Psyllid ID: psy17637

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150
Protein Sequence
RAGNKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGELRSQ
Secondary Structure (PSIPRED)
ccccccEEEEEEEcccHHHHHHHHHHHHHcccccccEEEEEcccccHHHHHHHHHHcccccccccccccHHHHHHHHHHHHcccccEEEEEEccccccccccccEEEEccccccccccccccccccccccccEEEEEEccccccHHHccc
Secondary Structure Prediction (SSPRO)
ccccccEEEEEEEEccHHHHHHHHHHHHHHccccccEEEEEccHHHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHcccccEEEEHHHHHccccccccEEEEEEcccccHHHHEEEccccccccccEEEEEEEccccHHHHHccc
Coil and Loop (DISEMBL)
ragnkgvaYTLVTDKDKEFAGHLVRNleganqevpPALMNLAMQLNAEELANSLTVKEYDVLLLhgdmdqsernsvITKFKRQECRILVATDVaargldiphirtVVNYDlardidththrigrtgragnkgvAYTLVtdkdkdgelrsq
Flexible Loop (DISEMBL)
ragnkgvaytlvtdkdkeFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHgdmdqsernsvitkfkrqecRILVAtdvaargldiphirTVVNYDlardidththrigrtgragnkgvaytlvtdkdkdgelrsq
Low Complexity Region (SEG)
RAGNKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGELRSQ
Disordered region (IsUnstruct)
******VAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLV************
Disordered Region (DISOPRED)
**GNKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK*G***S*
Disordered Region (DISEMBL)
RAGNKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD********
Disordered Region (DISPRO)
****KGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
RAGNKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGELRSQ
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	150	2.2.26 [Sep-21-2011]
Q5F485	944	ATP-dependent RNA helicas	yes	N/A	0.713	0.113	0.691	1e-36
Q5R7D1	942	ATP-dependent RNA helicas	yes	N/A	0.713	0.113	0.682	3e-36
Q86XP3	938	ATP-dependent RNA helicas	yes	N/A	0.713	0.114	0.682	3e-36
Q810A7	929	ATP-dependent RNA helicas	yes	N/A	0.713	0.115	0.672	1e-35
Q7ZY47	947	ATP-dependent RNA helicas	N/A	N/A	0.713	0.112	0.672	2e-34
Q54IV3	986	Probable ATP-dependent RN	yes	N/A	0.7	0.106	0.571	2e-28
O22907	760	DEAD-box ATP-dependent RN	yes	N/A	0.866	0.171	0.469	6e-25
Q10MH8	770	DEAD-box ATP-dependent RN	yes	N/A	0.7	0.136	0.509	2e-23
Q5VQL1	708	DEAD-box ATP-dependent RN	no	N/A	0.626	0.132	0.547	6e-23
Q5JKF2	792	DEAD-box ATP-dependent RN	no	N/A	0.633	0.119	0.531	2e-22

>sp|Q5F485|DDX42_CHICK ATP-dependent RNA helicase DDX42 OS=Gallus gallus GN=DDX42 PE=2 SV=1

 Score =  152 bits (383), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 74/107 (69%), Positives = 92/107 (85%)

Query: 38  LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
           L+ +  + NAEELAN+L  +++++ LLHGDMDQSERN VI++FK++   ILVATDVAARG
Sbjct: 502 LLFVTKKANAEELANNLKQEDHNLGLLHGDMDQSERNKVISEFKKKGIPILVATDVAARG 561

Query: 98  LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           LDIP I+TV+NYD+ARDIDTHTHRIGRTGRAG KGVAYTL+T KD +
Sbjct: 562 LDIPSIKTVINYDVARDIDTHTHRIGRTGRAGEKGVAYTLLTPKDSN 608

ATP-dependent RNA helicase. Binds to RNA. May be involved in the survival of cells.
Gallus gallus (taxid: 9031)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q5R7D1|DDX42_PONAB ATP-dependent RNA helicase DDX42 OS=Pongo abelii GN=DDX42 PE=2 SV=1

 Score =  150 bits (378), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 73/107 (68%), Positives = 91/107 (85%)

Query: 38  LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
           L+ +  + NAEELAN+L  + +++ LLHGDMDQSERN VI+ FK+++  +LVATDVAARG
Sbjct: 502 LLFVTKKANAEELANNLKQEGHNLGLLHGDMDQSERNKVISDFKKKDIPVLVATDVAARG 561

Query: 98  LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           LDIP I+TV+NYD+ARDIDTHTHRIGRTGRAG KGVAYTL+T KD +
Sbjct: 562 LDIPSIKTVINYDVARDIDTHTHRIGRTGRAGEKGVAYTLLTPKDSN 608

ATP-dependent RNA helicase. Binds to partially double-stranded RNAs (dsRNAs) in order to unwind RNA secondary structures. Unwinding is promoted in the presence of single-strand binding proteins. Mediates also RNA duplex formation thereby displacing the single-strand RNA binding protein. ATP and ADP modulate its activity: ATP binding and hydrolysis by DDX42 triggers RNA strand separation, whereas the ADP-bound form of the protein triggers annealing of complementary RNA strands. Involved in the survival of cells by interacting with TP53BP2 and thereby counteracting the apoptosis-stimulating activity of TP53BP2. Relocalizes TP53BP2 to the cytoplasm.

Pongo abelii (taxid: 9601)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q86XP3|DDX42_HUMAN ATP-dependent RNA helicase DDX42 OS=Homo sapiens GN=DDX42 PE=1 SV=1

 Score =  150 bits (378), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 73/107 (68%), Positives = 91/107 (85%)

Query: 38  LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
           L+ +  + NAEELAN+L  + +++ LLHGDMDQSERN VI+ FK+++  +LVATDVAARG
Sbjct: 502 LLFVTKKANAEELANNLKQEGHNLGLLHGDMDQSERNKVISDFKKKDIPVLVATDVAARG 561

Query: 98  LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           LDIP I+TV+NYD+ARDIDTHTHRIGRTGRAG KGVAYTL+T KD +
Sbjct: 562 LDIPSIKTVINYDVARDIDTHTHRIGRTGRAGEKGVAYTLLTPKDSN 608

ATP-dependent RNA helicase. Binds to partially double-stranded RNAs (dsRNAs) in order to unwind RNA secondary structures. Unwinding is promoted in the presence of single-strand binding proteins. Mediates also RNA duplex formation thereby displacing the single-strand RNA binding protein. ATP and ADP modulate its activity: ATP binding and hydrolysis by DDX42 triggers RNA strand separation, whereas the ADP-bound form of the protein triggers annealing of complementary RNA strands. Involved in the survival of cells by interacting with TP53BP2 and thereby counteracting the apoptosis-stimulating activity of TP53BP2. Relocalizes TP53BP2 to the cytoplasm.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q810A7|DDX42_MOUSE ATP-dependent RNA helicase DDX42 OS=Mus musculus GN=Ddx42 PE=1 SV=3

 Score =  148 bits (373), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 72/107 (67%), Positives = 91/107 (85%)

Query: 38  LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
           L+ +  + NAEELA++L  + +++ LLHGDMDQSERN VI+ FK+++  +LVATDVAARG
Sbjct: 502 LLFVTKKANAEELASNLKQEGHNLGLLHGDMDQSERNKVISDFKKKDIPVLVATDVAARG 561

Query: 98  LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           LDIP I+TV+NYD+ARDIDTHTHRIGRTGRAG KGVAYTL+T KD +
Sbjct: 562 LDIPSIKTVINYDVARDIDTHTHRIGRTGRAGEKGVAYTLLTPKDSN 608

ATP-dependent RNA helicase. Binds to partially double-stranded RNAs (dsRNAs) in order to unwind RNA secondary structures. Unwinding is promoted in the presence of single-strand binding proteins. Mediates also RNA duplex formation thereby displacing the single-strand RNA binding protein. ATP and ADP modulate its activity: ATP binding and hydrolysis by DDX42 triggers RNA strand separation, whereas the ADP-bound form of the protein triggers annealing of complementary RNA strands. Involved in the survival of cells by interacting with TP53BP2 and thereby counteracting the apoptosis-stimulating activity of TP53BP2. Relocalizes TP53BP2 to the cytoplasm.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q7ZY47|DDX42_XENLA ATP-dependent RNA helicase DDX42 OS=Xenopus laevis GN=ddx42 PE=2 SV=1

 Score =  144 bits (362), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 72/107 (67%), Positives = 88/107 (82%)

Query: 38  LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
           L+ +  + NAEELA +L   ++ + LLHGDMDQSERN VI+ FK++   +LVATDVAARG
Sbjct: 499 LVFVTKKANAEELAANLRQDDHPLGLLHGDMDQSERNKVISDFKKKSIPVLVATDVAARG 558

Query: 98  LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           LDIP I+TVVNYD+ARDIDTHTHRIGRTGRAG KGVAYTL+T K+ +
Sbjct: 559 LDIPSIKTVVNYDVARDIDTHTHRIGRTGRAGEKGVAYTLLTSKESN 605

ATP-dependent RNA helicase. Binds to RNA. May be involved in the survival of cells.

Xenopus laevis (taxid: 8355)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q54IV3|DDX42_DICDI Probable ATP-dependent RNA helicase ddx42 OS=Dictyostelium discoideum GN=ddx42 PE=3 SV=1

 Score =  124 bits (310), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 60/105 (57%), Positives = 79/105 (75%)

Query: 38  LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
           L+ ++ ++  E+L+++LT   +    LHGD +Q ER+  I  FK  +  IL+ATDVAARG
Sbjct: 554 LIFVSTKVAVEQLSSNLTKFGFQTCTLHGDKNQIERSQTIQTFKEGKINILIATDVAARG 613

Query: 98  LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
           LDIP I+ VVNYD +RDI++HTHRIGRTGRAGN GVAYTL+T KD
Sbjct: 614 LDIPLIKNVVNYDTSRDIESHTHRIGRTGRAGNTGVAYTLITPKD 658

probable ATP-dependent RNA helicase which may bind to partially double-stranded RNAs (dsRNAs) in order to unwind RNA secondary structures.

Dictyostelium discoideum (taxid: 44689)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|O22907|RH24_ARATH DEAD-box ATP-dependent RNA helicase 24 OS=Arabidopsis thaliana GN=RH24 PE=1 SV=2

 Score =  112 bits (281), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 62/132 (46%), Positives = 83/132 (62%), Gaps = 2/132 (1%)

Query: 12  VTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQS 71
           V   D E    L+  L G   E    L+  + +   +E+   LT+  + V  LHGD DQ+
Sbjct: 452 VIPSDAEKLPWLLEKLPGMIDEGD-VLVFASKKATVDEIEAQLTLNSFKVAALHGDKDQA 510

Query: 72  ERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNK 131
            R   + KFK     +L+ATDVAARGLDI  ++TVVNYD+A+D+D H HRIGRTGRAG++
Sbjct: 511 SRMETLQKFKSGVHHVLIATDVAARGLDIKSLKTVVNYDIAKDMDMHVHRIGRTGRAGDR 570

Query: 132 -GVAYTLVTDKD 142
            GVAYTLVT ++
Sbjct: 571 DGVAYTLVTQRE 582

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q10MH8|RH24_ORYSJ DEAD-box ATP-dependent RNA helicase 24 OS=Oryza sativa subsp. japonica GN=Os03g0308500 PE=2 SV=1

 Score =  107 bits (267), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 54/106 (50%), Positives = 74/106 (69%), Gaps = 1/106 (0%)

Query: 38  LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
           L+  A +   +E+ + L  + + +  LHGD DQ+ R   + KFK     +LVATDVAARG
Sbjct: 468 LVFAAKKARVDEIESQLNQRGFRIAALHGDKDQASRMETLQKFKSGVYHVLVATDVAARG 527

Query: 98  LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNK-GVAYTLVTDKD 142
           LDI  I+TVVN+D+A+++D H HRIGRTGRAG+K G AYTL+T K+
Sbjct: 528 LDIKSIKTVVNFDIAKEMDMHIHRIGRTGRAGDKDGTAYTLITQKE 573

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5VQL1|RH14_ORYSJ DEAD-box ATP-dependent RNA helicase 14 OS=Oryza sativa subsp. japonica GN=Os01g0172200 PE=2 SV=1

 Score =  106 bits (264), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 52/95 (54%), Positives = 68/95 (71%), Gaps = 1/95 (1%)

Query: 48  EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
           ++LA +L  ++Y    +HGD  Q+ER+SV+++F+   C ILVATDVAARGLDI  IR VV
Sbjct: 439 DQLARNLA-RQYGASAIHGDKSQAERDSVLSEFRSGRCPILVATDVAARGLDIKDIRVVV 497

Query: 108 NYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
           NYD    ++ + HRIGRTGRAG  GVAYT   D+D
Sbjct: 498 NYDFPTGVEDYVHRIGRTGRAGATGVAYTFFCDQD 532

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

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5JKF2|RH40_ORYSJ DEAD-box ATP-dependent RNA helicase 40 OS=Oryza sativa subsp. japonica GN=Os01g0549400 PE=2 SV=2

 Score =  104 bits (259), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 51/96 (53%), Positives = 65/96 (67%), Gaps = 1/96 (1%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
            ++LA +LT +++    +HGD  QSER  V++ F+     ILVATDVAARGLDI  IR V
Sbjct: 408 CDQLARTLT-RQFGASAIHGDKSQSEREKVLSHFRSGRSPILVATDVAARGLDIKDIRVV 466

Query: 107 VNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
           +NYD    I+ + HRIGRTGRAG  GVAYT   D+D
Sbjct: 467 INYDFPTGIEDYVHRIGRTGRAGATGVAYTFFCDQD 502

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

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

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	150
195127173	797	GI12051 [Drosophila mojavensis] gi|19391	0.78	0.146	0.717	2e-42
340723638	774	PREDICTED: ATP-dependent RNA helicase DD	0.713	0.138	0.775	4e-42
350426308	774	PREDICTED: ATP-dependent RNA helicase DD	0.713	0.138	0.775	4e-42
380022612	772	PREDICTED: LOW QUALITY PROTEIN: ATP-depe	0.713	0.138	0.775	4e-42
66522071	772	PREDICTED: ATP-dependent RNA helicase DD	0.713	0.138	0.775	5e-42
383857449	774	PREDICTED: ATP-dependent RNA helicase DD	0.713	0.138	0.785	7e-42
270012072	702	hypothetical protein TcasGA2_TC006173 [T	0.713	0.152	0.728	1e-41
195376889	797	GJ13322 [Drosophila virilis] gi|19415438	0.78	0.146	0.709	1e-41
312373386	615	hypothetical protein AND_17503 [Anophele	0.713	0.173	0.766	1e-41
189239856	699	PREDICTED: similar to CG6418 CG6418-PB [	0.713	0.153	0.728	2e-41

>gi|195127173|ref|XP_002008043.1| GI12051 [Drosophila mojavensis] gi|193919652|gb|EDW18519.1| GI12051 [Drosophila mojavensis]

 Score =  176 bits (447), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 89/124 (71%), Positives = 103/124 (83%), Gaps = 7/124 (5%)

Query: 22  HLVRNL-EGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKF 80
           HLV+ L EGA       L+ +  + +AE +AN+L VKEY+ LLLHGDMDQ++RN VIT+F
Sbjct: 513 HLVKFLSEGA------VLVFVTKKADAETVANNLLVKEYNCLLLHGDMDQADRNKVITQF 566

Query: 81  KRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTD 140
           KR+EC ILVATDVAARGLDIPHIR VVNYD+ARDIDTHTHRIGRTGRAG KG AYTLVTD
Sbjct: 567 KRKECDILVATDVAARGLDIPHIRNVVNYDIARDIDTHTHRIGRTGRAGEKGNAYTLVTD 626

Query: 141 KDKD 144
           KDK+
Sbjct: 627 KDKE 630

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340723638|ref|XP_003400196.1| PREDICTED: ATP-dependent RNA helicase DDX42-like [Bombus terrestris]

 Score =  176 bits (445), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 83/107 (77%), Positives = 95/107 (88%)

Query: 38  LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
           L+ +  +LNAEELAN+L +KE+DV+LLHGDMDQ ERN VIT FK++E   LVATDVAARG
Sbjct: 505 LIFVTKKLNAEELANNLKLKEFDVMLLHGDMDQIERNKVITAFKKKEVTTLVATDVAARG 564

Query: 98  LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           LDIPHIRTVVNYD+ARDIDTHTHRIGRTGRAG KG AYTLVT+KDK+
Sbjct: 565 LDIPHIRTVVNYDVARDIDTHTHRIGRTGRAGEKGTAYTLVTEKDKE 611

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350426308|ref|XP_003494399.1| PREDICTED: ATP-dependent RNA helicase DDX42-like [Bombus impatiens]

 Score =  175 bits (444), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 83/107 (77%), Positives = 95/107 (88%)

Query: 38  LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
           L+ +  +LNAEELAN+L +KE+DV+LLHGDMDQ ERN VIT FK++E   LVATDVAARG
Sbjct: 505 LIFVTKKLNAEELANNLKLKEFDVMLLHGDMDQIERNKVITAFKKKEVTTLVATDVAARG 564

Query: 98  LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           LDIPHIRTVVNYD+ARDIDTHTHRIGRTGRAG KG AYTLVT+KDK+
Sbjct: 565 LDIPHIRTVVNYDVARDIDTHTHRIGRTGRAGEKGTAYTLVTEKDKE 611

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380022612|ref|XP_003695134.1| PREDICTED: LOW QUALITY PROTEIN: ATP-dependent RNA helicase DDX42-like [Apis florea]

 Score =  175 bits (444), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 83/107 (77%), Positives = 95/107 (88%)

