v~~vi~~d   54 (135)
                      |+++..+||+.+..++...++.+..++.+|+|+|.-.-    .-++...+++||.-.
T Consensus        91 ~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~iViDE  147 (414)
T 3oiy_A           91 KVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDFVFVDD  147 (414)
T ss_dssp             SCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHHHTTCCCSEEEESC
T ss_pred             CceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHHhccccccEEEEeC
Confidence            67899999999999999999999999999999996321    124455778777544

>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=89.97  E-value=0.38  Score=40.91  Aligned_cols=51  Identities=14%  Similarity=0.247  Sum_probs=43.3

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecC-CCcccccccCCcEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATD-VAGRGIDIPDVAHVIN   52 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~-~~~~G~d~~~v~~vi~   52 (135)
                      ++++..+++..+..++...++.+..|+.+|+|+|. .+...+.+.++++||.
T Consensus       680 ~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~~~~~~~~l~lvIi  731 (1151)
T 2eyq_A          680 PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIV  731 (1151)
T ss_dssp             TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEEEE
T ss_pred             CCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhCCccccccceEEE
Confidence            56789999999999999999999999999999995 4445577788887774

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=84.09  E-value=1  Score=38.24  Aligned_cols=53  Identities=15%  Similarity=0.186  Sum_probs=42.4

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCc----ccccccCCcEEEEec
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAG----RGIDIPDVAHVINYD   54 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~----~G~d~~~v~~vi~~d   54 (135)
                      |+++..+||+++..++...++.+..|+.+|+|+|.-.-    .-+++.++++||.-+
T Consensus       148 ~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~l~~~~l~~lViDE  204 (1104)
T 4ddu_A          148 KVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDFVFVDD  204 (1104)
T ss_dssp             TSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHHHHTSCCSEEEESC
T ss_pred             CCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHhhcccCcCEEEEeC
Confidence            67899999999999999999999999999999996211    124567788887544

---

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	135
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	3e-26
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	1e-23
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	3e-23
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	2e-22
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	8e-19
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	1e-17
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	2e-16
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	2e-16
d2p6ra4	201	c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglob	4e-13
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	8e-13
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	1e-12
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	2e-12
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	3e-11
d1c4oa2	174	c.37.1.19 (A:410-583) Nucleotide excision repair e	1e-10
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	2e-10
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	4e-07
d1yksa2	299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	7e-07
d2eyqa5	211	c.37.1.19 (A:779-989) Transcription-repair couplin	2e-05
d1tf5a4	175	c.37.1.19 (A:396-570) Translocation ATPase SecA, n	2e-05
d1z3ix1	346	c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fi	0.003

>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 = 97.7 bits (243), Expect = 3e-26
 Identities = 17/95 (17%), Positives = 27/95 (28%), Gaps = 14/95 (14%)

Query: 1   LGYRVTTLHGGKSQEQREIS----------LEGFRTKRYNVLVATDVAGRGIDIPD---V 47
           LG      + G        S          L    T  ++ ++  +              
Sbjct: 59  LGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSLDPT 118

Query: 48  AHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFL 82
             +    +P +    T R GRTGR GK G+     
Sbjct: 119 FTIETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVA 152

>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 = 90.3 bits (223), Expect = 1e-23
 Identities = 28/98 (28%), Positives = 41/98 (41%), Gaps = 9/98 (9%)

Query: 2   GYRVTTLHGGKSQEQR--------EISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINY 53
           G +     G  S+E          ++ L+ F    +NVLVAT V   G+D+P+V  V+ Y
Sbjct: 185 GIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFY 244

Query: 54  DMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDTDVFY 91
           +   +      R GRTGR    G     +     D  Y
Sbjct: 245 EPVPSAIRSIQRRGRTGRHMP-GRVIILMAKGTRDEAY 281

>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 = 89.1 bits (220), Expect = 3e-23
 Identities = 17/108 (15%), Positives = 31/108 (28%), Gaps = 9/108 (8%)

Query: 8   LHGGKSQEQREISLEGFRTKRYNVLVAT----DVAGRGIDIPD-VAHVINYDMPGNIEMY 62
              G     ++   E F     + L+ T        RG+D+P+ +   +    P     +
Sbjct: 49  FRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCP----SF 104

Query: 63  THRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAK 110
              I          V      + + D    L   + +    V   L K
Sbjct: 105 RVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKK 152

>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 = 84.6 bits (208), Expect = 2e-22
 Identities = 39/110 (35%), Positives = 64/110 (58%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
             + V+ ++    Q++R+  ++ FR+    +L++TD+  RGID+  V+ VINYD+P N E
Sbjct: 50  DKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKE 109

Query: 61  MYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAK 110
            Y HRIGR GR G+ GVA  F+T  D     +L++        +P ++A 
Sbjct: 110 NYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIAT 159

>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 = 75.4 bits (184), Expect = 8e-19
 Identities = 43/107 (40%), Positives = 68/107 (63%)

Query: 3   YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMY 62
           + V+++HG   Q++RE  ++ FR+    VL++TDV  RG+D+P V+ +INYD+P N E+Y
Sbjct: 59  FTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELY 118

Query: 63  THRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELA 109
            HRIGR+GR G+ GVA  F+   D  +  D++Q        +P  +A
Sbjct: 119 IHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVA 165

>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 = 73.4 bits (179), Expect = 1e-17
 Identities = 25/86 (29%), Positives = 38/86 (44%)

Query: 3   YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMY 62
           + +  +    S+E+RE  LEGFRT R+  +V++ V   GID+PD    +     G+   Y
Sbjct: 113 FLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREY 172

Query: 63  THRIGRTGRAGKTGVATTFLTFHDTD 88
             R+GR  R  K              
Sbjct: 173 IQRLGRILRPSKGKKEAVLYELISRG 198

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]} Length = 181

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]

 Score = 69.4 bits (169), Expect = 2e-16
 Identities = 21/120 (17%), Positives = 44/120 (36%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G +V  LH      +R   +   R  +Y+VLV  ++   G+DIP+V+ V   D      +
Sbjct: 55  GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFL 114

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTI 121
            + R            A   +  +   +   ++  + ++      +   +      P T+
Sbjct: 115 RSERSLIQTIGRAARNANGHVIMYADTITKSMEIAIQETKRRRAIQEEYNRKHGIVPRTV 174