Query: 38  LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
           L+ +  +LNAEELAN+L +KE+DVLLLHGDMDQ ERN VIT FK++E   LVATDVAARG
Sbjct: 505 LIFVTKKLNAEELANNLKLKEFDVLLLHGDMDQIERNKVITAFKKKEVSTLVATDVAARG 564

Query: 98  LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           LDIPHIRTV+NYD+ARDIDTHTHRIGRTGRAG KG AYTLVT+KDK+
Sbjct: 565 LDIPHIRTVLNYDVARDIDTHTHRIGRTGRAGEKGTAYTLVTEKDKE 611

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66522071|ref|XP_624210.1| PREDICTED: ATP-dependent RNA helicase DDX42-like [Apis mellifera]

 Score =  175 bits (444), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 83/107 (77%), Positives = 95/107 (88%)

Query: 38  LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
           L+ +  +LNAEELAN+L +KE+DVLLLHGDMDQ ERN VIT FK++E   LVATDVAARG
Sbjct: 505 LIFVTKKLNAEELANNLKLKEFDVLLLHGDMDQIERNKVITAFKKKEVSTLVATDVAARG 564

Query: 98  LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           LDIPHIRTV+NYD+ARDIDTHTHRIGRTGRAG KG AYTLVT+KDK+
Sbjct: 565 LDIPHIRTVLNYDVARDIDTHTHRIGRTGRAGEKGTAYTLVTEKDKE 611

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383857449|ref|XP_003704217.1| PREDICTED: ATP-dependent RNA helicase DDX42-like [Megachile rotundata]

 Score =  175 bits (443), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 84/107 (78%), Positives = 94/107 (87%)

Query: 38  LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
           L+ +  +LNAEELAN+L +KE DVLLLHGDMDQ ERN VIT FK++E   LVATDVAARG
Sbjct: 505 LIFVTKKLNAEELANNLKLKELDVLLLHGDMDQIERNKVITAFKKKEVSTLVATDVAARG 564

Query: 98  LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           LDIPHIRTVVNYD+ARDIDTHTHRIGRTGRAG KG AYTLVT+KDK+
Sbjct: 565 LDIPHIRTVVNYDIARDIDTHTHRIGRTGRAGEKGTAYTLVTEKDKE 611

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270012072|gb|EFA08520.1| hypothetical protein TcasGA2_TC006173 [Tribolium castaneum]

 Score =  174 bits (441), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 78/107 (72%), Positives = 96/107 (89%)

Query: 38  LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
           L+ +  +++AE+LAN L VKE++ LLLHGD++Q+ERN VIT FK++EC +LVATDVAARG
Sbjct: 480 LVFVTKKVDAEQLANDLKVKEFECLLLHGDIEQAERNKVITAFKKKECSLLVATDVAARG 539

Query: 98  LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           LDIPHIRTVVNYD+ARDIDTHTHRIGRTGRAGN+G AYTL+T KDK+
Sbjct: 540 LDIPHIRTVVNYDIARDIDTHTHRIGRTGRAGNQGTAYTLITPKDKE 586

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195376889|ref|XP_002047225.1| GJ13322 [Drosophila virilis] gi|194154383|gb|EDW69567.1| GJ13322 [Drosophila virilis]

 Score =  174 bits (441), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 88/124 (70%), Positives = 103/124 (83%), Gaps = 7/124 (5%)

Query: 22  HLVRNL-EGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKF 80
           HLV+ L EGA       L+ +  + +AE +AN+L VKE++ LLLHGDMDQ++RN VIT+F
Sbjct: 517 HLVKFLSEGA------VLVFVTKKADAETVANNLIVKEHNCLLLHGDMDQADRNKVITQF 570

Query: 81  KRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTD 140
           KR+EC ILVATDVAARGLDIPHIR VVNYD+ARDIDTHTHRIGRTGRAG KG AYTLVTD
Sbjct: 571 KRKECDILVATDVAARGLDIPHIRNVVNYDIARDIDTHTHRIGRTGRAGEKGNAYTLVTD 630

Query: 141 KDKD 144
           KDK+
Sbjct: 631 KDKE 634

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312373386|gb|EFR21141.1| hypothetical protein AND_17503 [Anopheles darlingi]

 Score =  174 bits (440), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 82/107 (76%), Positives = 97/107 (90%)

Query: 38  LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
           L+ +  + +AE++ANSL VKE +V+LLHGDMDQSERNSVIT+FKR+E  ++VATDVAARG
Sbjct: 340 LIFVTKKADAEQVANSLRVKENEVVLLHGDMDQSERNSVITRFKRREVDMMVATDVAARG 399

Query: 98  LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           LDIPHIRTVVNYD+ARDIDTHTHRIGRTGRAG KG AYTL+TDKDK+
Sbjct: 400 LDIPHIRTVVNYDIARDIDTHTHRIGRTGRAGEKGTAYTLITDKDKE 446

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189239856|ref|XP_974261.2| PREDICTED: similar to CG6418 CG6418-PB [Tribolium castaneum]

 Score =  173 bits (439), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 78/107 (72%), Positives = 96/107 (89%)

Query: 38  LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
           L+ +  +++AE+LAN L VKE++ LLLHGD++Q+ERN VIT FK++EC +LVATDVAARG
Sbjct: 480 LVFVTKKVDAEQLANDLKVKEFECLLLHGDIEQAERNKVITAFKKKECSLLVATDVAARG 539

Query: 98  LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           LDIPHIRTVVNYD+ARDIDTHTHRIGRTGRAGN+G AYTL+T KDK+
Sbjct: 540 LDIPHIRTVVNYDIARDIDTHTHRIGRTGRAGNQGTAYTLITPKDKE 586

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	150
FB|FBgn0036104	791	CG6418 [Drosophila melanogaste	0.78	0.147	0.685	1.2e-38
UNIPROTKB|F1P0H1	703	DDX42 "ATP-dependent RNA helic	0.733	0.156	0.678	1.1e-34
UNIPROTKB|Q5F485	944	DDX42 "ATP-dependent RNA helic	0.733	0.116	0.678	2.4e-34
UNIPROTKB|F1NJ40	946	DDX42 "ATP-dependent RNA helic	0.733	0.116	0.678	2.4e-34
UNIPROTKB|E2RFF1	933	DDX42 "Uncharacterized protein	0.733	0.117	0.669	5e-34
UNIPROTKB|Q86XP3	938	DDX42 "ATP-dependent RNA helic	0.733	0.117	0.669	5e-34
UNIPROTKB|F1RSJ7	941	DDX42 "Uncharacterized protein	0.733	0.116	0.669	5.1e-34
UNIPROTKB|Q5R7D1	942	DDX42 "ATP-dependent RNA helic	0.733	0.116	0.669	5.1e-34
UNIPROTKB|E1BJD2	946	DDX42 "Uncharacterized protein	0.733	0.116	0.669	5.1e-34
RGD|1304909	929	Ddx42 "DEAD (Asp-Glu-Ala-Asp)	0.733	0.118	0.669	8.1e-34

FB|FBgn0036104 CG6418 [Drosophila melanogaster (taxid:7227)]

 Score = 421 (153.3 bits), Expect = 1.2e-38, P = 1.2e-38
 Identities = 85/124 (68%), Positives = 103/124 (83%)

Query:    22 HLVRNL-EGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKF 80
             HLV+ L EG+       L+ +  +++AE ++N+L +KEY+ LLLHGDMDQ++RN VIT+F
Sbjct:   507 HLVKFLSEGS------VLIFVTKKVDAETVSNNLLIKEYNCLLLHGDMDQADRNKVITQF 560

Query:    81 KRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTD 140
             KR+EC ILVATDVAARGLDIPHIR VVNYD ARDI+THTHRIGRTGRAG KG AYTLVTD
Sbjct:   561 KRKECDILVATDVAARGLDIPHIRNVVNYDTARDIETHTHRIGRTGRAGEKGNAYTLVTD 620

Query:   141 KDKD 144
             KDK+
Sbjct:   621 KDKE 624

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

GO:0004386 "helicase activity" evidence=ISS

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F1P0H1 DDX42 "ATP-dependent RNA helicase DDX42" [Gallus gallus (taxid:9031)]

 Score = 383 (139.9 bits), Expect = 1.1e-34, P = 1.1e-34
 Identities = 76/112 (67%), Positives = 95/112 (84%)

Query:    38 LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
             L+ +  + NAEELAN+L  +++++ LLHGDMDQSERN VI++FK++   ILVATDVAARG
Sbjct:   497 LLFVTKKANAEELANNLKQEDHNLGLLHGDMDQSERNKVISEFKKKGIPILVATDVAARG 556

Query:    98 LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD--GEL 147
             LDIP I+TV+NYD+ARDIDTHTHRIGRTGRAG KGVAYTL+T KD +  G+L
Sbjct:   557 LDIPSIKTVINYDVARDIDTHTHRIGRTGRAGEKGVAYTLLTPKDSNFAGDL 608

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|Q5F485 DDX42 "ATP-dependent RNA helicase DDX42" [Gallus gallus (taxid:9031)]

 Score = 383 (139.9 bits), Expect = 2.4e-34, P = 2.4e-34
 Identities = 76/112 (67%), Positives = 95/112 (84%)

Query:    38 LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
             L+ +  + NAEELAN+L  +++++ LLHGDMDQSERN VI++FK++   ILVATDVAARG
Sbjct:   502 LLFVTKKANAEELANNLKQEDHNLGLLHGDMDQSERNKVISEFKKKGIPILVATDVAARG 561

Query:    98 LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD--GEL 147
             LDIP I+TV+NYD+ARDIDTHTHRIGRTGRAG KGVAYTL+T KD +  G+L
Sbjct:   562 LDIPSIKTVINYDVARDIDTHTHRIGRTGRAGEKGVAYTLLTPKDSNFAGDL 613

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0008104 "protein localization" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

UNIPROTKB|F1NJ40 DDX42 "ATP-dependent RNA helicase DDX42" [Gallus gallus (taxid:9031)]

 Score = 383 (139.9 bits), Expect = 2.4e-34, P = 2.4e-34
 Identities = 76/112 (67%), Positives = 95/112 (84%)

Query:    38 LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
             L+ +  + NAEELAN+L  +++++ LLHGDMDQSERN VI++FK++   ILVATDVAARG
Sbjct:   504 LLFVTKKANAEELANNLKQEDHNLGLLHGDMDQSERNKVISEFKKKGIPILVATDVAARG 563

Query:    98 LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD--GEL 147
             LDIP I+TV+NYD+ARDIDTHTHRIGRTGRAG KGVAYTL+T KD +  G+L
Sbjct:   564 LDIPSIKTVINYDVARDIDTHTHRIGRTGRAGEKGVAYTLLTPKDSNFAGDL 615

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0008104 "protein localization" evidence=IEA

UNIPROTKB|E2RFF1 DDX42 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 380 (138.8 bits), Expect = 5.0e-34, P = 5.0e-34
 Identities = 75/112 (66%), Positives = 94/112 (83%)

Query:    38 LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
             L+ +  + NAEELAN+L  + +++ LLHGDMDQSERN VI+ FK+++  +LVATDVAARG
Sbjct:   502 LLFVTKKANAEELANNLKQEGHNLGLLHGDMDQSERNKVISDFKKKDIPVLVATDVAARG 561

Query:    98 LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD--GEL 147
             LDIP I+TV+NYD+ARDIDTHTHRIGRTGRAG KGVAYTL+T KD +  G+L
Sbjct:   562 LDIPSIKTVINYDVARDIDTHTHRIGRTGRAGEKGVAYTLLTPKDSNFAGDL 613

GO:0008104 "protein localization" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q86XP3 DDX42 "ATP-dependent RNA helicase DDX42" [Homo sapiens (taxid:9606)]

 Score = 380 (138.8 bits), Expect = 5.0e-34, P = 5.0e-34
 Identities = 75/112 (66%), Positives = 94/112 (83%)

Query:    38 LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
             L+ +  + NAEELAN+L  + +++ LLHGDMDQSERN VI+ FK+++  +LVATDVAARG
Sbjct:   502 LLFVTKKANAEELANNLKQEGHNLGLLHGDMDQSERNKVISDFKKKDIPVLVATDVAARG 561

Query:    98 LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD--GEL 147
             LDIP I+TV+NYD+ARDIDTHTHRIGRTGRAG KGVAYTL+T KD +  G+L
Sbjct:   562 LDIPSIKTVINYDVARDIDTHTHRIGRTGRAGEKGVAYTLLTPKDSNFAGDL 613

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0015030 "Cajal body" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0008104 "protein localization" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|F1RSJ7 DDX42 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 380 (138.8 bits), Expect = 5.1e-34, P = 5.1e-34
 Identities = 75/112 (66%), Positives = 94/112 (83%)

Query:    38 LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
             L+ +  + NAEELAN+L  + +++ LLHGDMDQSERN VI+ FK+++  +LVATDVAARG
Sbjct:   502 LLFVTKKANAEELANNLKQEGHNLGLLHGDMDQSERNKVISDFKKKDIPVLVATDVAARG 561

Query:    98 LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD--GEL 147
             LDIP I+TV+NYD+ARDIDTHTHRIGRTGRAG KGVAYTL+T KD +  G+L
Sbjct:   562 LDIPSIKTVINYDVARDIDTHTHRIGRTGRAGEKGVAYTLLTPKDSNFAGDL 613

GO:0008104 "protein localization" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q5R7D1 DDX42 "ATP-dependent RNA helicase DDX42" [Pongo abelii (taxid:9601)]

 Score = 380 (138.8 bits), Expect = 5.1e-34, P = 5.1e-34
 Identities = 75/112 (66%), Positives = 94/112 (83%)

Query:    38 LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
             L+ +  + NAEELAN+L  + +++ LLHGDMDQSERN VI+ FK+++  +LVATDVAARG
Sbjct:   502 LLFVTKKANAEELANNLKQEGHNLGLLHGDMDQSERNKVISDFKKKDIPVLVATDVAARG 561

Query:    98 LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD--GEL 147
             LDIP I+TV+NYD+ARDIDTHTHRIGRTGRAG KGVAYTL+T KD +  G+L
Sbjct:   562 LDIPSIKTVINYDVARDIDTHTHRIGRTGRAGEKGVAYTLLTPKDSNFAGDL 613

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0008104 "protein localization" evidence=ISS

UNIPROTKB|E1BJD2 DDX42 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 380 (138.8 bits), Expect = 5.1e-34, P = 5.1e-34
 Identities = 75/112 (66%), Positives = 94/112 (83%)

Query:    38 LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
             L+ +  + NAEELAN+L  + +++ LLHGDMDQSERN VI+ FK+++  +LVATDVAARG
Sbjct:   501 LLFVTKKANAEELANNLKQEGHNLGLLHGDMDQSERNKVISDFKKKDIPVLVATDVAARG 560

Query:    98 LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD--GEL 147
             LDIP I+TV+NYD+ARDIDTHTHRIGRTGRAG KGVAYTL+T KD +  G+L
Sbjct:   561 LDIPSIKTVINYDVARDIDTHTHRIGRTGRAGEKGVAYTLLTPKDSNFAGDL 612

GO:0008104 "protein localization" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

RGD|1304909 Ddx42 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 42" [Rattus norvegicus (taxid:10116)]

 Score = 378 (138.1 bits), Expect = 8.1e-34, P = 8.1e-34
 Identities = 75/112 (66%), Positives = 93/112 (83%)

Query:    38 LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
             L+ +  + NAEELAN+L  + +++ LLHGDMDQSERN VI  FK+++  +LVATDVAARG
Sbjct:   502 LLFVTKKANAEELANNLKQEGHNLGLLHGDMDQSERNKVILDFKKKDIPVLVATDVAARG 561

Query:    98 LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD--GEL 147
             LDIP I+TV+NYD+ARDIDTHTHRIGRTGRAG KGVAYTL+T KD +  G+L
Sbjct:   562 LDIPSIKTVINYDVARDIDTHTHRIGRTGRAGEKGVAYTLLTPKDSNFAGDL 613

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

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

GO:0008104 "protein localization" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=ISO

---

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)
Q54IV3	DDX42_DICDI	3, ., 6, ., 4, ., 1, 3	0.5714	0.7	0.1064	yes	N/A
Q49Z29	Y802_STAS1	3, ., 6, ., 4, ., 1, 3	0.5257	0.6466	0.1916	yes	N/A
Q7A4G0	Y1885_STAAN	3, ., 6, ., 4, ., 1, 3	0.5051	0.6466	0.1916	yes	N/A
Q5F485	DDX42_CHICK	3, ., 6, ., 4, ., 1, 3	0.6915	0.7133	0.1133	yes	N/A
Q86XP3	DDX42_HUMAN	3, ., 6, ., 4, ., 1, 3	0.6822	0.7133	0.1140	yes	N/A
Q5HME0	Y1688_STAEQ	3, ., 6, ., 4, ., 1, 3	0.5051	0.6466	0.1905	yes	N/A
Q10MH8	RH24_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.5094	0.7	0.1363	yes	N/A
Q2FWH5	Y2316_STAA8	3, ., 6, ., 4, ., 1, 3	0.5051	0.6466	0.1916	yes	N/A
Q7A0D2	Y2004_STAAW	3, ., 6, ., 4, ., 1, 3	0.5051	0.6466	0.1916	yes	N/A
Q6G7M9	Y1985_STAAS	3, ., 6, ., 4, ., 1, 3	0.5051	0.6466	0.1916	yes	N/A
Q5L3G9	CSHA_GEOKA	3, ., 6, ., 4, ., 1, 3	0.5157	0.6333	0.2034	yes	N/A
Q6GEZ3	Y2168_STAAR	3, ., 6, ., 4, ., 1, 3	0.5051	0.6466	0.1916	yes	N/A
Q5R7D1	DDX42_PONAB	3, ., 6, ., 4, ., 1, 3	0.6822	0.7133	0.1135	yes	N/A
Q5HEB9	Y2072_STAAC	3, ., 6, ., 4, ., 1, 3	0.5051	0.6466	0.1916	yes	N/A
Q99SH6	Y2081_STAAM	3, ., 6, ., 4, ., 1, 3	0.5051	0.6466	0.1916	yes	N/A
Q810A7	DDX42_MOUSE	3, ., 6, ., 4, ., 1, 3	0.6728	0.7133	0.1151	yes	N/A
Q8CRP6	Y1679_STAES	3, ., 6, ., 4, ., 1, 3	0.5051	0.6466	0.1905	yes	N/A
Q2YUH3	Y1965_STAAB	3, ., 6, ., 4, ., 1, 3	0.5051	0.6466	0.1916	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4	0.691