>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 = 68.8 bits (167), Expect = 2e-16
 Identities = 37/84 (44%), Positives = 52/84 (61%)

Query: 14  QEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAG 73
           Q QRE  +  F+ K+  +L+ATDV  RGID+ D+  VINY +P N E Y HRIGRTGRAG
Sbjct: 64  QSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAG 123

Query: 74  KTGVATTFLTFHDTDVFYDLKQML 97
           K G A + +   +      +++ +
Sbjct: 124 KKGKAISIINRREYKKLRYIERAM 147

>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 = 61.5 bits (148), Expect = 4e-13
 Identities = 21/105 (20%), Positives = 35/105 (33%), Gaps = 7/105 (6%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVI-------NY 53
           +       H G    QR +  + FR     V+VAT     G+++P    ++        Y
Sbjct: 93  VRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGY 152

Query: 54  DMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLI 98
                +  Y    GR GR G        +     D    +K+ + 
Sbjct: 153 SKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDREIAVKRYIF 197

>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 = 59.7 bits (143), Expect = 8e-13
 Identities = 32/82 (39%), Positives = 45/82 (54%)

Query: 29  YNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDTD 88
              LV +D+  RGIDI  V  VIN+D P   E Y HRIGR+GR G  G+A   + ++D  
Sbjct: 83  VRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRF 142

Query: 89  VFYDLKQMLIQSNSPVPPELAK 110
             Y ++Q L    + +P  + K
Sbjct: 143 NLYKIEQELGTEIAAIPATIDK 164

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]} 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: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 59.7 bits (143), Expect = 1e-12
 Identities = 30/98 (30%), Positives = 40/98 (40%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G      H G     R    E F+     ++VAT   G GI+ P+V  V+++D+P NIE 
Sbjct: 54  GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIES 113

Query: 62  YTHRIGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQ 99
           Y    GR GR G    A  F    D        +   Q
Sbjct: 114 YYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPQ 151

>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 = 60.3 bits (145), Expect = 2e-12
 Identities = 18/100 (18%), Positives = 29/100 (29%), Gaps = 23/100 (23%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIP---------DVAHVI 51
            G +V  L       +        RT  ++ +V TD++  G +            +  VI
Sbjct: 201 NGKKVIQLSRKTFDSEYI----KTRTNDWDFVVTTDISEMGANFKAERVIDPRRCMKPVI 256

Query: 52  NYDMPGNIEM----------YTHRIGRTGRAGKTGVATTF 81
             D    + +             R GR GR  K       
Sbjct: 257 LTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYI 296

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]} Length = 174

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]

 Score = 53.9 bits (129), Expect = 1e-10
 Identities = 26/122 (21%), Positives = 49/122 (40%), Gaps = 4/122 (3%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEM 61
           G R   LH      +R+  +   R   Y+ LV  ++   G+DIP+V+ V   D      +
Sbjct: 55  GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFL 114

Query: 62  YTHR--IGRTGRAGKTGVATTFLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPG 119
            + R  I   GRA +      +   +   V   +++ + ++N     + A +      P 
Sbjct: 115 RSERSLIQTIGRAARNARGEVW--LYADRVSEAMQRAIEETNRRRALQEAYNLEHGITPE 172

Query: 120 TI 121
           T+
Sbjct: 173 TV 174

>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 = 52.8 bits (126), Expect = 2e-10
 Identities = 18/62 (29%), Positives = 23/62 (37%), Gaps = 4/62 (6%)

Query: 24  FRTKRYNVLVATDVAGRGIDIPDVA---HVINYDMPGNIEMYTHRIGRTGRAGKTGVATT 80
             T    V+VATD    G      +      +   P +    T R GRTGR GK G+   
Sbjct: 74  IPTNGDVVVVATDALMTGFTGDFDSVIDCNTSDGKPQDAVSRTQRRGRTGR-GKPGIYRF 132

Query: 81  FL 82
             
Sbjct: 133 VA 134

>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 = 44.7 bits (104), Expect = 4e-07
 Identities = 28/75 (37%), Positives = 44/75 (58%), Gaps = 1/75 (1%)

Query: 35  TDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTF-HDTDVFYDL 93
           T++ GRG+DI  V    NYDMP + + Y HR+ R GR G  G+A TF++  +D  +  D+
Sbjct: 84  TNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDV 143

Query: 94  KQMLIQSNSPVPPEL 108
           +     + S +P E+
Sbjct: 144 QDRFEVNISELPDEI 158

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]} 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: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

 Score = 44.6 bits (105), Expect = 7e-07
 Identities = 15/108 (13%), Positives = 33/108 (30%), Gaps = 21/108 (19%)

Query: 1   LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIE 60
            G  V  L+    + +        + K+ + ++ATD+A  G ++  V  V++        
Sbjct: 59  AGKSVVVLNRKTFEREYP----TIKQKKPDFILATDIAEMGANL-CVERVLDCRTAFKPV 113

Query: 61  MYTHRIG----------------RTGRAGKTGVATTFLTFHDTDVFYD 92
           +                      R GR G+         ++      +
Sbjct: 114 LVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPTSEN 161

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]} Length = 211

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]

 Score = 40.0 bits (93), Expect = 2e-05
 Identities = 30/123 (24%), Positives = 46/123 (37%), Gaps = 4/123 (3%)

Query: 3   YRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMY 62
            R+   HG   + + E  +  F  +R+NVLV T +   GIDIP    +I           
Sbjct: 58  ARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQ 117

Query: 63  THRI-GRTGRAGKTGVATTFL---TFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKP 118
            H++ GR GR+     A           TD    L+ +    +      LA H+      
Sbjct: 118 LHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGA 177

Query: 119 GTI 121
           G +
Sbjct: 178 GEL 180

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]} Length = 175

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]

 Score = 39.9 bits (93), Expect = 2e-05
 Identities = 22/93 (23%), Positives = 39/93 (41%), Gaps = 10/93 (10%)

Query: 2   GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDI--------PDVAHVINY 53
           G     L+    + + +I  E    ++  V +AT++AGRG DI             V+  
Sbjct: 58  GIPHQVLNAKNHEREAQIIEE--AGQKGAVTIATNMAGRGTDIKLGEGVKELGGLAVVGT 115

Query: 54  DMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHD 86
           +   +  +     GR+GR G  G+   +L+  D
Sbjct: 116 ERHESRRIDNQLRGRSGRQGDPGITQFYLSMED 148

>d1z3ix1 c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]} Length = 346

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]

 Score = 34.2 bits (77), Expect = 0.003
 Identities = 7/52 (13%), Positives = 21/52 (40%)

Query: 24  FRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKT 75
             +  +  ++++   G G+++     ++ +D   N       + R  R G+ 
Sbjct: 167 PSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQK 218

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	135
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.97
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.96
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.96
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.96
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.95
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.95
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.95
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.93
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.92
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.9
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.85
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.84
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.83
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.82
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.79
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.72
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.66
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.48
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.43
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.33
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.32
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	98.82
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	97.87
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	97.69
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	97.02

>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=99.97  E-value=5.5e-31  Score=175.97  Aligned_cols=111  Identities=35%  Similarity=0.635  Sum_probs=101.0

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      .|+.+..+||+|++.+|..+++.|+.|+.+|||||+++++|+|+|+|++||+||+|+++..|+||+||+||.|+.|.+++
T Consensus        50 ~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Tdv~~rGiDi~~v~~VI~~d~P~~~~~yihR~GR~gR~g~~g~~i~  129 (162)
T d1fuka_          50 DKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAIN  129 (162)
T ss_dssp             TTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEE
T ss_pred             cCceEEEeccCCchhhHHHHHHHHhhcccceeeccccccccccCCCceEEEEeccchhHHHHHhhccccccCCCccEEEE
Confidence            37889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHHHHHHHHHhhCCCCCChHHHHH
Q 037139           81 FLTFHDTDVFYDLKQMLIQSNSPVPPELAKH  111 (135)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  111 (135)
                      ++++.+...++.+++.++....++|.++.+.
T Consensus       130 ~~~~~d~~~~~~i~~~~~~~~~~ip~~~~~l  160 (162)
T d1fuka_         130 FVTNEDVGAMRELEKFYSTQIEELPSDIATL  160 (162)
T ss_dssp             EEETTTHHHHHHHHHHSSCCCEECCSCCTTT
T ss_pred             EcCHHHHHHHHHHHHHHcCcCCCCChHHHHh
Confidence            9999999999999999999999999887653

>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=99.96  E-value=1.2e-30  Score=175.17  Aligned_cols=109  Identities=39%  Similarity=0.734  Sum_probs=102.3

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      .|+.+..+||+|++++|..++++|++|++++||||+++++|+|+|++++|||||+|++...|+||+||+||.|+.|.+++
T Consensus        57 ~~~~~~~~~~~~~~~~r~~~~~~fk~g~~~iLv~Td~~~rGiDi~~v~~VIn~d~P~~~~~yihR~GR~gR~g~~G~~i~  136 (168)
T d2j0sa2          57 ANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAIN  136 (168)
T ss_dssp             TTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEE
T ss_pred             cccchhhhhhhhhHHHHHHHHHHHhcCCccEEeccchhcccccccCcceEEEecCCcCHHHHHhhhccccccCCCcEEEE
Confidence            47889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHHHHHHHHHhhCCCCCChHHH
Q 037139           81 FLTFHDTDVFYDLKQMLIQSNSPVPPELA  109 (135)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  109 (135)
                      ++.+.+...++.+++.++....++|..+.
T Consensus       137 ~~~~~d~~~~~~i~~~~~~~i~e~p~~~~  165 (168)
T d2j0sa2         137 FVKNDDIRILRDIEQYYSTQIDEMPMNVA  165 (168)
T ss_dssp             EEEGGGHHHHHHHHHHTTCCCEECCSCCT
T ss_pred             EECHHHHHHHHHHHHHHcCcCCCCCcChH
Confidence            99999998999998888888777776544

>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=99.96  E-value=8.2e-30  Score=171.51  Aligned_cols=109  Identities=36%  Similarity=0.620  Sum_probs=104.7

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTF   81 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~   81 (135)
                      |+.+..+||+|++++|.+++++|+.|+.++||||+++++|+|+|++++||+||+|+++..|+||+||+||.|+.|.+++|
T Consensus        56 g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~~~~Gid~~~v~~VI~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~  135 (171)
T d1s2ma2          56 GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINL  135 (171)
T ss_dssp             TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEE
T ss_pred             cccccccccccchhhhhhhhhhcccCccccccchhHhhhccccceeEEEEecCCcchHHHHHHHhhhcccCCCccEEEEE
Confidence            78899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCChhHHHHHHHHHhhCCCCCChHHHH
Q 037139           82 LTFHDTDVFYDLKQMLIQSNSPVPPELAK  110 (135)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  110 (135)
                      +.+.+...++.+++.++....++|..+.+
T Consensus       136 v~~~e~~~~~~i~~~l~~~~~~~p~~~d~  164 (171)
T d1s2ma2         136 INWNDRFNLYKIEQELGTEIAAIPATIDK  164 (171)
T ss_dssp             ECGGGHHHHHHHHHHHTCCCEECCSSCCG
T ss_pred             eCHHHHHHHHHHHHHHCCCCCCCCcccch
Confidence            99999999999999999998888887664

>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=99.96  E-value=1.1e-28  Score=163.59  Aligned_cols=104  Identities=39%  Similarity=0.667  Sum_probs=97.8

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      .|+.+..+||++++.+|..++++|+.|+.++||||+++++|+|+|.+++||+||+|+++..|+||+||+||.|+.|.+++
T Consensus        51 ~g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~~~~~Gid~~~v~~Vi~~d~p~~~~~y~qr~GR~gR~g~~g~~i~  130 (155)
T d1hv8a2          51 IGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAIS  130 (155)
T ss_dssp             TTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEE
T ss_pred             cccccccccccchhhhhhhhhhhhhcccceeeeehhHHhhhhhhccCcEEEEecCCCCHHHHHHHHHhcCcCCCCceEEE
Confidence            47889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHHHHHHHHHhhCCCCC
Q 037139           81 FLTFHDTDVFYDLKQMLIQSNSPV  104 (135)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~  104 (135)
                      ++.+.+...++.+++.++....++
T Consensus       131 ~~~~~d~~~~~~i~~~~~~~i~~l  154 (155)
T d1hv8a2         131 IINRREYKKLRYIERAMKLKIKKL  154 (155)
T ss_dssp             EECTTSHHHHHHHHHHHTCCCCCB
T ss_pred             EEchHHHHHHHHHHHHHCCCcccc
Confidence            999999988888888887765543