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	150
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	8e-41
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	2e-37
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	4e-34
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	1e-30
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	6e-30
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	2e-29
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	1e-27
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	3e-24
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	8e-23
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	2e-21
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	9e-19
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	9e-18
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	2e-17
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	3e-16
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	4e-13
COG1111	542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	2e-12
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	2e-10
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	3e-10
PRK11057	607	PRK11057, PRK11057, ATP-dependent DNA helicase Rec	1e-09
TIGR00643	630	TIGR00643, recG, ATP-dependent DNA helicase RecG	4e-09
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	4e-09
COG1200	677	COG1200, RecG, RecG-like helicase [DNA replication	1e-08
TIGR00580	926	TIGR00580, mfd, transcription-repair coupling fact	8e-08
COG1202	830	COG1202, COG1202, Superfamily II helicase, archaea	3e-07
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	4e-07
PRK10917	681	PRK10917, PRK10917, ATP-dependent DNA helicase Rec	4e-07
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	5e-07
COG1197	1139	COG1197, Mfd, Transcription-repair coupling factor	1e-06
PLN03137	1195	PLN03137, PLN03137, ATP-dependent DNA helicase; Q4	1e-06
COG1643	845	COG1643, HrpA, HrpA-like helicases [DNA replicatio	3e-05
PRK10689	1147	PRK10689, PRK10689, transcription-repair coupling	6e-05
COG0556	663	COG0556, UvrB, Helicase subunit of the DNA excisio	5e-04
cd09639	353	cd09639, Cas3_I, CRISPR/Cas system-associated prot	6e-04
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	7e-04
TIGR01587	358	TIGR01587, cas3_core, CRISPR-associated helicase C	7e-04
COG1203	733	COG1203, COG1203, CRISPR-associated helicase Cas3	0.001

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

 Score =  141 bits (358), Expect = 8e-41
 Identities = 49/94 (52%), Positives = 71/94 (75%)

Query: 49  ELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVN 108
           E+A++L  + +  L LHGD++Q +R+ V+ +F  + C +LVATDVAARGLDI  +  V+N
Sbjct: 257 EVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVIN 316

Query: 109 YDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
           Y+LARD + H HRIGRTGRAG+KG+A +LV  ++
Sbjct: 317 YELARDPEVHVHRIGRTGRAGSKGLALSLVAPEE 350

Length = 460

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

 Score =  132 bits (335), Expect = 2e-37
 Identities = 56/103 (54%), Positives = 73/103 (70%)

Query: 46  NAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRT 105
             EELA SL  + + V  LHGD+ Q ER+  + KFK  E R+LVATDVAARGLDIP +  
Sbjct: 285 LVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSH 344

Query: 106 VVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGELR 148
           V+NYDL  D + + HRIGRTGRAG KGVA + VT++++  +L+
Sbjct: 345 VINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLK 387

Length = 513

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

 Score =  115 bits (291), Expect = 4e-34
 Identities = 43/91 (47%), Positives = 54/91 (59%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
            +ELA  L      V  LHGD  Q ER  V+  F+  E  +LVATDV ARG+D+P++  V
Sbjct: 41  LDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVV 100

Query: 107 VNYDLARDIDTHTHRIGRTGRAGNKGVAYTL 137
           +NYDL     ++  RIGR GRAG KG A  L
Sbjct: 101 INYDLPWSPSSYLQRIGRAGRAGQKGTAILL 131

Length = 131

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

 Score =  104 bits (263), Expect = 1e-30
 Identities = 33/76 (43%), Positives = 47/76 (61%)

Query: 54  LTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLAR 113
           L      V  LHG + Q ER  ++  F+  + ++LVATDVA RG+D+P +  V+NYDL  
Sbjct: 3   LRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLPW 62

Query: 114 DIDTHTHRIGRTGRAG 129
           +  ++  RIGR GRAG
Sbjct: 63  NPASYIQRIGRAGRAG 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 =  103 bits (259), Expect = 6e-30
 Identities = 38/82 (46%), Positives = 49/82 (59%)

Query: 48  EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
           EELA  L      V  LHG + Q ER  ++ KF   + ++LVATDVA RGLD+P +  V+
Sbjct: 1   EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60

Query: 108 NYDLARDIDTHTHRIGRTGRAG 129
            YDL     ++  RIGR GRAG
Sbjct: 61  IYDLPWSPASYIQRIGRAGRAG 82

Length = 82

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

 Score =  110 bits (277), Expect = 2e-29
 Identities = 44/91 (48%), Positives = 57/91 (62%)

Query: 48  EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
            ELA  L     +   L G+M Q++RN  I +       +LVATDVAARG+DI  +  V+
Sbjct: 259 HELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVI 318

Query: 108 NYDLARDIDTHTHRIGRTGRAGNKGVAYTLV 138
           N+D+ R  DT+ HRIGRTGRAG KG A +LV
Sbjct: 319 NFDMPRSADTYLHRIGRTGRAGRKGTAISLV 349

Length = 434

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

 Score =  106 bits (266), Expect = 1e-27
 Identities = 44/99 (44%), Positives = 64/99 (64%), Gaps = 1/99 (1%)

Query: 46  NAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRT 105
            A+ L   L +  +  L +HGD  Q ER  V+ +FK  +  I++ATDVA+RGLD+  ++ 
Sbjct: 389 GADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKY 448

Query: 106 VVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVT-DKDK 143
           V+N+D    I+ + HRIGRTGRAG KG +YT +T DK +
Sbjct: 449 VINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYR 487

Length = 545

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

 Score = 96.0 bits (239), Expect = 3e-24
 Identities = 38/95 (40%), Positives = 60/95 (63%)

Query: 50  LANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNY 109
           L   +  +++ V  +HGDMDQ +R+ ++ +F+    R+L+ TD+ ARG+D+  +  V+NY
Sbjct: 283 LTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINY 342

Query: 110 DLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           DL    + + HRIGR+GR G KGVA   VT  D +
Sbjct: 343 DLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIE 377

Length = 401

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

 Score = 92.3 bits (230), Expect = 8e-23
 Identities = 44/90 (48%), Positives = 57/90 (63%)

Query: 48  EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
           EE+   L    + V LL GD+ Q +R  ++ +F R +  ILVATDVAARGL IP +  V 
Sbjct: 269 EEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVF 328

Query: 108 NYDLARDIDTHTHRIGRTGRAGNKGVAYTL 137
           NYDL  D + + HRIGRTGRAG  G + +L
Sbjct: 329 NYDLPDDCEDYVHRIGRTGRAGASGHSISL 358

Length = 423

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

 Score = 88.8 bits (220), Expect = 2e-21
 Identities = 43/95 (45%), Positives = 61/95 (64%)

Query: 49  ELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVN 108
           E+A +L    Y+   L+GDM+Q+ R   + + K     IL+ATDVAARGLD+  I  VVN
Sbjct: 260 EVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVN 319

Query: 109 YDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK 143
           YD+  D +++ HRIGRTGRAG  G A   V ++++
Sbjct: 320 YDIPMDSESYVHRIGRTGRAGRAGRALLFVENRER 354

Length = 629

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

 Score = 81.2 bits (200), Expect = 9e-19
 Identities = 41/94 (43%), Positives = 60/94 (63%)

Query: 48  EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
           E +A +L    Y V +L GD+ Q +R S++ +F++ +  ILVATDVAARGL I  ++ V 
Sbjct: 271 ERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVY 330

Query: 108 NYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDK 141
           NYDL  D + + HRIGRT R G +G A +   ++
Sbjct: 331 NYDLPFDAEDYVHRIGRTARLGEEGDAISFACER 364

Length = 572

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

 Score = 78.4 bits (193), Expect = 9e-18
 Identities = 37/89 (41%), Positives = 51/89 (57%)

Query: 54  LTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLAR 113
           L     +   L GD+ Q +R   +  F+  + R+LVATDVA RG+ I  I  V+N+ L  
Sbjct: 355 LVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPE 414

Query: 114 DIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
           D D + HRIGRTGRAG  GV+ +   + D
Sbjct: 415 DPDDYVHRIGRTGRAGASGVSISFAGEDD 443

Length = 475

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

 Score = 77.5 bits (191), Expect = 2e-17
 Identities = 46/114 (40%), Positives = 61/114 (53%), Gaps = 17/114 (14%)

Query: 25  RNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE 84
           R   GAN         LA QLN + + ++          +HG+  Q  R   +  FK  +
Sbjct: 253 RTKHGANH--------LAEQLNKDGIRSAA---------IHGNKSQGARTRALADFKSGD 295

Query: 85  CRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLV 138
            R+LVATD+AARGLDI  +  VVNY+L    + + HRIGRTGRA   G A +LV
Sbjct: 296 IRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLV 349

Length = 456

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

 Score = 73.7 bits (181), Expect = 3e-16
 Identities = 40/110 (36%), Positives = 64/110 (58%), Gaps = 1/110 (0%)

Query: 35  PPALMNLAMQLNAEELANSLTV-KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDV 93
           PPA++ ++ +L A+ LAN++TV      L +HG+    ER  V+  F   E  ++VAT V
Sbjct: 368 PPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGV 427

Query: 94  AARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK 143
             RG+D+  +R V+ +D+   I  + H+IGR  R G KG A   V ++D+
Sbjct: 428 LGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDR 477

Length = 518

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

 Score = 65.0 bits (159), Expect = 4e-13
 Identities = 31/98 (31%), Positives = 45/98 (45%)

Query: 46  NAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRT 105
             EELA  L          H  +   ER  V   F   E +++VAT+    G+D P +R 
Sbjct: 242 KVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRF 301

Query: 106 VVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK 143
           V++YDL   I+++    GR GR G    A  L + +D 
Sbjct: 302 VIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDI 339

Length = 590

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

 Score = 62.7 bits (153), Expect = 2e-12
 Identities = 31/78 (39%), Positives = 45/78 (57%), Gaps = 3/78 (3%)

Query: 68  MDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYD-LARDIDTHTHRIGRTG 126
           M Q E+  +I +F++ E  +LVAT V   GLDIP +  V+ Y+ +  +I +   R GRTG
Sbjct: 409 MSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRS-IQRKGRTG 467

Query: 127 RAGNKGVAYTLVTDKDKD 144
           R   KG    LVT+  +D
Sbjct: 468 R-KRKGRVVVLVTEGTRD 484

Length = 542

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

 Score = 57.4 bits (139), Expect = 2e-10
 Identities = 27/95 (28%), Positives = 46/95 (48%)

Query: 48  EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
           EELA  L  +    L  H  +    R      F   + +++VAT+    G+D P++R V+
Sbjct: 238 EELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVI 297

Query: 108 NYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
           +YD+  +++++    GR GR G    A  L +  D
Sbjct: 298 HYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPAD 332

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 = 57.1 bits (138), Expect = 3e-10
 Identities = 25/82 (30%), Positives = 44/82 (53%)

Query: 48  EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
           E++  SL          H  ++ S R+ V  KF+R E +++VAT     G++ P +R V+
Sbjct: 240 EQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVI 299

Query: 108 NYDLARDIDTHTHRIGRTGRAG 129
           +Y L + ++++    GR GR G
Sbjct: 300 HYSLPKSMESYYQESGRAGRDG 321

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

 Score = 54.7 bits (132), Expect = 1e-09
 Identities = 26/82 (31%), Positives = 44/82 (53%)

Query: 48  EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
           E+ A  L  +       H  +D   R  V   F+R + +I+VAT     G++ P++R VV
Sbjct: 250 EDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVV 309

Query: 108 NYDLARDIDTHTHRIGRTGRAG 129
           ++D+ R+I+++    GR GR G
Sbjct: 310 HFDIPRNIESYYQETGRAGRDG 331

Length = 607

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

 Score = 53.5 bits (129), Expect = 4e-09
 Identities = 34/107 (31%), Positives = 54/107 (50%), Gaps = 4/107 (3%)

Query: 46  NAEELANSLTVK--EYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHI 103
            AE L   L     +Y+V LLHG M   E+ +V+ +F+  E  ILVAT V   G+D+P+ 
Sbjct: 468 AAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNA 527

Query: 104 RTVVNYDLARDIDTHTHRI-GRTGRAGNKGVAYTLVTD-KDKDGELR 148
             +V  D  R   +  H++ GR GR  ++     +  + K +  + R
Sbjct: 528 TVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKNPKSESAKKR 574

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

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

 Score = 53.3 bits (129), Expect = 4e-09
 Identities = 29/81 (35%), Positives = 41/81 (50%), Gaps = 9/81 (11%)

Query: 68  MDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLA----RDIDTHTHRIG 123
           M Q E+  ++ KF+  E  +LV+T VA  GLDIP +  V+ Y+      R I     R G
Sbjct: 407 MSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSI----QRKG 462

Query: 124 RTGRAGNKGVAYTLVTDKDKD 144
           RTGR   +G    L+    +D
Sbjct: 463 RTGR-QEEGRVVVLIAKGTRD 482

Length = 773

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

 Score = 52.2 bits (126), Expect = 1e-08
 Identities = 25/58 (43%), Positives = 34/58 (58%), Gaps = 2/58 (3%)

Query: 46  NAEELANSLT--VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIP 101
            AEEL   L   + E  V L+HG M  +E+++V+  FK  E  ILVAT V   G+D+P
Sbjct: 493 AAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVP 550

Length = 677

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

 Score = 50.0 bits (120), Expect = 8e-08
 Identities = 28/93 (30%), Positives = 46/93 (49%), Gaps = 9/93 (9%)

Query: 56  VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV-----NYD 110
           V E  + + HG M ++E   V+ +F + E ++LV T +   G+DIP+  T++      + 
Sbjct: 684 VPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFG 743

Query: 111 LARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK 143
           LA     +  R GR GR+  K  AY L   +  
Sbjct: 744 LA---QLYQLR-GRVGRSKKKAYAYLLYPHQKA 772

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|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific [General function prediction only]

 Score = 48.2 bits (115), Expect = 3e-07
 Identities = 33/100 (33%), Positives = 44/100 (44%), Gaps = 8/100 (8%)

Query: 46  NAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRT 105
              ELA++LT K       H  +   ER SV   F  QE   +V T   A G+D P    
Sbjct: 452 RCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAGVDFP-ASQ 510

Query: 106 VVNYDLARDIDTHTHR-----IGRTGRAG--NKGVAYTLV 138
           V+   LA  I+  + R     +GR GR    ++G  Y LV
Sbjct: 511 VIFESLAMGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLV 550

Length = 830

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

 Score = 47.8 bits (114), Expect = 4e-07
 Identities = 32/137 (23%), Positives = 56/137 (40%), Gaps = 21/137 (15%)

Query: 15  KDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERN 74
           K     G L+++  G    +  + +      +A E+A         V  + G+  + ER 
Sbjct: 269 KIAAVRGLLLKHARGDKTLIFASDVE-----HAYEIAKLFLAPGI-VEAITGETPKEERE 322

Query: 75  SVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHR--IGRTGR----A 128
           +++ +F+    ++LV   V   G+DIP    ++   + R   T + R  I R GR    A
Sbjct: 323 AILERFRTGGIKVLVTVKVLDEGVDIPDADVLI---ILR--PTGSRRLFIQRLGRGLRPA 377

Query: 129 GNKGVA----YTLVTDK 141
             K       Y+LV D 
Sbjct: 378 EGKEDTLALDYSLVPDD 394

Length = 442

>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional

 Score = 47.8 bits (115), Expect = 4e-07
 Identities = 25/59 (42%), Positives = 33/59 (55%), Gaps = 2/59 (3%)

Query: 45  LNAEELANSLT--VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIP 101
            +AEE    L     E  V LLHG M  +E+++V+  FK  E  ILVAT V   G+D+P
Sbjct: 490 QSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVP 548

Length = 681

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

 Score = 47.5 bits (113), Expect = 5e-07
 Identities = 19/44 (43%), Positives = 24/44 (54%)

Query: 1   RAGNKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQ 44
           RAG KG +YT +T      A  LV+ L  A Q VPP L  L+ +
Sbjct: 470 RAGAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELEKLSNE 513

Length = 545

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

 Score = 46.5 bits (111), Expect = 1e-06
 Identities = 30/102 (29%), Positives = 45/102 (44%), Gaps = 11/102 (10%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
           AE L     V E  + + HG M + E   V+  F   E  +LV T +   G+DIP+  T+
Sbjct: 820 AERLREL--VPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTI 877

Query: 107 V-----NYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK 143
           +      + LA     +  R GR GR+  +  AY L   +  
Sbjct: 878 IIERADKFGLA---QLYQLR-GRVGRSNKQAYAYFLYPPQKA 915

Length = 1139

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

 Score = 46.4 bits (110), Expect = 1e-06
 Identities = 27/99 (27%), Positives = 50/99 (50%), Gaps = 2/99 (2%)