>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=99.95  E-value=2e-28  Score=164.28  Aligned_cols=109  Identities=34%  Similarity=0.608  Sum_probs=97.5

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      .|+.+..+||+|++++|..++++|++|++++||||+++++|+|+|.+++||+||+|+++..|+||+||+||.|+.|.+++
T Consensus        50 ~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~~~~Gid~~~~~~vi~~~~p~~~~~yiqr~GR~gR~g~~g~~i~  129 (168)
T d1t5ia_          50 QNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAIT  129 (168)
T ss_dssp             TTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEE
T ss_pred             ccccccccccccchhhhhhhhhhhccccceeeeccccccchhhcccchhhhhhhcccchhhHhhhhhhcccCCCccEEEE
Confidence            47889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecC-ChhHHHHHHHHHhhCCCCCChHHH
Q 037139           81 FLTFH-DTDVFYDLKQMLIQSNSPVPPELA  109 (135)
Q Consensus        81 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~  109 (135)
                      ++.+. +...+..+++.++....++|+.+.
T Consensus       130 l~~~~~~~~~~~~i~~~~~~~~~elp~~~~  159 (168)
T d1t5ia_         130 FVSDENDAKILNDVQDRFEVNISELPDEID  159 (168)
T ss_dssp             EECSHHHHHHHHHHHHHHCCCEEECC----
T ss_pred             EECchHHHHHHHHHHHHHcCCcccCCchhh
Confidence            99875 455667788888888888888764

>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=99.95  E-value=1.2e-27  Score=164.44  Aligned_cols=91  Identities=32%  Similarity=0.500  Sum_probs=85.5

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEE
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      .|+.+..+||+|++++|.++++.|++|+++|||||+++++|+|+|+|++||+||+|.++.+|+||+||+||.|..|.+++
T Consensus        53 ~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd~~~~GiD~p~v~~VI~~~~P~~~~~y~qr~GR~gR~g~~g~ai~  132 (200)
T d1oywa3          53 KGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAML  132 (200)
T ss_dssp             TTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEE
T ss_pred             CCceeEEecCCCcHHHHHHHHHHHhcccceEEEecchhhhccCCCCCCEEEECCCccchHHHHHHhhhhhcCCCCceEEE
Confidence            37889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCChhHHH
Q 037139           81 FLTFHDTDVFY   91 (135)
Q Consensus        81 ~~~~~~~~~~~   91 (135)
                      |+.+.+...++
T Consensus       133 ~~~~~d~~~l~  143 (200)
T d1oywa3         133 FYDPADMAWLR  143 (200)
T ss_dssp             EECHHHHHHHH
T ss_pred             ecCHHHHHHHH
Confidence            99876554443

>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=99.93  E-value=9.2e-26  Score=152.72  Aligned_cols=89  Identities=25%  Similarity=0.378  Sum_probs=77.9

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCC-----CHHHHHHHhhhcCCCCCC
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPG-----NIEMYTHRIGRTGRAGKT   75 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~-----~~~~~~qr~GR~gR~~~~   75 (135)
                      .|+++..+||+|++.+|.+++++|++|+++|||||+++++|+|+|+|++||+||+|.     +...|+||+||+||.|. 
T Consensus        54 ~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~~rGiDip~v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~-  132 (181)
T d1t5la2          54 AGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAN-  132 (181)
T ss_dssp             TTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCCSSSCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTT-
T ss_pred             CCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHHHccCCCCCCCEEEEecCCcccccccHHHHHHHHHhhccccC-
Confidence            488999999999999999999999999999999999999999999999999999995     68999999999999875 


Q ss_pred             ceEEEEeecCChhHH
Q 037139           76 GVATTFLTFHDTDVF   90 (135)
Q Consensus        76 g~~~~~~~~~~~~~~   90 (135)
                      +.++.+.........
T Consensus       133 ~~~~~~~~~~~~~~~  147 (181)
T d1t5la2         133 GHVIMYADTITKSME  147 (181)
T ss_dssp             CEEEEECSSCCHHHH
T ss_pred             ceeEeecchhhHHHH
Confidence            445555544444433

>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=99.92  E-value=8.9e-25  Score=146.47  Aligned_cols=92  Identities=23%  Similarity=0.344  Sum_probs=80.1

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCC-----CHHHHHHHhhhcCCCCCC
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPG-----NIEMYTHRIGRTGRAGKT   75 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~-----~~~~~~qr~GR~gR~~~~   75 (135)
                      .|+++..+||+|++.+|.+++++|++|+++|||||+++++|+|+|+|++||+||+|.     +..+|+||+||+||.+. 
T Consensus        54 ~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~GiDip~V~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~~-  132 (174)
T d1c4oa2          54 HGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAR-  132 (174)
T ss_dssp             TTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTT-
T ss_pred             cCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeeeeeccCCCCcEEEEeccccccccchhHHHHHHhhhhhhcCC-
Confidence            489999999999999999999999999999999999999999999999999999776     56889999999999874 


Q ss_pred             ceEEEEeecCChhHHHHH
Q 037139           76 GVATTFLTFHDTDVFYDL   93 (135)
Q Consensus        76 g~~~~~~~~~~~~~~~~~   93 (135)
                      |.++++.........+.+
T Consensus       133 g~~~~~~~~~~~~~~~~i  150 (174)
T d1c4oa2         133 GEVWLYADRVSEAMQRAI  150 (174)
T ss_dssp             CEEEEECSSCCHHHHHHH
T ss_pred             CeeEEeecCCCHHHHHHH
Confidence            777777665554433333

>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=99.90  E-value=8.2e-25  Score=150.47  Aligned_cols=117  Identities=21%  Similarity=0.354  Sum_probs=93.3

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCC-CHHHHHHHhhhcCCCCCCceEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPG-NIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~-~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      ++++..+||.|++++|++++++|++|+++|||||+++++|+|+|++++||++|.|. ..++|.|..||+||.+..|+|++
T Consensus        64 ~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLVaTtViE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l  143 (206)
T d1gm5a4          64 EFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFL  143 (206)
T ss_dssp             --CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEEC
T ss_pred             CCeEEEEeecccHHHHHHHHHHHHCCCEEEEEEehhhhccccccCCcEEEEEccCCccHHHHHhhhhheeeccccceeEe
Confidence            45788899999999999999999999999999999999999999999999999987 79999999999999999999999