Query: 44  QLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHI 103
           +++ E++A  L    +     HG MD ++R  V  ++ + E  I+ AT     G++ P +
Sbjct: 690 RMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDV 749

Query: 104 RTVVNYDLARDIDTHTHRIGRTGRAGNKG--VAYTLVTD 140
           R V+++ L + I+ +    GR GR G +   V Y   +D
Sbjct: 750 RFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSD 788

Length = 1195

>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination, and repair]

 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 31/113 (27%), Positives = 52/113 (46%), Gaps = 17/113 (15%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
           AE L  +    + ++L L+G +   E+  V       + ++++AT++A   L IP IR V
Sbjct: 276 AEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYV 335

Query: 107 VNYDLAR----DIDTHTHR-----------IGRTGRAGN--KGVAYTLVTDKD 142
           ++  LA+    D  T   R             R GRAG    G+ Y L +++D
Sbjct: 336 IDSGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGRTGPGICYRLYSEED 388

Length = 845

>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor; Provisional

 Score = 41.7 bits (98), Expect = 6e-05
 Identities = 30/99 (30%), Positives = 48/99 (48%), Gaps = 11/99 (11%)

Query: 46  NAEELANSLT--VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHI 103
           N ++ A  L   V E  + + HG M + E   V+  F  Q   +LV T +   G+DIP  
Sbjct: 821 NIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTA 880

Query: 104 RTVV-----NYDLARDIDTHTHRIGRTGRAGNKGVAYTL 137
            T++     ++ LA+    H  R GR GR+ ++  A+ L
Sbjct: 881 NTIIIERADHFGLAQ---LHQLR-GRVGRSHHQAYAWLL 915

Length = 1147

>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]

 Score = 38.7 bits (91), Expect = 5e-04
 Identities = 26/86 (30%), Positives = 36/86 (41%), Gaps = 5/86 (5%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
           AE+L   L      V  LH D+D  ER  +I   +  E  +LV  ++   GLD+P +  V
Sbjct: 459 AEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLV 518

Query: 107 VNYD-----LARDIDTHTHRIGRTGR 127
              D       R   +    IGR  R
Sbjct: 519 AILDADKEGFLRSERSLIQTIGRAAR 544

Length = 663

>gnl|CDD|187770 cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3

 Score = 38.6 bits (90), Expect = 6e-04
 Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 7/80 (8%)

Query: 56  VKEYDVLLLHGDMDQSER----NSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDL 111
             E +++L+H    + +R      ++ +FK+ E  ++VAT V    LDI     V+  +L
Sbjct: 242 GPEEEIMLIHSRFTEKDRAKKEAELLLEFKKSEKFVIVATQVIEASLDISV--DVMITEL 299

Query: 112 ARDIDTHTHRIGRTGRAGNK 131
           A  ID+   R+GR  R G K
Sbjct: 300 A-PIDSLIQRLGRLHRYGEK 318

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I. Length = 353

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

 Score = 38.4 bits (90), Expect = 7e-04
 Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 1/82 (1%)

Query: 47  AEELANSL-TVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRT 105
           AE LA  L  +    + + HG + +  R  V  + K  E + +VAT     G+DI  I  
Sbjct: 266 AERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELGIDIGDIDL 325

Query: 106 VVNYDLARDIDTHTHRIGRTGR 127
           V+     + ++    RIGR G 
Sbjct: 326 VIQLGSPKSVNRFLQRIGRAGH 347

Length = 814

>gnl|CDD|233483 TIGR01587, cas3_core, CRISPR-associated helicase Cas3

 Score = 38.2 bits (89), Expect = 7e-04
 Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 7/78 (8%)

Query: 58  EYDVLLLHGDMDQSER----NSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLAR 113
           E +++LLH    + +R      ++ + K+ E  ++VAT V    LDI     V+  +LA 
Sbjct: 248 EEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDISA--DVMITELA- 304

Query: 114 DIDTHTHRIGRTGRAGNK 131
            ID+   R+GR  R G K
Sbjct: 305 PIDSLIQRLGRLHRYGRK 322

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 [Mobile and extrachromosomal element functions, Other]. Length = 358

>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]

 Score = 37.8 bits (88), Expect = 0.001
 Identities = 34/114 (29%), Positives = 46/114 (40%), Gaps = 17/114 (14%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSER----NSVITKFKRQECRILVATDVAARGLDIPH 102
           A EL   L  K   VLLLH      +R      +   FK+ E  I+VAT V   G+DI  
Sbjct: 453 AIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDI-- 510

Query: 103 IRTVVNYDLA-RD---IDTHTHRIGRTGRAGNK--GVAYTLVTDKDKDGELRSQ 150
                ++D+   +   ID+   R GR  R G K  G  Y    ++       S 
Sbjct: 511 -----DFDVLITELAPIDSLIQRAGRVNRHGKKENGKIYVYNDEERGPYLKYSY 559

Length = 733

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	150
KOG0331|consensus	519		99.97
KOG0328|consensus	400		99.97
KOG0333|consensus	673		99.96
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.96
PTZ00110	545	helicase; Provisional	99.96
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.96
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.96
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.96
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.96
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.96
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.95
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.95
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.95
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.95
KOG0330|consensus	476		99.95
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.95
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.95
PTZ00424	401	helicase 45; Provisional	99.95
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.95
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.95
KOG0332|consensus	477		99.94
KOG0341|consensus	610		99.93
KOG0326|consensus	459		99.93
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.93
KOG0340|consensus	442		99.93
KOG0335|consensus	482		99.93
KOG0336|consensus	629		99.92
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.92
KOG0342|consensus	543		99.91
KOG0344|consensus	593		99.91
KOG0345|consensus	567		99.9
KOG0351|consensus	941		99.9
PRK04914	956	ATP-dependent helicase HepA; Validated	99.9
PRK13767	876	ATP-dependent helicase; Provisional	99.9
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.9
KOG0347|consensus	731		99.9
KOG0327|consensus	397		99.89
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.89
KOG0338|consensus	691		99.89
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.88
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.88
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.88
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.88
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.88
KOG0348|consensus	708		99.88
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.87
KOG0343|consensus	758		99.87
KOG0339|consensus	731		99.87
KOG0350|consensus	620		99.87
PRK10689	1147	transcription-repair coupling factor; Provisional	99.87
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.86
PRK05298	652	excinuclease ABC subunit B; Provisional	99.86
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.86
PRK02362	737	ski2-like helicase; Provisional	99.86
PRK13766	773	Hef nuclease; Provisional	99.85
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.85
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.85
PHA02558	501	uvsW UvsW helicase; Provisional	99.85
KOG0334|consensus	997		99.85
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.85
PHA02653	675	RNA helicase NPH-II; Provisional	99.85
KOG4284|consensus	980		99.85
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.84
KOG0352|consensus	641		99.83
KOG0346|consensus	569		99.83
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.83
KOG0354|consensus	746		99.82
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.82
PRK00254	720	ski2-like helicase; Provisional	99.81
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.81
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.81
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.81
PRK01172	674	ski2-like helicase; Provisional	99.81
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.8
COG1202	830	Superfamily II helicase, archaea-specific [General	99.8
KOG0353|consensus	695		99.79
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.76
KOG0337|consensus	529		99.74
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.74
KOG0349|consensus	725		99.73
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.73
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.73
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.7
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.7
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.69
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.69
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.68
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.67
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.66
PRK09694	878	helicase Cas3; Provisional	99.64
PRK14701	1638	reverse gyrase; Provisional	99.64
COG1204	766	Superfamily II helicase [General function predicti	99.63
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.59
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.59
PRK09401	1176	reverse gyrase; Reviewed	99.59
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.57
KOG0947|consensus	1248		99.56
KOG0948|consensus	1041		99.54
KOG0384|consensus	1373		99.5
COG1205	851	Distinct helicase family with a unique C-terminal	99.5
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.5
KOG4150|consensus	1034		99.49
PRK05580	679	primosome assembly protein PriA; Validated	99.49
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.41
KOG0387|consensus	923		99.4
KOG0390|consensus	776		99.4
KOG0329|consensus	387		99.39
KOG0385|consensus	971		99.39
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	99.38
KOG0950|consensus	1008		99.37
KOG0951|consensus	1674		99.37
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.37
KOG0922|consensus	674		99.36
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.34
KOG0953|consensus	700		99.33
KOG0391|consensus	1958		99.33
KOG0952|consensus	1230		99.27
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	99.25
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.23
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.21
KOG0392|consensus	1549		99.2
KOG0389|consensus	941		99.2
KOG0923|consensus	902		99.19
KOG0388|consensus	1185		99.17
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.12
KOG0920|consensus	924		99.1
KOG0924|consensus	1042		99.09
CHL00122	870	secA preprotein translocase subunit SecA; Validate	99.08
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	99.05
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.03
KOG1000|consensus	689		99.0
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	98.99
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.98
COG4096	875	HsdR Type I site-specific restriction-modification	98.96
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	98.89
KOG1123|consensus	776		98.88
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	98.85
KOG0949|consensus	1330		98.8
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.73
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	98.68
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.67
KOG0926|consensus	1172		98.67
KOG1015|consensus	1567		98.67
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.66
KOG0386|consensus	1157		98.63
KOG4439|consensus	901		98.62
COG4889	1518	Predicted helicase [General function prediction on	98.61
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.6
KOG1002|consensus	791		98.56
KOG0925|consensus	699		98.52
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	98.5
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	98.43
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.41
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	98.3
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	98.22
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	98.21
PF13871	278	Helicase_C_4: Helicase_C-like	97.87
KOG1016|consensus	1387		97.85
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	97.83
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	97.62
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	97.42
PRK05580	679	primosome assembly protein PriA; Validated	97.3
KOG1001|consensus	674		97.3
TIGR00595	505	priA primosomal protein N'. All proteins in this f	97.27
PRK14873	665	primosome assembly protein PriA; Provisional	97.21
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	97.2
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	97.15
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	97.14
KOG0951|consensus	1674		97.12
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	97.08
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	96.99
COG1198	730	PriA Primosomal protein N' (replication factor Y)	96.97
PRK14873	665	primosome assembly protein PriA; Provisional	96.94
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	96.63
KOG0921|consensus	1282		96.5
PRK10689	1147	transcription-repair coupling factor; Provisional	96.4
KOG0298|consensus	1394		96.31
PRK14701	1638	reverse gyrase; Provisional	96.2
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	96.17
KOG2340|consensus	698		96.0
KOG0701|consensus	1606		96.0
KOG1133|consensus	821		95.7
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	95.48
KOG0347|consensus	731		95.42
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	95.06
KOG1513|consensus	1300		94.98
PF10593	239	Z1: Z1 domain; InterPro: IPR018310 This entry repr	94.85
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	94.73
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	94.48
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	94.33
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	93.53
KOG0339|consensus	731		93.45
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	92.5
KOG0330|consensus	476		92.39
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	92.08
PF04364	137	DNA_pol3_chi: DNA polymerase III chi subunit, HolC	92.06
cd01524	90	RHOD_Pyr_redox Member of the Rhodanese Homology Do	91.24
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	91.24
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	91.18
PRK09401	1176	reverse gyrase; Reviewed	91.1
KOG0331|consensus	519		90.96
KOG0383|consensus	696		90.89
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	90.8
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	90.69
COG1205	851	Distinct helicase family with a unique C-terminal	90.67
KOG0338|consensus	691		90.42
cd01523	100	RHOD_Lact_B Member of the Rhodanese Homology Domai	90.33
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	90.3
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	89.57
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	88.77
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	88.27
smart00450	100	RHOD Rhodanese Homology Domain. An alpha beta fold	88.23
KOG0335|consensus	482		87.29
cd01529	96	4RHOD_Repeats Member of the Rhodanese Homology Dom	86.98
cd01520	128	RHOD_YbbB Member of the Rhodanese Homology Domain	86.91
PTZ00110	545	helicase; Provisional	86.54
KOG0389|consensus	941		86.43
cd01449	118	TST_Repeat_2 Thiosulfate sulfurtransferase (TST),	86.41
cd01534	95	4RHOD_Repeat_3 Member of the Rhodanese Homology Do	85.93
TIGR00696	177	wecB_tagA_cpsF bacterial polymer biosynthesis prot	85.92
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	85.72
PRK13766	773	Hef nuclease; Provisional	85.57
cd01448	122	TST_Repeat_1 Thiosulfate sulfurtransferase (TST),	84.51
cd01533	109	4RHOD_Repeat_2 Member of the Rhodanese Homology Do	84.34
cd01518	101	RHOD_YceA Member of the Rhodanese Homology Domain	84.27
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	84.19
PF03808	172	Glyco_tran_WecB: Glycosyl transferase WecB/TagA/Cp	83.86
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	83.54
cd01521	110	RHOD_PspE2 Member of the Rhodanese Homology Domain	83.4
cd01526	122	RHOD_ThiF Member of the Rhodanese Homology Domain	83.06
PF12683	275	DUF3798: Protein of unknown function (DUF3798); In	83.02
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	82.84
KOG0350|consensus	620		82.55
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	82.52
cd01528	101	RHOD_2 Member of the Rhodanese Homology Domain sup	82.37
cd01444	96	GlpE_ST GlpE sulfurtransferase (ST) and homologs a	82.27
cd01447	103	Polysulfide_ST Polysulfide-sulfurtransferase - Rho	82.15
cd01519	106	RHOD_HSP67B2 Member of the Rhodanese Homology Doma	81.99
cd01527	99	RHOD_YgaP Member of the Rhodanese Homology Domain	81.68
KOG0348|consensus	708		81.15
cd01532	92	4RHOD_Repeat_1 Member of the Rhodanese Homology Do	81.11
cd06533	171	Glyco_transf_WecG_TagA The glycosyltransferase Wec	81.07
KOG1132|consensus	945		81.06
COG0610	962	Type I site-specific restriction-modification syst	80.03

>KOG0331|consensus

Probab=99.97  E-value=1.1e-30  Score=197.47  Aligned_cols=138  Identities=36%  Similarity=0.563  Sum_probs=118.3

Q ss_pred             CeeEEEeecchhhHHHHHHHHHHhcc-CCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC
Q psy17637          6 GVAYTLVTDKDKEFAGHLVRNLEGAN-QEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE   84 (150)
Q Consensus         6 ~~~~~~~~~~~~~~~~~ll~~l~~~~-~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~   84 (150)
                      ++.++....+...+...|.+.|.... ....++||||+|++.|++|...|...++++..+||+.++.+|..+++.|++|+
T Consensus       312 ~i~qive~~~~~~K~~~l~~lL~~~~~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~  391 (519)
T KOG0331|consen  312 NIRQIVEVCDETAKLRKLGKLLEDISSDSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGK  391 (519)
T ss_pred             chhhhhhhcCHHHHHHHHHHHHHHHhccCCCcEEEEecchhhHHHHHHHHHhcCcceeeecccccHHHHHHHHHhcccCC
Confidence            34444444444444444444444331 46779999999999999999999998999999999999999999999999999


Q ss_pred             ceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         85 CRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        85 ~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      ..|||||+++++|+|+|++++|||||+|.+.++|+||+||+||.|+.|.++.|++..+.
T Consensus       392 ~~vLVATdVAaRGLDi~dV~lVInydfP~~vEdYVHRiGRTGRa~~~G~A~tfft~~~~  450 (519)
T KOG0331|consen  392 SPVLVATDVAARGLDVPDVDLVINYDFPNNVEDYVHRIGRTGRAGKKGTAITFFTSDNA  450 (519)
T ss_pred             cceEEEcccccccCCCccccEEEeCCCCCCHHHHHhhcCccccCCCCceEEEEEeHHHH
Confidence            99999999999999999999999999999999999999999999999999999987643

>KOG0328|consensus

Probab=99.97  E-value=9.2e-31  Score=183.17  Aligned_cols=139  Identities=31%  Similarity=0.550  Sum_probs=125.1

Q ss_pred             cCeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC
Q psy17637          5 KGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE   84 (150)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~   84 (150)
                      +|++.++...+..+|...-+..+... ....+++|||||+..++.|.+++...++.+...||+|++++|.+++..|++|.
T Consensus       238 EgIKqf~v~ve~EewKfdtLcdLYd~-LtItQavIFcnTk~kVdwLtekm~~~nftVssmHGDm~qkERd~im~dFRsg~  316 (400)
T KOG0328|consen  238 EGIKQFFVAVEKEEWKFDTLCDLYDT-LTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMEQKERDKIMNDFRSGK  316 (400)
T ss_pred             hhhhhheeeechhhhhHhHHHHHhhh-hehheEEEEecccchhhHHHHHHHhhCceeeeccCCcchhHHHHHHHHhhcCC
Confidence            46777777777777555555555444 47789999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCc
Q psy17637         85 CRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD  144 (150)
Q Consensus        85 ~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~  144 (150)
                      .+||++|+++++|+|+|.+++|||||+|.+.+.|++|+||+||.|+.|.++.|+..++.+
T Consensus       317 SrvLitTDVwaRGiDv~qVslviNYDLP~nre~YIHRIGRSGRFGRkGvainFVk~~d~~  376 (400)
T KOG0328|consen  317 SRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKSDDLR  376 (400)
T ss_pred             ceEEEEechhhccCCcceeEEEEecCCCccHHHHhhhhccccccCCcceEEEEecHHHHH
Confidence            999999999999999999999999999999999999999999999999999999887653

>KOG0333|consensus

Probab=99.96  E-value=2.7e-29  Score=187.62  Aligned_cols=134  Identities=39%  Similarity=0.613  Sum_probs=120.7