Q ss_pred             EeecCChhHHHHHHHHHhhCCCCCChHHHHHHHhhCCCCCC
Q 037139           81 FLTFHDTDVFYDLKQMLIQSNSPVPPELAKHEASKFKPGTI  121 (135)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  121 (135)
                      ++.+.+....+.++.+. ....  --.++....+.-.++.+
T Consensus       144 ~~~~~~~~~~~rl~~~~-~~~d--Gf~ia~~Dl~lRG~G~~  181 (206)
T d1gm5a4         144 VVGDVGEEAMERLRFFT-LNTD--GFKIAEYDLKTRGPGEF  181 (206)
T ss_dssp             CCCSCCHHHHHHHHHHH-TCCC--SHHHHHHHHHSSCCCC-
T ss_pred             eeccccccchhhhhhcc-ccCC--CchHHHHHHhccCCccc
Confidence            99876665555554443 3332  23344444444444443

>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=99.85  E-value=8.9e-22  Score=135.01  Aligned_cols=84  Identities=26%  Similarity=0.434  Sum_probs=75.6

Q ss_pred             eEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEE-------ecCCCCHHHHHHHhhhcCCCCC--
Q 037139            4 RVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVIN-------YDMPGNIEMYTHRIGRTGRAGK--   74 (135)
Q Consensus         4 ~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~-------~d~p~~~~~~~qr~GR~gR~~~--   74 (135)
                      .|++|||+|++++|..+++.|++|.++|||||+++++|+|+|..++||.       ++.|.+..+|+||+|||||.|.  
T Consensus        96 GIa~hh~~l~~~~r~~ie~~f~~g~i~vlvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~q~~GRAGR~g~~~  175 (201)
T d2p6ra4          96 GAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDE  175 (201)
T ss_dssp             TCCEECTTSCHHHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCS
T ss_pred             cHHHHHHHhhhhhHHHHHHHHhCCCceEEEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHHHHhcccCCCCCCC
Confidence            4788999999999999999999999999999999999999999999985       6778899999999999999874  


Q ss_pred             CceEEEEeecCCh
Q 037139           75 TGVATTFLTFHDT   87 (135)
Q Consensus        75 ~g~~~~~~~~~~~   87 (135)
                      .|.+++++...+.
T Consensus       176 ~G~~~l~~~~~~~  188 (201)
T d2p6ra4         176 RGEAIIIVGKRDR  188 (201)
T ss_dssp             CEEEEEECCGGGH
T ss_pred             eeEEEEEeCCCCh
Confidence            6788887766544

>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=99.84  E-value=2.2e-21  Score=139.03  Aligned_cols=86  Identities=33%  Similarity=0.518  Sum_probs=74.0

Q ss_pred             CceEEEecC--------CCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCC
Q 037139            2 GYRVTTLHG--------GKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAG   73 (135)
Q Consensus         2 g~~v~~~hg--------~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~   73 (135)
                      |+++..+||        +|+..+|..++++|++|+++|||||+++++|+|+|+|++||+||+|+++..|+||+||+||.+
T Consensus       185 ~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv~T~~~~~Gld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR~~  264 (286)
T d1wp9a2         185 GIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHM  264 (286)
T ss_dssp             TCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCC
T ss_pred             CCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEEEccceeccccCCCCCEEEEeCCCCCHHHHHHHHHhCCCCC
Confidence            455566654        677889999999999999999999999999999999999999999999999999999999975


Q ss_pred             CCceEEEEeecCChh
Q 037139           74 KTGVATTFLTFHDTD   88 (135)
Q Consensus        74 ~~g~~~~~~~~~~~~   88 (135)
                       .|.++.++.....+
T Consensus       265 -~~~~~~l~~~~~~e  278 (286)
T d1wp9a2         265 -PGRVIILMAKGTRD  278 (286)
T ss_dssp             -CSEEEEEEETTSHH
T ss_pred             -CCEEEEEEeCCCHH
Confidence             68888888877553

>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=99.83  E-value=2.2e-20  Score=127.83  Aligned_cols=84  Identities=26%  Similarity=0.384  Sum_probs=79.3

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCC-CHHHHHHHhhhcCCCCCCceEEE
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPG-NIEMYTHRIGRTGRAGKTGVATT   80 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~-~~~~~~qr~GR~gR~~~~g~~~~   80 (135)
                      ++++.++||.|+++++++++.+|.+|+++|||||++++.|+|+|+++++|..+... ..+++.|..||+||.+..++|++
T Consensus        57 ~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~TtvIEvGiDvpnA~~iiI~~a~rfGLaQLhQLRGRVGR~~~~s~c~l  136 (211)
T d2eyqa5          57 EARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWL  136 (211)
T ss_dssp             TSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEE
T ss_pred             ceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehhhhhccCCCCCcEEEEecchhccccccccccceeeecCccceEEE
Confidence            46899999999999999999999999999999999999999999999999999885 89999999999999999999999


Q ss_pred             EeecC
Q 037139           81 FLTFH   85 (135)
Q Consensus        81 ~~~~~   85 (135)
                      ++...
T Consensus       137 ~~~~~  141 (211)
T d2eyqa5         137 LTPHP  141 (211)
T ss_dssp             EECCG
T ss_pred             EecCC
Confidence            98653

>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=99.82  E-value=5.2e-21  Score=123.95  Aligned_cols=76  Identities=33%  Similarity=0.429  Sum_probs=66.9

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEec----CCCCHHHHHHHhhhcCCCCCCc
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYD----MPGNIEMYTHRIGRTGRAGKTG   76 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d----~p~~~~~~~qr~GR~gR~~~~g   76 (135)
                      +|+.+..+|++|+.+       .|++|+.++||||+++++|+| |++++||++|    +|.+..+|+||+||+|| |++|
T Consensus        58 ~G~~~~~~H~~~~~~-------~~~~~~~~vlvaTd~~~~GiD-~~v~~Vi~~~~~~~~P~~~~~y~qr~GR~gR-g~~G  128 (138)
T d1jr6a_          58 LGINAVAYYRGLDVS-------VIPTNGDVVVVATDALMTGFT-GDFDSVIDCNTSDGKPQDAVSRTQRRGRTGR-GKPG  128 (138)
T ss_dssp             HTCEEEEECTTCCSC-------CCTTSSCEEEEESSSSCSSSC-CCBSEEEECSEETTEECCHHHHHHHHTTBCS-SSCE
T ss_pred             cccchhhhhccchhh-------hhhhhhcceeehhHHHHhccc-cccceEEEEEecCCCCCCHHHHHhHhccccC-CCCc
Confidence            378899999999855       478899999999999999999 9999999855    69999999999999999 8898