Q ss_pred             EEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEE
Q psy17637          9 YTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRIL   88 (150)
Q Consensus         9 ~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vl   88 (150)
                      +.+....+.++...|+..+...  -.+|+|||+|+++.|+.|++.|.+.++++..+||+-++++|+.+++.|+.|...||
T Consensus       494 Q~v~m~~ed~k~kkL~eil~~~--~~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIl  571 (673)
T KOG0333|consen  494 QKVEMVSEDEKRKKLIEILESN--FDPPIIIFVNTKKGADALAKILEKAGYKVTTLHGGKSQEQRENALADFREGTGDIL  571 (673)
T ss_pred             eEEEEecchHHHHHHHHHHHhC--CCCCEEEEEechhhHHHHHHHHhhccceEEEeeCCccHHHHHHHHHHHHhcCCCEE
Confidence            3333334444455677777665  67899999999999999999999999999999999999999999999999999999


Q ss_pred             EEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCc
Q psy17637         89 VATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD  144 (150)
Q Consensus        89 v~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~  144 (150)
                      |||+++++|||+|++++|||||+++++.+|.||+||+||.|+.|.++.|+++.+..
T Consensus       572 VaTDvAgRGIDIpnVSlVinydmaksieDYtHRIGRTgRAGk~GtaiSflt~~dt~  627 (673)
T KOG0333|consen  572 VATDVAGRGIDIPNVSLVINYDMAKSIEDYTHRIGRTGRAGKSGTAISFLTPADTA  627 (673)
T ss_pred             EEecccccCCCCCccceeeecchhhhHHHHHHHhccccccccCceeEEEeccchhH
Confidence            99999999999999999999999999999999999999999999999999998754

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

Probab=99.96  E-value=4.7e-29  Score=192.50  Aligned_cols=135  Identities=44%  Similarity=0.637  Sum_probs=118.4

Q ss_pred             cCeeEEEeecchhh-HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcC
Q psy17637          5 KGVAYTLVTDKDKE-FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQ   83 (150)
Q Consensus         5 ~~~~~~~~~~~~~~-~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g   83 (150)
                      ..+.+.+...+... +. .++..+... ....++||||+|+..++.|+..|...|+++..+||+|++++|.+.++.|++|
T Consensus       245 ~~i~q~~~~v~~~~~k~-~~L~~ll~~-~~~~~~IVF~~tk~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g  322 (513)
T COG0513         245 KKIKQFYLEVESEEEKL-ELLLKLLKD-EDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDG  322 (513)
T ss_pred             cCceEEEEEeCCHHHHH-HHHHHHHhc-CCCCeEEEEeCcHHHHHHHHHHHHHCCCeEEEecCCCCHHHHHHHHHHHHcC
Confidence            44555555555443 44 444444444 3445799999999999999999999999999999999999999999999999


Q ss_pred             CceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecC
Q psy17637         84 ECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus        84 ~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                      +.+|||||+++++|+|+|++++|||||+|.+++.|+||+||+||.|..|.++.|+++.
T Consensus       323 ~~~vLVaTDvaaRGiDi~~v~~VinyD~p~~~e~yvHRiGRTgRaG~~G~ai~fv~~~  380 (513)
T COG0513         323 ELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEE  380 (513)
T ss_pred             CCCEEEEechhhccCCccccceeEEccCCCCHHHheeccCccccCCCCCeEEEEeCcH
Confidence            9999999999999999999999999999999999999999999999999999999874

>PTZ00110 helicase; Provisional

Probab=99.96  E-value=1.4e-28  Score=191.30  Aligned_cols=126  Identities=37%  Similarity=0.604  Sum_probs=113.9

Q ss_pred             hHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCccc
Q psy17637         18 EFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG   97 (150)
Q Consensus        18 ~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G   97 (150)
                      .+...|.+.+........++||||++++.++.++..|...++.+..+||++++++|..+++.|++|+.+|||||+++++|
T Consensus       361 ~k~~~L~~ll~~~~~~~~k~LIF~~t~~~a~~l~~~L~~~g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTdv~~rG  440 (545)
T PTZ00110        361 EKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRG  440 (545)
T ss_pred             hHHHHHHHHHHHhcccCCeEEEEecChHHHHHHHHHHHHcCCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcchhhcC
Confidence            33445555554442356799999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         98 LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        98 idi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +|+|++++||+|++|.++.+|+||+||+||.|..|.+++|+++.+.
T Consensus       441 IDi~~v~~VI~~d~P~s~~~yvqRiGRtGR~G~~G~ai~~~~~~~~  486 (545)
T PTZ00110        441 LDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKY  486 (545)
T ss_pred             CCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEECcchH
Confidence            9999999999999999999999999999999999999999987654

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.96  E-value=6.1e-29  Score=188.58  Aligned_cols=125  Identities=38%  Similarity=0.527  Sum_probs=112.8

Q ss_pred             hhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcc
Q psy17637         17 KEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAAR   96 (150)
Q Consensus        17 ~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~   96 (150)
                      ..+...+...+..  ....++||||++++.++.++..|...++.+..+||+|++++|..+++.|++|+.+|||||+++++
T Consensus       240 ~~k~~~l~~ll~~--~~~~~~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTdv~~r  317 (423)
T PRK04837        240 EEKMRLLQTLIEE--EWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAAR  317 (423)
T ss_pred             HHHHHHHHHHHHh--cCCCeEEEEECCHHHHHHHHHHHHhCCCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEechhhc
Confidence            3344444444443  35678999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         97 GLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        97 Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |+|+|++++||+|++|.+..+|+||+||+||.|+.|.+++|+++++.
T Consensus       318 GiDip~v~~VI~~d~P~s~~~yiqR~GR~gR~G~~G~ai~~~~~~~~  364 (423)
T PRK04837        318 GLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLACEEYA  364 (423)
T ss_pred             CCCccccCEEEEeCCCCchhheEeccccccCCCCCeeEEEEeCHHHH
Confidence            99999999999999999999999999999999999999999987643

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.96  E-value=2.8e-28  Score=186.99  Aligned_cols=124  Identities=23%  Similarity=0.355  Sum_probs=114.0

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccC
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGL   98 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gi   98 (150)
                      ....++..+... .+..++||||++++.++.++..|...++.+..+||+|++++|..+++.|++|+++|||||+++++|+
T Consensus       212 ~~~~l~~~l~~~-~~~~~~IIF~~s~~~~e~la~~L~~~g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~GI  290 (470)
T TIGR00614       212 ILEDLLRFIRKE-FKGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGI  290 (470)
T ss_pred             HHHHHHHHHHHh-cCCCceEEEECcHHHHHHHHHHHHhcCCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhccC
Confidence            445666666643 4566789999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         99 DIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        99 di~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |+|++++||++++|.+++.|+|++||+||.|..+.++++++..|.
T Consensus       291 D~p~V~~VI~~~~P~s~~~y~Qr~GRaGR~G~~~~~~~~~~~~d~  335 (470)
T TIGR00614       291 NKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPADI  335 (470)
T ss_pred             CcccceEEEEeCCCCCHHHHHhhhcCcCCCCCCceEEEEechhHH
Confidence            999999999999999999999999999999999999999987654

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

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.96  E-value=4.6e-28  Score=185.49  Aligned_cols=131  Identities=40%  Similarity=0.674  Sum_probs=115.7

Q ss_pred             EEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEE
Q psy17637         10 TLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILV   89 (150)
Q Consensus        10 ~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv   89 (150)
                      .+.......+...+...+...  ...++||||++++.++.+++.|...++.+..+||+|++.+|+.+++.|++|+.+|||
T Consensus       220 ~~~~~~~~~k~~~l~~ll~~~--~~~~~lVF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLV  297 (460)
T PRK11776        220 RFYEVSPDERLPALQRLLLHH--QPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLV  297 (460)
T ss_pred             EEEEeCcHHHHHHHHHHHHhc--CCCceEEEECCHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEE
Confidence            333333333445555555443  567899999999999999999999999999999999999999999999999999999


Q ss_pred             EcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637         90 ATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus        90 ~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      ||+++++|+|+|++++||++++|.+..+|+||+||+||.|..|.+++|+++.+
T Consensus       298 aTdv~~rGiDi~~v~~VI~~d~p~~~~~yiqR~GRtGR~g~~G~ai~l~~~~e  350 (460)
T PRK11776        298 ATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEE  350 (460)
T ss_pred             EecccccccchhcCCeEEEecCCCCHhHhhhhcccccCCCCcceEEEEEchhH
Confidence            99999999999999999999999999999999999999999999999998764

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.96  E-value=7.4e-28  Score=183.19  Aligned_cols=121  Identities=40%  Similarity=0.594  Sum_probs=111.2

Q ss_pred             HHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCc
Q psy17637         21 GHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDI  100 (150)
Q Consensus        21 ~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi  100 (150)
                      ..++..+... ....++||||++++.++.++..|...++.+..+||+|++.+|..+++.|++|+++|||||+.+++|+|+
T Consensus       233 ~~~l~~l~~~-~~~~~~lVF~~s~~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd~~~~GiDi  311 (434)
T PRK11192        233 TALLCHLLKQ-PEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDI  311 (434)
T ss_pred             HHHHHHHHhc-CCCCeEEEEeCChHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEccccccCccC
Confidence            3455555543 356799999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637        101 PHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus       101 ~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      |++++||+|++|.+...|+||+||+||.|..|.++++++..+
T Consensus       312 p~v~~VI~~d~p~s~~~yiqr~GR~gR~g~~g~ai~l~~~~d  353 (434)
T PRK11192        312 DDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHD  353 (434)
T ss_pred             CCCCEEEEECCCCCHHHHhhcccccccCCCCceEEEEecHHH
Confidence            999999999999999999999999999999999999997654

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

Probab=99.96  E-value=4.7e-28  Score=195.80  Aligned_cols=137  Identities=21%  Similarity=0.350  Sum_probs=117.7

Q ss_pred             CcCeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcC
Q psy17637          4 NKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQ   83 (150)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g   83 (150)
                      +.++.|.+.. +.......+...+... ....++||||.+++.++.++..|...|+.+..+||+|++++|..+++.|..|
T Consensus       652 RpNL~y~Vv~-k~kk~le~L~~~I~~~-~~~esgIIYC~SRke~E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~F~~G  729 (1195)
T PLN03137        652 RPNLWYSVVP-KTKKCLEDIDKFIKEN-HFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKD  729 (1195)
T ss_pred             ccceEEEEec-cchhHHHHHHHHHHhc-ccCCCceeEeCchhHHHHHHHHHHHCCCCeeeeeCCCCHHHHHHHHHHHhcC
Confidence            3455555443 3333334555555433 3456899999999999999999999999999999999999999999999999


Q ss_pred             CceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637         84 ECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus        84 ~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      +++|||||+++++|||+|++++||+|++|++++.|+|++|||||.|.++.|++|+...|
T Consensus       730 ei~VLVATdAFGMGIDkPDVR~VIHydlPkSiEsYyQriGRAGRDG~~g~cILlys~~D  788 (1195)
T PLN03137        730 EINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSD  788 (1195)
T ss_pred             CCcEEEEechhhcCCCccCCcEEEEcCCCCCHHHHHhhhcccCCCCCCceEEEEecHHH
Confidence            99999999999999999999999999999999999999999999999999999997543

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

Probab=99.95  E-value=1.1e-27  Score=185.46  Aligned_cols=125  Identities=34%  Similarity=0.560  Sum_probs=111.9

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccc-cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCccc
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTV-KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG   97 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~-~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G   97 (150)
                      +...+.+.+........++||||+++..++.++..|.. .++.+..+||+|++++|..+++.|++|+.+|||||+++++|
T Consensus       352 k~~~l~~~l~~~~~~~~~~iVFv~s~~~a~~l~~~L~~~~g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTdvl~rG  431 (518)
T PLN00206        352 KKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRG  431 (518)
T ss_pred             HHHHHHHHHHhhcccCCCEEEEcCCchhHHHHHHHHhhccCcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEecHhhcc
Confidence            34456666654433456899999999999999999974 58899999999999999999999999999999999999999


Q ss_pred             CCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         98 LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        98 idi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +|+|++++||+|++|.+..+|+||+||+||.|..|.+++|++.++.
T Consensus       432 iDip~v~~VI~~d~P~s~~~yihRiGRaGR~g~~G~ai~f~~~~~~  477 (518)
T PLN00206        432 VDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDR  477 (518)
T ss_pred             CCcccCCEEEEeCCCCCHHHHHHhccccccCCCCeEEEEEEchhHH
Confidence            9999999999999999999999999999999999999999987653

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.95  E-value=1.2e-27  Score=186.73  Aligned_cols=128  Identities=36%  Similarity=0.519  Sum_probs=114.8

Q ss_pred             ecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC
Q psy17637         13 TDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD   92 (150)
Q Consensus        13 ~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~   92 (150)
                      ...+..+...++..+...  ...++||||++++.++.+++.|...++.+..+||+|++.+|..+++.|++|+.+|||||+
T Consensus       238 ~~~~~~k~~~L~~ll~~~--~~~k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTd  315 (572)
T PRK04537        238 FPADEEKQTLLLGLLSRS--EGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATD  315 (572)
T ss_pred             ecCHHHHHHHHHHHHhcc--cCCcEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEeh
Confidence            333444445555555443  677999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637         93 VAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus        93 ~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      ++++|+|+|++++||+|+.|.+...|+||+||+||.|..|.+++|+.+.+
T Consensus       316 v~arGIDip~V~~VInyd~P~s~~~yvqRiGRaGR~G~~G~ai~~~~~~~  365 (572)
T PRK04537        316 VAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERY  365 (572)
T ss_pred             hhhcCCCccCCCEEEEcCCCCCHHHHhhhhcccccCCCCceEEEEecHHH
Confidence            99999999999999999999999999999999999999999999997653

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.95  E-value=1.5e-27  Score=187.57  Aligned_cols=120  Identities=25%  Similarity=0.423  Sum_probs=112.2

Q ss_pred             HHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCc
Q psy17637         21 GHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDI  100 (150)
Q Consensus        21 ~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi  100 (150)
                      ..++..+...  ...++||||+|++.++.++..|...++.+..+||+|++++|.++++.|+.|+.+|||||+++++|+|+
T Consensus       225 ~~l~~~l~~~--~~~~~IIFc~tr~~~e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GIDi  302 (607)
T PRK11057        225 DQLMRYVQEQ--RGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINK  302 (607)
T ss_pred             HHHHHHHHhc--CCCCEEEEECcHHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccCCC
Confidence            4566666554  67799999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637        101 PHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus       101 ~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      |++++||++++|.+.++|+|++||+||.|.++.+++|++..+
T Consensus       303 p~V~~VI~~d~P~s~~~y~Qr~GRaGR~G~~~~~ill~~~~d  344 (607)
T PRK11057        303 PNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPAD  344 (607)
T ss_pred             CCcCEEEEeCCCCCHHHHHHHhhhccCCCCCceEEEEeCHHH
Confidence            999999999999999999999999999999999999998765

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.95  E-value=1.8e-27  Score=181.99  Aligned_cols=121  Identities=36%  Similarity=0.542  Sum_probs=111.4

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCcc
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIP  101 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~  101 (150)
                      .++..+... ....++||||++++.++.+++.|...++.+..+||+|++++|.++++.|++|+++|||||+++++|+|+|
T Consensus       234 ~~l~~l~~~-~~~~~~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTdv~~rGiDip  312 (456)
T PRK10590        234 ELLSQMIGK-GNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIE  312 (456)
T ss_pred             HHHHHHHHc-CCCCcEEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEccHHhcCCCcc
Confidence            455555544 4567899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637        102 HIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus       102 ~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      ++++||+|++|.++.+|+||+||+||.|..|.+++|++..+.
T Consensus       313 ~v~~VI~~~~P~~~~~yvqR~GRaGR~g~~G~ai~l~~~~d~  354 (456)
T PRK10590        313 ELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEH  354 (456)
T ss_pred             cCCEEEEeCCCCCHHHhhhhccccccCCCCeeEEEEecHHHH
Confidence            999999999999999999999999999999999999987653

>KOG0330|consensus

Probab=99.95  E-value=4.8e-28  Score=175.46  Aligned_cols=125  Identities=41%  Similarity=0.512  Sum_probs=115.7

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCcc
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIP  101 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~  101 (150)
                      .|+..+.+.  .+.++||||++-.....++-.|...|+.+..+||.|+++.|...++.|+.|...|||||++.++|+|+|
T Consensus       290 yLV~ll~e~--~g~s~iVF~~t~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~TDVaSRGLDip  367 (476)
T KOG0330|consen  290 YLVYLLNEL--AGNSVIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGALNKFKAGARSILVCTDVASRGLDIP  367 (476)
T ss_pred             hHHHHHHhh--cCCcEEEEEeccchHHHHHHHHHhcCcceecccchhhHHHHHHHHHHHhccCCcEEEecchhcccCCCC
Confidence            455555554  678999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCccccc
Q psy17637        102 HIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGELR  148 (150)
Q Consensus       102 ~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~~~~~  148 (150)
                      .+++|||||.|.+..+|++|+||++|.|+.|.++.|++..|.+-++|
T Consensus       368 ~Vd~VVNyDiP~~skDYIHRvGRtaRaGrsG~~ItlVtqyDve~~qr  414 (476)
T KOG0330|consen  368 HVDVVVNYDIPTHSKDYIHRVGRTARAGRSGKAITLVTQYDVELVQR  414 (476)
T ss_pred             CceEEEecCCCCcHHHHHHHcccccccCCCcceEEEEehhhhHHHHH
Confidence            99999999999999999999999999999999999999877665554

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.95  E-value=3.5e-27  Score=181.27  Aligned_cols=111  Identities=33%  Similarity=0.528  Sum_probs=106.2

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDL  111 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~  111 (150)
                      ....++||||++++.++.+++.|...++.+..+||++++++|.++++.|++|++.+||||+++++|+|+|++++||++++
T Consensus       333 ~~~~~~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~~l~~GIDi~~v~~VI~~~~  412 (475)
T PRK01297        333 NPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTL  412 (475)
T ss_pred             cCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEccccccCCcccCCCEEEEeCC
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637        112 ARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus       112 ~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      |.+..+|+||+||+||.|..|.+++|++++|
T Consensus       413 P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~~d  443 (475)
T PRK01297        413 PEDPDDYVHRIGRTGRAGASGVSISFAGEDD  443 (475)
T ss_pred             CCCHHHHHHhhCccCCCCCCceEEEEecHHH
Confidence            9999999999999999999999999998763

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.95  E-value=7.7e-27  Score=183.55  Aligned_cols=123  Identities=40%  Similarity=0.605  Sum_probs=112.4

Q ss_pred             hHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCccc
Q psy17637         18 EFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG   97 (150)
Q Consensus        18 ~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G   97 (150)
                      .+...+...+...  ...++||||+|+..++.+++.|...++.+..+||+|++.+|.++++.|++|+++|||||+++++|
T Consensus       231 ~k~~~L~~~L~~~--~~~~~IVF~~tk~~a~~l~~~L~~~g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATdv~arG  308 (629)
T PRK11634        231 RKNEALVRFLEAE--DFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARG  308 (629)
T ss_pred             hHHHHHHHHHHhc--CCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcchHhcC
Confidence            3444555555443  56789999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637         98 LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus        98 idi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      +|+|++++||+|++|.+..+|+||+||+||.|+.|.+++|+++.+
T Consensus       309 IDip~V~~VI~~d~P~~~e~yvqRiGRtGRaGr~G~ai~~v~~~e  353 (629)
T PRK11634        309 LDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRE  353 (629)
T ss_pred             CCcccCCEEEEeCCCCCHHHHHHHhccccCCCCcceEEEEechHH
Confidence            999999999999999999999999999999999999999998654

>PTZ00424 helicase 45; Provisional

Probab=99.95  E-value=3.6e-27  Score=177.72  Aligned_cols=112  Identities=35%  Similarity=0.668  Sum_probs=106.7

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLA  112 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~  112 (150)
                      ...++||||++++.++.+++.|...++.+..+||+|++++|..+++.|++|+++|||||+.+++|+|+|++++||++++|
T Consensus       266 ~~~~~ivF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~~l~~GiDip~v~~VI~~~~p  345 (401)
T PTZ00424        266 TITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLP  345 (401)
T ss_pred             CCCeEEEEecCcHHHHHHHHHHHHCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcccccCCcCcccCCEEEEECCC
Confidence            56789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CChhHHHHhhccccCCCCccEEEEEEecCCCc
Q psy17637        113 RDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD  144 (150)
Q Consensus       113 ~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~  144 (150)
                      .+..+|+||+||+||.|..|.++.|+++.+..
T Consensus       346 ~s~~~y~qr~GRagR~g~~G~~i~l~~~~~~~  377 (401)
T PTZ00424        346 ASPENYIHRIGRSGRFGRKGVAINFVTPDDIE  377 (401)
T ss_pred             CCHHHEeecccccccCCCCceEEEEEcHHHHH
Confidence            99999999999999999999999999876543

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

Probab=99.95  E-value=6.3e-27  Score=179.81  Aligned_cols=112  Identities=29%  Similarity=0.418  Sum_probs=108.3

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDL  111 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~  111 (150)
                      ....+.||||.|++.+|.++++|...|+.+..||++|+.++|+.+.++|..++..|+|||.+++||||-|++.+||||++
T Consensus       228 ~~~~~GIIYc~sRk~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfViH~~l  307 (590)
T COG0514         228 QLSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDL  307 (590)
T ss_pred             ccCCCeEEEEeeHHhHHHHHHHHHHCCCceEEecCCCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCceEEEEecC
Confidence            46677999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637        112 ARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus       112 ~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |.|+++|+|.+|||||.|.++.+++|+.+.|.
T Consensus       308 P~s~EsYyQE~GRAGRDG~~a~aill~~~~D~  339 (590)
T COG0514         308 PGSIESYYQETGRAGRDGLPAEAILLYSPEDI  339 (590)
T ss_pred             CCCHHHHHHHHhhccCCCCcceEEEeeccccH
Confidence            99999999999999999999999999998874

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.95  E-value=1.3e-26  Score=182.17  Aligned_cols=134  Identities=22%  Similarity=0.399  Sum_probs=116.6

Q ss_pred             cCeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC
Q psy17637          5 KGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE   84 (150)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~   84 (150)
                      +++.+.......  ....+++.+...  ...++||||+|++.++.+++.|...++.+..+||+|++++|..+++.|..|+
T Consensus       199 ~nl~~~v~~~~~--~~~~l~~~l~~~--~~~~~IIf~~sr~~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F~~g~  274 (591)
T TIGR01389       199 PNLRFSVVKKNN--KQKFLLDYLKKH--RGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDD  274 (591)
T ss_pred             CCcEEEEEeCCC--HHHHHHHHHHhc--CCCCEEEEECcHHHHHHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHHHcCC
Confidence            344444433332  234566666554  4678999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637         85 CRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus        85 ~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      ++|||||+++++|+|+|++++||++++|.++++|+|++||+||.|.++.++++++..+
T Consensus       275 ~~vlVaT~a~~~GID~p~v~~VI~~~~p~s~~~y~Q~~GRaGR~G~~~~~il~~~~~d  332 (591)
T TIGR01389       275 VKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPAD  332 (591)
T ss_pred             CcEEEEechhhccCcCCCCCEEEEcCCCCCHHHHhhhhccccCCCCCceEEEecCHHH
Confidence            9999999999999999999999999999999999999999999999999998887654

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.

>KOG0332|consensus

Probab=99.94  E-value=3.5e-26  Score=165.18  Aligned_cols=129  Identities=36%  Similarity=0.567  Sum_probs=115.6

Q ss_pred             chhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCC
Q psy17637         15 KDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVA   94 (150)
Q Consensus        15 ~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~   94 (150)
                      ....+...|.+ |... -..++.||||.|++.+.+|+..|...|+.+..+||.|+-.+|..++..|+.|..+|||+|+++
T Consensus       313 ~~~~K~~~l~~-lyg~-~tigqsiIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l~~~~R~~ii~~Fr~g~~kVLitTnV~  390 (477)
T KOG0332|consen  313 CRDDKYQALVN-LYGL-LTIGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLTVEQRAAIIDRFREGKEKVLITTNVC  390 (477)
T ss_pred             chhhHHHHHHH-HHhh-hhhhheEEEEeehhhHHHHHHHHHhcCceeEEeeccchhHHHHHHHHHHhcCcceEEEEechh
Confidence            34444455555 5444 477899999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCccCCcEEEEecCCC------ChhHHHHhhccccCCCCccEEEEEEecCCCcc
Q psy17637         95 ARGLDIPHIRTVVNYDLAR------DIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDG  145 (150)
Q Consensus        95 ~~Gidi~~~~~vi~~~~~~------~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~~  145 (150)
                      .+|+|++.++.|||||+|.      +.+.|++|+||+||.|+.|.++.++...+...
T Consensus       391 ARGiDv~qVs~VvNydlP~~~~~~pD~etYlHRiGRtGRFGkkG~a~n~v~~~~s~~  447 (477)
T KOG0332|consen  391 ARGIDVAQVSVVVNYDLPVKYTGEPDYETYLHRIGRTGRFGKKGLAINLVDDKDSMN  447 (477)
T ss_pred             hcccccceEEEEEecCCccccCCCCCHHHHHHHhcccccccccceEEEeecccCcHH
Confidence            9999999999999999996      78999999999999999999999988776543

>KOG0341|consensus

Probab=99.93  E-value=1.9e-26  Score=167.76  Aligned_cols=125  Identities=35%  Similarity=0.652  Sum_probs=116.0

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCcc
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIP  101 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~  101 (150)
                      .++-.+....+..+|++|||..+..++.+.++|.-+|+.++.+||+-++++|...++.|+.|+..|||+|++.+.|+|+|
T Consensus       409 KiVylLeCLQKT~PpVLIFaEkK~DVD~IhEYLLlKGVEavaIHGGKDQedR~~ai~afr~gkKDVLVATDVASKGLDFp  488 (610)
T KOG0341|consen  409 KIVYLLECLQKTSPPVLIFAEKKADVDDIHEYLLLKGVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATDVASKGLDFP  488 (610)
T ss_pred             hhhhHHHHhccCCCceEEEeccccChHHHHHHHHHccceeEEeecCcchhHHHHHHHHHhcCCCceEEEecchhccCCCc
Confidence            45555555556789999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCccc
Q psy17637        102 HIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGE  146 (150)
Q Consensus       102 ~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~~~  146 (150)
                      ++.+|||||+|..++.|++|+||+||.|..|.+.+|+++......
T Consensus       489 ~iqHVINyDMP~eIENYVHRIGRTGRsg~~GiATTfINK~~~esv  533 (610)
T KOG0341|consen  489 DIQHVINYDMPEEIENYVHRIGRTGRSGKTGIATTFINKNQEESV  533 (610)
T ss_pred             cchhhccCCChHHHHHHHHHhcccCCCCCcceeeeeecccchHHH
Confidence            999999999999999999999999999999999999998766544

>KOG0326|consensus

Probab=99.93  E-value=2.2e-26  Score=163.71  Aligned_cols=113  Identities=35%  Similarity=0.603  Sum_probs=108.9

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLA  112 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~  112 (150)
                      ..++.|||||+...+|.++.+..+.|+.+.++|+.|.++.|..+.-.|++|.++.||||+.+.+|+|++.+++|||||+|
T Consensus       321 qINQsIIFCNS~~rVELLAkKITelGyscyyiHakM~Q~hRNrVFHdFr~G~crnLVctDL~TRGIDiqavNvVINFDfp  400 (459)
T KOG0326|consen  321 QINQSIIFCNSTNRVELLAKKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLVCTDLFTRGIDIQAVNVVINFDFP  400 (459)
T ss_pred             cccceEEEeccchHhHHHHHHHHhccchhhHHHHHHHHhhhhhhhhhhhccccceeeehhhhhcccccceeeEEEecCCC
Confidence            67799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CChhHHHHhhccccCCCCccEEEEEEecCCCcc
Q psy17637        113 RDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDG  145 (150)
Q Consensus       113 ~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~~  145 (150)
                      ++.++|++|+||+||.|..|.++.+++-+|...
T Consensus       401 k~aEtYLHRIGRsGRFGhlGlAInLityedrf~  433 (459)
T KOG0326|consen  401 KNAETYLHRIGRSGRFGHLGLAINLITYEDRFN  433 (459)
T ss_pred             CCHHHHHHHccCCccCCCcceEEEEEehhhhhh
Confidence            999999999999999999999999999876544

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

Probab=99.93  E-value=9.9e-26  Score=180.18  Aligned_cols=111  Identities=18%  Similarity=0.169  Sum_probs=102.0

Q ss_pred             CCCeeEEehhhhhHHHHHhhcccc--------CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcE
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVK--------EYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRT  105 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~--------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~  105 (150)
                      ..++||||+|++.++.++..|...        +.++..+||++++++|.++++.|++|++++||||+++++|+|+|++++
T Consensus       271 ~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~~f~~G~i~vLVaTd~lerGIDI~~vd~  350 (742)
T TIGR03817       271 GARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELERALRDGELLGVATTNALELGVDISGLDA  350 (742)
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHHHHHcCCceEEEECchHhccCCcccccE
Confidence            579999999999999999987653        467889999999999999999999999999999999999999999999


Q ss_pred             EEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCc
Q psy17637        106 VVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD  144 (150)
Q Consensus       106 vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~  144 (150)
                      ||+++.|.+..+|+||+||+||.|+.|.+++++.....+
T Consensus       351 VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~~~~d  389 (742)
T TIGR03817       351 VVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARDDPLD  389 (742)
T ss_pred             EEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCCChHH
Confidence            999999999999999999999999999999888754333

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.

>KOG0340|consensus

Probab=99.93  E-value=3.2e-25  Score=159.31  Aligned_cols=122  Identities=40%  Similarity=0.594  Sum_probs=111.6

Q ss_pred             HHHHHHHhccC-CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCc
Q psy17637         22 HLVRNLEGANQ-EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDI  100 (150)
Q Consensus        22 ~ll~~l~~~~~-~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi  100 (150)
                      .++..+....+ +...++||+++...|+.|+..|+...+.+..+|+.|++.+|...+.+|+++..+|||||+++++|+|+
T Consensus       241 YLv~~Lr~~~~~~~~simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFrs~~~~iliaTDVAsRGLDI  320 (442)
T KOG0340|consen  241 YLVHLLRDFENKENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFRSNAARILIATDVASRGLDI  320 (442)
T ss_pred             HHHHHHhhhhhccCceEEEEeehhHHHHHHHHHHhhhceeeeehhhcchHHHHHHHHHHHhhcCccEEEEechhhcCCCC
Confidence            44444444322 57899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637        101 PHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus       101 ~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |.+.+|+|+|.|.++.+|++|+||+.|.|+.|.++.++++.|-
T Consensus       321 P~V~LVvN~diPr~P~~yiHRvGRtARAGR~G~aiSivt~rDv  363 (442)
T KOG0340|consen  321 PTVELVVNHDIPRDPKDYIHRVGRTARAGRKGMAISIVTQRDV  363 (442)
T ss_pred             CceeEEEecCCCCCHHHHHHhhcchhcccCCcceEEEechhhH
Confidence            9999999999999999999999999999999999999996553

>KOG0335|consensus

Probab=99.93  E-value=4.5e-25  Score=165.00  Aligned_cols=138  Identities=36%  Similarity=0.583  Sum_probs=122.4

Q ss_pred             CcCeeEEEeecchhhHHHHHHHHHHhccC--CC-----CCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHH
Q psy17637          4 NKGVAYTLVTDKDKEFAGHLVRNLEGANQ--EV-----PPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSV   76 (150)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~ll~~l~~~~~--~~-----~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~   76 (150)
                      .+++.+.+....+..+...|++.+.....  ..     ..++|||.|++.++++...|...++++..+||.-++.+|.+.
T Consensus       300 ~~ni~q~i~~V~~~~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~a  379 (482)
T KOG0335|consen  300 SENITQKILFVNEMEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNGYPAKSIHGDRTQIEREQA  379 (482)
T ss_pred             cccceeEeeeecchhhHHHHHHHhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcCCCCceeecchhhhhHHHHH
Confidence            45555555556666666778888875531  22     379999999999999999999999999999999999999999


Q ss_pred             HHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecC
Q psy17637         77 ITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus        77 ~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                      ++.|++|...+||||+++++|+|+|++++||+||+|.+..+|++||||+||.|..|.+..|++..
T Consensus       380 l~~Fr~g~~pvlVaT~VaaRGlDi~~V~hVInyDmP~d~d~YvHRIGRTGR~Gn~G~atsf~n~~  444 (482)
T KOG0335|consen  380 LNDFRNGKAPVLVATNVAARGLDIPNVKHVINYDMPADIDDYVHRIGRTGRVGNGGRATSFFNEK  444 (482)
T ss_pred             HHHhhcCCcceEEEehhhhcCCCCCCCceeEEeecCcchhhHHHhccccccCCCCceeEEEeccc
Confidence            99999999999999999999999999999999999999999999999999999999999999843

>KOG0336|consensus

Probab=99.92  E-value=6.6e-25  Score=160.64  Aligned_cols=136  Identities=35%  Similarity=0.587  Sum_probs=120.0

Q ss_pred             eeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCce
Q psy17637          7 VAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECR   86 (150)
Q Consensus         7 ~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~   86 (150)
                      +.+.+....+.++. .+++.+...-....++||||.++..++.|...|...|+..-.+||+-++.+|+..++.|++|+++
T Consensus       439 VkQ~i~v~~d~~k~-~~~~~f~~~ms~ndKvIiFv~~K~~AD~LSSd~~l~gi~~q~lHG~r~Q~DrE~al~~~ksG~vr  517 (629)
T KOG0336|consen  439 VKQNIIVTTDSEKL-EIVQFFVANMSSNDKVIIFVSRKVMADHLSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEVR  517 (629)
T ss_pred             eeeeEEecccHHHH-HHHHHHHHhcCCCceEEEEEechhhhhhccchhhhcccchhhccCChhhhhHHHHHHhhhcCceE
Confidence            33444444444443 56666666557788999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         87 ILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        87 vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |||+|+..++|+|+++++||++||+|.++++|++|+||+||.|+.|..+.|++..|-
T Consensus       518 ILvaTDlaSRGlDv~DiTHV~NyDFP~nIeeYVHRvGrtGRaGr~G~sis~lt~~D~  574 (629)
T KOG0336|consen  518 ILVATDLASRGLDVPDITHVYNYDFPRNIEEYVHRVGRTGRAGRTGTSISFLTRNDW  574 (629)
T ss_pred             EEEEechhhcCCCchhcceeeccCCCccHHHHHHHhcccccCCCCcceEEEEehhhH
Confidence            999999999999999999999999999999999999999999999999999987654

>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=99.92  E-value=9.9e-24  Score=135.73  Aligned_cols=119  Identities=39%  Similarity=0.529  Sum_probs=107.7

Q ss_pred             hHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCccc
Q psy17637         18 EFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG   97 (150)
Q Consensus        18 ~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G   97 (150)
                      .+...+.+.+.+......++||||++.+.++.++..|...+..+..+||++++.++..+++.|..+...+|++|+.+++|
T Consensus        12 ~k~~~i~~~i~~~~~~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~~~~~G   91 (131)
T cd00079          12 EKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARG   91 (131)
T ss_pred             HHHHHHHHHHHhcccCCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcChhhcC
Confidence            34456666666653467899999999999999999998888899999999999999999999999999999999999999