Q ss_pred             eEEEEeecCC
Q 037139           77 VATTFLTFHD   86 (135)
Q Consensus        77 ~~~~~~~~~~   86 (135)
                      . +.|+.+.+
T Consensus       129 ~-~~~i~~~e  137 (138)
T d1jr6a_         129 I-YRFVAPGE  137 (138)
T ss_dssp             E-EEECCSSC
T ss_pred             E-EEEEcCCC
Confidence            4 66777654

>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=99.79  E-value=2.6e-20  Score=127.20  Aligned_cols=81  Identities=32%  Similarity=0.518  Sum_probs=72.6

Q ss_pred             eEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCC---ceEEE
Q 037139            4 RVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKT---GVATT   80 (135)
Q Consensus         4 ~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~---g~~~~   80 (135)
                      .+..+||+++.++|+.++++|++|+++|||||+++++|+|+|.+++||++|+|+++..|+||+||++|.++.   ..++.
T Consensus       114 ~~~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~~~~~Gidl~~~~~vi~~~~~~s~~~~~Q~iGR~~R~~~~k~~~~i~~  193 (200)
T d2fwra1         114 LIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYE  193 (200)
T ss_dssp             TCCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEE
T ss_pred             CcceeeCCCCHHHHHHHHHHhhcCCeeeeeecchhhcccCCCCCCEEEEeCCCCCHHHHHHHHHhcCCCCCCCcEEEEEE
Confidence            455689999999999999999999999999999999999999999999999999999999999999998753   34555


Q ss_pred             Eeec
Q 037139           81 FLTF   84 (135)
Q Consensus        81 ~~~~   84 (135)
                      |+..
T Consensus       194 ~v~~  197 (200)
T d2fwra1         194 LISR  197 (200)
T ss_dssp             EEEC
T ss_pred             EecC
Confidence            5544

>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=99.72  E-value=3.2e-21  Score=135.82  Aligned_cols=79  Identities=16%  Similarity=0.265  Sum_probs=68.0

Q ss_pred             ecCCCCHHHHHHHHHHHhcCCCcEEEec----CCCcccccccC-CcEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEEe
Q 037139            8 LHGGKSQEQREISLEGFRTKRYNVLVAT----DVAGRGIDIPD-VAHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFL   82 (135)
Q Consensus         8 ~hg~~~~~~r~~~~~~f~~g~~~ilv~T----~~~~~G~d~~~-v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~~   82 (135)
                      +||+|++.+|.+++++|++|+++|||||    +++++|+|+|+ |++||+||+|+    |.||+||+||.|..+.+++++
T Consensus        49 ~hg~~~~~~R~~~~~~f~~g~~~vLVaT~a~~~v~~rGlDip~~v~~VI~~d~P~----~~~r~gR~~R~g~~~~~~~~~  124 (248)
T d1gkub2          49 FRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLLAY  124 (248)
T ss_dssp             SCEEECTTSSSHHHHHHHHTSCSEEEEECC------CCSCCTTTCCEEEEESCCE----EEEECSCGGGSCHHHHHHHHT
T ss_pred             ccCCCCHHHHHHHHHHHHhCCCeEEEEeccccchhhhccCccccccEEEEeCCCc----chhhhhhhhccCcceEeeeec
Confidence            7999999999999999999999999999    78999999996 99999999996    889999999999888888777


Q ss_pred             ecCChhHH
Q 037139           83 TFHDTDVF   90 (135)
Q Consensus        83 ~~~~~~~~   90 (135)
                      ...+....
T Consensus       125 ~~~~~~~~  132 (248)
T d1gkub2         125 LYRNVDEI  132 (248)
T ss_dssp             TTSCHHHH
T ss_pred             cHhhHHHH
Confidence            76655443

>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=99.66  E-value=1.3e-17  Score=118.85  Aligned_cols=82  Identities=20%  Similarity=0.238  Sum_probs=69.0

Q ss_pred             CCceEEEecCCCCHHHH----------HHHHHHHhcCCCcEEEecCCCcc---cccccCCcEEEEecCCCCHHHHHHHhh
Q 037139            1 LGYRVTTLHGGKSQEQR----------EISLEGFRTKRYNVLVATDVAGR---GIDIPDVAHVINYDMPGNIEMYTHRIG   67 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r----------~~~~~~f~~g~~~ilv~T~~~~~---G~d~~~v~~vi~~d~p~~~~~~~qr~G   67 (135)
                      .|+++..+|++|+++.|          ..+++.|..|+.+++|+|+++.+   |+|++.+..|+++|.|.+.++|+||+|
T Consensus        59 ~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~g~~giDid~V~~VI~~d~P~SvesyIQRiG  138 (299)
T d1a1va2          59 LGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRG  138 (299)
T ss_dssp             TTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEEEEEECCCSSSCEEEEEEEECBHHHHHHHHT
T ss_pred             CCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhccCCCCCCCcceEEEeCCCCCCHHHHHhhcc
Confidence            47889999999999887          56889999999999999999888   567777889999999999999999999


Q ss_pred             hcCCCCCCceEEEEee
Q 037139           68 RTGRAGKTGVATTFLT   83 (135)
Q Consensus        68 R~gR~~~~g~~~~~~~   83 (135)
                      |+|| |++|....+..
T Consensus       139 RTGR-Gr~G~~~~l~~  153 (299)
T d1a1va2         139 RTGR-GKPGIYRFVAP  153 (299)
T ss_dssp             TBCS-SSCEEEEESCS
T ss_pred             ccCC-CCCceEEEEec
Confidence            9999 88886654443

>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=99.48  E-value=1.9e-13  Score=99.98  Aligned_cols=84  Identities=18%  Similarity=0.265  Sum_probs=73.4

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCc---EEEecCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCCc--
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYN---VLVATDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKTG--   76 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~---ilv~T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~g--   76 (135)
                      |+.+..++|+++.++|..+++.|+++...   +|++|.+++.|+|++.++.||+||++|++..+.|++||+.|.|+..  
T Consensus       142 g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~vlLls~~agg~GlnL~~a~~vi~~d~~wnp~~~~Qa~~R~~R~GQ~~~V  221 (346)
T d1z3ix1         142 RYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTC  221 (346)
T ss_dssp             TCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCE
T ss_pred             hccccccccchhHHHHHHHHHhhhcccccceeeeecchhhhhccccccceEEEEecCCCccchHhHhhhcccccCCCCce
Confidence            67888999999999999999999987543   5678899999999999999999999999999999999999998754  