Q ss_pred             CCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEE
Q psy17637         98 LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYT  136 (150)
Q Consensus        98 idi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~  136 (150)
                      +|+|.+++||++++|++...+.|++||++|.|+.+.+++
T Consensus        92 ~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~  130 (131)
T cd00079          92 IDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAIL  130 (131)
T ss_pred             cChhhCCEEEEeCCCCCHHHheecccccccCCCCceEEe
Confidence            999999999999999999999999999999998777665

>KOG0342|consensus

Probab=99.91  E-value=2.1e-24  Score=160.30  Aligned_cols=131  Identities=34%  Similarity=0.454  Sum_probs=116.2

Q ss_pred             EeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEE
Q psy17637         11 LVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVA   90 (150)
Q Consensus        11 ~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~   90 (150)
                      .+.+.+.. +..+...+.+. -...++||||+|-..+..+++.|....+++..+||+.++..|..+...|...+.-||||
T Consensus       309 vv~~~~~~-f~ll~~~LKk~-~~~~KiiVF~sT~~~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~~~F~kaesgIL~c  386 (543)
T KOG0342|consen  309 VVAPSDSR-FSLLYTFLKKN-IKRYKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFCKAESGILVC  386 (543)
T ss_pred             Eeccccch-HHHHHHHHHHh-cCCceEEEEechhhHHHHHHHHHhhcCCchhhhhcCCcccccchHHHHHhhcccceEEe
Confidence            33444443 44566666665 33389999999999999999999988999999999999999999999999999999999


Q ss_pred             cCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         91 TDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        91 T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |++.++|+|+|++++||.+++|.++.+|+||+||+||.|..|.+++++.+.+.
T Consensus       387 TDVaARGlD~P~V~~VvQ~~~P~d~~~YIHRvGRTaR~gk~G~alL~l~p~El  439 (543)
T KOG0342|consen  387 TDVAARGLDIPDVDWVVQYDPPSDPEQYIHRVGRTAREGKEGKALLLLAPWEL  439 (543)
T ss_pred             cchhhccCCCCCceEEEEeCCCCCHHHHHHHhccccccCCCceEEEEeChhHH
Confidence            99999999999999999999999999999999999999999999999987654

>KOG0344|consensus

Probab=99.91  E-value=8e-24  Score=159.96  Aligned_cols=122  Identities=33%  Similarity=0.520  Sum_probs=111.6

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhc-cccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCccc
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSL-TVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG   97 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L-~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G   97 (150)
                      ++..+-+.+...  -.+|++||+.+.+.+..|+..| ...++.+..+||+.++.+|...+++|+.|++++|+||+.+++|
T Consensus       374 K~lA~rq~v~~g--~~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicTdll~RG  451 (593)
T KOG0344|consen  374 KLLALRQLVASG--FKPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGERSQKQRDETMERFRIGKIWVLICTDLLARG  451 (593)
T ss_pred             HHHHHHHHHhcc--CCCCeEEEEecHHHHHHHHHHhhhccCcceeeEecccchhHHHHHHHHHhccCeeEEEehhhhhcc
Confidence            334444444444  5679999999999999999999 7789999999999999999999999999999999999999999


Q ss_pred             CCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637         98 LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus        98 idi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      +|+.+++.||+||+|.+.-+|++|+||+||.|+.|.+++|+++++
T Consensus       452 iDf~gvn~VInyD~p~s~~syihrIGRtgRag~~g~Aitfytd~d  496 (593)
T KOG0344|consen  452 IDFKGVNLVINYDFPQSDLSYIHRIGRTGRAGRSGKAITFYTDQD  496 (593)
T ss_pred             ccccCcceEEecCCCchhHHHHHHhhccCCCCCCcceEEEecccc
Confidence            999999999999999999999999999999999999999999854

>KOG0345|consensus

Probab=99.90  E-value=1.3e-23  Score=155.55  Aligned_cols=134  Identities=30%  Similarity=0.482  Sum_probs=116.8

Q ss_pred             eeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhcccc--CceEEEecCCCCHHHHHHHHHHhhcCC
Q psy17637          7 VAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVK--EYDVLLLHGDMDQSERNSVITKFKRQE   84 (150)
Q Consensus         7 ~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~   84 (150)
                      +..++...+..++...++..+.+.  ...++|||++|=..++.....|...  ...+..+||.|.+..|.+++..|....
T Consensus       230 L~~~Y~v~~a~eK~~~lv~~L~~~--~~kK~iVFF~TCasVeYf~~~~~~~l~~~~i~~iHGK~~q~~R~k~~~~F~~~~  307 (567)
T KOG0345|consen  230 LALEYLVCEADEKLSQLVHLLNNN--KDKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIHGKMSQKARAKVLEAFRKLS  307 (567)
T ss_pred             hcceeeEecHHHHHHHHHHHHhcc--ccccEEEEecCcchHHHHHHHHHHHhCCCcEEEecchhcchhHHHHHHHHHhcc
Confidence            444555555566667888888775  7889999999988888777776543  567999999999999999999999977


Q ss_pred             ceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637         85 CRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus        85 ~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      ..+|+||+++++|+|+|++++||+||+|.+++.|+||+||++|.|+.|.+++|+.+.+
T Consensus       308 ~~vl~~TDVaARGlDip~iD~VvQ~DpP~~~~~FvHR~GRTaR~gr~G~Aivfl~p~E  365 (567)
T KOG0345|consen  308 NGVLFCTDVAARGLDIPGIDLVVQFDPPKDPSSFVHRCGRTARAGREGNAIVFLNPRE  365 (567)
T ss_pred             CceEEeehhhhccCCCCCceEEEecCCCCChhHHHhhcchhhhccCccceEEEecccH
Confidence            7899999999999999999999999999999999999999999999999999988743

>KOG0351|consensus

Probab=99.90  E-value=1.1e-23  Score=169.54  Aligned_cols=141  Identities=19%  Similarity=0.306  Sum_probs=128.4

Q ss_pred             CCcCeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhc
Q psy17637          3 GNKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKR   82 (150)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~   82 (150)
                      +++++.|.+...+.......++..+... .+..+.||||.++..||.+...|...++.+..||+||++++|..+...|..
T Consensus       455 nR~NL~yeV~~k~~~~~~~~~~~~~~~~-~~~~s~IIYC~sr~~ce~vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~~w~~  533 (941)
T KOG0351|consen  455 NRPNLKYEVSPKTDKDALLDILEESKLR-HPDQSGIIYCLSRKECEQVSAVLRSLGKSAAFYHAGLPPKERETVQKAWMS  533 (941)
T ss_pred             CCCCceEEEEeccCccchHHHHHHhhhc-CCCCCeEEEeCCcchHHHHHHHHHHhchhhHhhhcCCCHHHHHHHHHHHhc
Confidence            3567778777777555556677777666 788999999999999999999999999999999999999999999999999


Q ss_pred             CCceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCc
Q psy17637         83 QECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD  144 (150)
Q Consensus        83 g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~  144 (150)
                      ++++|+|||=+++||||.|++..||+|+.|++.+.|+|.+|||||.|..+.|++|+...+..
T Consensus       534 ~~~~VivATVAFGMGIdK~DVR~ViH~~lPks~E~YYQE~GRAGRDG~~s~C~l~y~~~D~~  595 (941)
T KOG0351|consen  534 DKIRVIVATVAFGMGIDKPDVRFVIHYSLPKSFEGYYQEAGRAGRDGLPSSCVLLYGYADIS  595 (941)
T ss_pred             CCCeEEEEEeeccCCCCCCceeEEEECCCchhHHHHHHhccccCcCCCcceeEEecchhHHH
Confidence            99999999999999999999999999999999999999999999999999999999887543

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.90  E-value=5.2e-23  Score=166.67  Aligned_cols=118  Identities=22%  Similarity=0.300  Sum_probs=104.6

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhc-cccCceEEEecCCCCHHHHHHHHHHhhcC--CceEEEEcCCCc
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSL-TVKEYDVLLLHGDMDQSERNSVITKFKRQ--ECRILVATDVAA   95 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L-~~~~~~~~~~~~~~~~~~r~~~~~~f~~g--~~~vlv~T~~~~   95 (150)
                      ++..|++.+...  ...++||||++++.++.+.+.| ...|+++..+||+|++.+|.++++.|+++  ...|||||++++
T Consensus       480 Ki~~L~~~L~~~--~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~~~F~~~~~~~~VLIsTdvgs  557 (956)
T PRK04914        480 RVEWLIDFLKSH--RSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLLCSEIGS  557 (956)
T ss_pred             HHHHHHHHHHhc--CCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHHHHHhcCCCCccEEEechhhc
Confidence            445666666554  5779999999999999999999 46699999999999999999999999984  589999999999


Q ss_pred             ccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEE
Q psy17637         96 RGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLV  138 (150)
Q Consensus        96 ~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~  138 (150)
                      +|+|++.+++||+||+|+++..|.||+||++|.|+.+.+.+++
T Consensus       558 eGlNlq~a~~VInfDlP~nP~~~eQRIGR~~RiGQ~~~V~i~~  600 (956)
T PRK04914        558 EGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQKHDIQIHV  600 (956)
T ss_pred             cCCCcccccEEEEecCCCCHHHHHHHhcccccCCCCceEEEEE
Confidence            9999999999999999999999999999999999887654443

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.90  E-value=4.4e-23  Score=167.66  Aligned_cols=119  Identities=24%  Similarity=0.297  Sum_probs=100.3

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhhHHHHHhhcccc------CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCc
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVK------EYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAA   95 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~   95 (150)
                      .+...+........++||||+|++.++.++..|...      +..+..+||+|++++|..+++.|++|++++||||+.++
T Consensus       272 ~l~~~L~~~i~~~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~i~vLVaTs~Le  351 (876)
T PRK13767        272 ALYETLHELIKEHRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLE  351 (876)
T ss_pred             HHHHHHHHHHhcCCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCCCeEEEECChHH
Confidence            334444433234678999999999999999998762      45799999999999999999999999999999999999


Q ss_pred             ccCCccCCcEEEEecCCCChhHHHHhhccccCCC-CccEEEEEEec
Q psy17637         96 RGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAG-NKGVAYTLVTD  140 (150)
Q Consensus        96 ~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g-~~~~~~~~~~~  140 (150)
                      +|+|+|++++||+++.|.+..+|+||+||+||.+ ..+..++++..
T Consensus       352 ~GIDip~Vd~VI~~~~P~sv~~ylQRiGRaGR~~g~~~~g~ii~~~  397 (876)
T PRK13767        352 LGIDIGYIDLVVLLGSPKSVSRLLQRIGRAGHRLGEVSKGRIIVVD  397 (876)
T ss_pred             hcCCCCCCcEEEEeCCCCCHHHHHHhcccCCCCCCCCCcEEEEEcC
Confidence            9999999999999999999999999999999864 34445544443

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

Probab=99.90  E-value=7.3e-23  Score=152.95  Aligned_cols=125  Identities=28%  Similarity=0.391  Sum_probs=107.4

Q ss_pred             HHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEE-Eec--------CCCCHHHHHHHHHHhhcCCceEEEE
Q psy17637         20 AGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVL-LLH--------GDMDQSERNSVITKFKRQECRILVA   90 (150)
Q Consensus        20 ~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~-~~~--------~~~~~~~r~~~~~~f~~g~~~vlv~   90 (150)
                      +..++...... ....++|||++.++.++.+.+.|...+..+. .+-        .||+++++.+++++|+.|+.+||||
T Consensus       353 l~eilke~~~k-~~~~RvIVFT~yRdTae~i~~~L~~~~~~~~~rFiGQa~r~~~~GMsQkeQ~eiI~~Fr~Ge~nVLVa  431 (542)
T COG1111         353 LREILKEQLEK-NGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNVLVA  431 (542)
T ss_pred             HHHHHHHHHhc-CCCceEEEEehhHhHHHHHHHHHHhcCCcceeEEeeccccccccccCHHHHHHHHHHHhcCCceEEEE
Confidence            33444444433 4568999999999999999999998877663 222        4699999999999999999999999


Q ss_pred             cCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCccc
Q psy17637         91 TDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGE  146 (150)
Q Consensus        91 T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~~~  146 (150)
                      |++.++|+|+|.++.||+|++..|+-.++||.||+||. +.|.+++|+++.+.++.
T Consensus       432 TSVgEEGLDIp~vDlVifYEpvpSeIR~IQR~GRTGR~-r~Grv~vLvt~gtrdea  486 (542)
T COG1111         432 TSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRK-RKGRVVVLVTEGTRDEA  486 (542)
T ss_pred             cccccccCCCCcccEEEEecCCcHHHHHHHhhCccccC-CCCeEEEEEecCchHHH
Confidence            99999999999999999999999999999999999999 68999999998866554

>KOG0347|consensus

Probab=99.90  E-value=4.7e-24  Score=160.55  Aligned_cols=128  Identities=32%  Similarity=0.406  Sum_probs=115.5

Q ss_pred             hHHHHHHHHHHhccC-------------CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC
Q psy17637         18 EFAGHLVRNLEGANQ-------------EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE   84 (150)
Q Consensus        18 ~~~~~ll~~l~~~~~-------------~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~   84 (150)
                      .....|++.+.++..             =.+++|||||+++.+..|+..|+..++....+|+.|.+++|.+.+++|++..
T Consensus       434 ~ta~~l~Es~I~C~~~eKD~ylyYfl~ryPGrTlVF~NsId~vKRLt~~L~~L~i~p~~LHA~M~QKqRLknLEkF~~~~  513 (731)
T KOG0347|consen  434 ATASTLTESLIECPPLEKDLYLYYFLTRYPGRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHASMIQKQRLKNLEKFKQSP  513 (731)
T ss_pred             hHHHHHHHHhhcCCccccceeEEEEEeecCCceEEEechHHHHHHHHHHHhhcCCCCchhhHHHHHHHHHHhHHHHhcCC
Confidence            344566666665521             1478999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCcc
Q psy17637         85 CRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDG  145 (150)
Q Consensus        85 ~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~~  145 (150)
                      ..|||||+++.+|+|||++.|||+|.+|.+.+.|++|.||+.|.+..|..+.++.+.+...
T Consensus       514 ~~VLiaTDVAARGLDIp~V~HVIHYqVPrtseiYVHRSGRTARA~~~Gvsvml~~P~e~~~  574 (731)
T KOG0347|consen  514 SGVLIATDVAARGLDIPGVQHVIHYQVPRTSEIYVHRSGRTARANSEGVSVMLCGPQEVGP  574 (731)
T ss_pred             CeEEEeehhhhccCCCCCcceEEEeecCCccceeEecccccccccCCCeEEEEeChHHhHH
Confidence            9999999999999999999999999999999999999999999999999999999887443

>KOG0327|consensus

Probab=99.89  E-value=4.2e-23  Score=149.49  Aligned_cols=137  Identities=33%  Similarity=0.582  Sum_probs=123.2

Q ss_pred             cCeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC
Q psy17637          5 KGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE   84 (150)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~   84 (150)
                      +++.+++.......++..+.+...    ...+.+|||||++.+..+..+|...+..+..+||.|.+.+|..++..|+.|.
T Consensus       238 ~gikq~~i~v~k~~k~~~l~dl~~----~~~q~~if~nt~r~v~~l~~~L~~~~~~~s~~~~d~~q~~R~~~~~ef~~gs  313 (397)
T KOG0327|consen  238 EGIKQFYINVEKEEKLDTLCDLYR----RVTQAVIFCNTRRKVDNLTDKLRAHGFTVSAIHGDMEQNERDTLMREFRSGS  313 (397)
T ss_pred             hheeeeeeeccccccccHHHHHHH----hhhcceEEecchhhHHHHHHHHhhCCceEEEeecccchhhhhHHHHHhhcCC
Confidence            456677776666656666666555    4568999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCcc
Q psy17637         85 CRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDG  145 (150)
Q Consensus        85 ~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~~  145 (150)
                      .+|||+|+.+++|+|+..++.|++|+.|.....|++|+||+||.|..|.++.++++.+..+
T Consensus       314 srvlIttdl~argidv~~~slvinydlP~~~~~yihR~gr~gr~grkg~~in~v~~~d~~~  374 (397)
T KOG0327|consen  314 SRVLITTDLLARGIDVQQVSLVVNYDLPARKENYIHRIGRAGRFGRKGVAINFVTEEDVRD  374 (397)
T ss_pred             ceEEeeccccccccchhhcceeeeeccccchhhhhhhcccccccCCCceeeeeehHhhHHH
Confidence            9999999999999999999999999999999999999999999999999999999876654

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.89  E-value=3.9e-22  Score=161.80  Aligned_cols=110  Identities=25%  Similarity=0.371  Sum_probs=102.1

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhcccc--CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEe
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVK--EYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNY  109 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~  109 (150)
                      ..+.++++||++++.++.+++.|...  +.++..+||+|++++|.+++++|++|+.+|||||+++++|+|+|++++||++
T Consensus       658 ~~g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~iie~GIDIp~v~~VIi~  737 (926)
T TIGR00580       658 LRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIE  737 (926)
T ss_pred             HcCCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcccccccCCEEEEe
Confidence            34678999999999999999999863  7789999999999999999999999999999999999999999999999999


Q ss_pred             cCCC-ChhHHHHhhccccCCCCccEEEEEEecC
Q psy17637        110 DLAR-DIDTHTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus       110 ~~~~-~~~~~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                      +.|. +..+|.|++||+||.|+.|.|++++...
T Consensus       738 ~a~~~gls~l~Qr~GRvGR~g~~g~aill~~~~  770 (926)
T TIGR00580       738 RADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQ  770 (926)
T ss_pred             cCCCCCHHHHHHHhcCCCCCCCCeEEEEEECCc
Confidence            9875 7889999999999999999999998764

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.