Q ss_pred             eEEEEeecC
Q 037139           77 VATTFLTFH   85 (135)
Q Consensus        77 ~~~~~~~~~   85 (135)
                      .++.++..+
T Consensus       222 ~v~rli~~~  230 (346)
T d1z3ix1         222 YIYRLLSTG  230 (346)
T ss_dssp             EEEEEEETT
T ss_pred             EEEEEEeCC
Confidence            445555554

>d1z5za1 c.37.1.19 (A:663-906) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.43  E-value=1.3e-13  Score=96.09  Aligned_cols=85  Identities=21%  Similarity=0.310  Sum_probs=60.7

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCC-CcEEEe-cCCCcccccccCCcEEEEecCCCCHHHHHHHhhhcCCCCCC--ce
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKR-YNVLVA-TDVAGRGIDIPDVAHVINYDMPGNIEMYTHRIGRTGRAGKT--GV   77 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~-~~ilv~-T~~~~~G~d~~~v~~vi~~d~p~~~~~~~qr~GR~gR~~~~--g~   77 (135)
                      |..+..+||+++.++|..+++.|+++. ..++++ |.+.+.|+|++.+++||++|+||++..+.|+.||+.|.|+.  ..
T Consensus       110 ~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vll~~~~~~g~Glnl~~a~~vi~~~~~wn~~~~~Qa~~R~~R~Gq~~~v~  189 (244)
T d1z5za1         110 NTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVI  189 (244)
T ss_dssp             CSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCTTCCCCCCTTCSEEEECSCCSCTTTC--------------CCE
T ss_pred             cceEEEEecccchhccchhhhhhhccccchhccccccccccccccchhhhhhhcCchhhhHHHhhhcceeeecCCCCceE
Confidence            567778999999999999999998764 677755 57899999999999999999999999999999999998854  45


Q ss_pred             EEEEeecCC
Q 037139           78 ATTFLTFHD   86 (135)
Q Consensus        78 ~~~~~~~~~   86 (135)
                      ++.++..+.
T Consensus       190 i~~l~~~~T  198 (244)
T d1z5za1         190 VHKLISVGT  198 (244)
T ss_dssp             EEEEEETTS
T ss_pred             EEEEeeCCC
Confidence            555666553

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=99.33  E-value=9.1e-13  Score=93.50  Aligned_cols=78  Identities=26%  Similarity=0.313  Sum_probs=61.6

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEE----------Eec----------CCCCHHH
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVI----------NYD----------MPGNIEM   61 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi----------~~d----------~p~~~~~   61 (135)
                      |+.+..+||+++++.    ...|++|..+++|+|+++++|+|++ ++.||          ++|          .|.|..+
T Consensus       202 ~~~~~~l~~~~~~~~----~~~~~~~~~~~lvaT~~~~~G~~~~-~~~Vi~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~  276 (305)
T d2bmfa2         202 GKKVIQLSRKTFDSE----YIKTRTNDWDFVVTTDISEMGANFK-AERVIDPRRCMKPVILTDGEERVILAGPMPVTHSS  276 (305)
T ss_dssp             TCCCEECCTTCHHHH----GGGGGTSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHH
T ss_pred             CCCEEEeCCcChHHH----HhhhhccchhhhhhhHHHHhcCCCC-ccEEEEcCCceeeeEecCCCCceEEeccccCCHHH
Confidence            677889999986554    4468999999999999999999995 44443          333          4568999


Q ss_pred             HHHHhhhcCCCCCCceEEEEeec
Q 037139           62 YTHRIGRTGRAGKTGVATTFLTF   84 (135)
Q Consensus        62 ~~qr~GR~gR~~~~g~~~~~~~~   84 (135)
                      |+||+||+||.|+.+....++..
T Consensus       277 ~~Qr~GR~GR~~~~~~~~~~~~~  299 (305)
T d2bmfa2         277 AAQRRGRVGRNPKNENDQYIYMG  299 (305)
T ss_dssp             HHHHHTTSSCSSSCCCEEEEECS
T ss_pred             HhhhhcCcCcCCCCceEEEEECC
Confidence            99999999999987766666554

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=99.32  E-value=2e-12  Score=92.55  Aligned_cols=78  Identities=21%  Similarity=0.304  Sum_probs=57.4

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccCCcEEEEecC-------------------CCCHHH
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPDVAHVINYDM-------------------PGNIEM   61 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~v~~vi~~d~-------------------p~~~~~   61 (135)
                      .|++|.++||.+..++++    +|++++.+|||||++++.|+|+ ++.+||+.+.                   |.+..+
T Consensus        59 ~g~~V~~l~~~~~~~e~~----~~~~~~~~~~~~t~~~~~~~~~-~~~~vid~g~~~~~~~~~~~~~~~~~~~~~~~~~~  133 (299)
T d1yksa2          59 AGKSVVVLNRKTFEREYP----TIKQKKPDFILATDIAEMGANL-CVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASS  133 (299)
T ss_dssp             TTCCEEECCSSSCC------------CCCSEEEESSSTTCCTTC-CCSEEEECCEEEEEEEETTTTEEEEEEEEECCHHH
T ss_pred             cCCeEEEEcCcCcHhHHh----hhhcCCcCEEEEechhhhceec-CceEEEecCceeceeeecCCCCeeEEeeeecCHHH
Confidence            378899999999988765    4788999999999999999999 5998885442                   347888


Q ss_pred             HHHHhhhcCCCCCCceEEEEee
Q 037139           62 YTHRIGRTGRAGKTGVATTFLT   83 (135)
Q Consensus        62 ~~qr~GR~gR~~~~g~~~~~~~   83 (135)
                      ..||.||+||.+..+.++.++.
T Consensus       134 ~~qr~gr~gr~~~~~~~~~~y~  155 (299)
T d1yksa2         134 AAQRRGRIGRNPNRDGDSYYYS  155 (299)
T ss_dssp             HHHHHTTSSCCTTCCCEEEEEC
T ss_pred             HHHhcccccccCCCceEEEEeC
Confidence            9999999999865544555544

>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=98.82  E-value=1.2e-08  Score=67.02  Aligned_cols=84  Identities=27%  Similarity=0.424  Sum_probs=64.0

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCcccccccC---C-----cEEEEecCCCCHHHHHHHhhhcCCCC
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAGRGIDIPD---V-----AHVINYDMPGNIEMYTHRIGRTGRAG   73 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~~G~d~~~---v-----~~vi~~d~p~~~~~~~qr~GR~gR~~   73 (135)
                      |++..++++....++-+-+-+.-+  .-.|.|+|+++++|.|+.-   |     -+||....|.+.....|..||+||.|
T Consensus        58 gi~h~vLnAk~~~~Ea~II~~Ag~--~g~VtIATNmAGRGtDikl~~~v~~~GGLhVI~t~~~~s~Rid~Ql~GR~gRQG  135 (175)
T d1tf5a4          58 GIPHQVLNAKNHEREAQIIEEAGQ--KGAVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQG  135 (175)
T ss_dssp             TCCCEEECSSCHHHHHHHHTTTTS--TTCEEEEETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGG
T ss_pred             CCCceeehhhhHHHHHHHHHhccC--CCceeehhhHHHcCCCccchHHHHhCCCcEEEEeccCcchhHHHHHhcchhhhC
Confidence            566677887764444333333222  3368999999999999842   2     27899999999999999999999999


Q ss_pred             CCceEEEEeecCCh
Q 037139           74 KTGVATTFLTFHDT   87 (135)
Q Consensus        74 ~~g~~~~~~~~~~~   87 (135)
                      .+|....+++-+|.
T Consensus       136 dpGs~~~~~sleD~  149 (175)
T d1tf5a4         136 DPGITQFYLSMEDE  149 (175)
T ss_dssp             CCEEEEEEEETTSS
T ss_pred             CCcccEEEEEcCHH
Confidence            99999988876653

>d1nkta4 c.37.1.19 (A:397-615) Translocation ATPase SecA, nucleotide-binding domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.87  E-value=1.7e-05  Score=53.11  Aligned_cols=83  Identities=27%  Similarity=0.358  Sum_probs=60.8

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCC-CcEEEecCCCcccccccC----------------------------------
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKR-YNVLVATDVAGRGIDIPD----------------------------------   46 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~-~~ilv~T~~~~~G~d~~~----------------------------------   46 (135)
                      |++..++++..-.++ .+++.  +.|. -.|-|+|+++++|.|+.=                                  
T Consensus        58 gi~h~vLNAK~herE-AeIIA--qAG~~GaVTIATNMAGRGTDI~LGgn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  134 (219)
T d1nkta4          58 RIPHNVLNAKYHEQE-ATIIA--VAGRRGGVTVATNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSEL  134 (219)
T ss_dssp             TCCCEEECSSCHHHH-HHHHH--TTTSTTCEEEEETTCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHH
T ss_pred             ccchhccchhhHHHH-HHHHH--hcccCCcEEeeccccCCCCceeecCchhhhhHHHhhhcccCcccCHHHHHHHHHHHH
Confidence            566677887643322 22222  2333 358899999999999921                                  


Q ss_pred             -------------C-----cEEEEecCCCCHHHHHHHhhhcCCCCCCceEEEEeecCCh
Q 037139           47 -------------V-----AHVINYDMPGNIEMYTHRIGRTGRAGKTGVATTFLTFHDT   87 (135)
Q Consensus        47 -------------v-----~~vi~~d~p~~~~~~~qr~GR~gR~~~~g~~~~~~~~~~~   87 (135)
                                   |     =+||-.....|..-=.|..||+||.|.+|....|++-.|.
T Consensus       135 ~~~~~~~~~~~~~V~~~GGL~VIGTErHeSrRIDnQLRGRsGRQGDPGsSrFflSLeDd  193 (219)
T d1nkta4         135 PIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGDE  193 (219)
T ss_dssp             HHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTSH
T ss_pred             HHHHHHHHHHHHHHHhcCCcEEEeccccccccccccccccccccCCCccceeEEeccHH
Confidence                         1     1577888888888889999999999999999999887665

>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=97.69  E-value=2.7e-05  Score=54.00  Aligned_cols=65  Identities=17%  Similarity=0.223  Sum_probs=49.3

Q ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCc-ccccccCCcEEEEecCCCCHHHHHHHhh
Q 037139            1 LGYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAG-RGIDIPDVAHVINYDMPGNIEMYTHRIG   67 (135)
Q Consensus         1 ~g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~-~G~d~~~v~~vi~~d~p~~~~~~~qr~G   67 (135)
                      +|+.+..+||+++..+|.+++.++++|+++|+|+|-.+- ..+.+.++.+||.-.--.  -.|.||..
T Consensus       159 ~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~~~~f~~LglviiDEqH~--fgv~Qr~~  224 (264)
T d1gm5a3         159 FNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVIIDEQHR--FGVKQREA  224 (264)
T ss_dssp             SSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEEEESCCC--C-----CC
T ss_pred             ccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcCCCCccccceeeeccccc--cchhhHHH
Confidence            377899999999999999999999999999999997654 468888999888655332  24667643

>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=97.02  E-value=0.00048  Score=46.69  Aligned_cols=64  Identities=13%  Similarity=0.121  Sum_probs=50.7

Q ss_pred             CceEEEecCCCCHHHHHHHHHHHhcCCCcEEEecCCCc-ccccccCCcEEEEecCCCCHHHHHHHhh
Q 037139            2 GYRVTTLHGGKSQEQREISLEGFRTKRYNVLVATDVAG-RGIDIPDVAHVINYDMPGNIEMYTHRIG   67 (135)
Q Consensus         2 g~~v~~~hg~~~~~~r~~~~~~f~~g~~~ilv~T~~~~-~G~d~~~v~~vi~~d~p~~~~~~~qr~G   67 (135)
                      |..+..+||.++..+|.++++.+.+|+++|+|+|-.+. ..+.+++..+||.-.--.  ..|.|+.+
T Consensus       132 ~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~~~~~f~~LgLiIiDEeH~--fg~kQ~~~  196 (233)
T d2eyqa3         132 PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIVDEEHR--FGVRHKER  196 (233)
T ss_dssp             TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEEEEESGGG--SCHHHHHH
T ss_pred             CCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhccCCccccccceeeechhh--hhhHHHHH
Confidence            57889999999999999999999999999999997554 468888988887654332  23455543