>KOG0338|consensus

Probab=99.89  E-value=4.6e-23  Score=154.18  Aligned_cols=110  Identities=37%  Similarity=0.583  Sum_probs=105.3

Q ss_pred             CCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCCC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLAR  113 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~  113 (150)
                      ..++|||+.|++.+..+.-.|--.|+++.-+||.+++.+|...++.|+.+++++||||+++++|+||+++..||||++|.
T Consensus       426 ~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGsLtQ~QRlesL~kFk~~eidvLiaTDvAsRGLDI~gV~tVINy~mP~  505 (691)
T KOG0338|consen  426 QDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGSLTQEQRLESLEKFKKEEIDVLIATDVASRGLDIEGVQTVINYAMPK  505 (691)
T ss_pred             ccceEEEEehHHHHHHHHHHHHHhhchhhhhcccccHHHHHHHHHHHHhccCCEEEEechhhccCCccceeEEEeccCch
Confidence            46899999999999999888888899999999999999999999999999999999999999999999999999999999


Q ss_pred             ChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637        114 DIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus       114 ~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +...|+||+||+.|.|+.|..+.|+.+.+.
T Consensus       506 t~e~Y~HRVGRTARAGRaGrsVtlvgE~dR  535 (691)
T KOG0338|consen  506 TIEHYLHRVGRTARAGRAGRSVTLVGESDR  535 (691)
T ss_pred             hHHHHHHHhhhhhhcccCcceEEEeccccH
Confidence            999999999999999999999999988753

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.88  E-value=3.4e-22  Score=158.95  Aligned_cols=125  Identities=19%  Similarity=0.273  Sum_probs=111.9

Q ss_pred             hhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcc
Q psy17637         17 KEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAAR   96 (150)
Q Consensus        17 ~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~   96 (150)
                      ..+...++..+........|+||||+|.+.++.++..|...++++..+||.+.+.++..+...++.|  .|+|||+++++
T Consensus       411 ~~K~~al~~~i~~~~~~~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L~~~~~~~e~~~i~~ag~~g--~VlIATdmAgR  488 (790)
T PRK09200        411 DEKYKAVIEEVKERHETGRPVLIGTGSIEQSETFSKLLDEAGIPHNLLNAKNAAKEAQIIAEAGQKG--AVTVATNMAGR  488 (790)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEecCCccHHHHHHHHHcCCCC--eEEEEccchhc
Confidence            3455677777766545788999999999999999999999999999999999998888887777766  79999999999


Q ss_pred             cCCc---cCCc-----EEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         97 GLDI---PHIR-----TVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        97 Gidi---~~~~-----~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |+|+   |.+.     +||++++|.+...|.|++||+||.|++|.++.|++.+|.
T Consensus       489 G~DI~l~~~V~~~GGL~VI~~d~p~s~r~y~qr~GRtGR~G~~G~s~~~is~eD~  543 (790)
T PRK09200        489 GTDIKLGEGVHELGGLAVIGTERMESRRVDLQLRGRSGRQGDPGSSQFFISLEDD  543 (790)
T ss_pred             CcCCCcccccccccCcEEEeccCCCCHHHHHHhhccccCCCCCeeEEEEEcchHH
Confidence            9999   6898     999999999999999999999999999999999987654

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.88  E-value=8.2e-22  Score=156.87  Aligned_cols=120  Identities=28%  Similarity=0.373  Sum_probs=101.3

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhh--------hHHHHHhhcccc--CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEc
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQL--------NAEELANSLTVK--EYDVLLLHGDMDQSERNSVITKFKRQECRILVAT   91 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~--------~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T   91 (150)
                      .+++.+......+.+++|||+..+        .++.+++.|...  ++++..+||+|++++|..++++|++|+.+|||||
T Consensus       459 ~~~~~i~~~~~~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT  538 (681)
T PRK10917        459 EVYERIREEIAKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVAT  538 (681)
T ss_pred             HHHHHHHHHHHcCCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEC
Confidence            344444443356789999998543        455666666544  4689999999999999999999999999999999


Q ss_pred             CCCcccCCccCCcEEEEecCCC-ChhHHHHhhccccCCCCccEEEEEEecC
Q psy17637         92 DVAARGLDIPHIRTVVNYDLAR-DIDTHTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus        92 ~~~~~Gidi~~~~~vi~~~~~~-~~~~~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                      +++++|+|+|++++||+++.|. +.+.+.|++||+||.|..|.|++++...
T Consensus       539 ~vie~GiDip~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~ill~~~~  589 (681)
T PRK10917        539 TVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDP  589 (681)
T ss_pred             cceeeCcccCCCcEEEEeCCCCCCHHHHHHHhhcccCCCCceEEEEEECCC
Confidence            9999999999999999999987 6889999999999999999999999643

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.88  E-value=4.9e-22  Score=155.29  Aligned_cols=125  Identities=22%  Similarity=0.262  Sum_probs=106.0

Q ss_pred             hhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcc
Q psy17637         17 KEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAAR   96 (150)
Q Consensus        17 ~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~   96 (150)
                      ..+...|++.+........++||||+|++.++.++..|...++++..+||.+++  ++..+..|..+...|+|||+++++
T Consensus       456 ~~K~~aL~~~i~~~~~~~~pvLIft~t~~~se~L~~~L~~~gi~~~~Lhg~~~~--rE~~ii~~ag~~g~VlVATdmAgR  533 (656)
T PRK12898        456 AAKWAAVAARVRELHAQGRPVLVGTRSVAASERLSALLREAGLPHQVLNAKQDA--EEAAIVARAGQRGRITVATNMAGR  533 (656)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEeeCCcHH--HHHHHHHHcCCCCcEEEEccchhc
Confidence            334556777776654456789999999999999999999999999999998654  445555566666689999999999


Q ss_pred             cCCcc---CCc-----EEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         97 GLDIP---HIR-----TVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        97 Gidi~---~~~-----~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |+|++   ++.     +||+++.|.+...|.|++||+||.|++|.+++|++.+|.
T Consensus       534 GtDI~l~~~V~~~GGLhVI~~d~P~s~r~y~hr~GRTGRqG~~G~s~~~is~eD~  588 (656)
T PRK12898        534 GTDIKLEPGVAARGGLHVILTERHDSARIDRQLAGRCGRQGDPGSYEAILSLEDD  588 (656)
T ss_pred             ccCcCCccchhhcCCCEEEEcCCCCCHHHHHHhcccccCCCCCeEEEEEechhHH
Confidence            99998   565     999999999999999999999999999999999987653

>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=99.88  E-value=1.2e-22  Score=120.02  Aligned_cols=77  Identities=40%  Similarity=0.700  Sum_probs=74.3

Q ss_pred             hccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCC
Q psy17637         53 SLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAG  129 (150)
Q Consensus        53 ~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g  129 (150)
                      .|...++++..+||++++++|..+++.|+++...+||+|+.+++|+|+|.+++||++++|+++..|.|++||++|.|
T Consensus         2 ~L~~~~~~~~~i~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gid~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~g   78 (78)
T PF00271_consen    2 FLEKKGIKVAIIHGDMSQKERQEILKKFNSGEIRVLIATDILGEGIDLPDASHVIFYDPPWSPEEYIQRIGRAGRIG   78 (78)
T ss_dssp             HHHHTTSSEEEESTTSHHHHHHHHHHHHHTTSSSEEEESCGGTTSSTSTTESEEEESSSESSHHHHHHHHTTSSTTT
T ss_pred             ChHHCCCcEEEEECCCCHHHHHHHHHHhhccCceEEEeeccccccccccccccccccccCCCHHHHHHHhhcCCCCC
Confidence            46678999999999999999999999999999999999999999999999999999999999999999999999986

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 ....

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.88  E-value=9.5e-22  Score=155.14  Aligned_cols=123  Identities=23%  Similarity=0.330  Sum_probs=113.5

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccC
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGL   98 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gi   98 (150)
                      .+..++..+......+.++||||+|++.++.+++.|...++++..+||++++.+|.+++..|+.|++.|||||+.+++|+
T Consensus       427 qi~~Ll~eI~~~~~~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~L~rGf  506 (655)
T TIGR00631       427 QVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGL  506 (655)
T ss_pred             hHHHHHHHHHHHHcCCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcChhcCCe
Confidence            45578888877666788999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccCCcEEEEec-----CCCChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637         99 DIPHIRTVVNYD-----LARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus        99 di~~~~~vi~~~-----~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      |+|++++|++++     .|.+..+|+|++||+||. ..|.++++++..+
T Consensus       507 DiP~v~lVvi~DadifG~p~~~~~~iqriGRagR~-~~G~vi~~~~~~~  554 (655)
T TIGR00631       507 DLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVIMYADKIT  554 (655)
T ss_pred             eeCCCcEEEEeCcccccCCCCHHHHHHHhcCCCCC-CCCEEEEEEcCCC
Confidence            999999999988     799999999999999998 5788988888654

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

>KOG0348|consensus

Probab=99.88  E-value=7e-22  Score=148.55  Aligned_cols=113  Identities=35%  Similarity=0.529  Sum_probs=102.3

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccc----------------------cCceEEEecCCCCHHHHHHHHHHhhcCCceEEE
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTV----------------------KEYDVLLLHGDMDQSERNSVITKFKRQECRILV   89 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~----------------------~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv   89 (150)
                      ++..++|||+++.+.+++-+..|..                      .+.++..+||+|++++|..+++.|....-.||+
T Consensus       423 ~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~e~~s~~~~s~g~~~l~~~~k~~rLHGsm~QeeRts~f~~Fs~~~~~VLL  502 (708)
T KOG0348|consen  423 EEKQKMIVFFSCSDSVEFHYSLFSEALLSHLEGSSGAPDSEGLPPLFMDLKFYRLHGSMEQEERTSVFQEFSHSRRAVLL  502 (708)
T ss_pred             hhhceeEEEEechhHHHHHHHHHHhhhhcccccccCCcccCCChhhhhcceEEEecCchhHHHHHHHHHhhccccceEEE
Confidence            4566999999999999988777743                      144588999999999999999999998888999


Q ss_pred             EcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCc
Q psy17637         90 ATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD  144 (150)
Q Consensus        90 ~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~  144 (150)
                      ||++.++|+|+|.+.+||.||+|.+.++|++|+||+.|.|..|..++|+.+.+.+
T Consensus       503 cTDVAaRGLDlP~V~~vVQYd~P~s~adylHRvGRTARaG~kG~alLfL~P~Eae  557 (708)
T KOG0348|consen  503 CTDVAARGLDLPHVGLVVQYDPPFSTADYLHRVGRTARAGEKGEALLFLLPSEAE  557 (708)
T ss_pred             ehhhhhccCCCCCcCeEEEeCCCCCHHHHHHHhhhhhhccCCCceEEEecccHHH
Confidence            9999999999999999999999999999999999999999999999998877654

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.87  E-value=2.3e-21  Score=153.27  Aligned_cols=118  Identities=28%  Similarity=0.401  Sum_probs=101.4

Q ss_pred             HHHHHHHhccCCCCCeeEEehhh--------hhHHHHHhhccc--cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEc
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQ--------LNAEELANSLTV--KEYDVLLLHGDMDQSERNSVITKFKRQECRILVAT   91 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~--------~~~~~l~~~L~~--~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T   91 (150)
                      .++..+.+....+.+++|||+..        ..++.+++.|..  .++.+..+||+|++++|..+++.|++|+.+|||||
T Consensus       436 ~~~~~i~~~l~~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT  515 (630)
T TIGR00643       436 IVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVAT  515 (630)
T ss_pred             HHHHHHHHHHHhCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEC
Confidence            45555554434678999999875        345566666654  36789999999999999999999999999999999


Q ss_pred             CCCcccCCccCCcEEEEecCCC-ChhHHHHhhccccCCCCccEEEEEEe
Q psy17637         92 DVAARGLDIPHIRTVVNYDLAR-DIDTHTHRIGRTGRAGNKGVAYTLVT  139 (150)
Q Consensus        92 ~~~~~Gidi~~~~~vi~~~~~~-~~~~~~q~~GR~~R~g~~~~~~~~~~  139 (150)
                      +++++|+|+|++++||+++.|. +.+.|.|++||+||.|..|.|++++.
T Consensus       516 ~vie~GvDiP~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~il~~~  564 (630)
T TIGR00643       516 TVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYK  564 (630)
T ss_pred             ceeecCcccCCCcEEEEeCCCcCCHHHHHHHhhhcccCCCCcEEEEEEC
Confidence            9999999999999999999986 78899999999999999999999984

>KOG0343|consensus

Probab=99.87  E-value=7.3e-22  Score=149.01  Aligned_cols=132  Identities=30%  Similarity=0.412  Sum_probs=114.2

Q ss_pred             EEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccc--cCceEEEecCCCCHHHHHHHHHHhhcCCceE
Q psy17637         10 TLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTV--KEYDVLLLHGDMDQSERNSVITKFKRQECRI   87 (150)
Q Consensus        10 ~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~--~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~v   87 (150)
                      +++......++..|-..|..  +...+.|||++|-+++..+++.+..  .|+++..+||.|++..|..+...|-.....|
T Consensus       291 ~y~~v~l~~Ki~~L~sFI~s--hlk~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~Q~~R~ev~~~F~~~~~~v  368 (758)
T KOG0343|consen  291 SYVIVPLEDKIDMLWSFIKS--HLKKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMSQKKRIEVYKKFVRKRAVV  368 (758)
T ss_pred             eEEEEehhhHHHHHHHHHHh--ccccceEEEEehhhHHHHHHHHHHhcCCCCceeeeccchhHHHHHHHHHHHHHhcceE
Confidence            33333333344455555544  4777999999999999999998864  5889999999999999999999999988899


Q ss_pred             EEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         88 LVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        88 lv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |+||+++++|+|+|.++|||.+|.|.+.++|++|+||+.|.+..|.+++++++.+.
T Consensus       369 LF~TDv~aRGLDFpaVdwViQ~DCPedv~tYIHRvGRtAR~~~~G~sll~L~psEe  424 (758)
T KOG0343|consen  369 LFCTDVAARGLDFPAVDWVIQVDCPEDVDTYIHRVGRTARYKERGESLLMLTPSEE  424 (758)
T ss_pred             EEeehhhhccCCCcccceEEEecCchhHHHHHHHhhhhhcccCCCceEEEEcchhH
Confidence            99999999999999999999999999999999999999999999999999998774

>KOG0339|consensus

Probab=99.87  E-value=9.8e-22  Score=147.17  Aligned_cols=132  Identities=58%  Similarity=0.857  Sum_probs=122.1

Q ss_pred             eecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEc
Q psy17637         12 VTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVAT   91 (150)
Q Consensus        12 ~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T   91 (150)
                      +.+.+..++.+|+..|... ...+++|+|+.-+..+++++..|+-.++.+..+||+|.+.+|.+++..|+.+...|||+|
T Consensus       447 V~~s~~~Kl~wl~~~L~~f-~S~gkvlifVTKk~~~e~i~a~Lklk~~~v~llhgdkdqa~rn~~ls~fKkk~~~Vlvat  525 (731)
T KOG0339|consen  447 VCPSEEKKLNWLLRHLVEF-SSEGKVLIFVTKKADAEEIAANLKLKGFNVSLLHGDKDQAERNEVLSKFKKKRKPVLVAT  525 (731)
T ss_pred             eccCcHHHHHHHHHHhhhh-ccCCcEEEEEeccCCHHHHHHHhccccceeeeecCchhhHHHHHHHHHHhhcCCceEEEe
Confidence            3344555678999999887 556799999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCc
Q psy17637         92 DVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD  144 (150)
Q Consensus        92 ~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~  144 (150)
                      ++..+|+|++.+..||+||+..+++.|.||+||+||.|..|..|.++++.|..
T Consensus       526 DvaargldI~~ikTVvnyD~ardIdththrigrtgRag~kGvayTlvTeKDa~  578 (731)
T KOG0339|consen  526 DVAARGLDIPSIKTVVNYDFARDIDTHTHRIGRTGRAGEKGVAYTLVTEKDAE  578 (731)
T ss_pred             eHhhcCCCccccceeecccccchhHHHHHHhhhcccccccceeeEEechhhHH
Confidence            99999999999999999999999999999999999999999999999987654

>KOG0350|consensus

Probab=99.87  E-value=5.3e-22  Score=148.07  Aligned_cols=130  Identities=27%  Similarity=0.416  Sum_probs=113.2

Q ss_pred             cchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhcc----ccCceEEEecCCCCHHHHHHHHHHhhcCCceEEE
Q psy17637         14 DKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLT----VKEYDVLLLHGDMDQSERNSVITKFKRQECRILV   89 (150)
Q Consensus        14 ~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~----~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv   89 (150)
                      .+...+...+...+...  +..++|+|+++.+.+..++..|+    ..+.++..++|+++.+.|.+.+..|..|++++||
T Consensus       411 ~~~~~kpl~~~~lI~~~--k~~r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~~l~~k~r~k~l~~f~~g~i~vLI  488 (620)
T KOG0350|consen  411 TEPKFKPLAVYALITSN--KLNRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTGQLNGKRRYKMLEKFAKGDINVLI  488 (620)
T ss_pred             cccccchHhHHHHHHHh--hcceEEEEecchHHHHHHHHHHHHHhccccchhhhhhhhhhHHHHHHHHHHHhcCCceEEE
Confidence            33333344555555554  78899999999999988888776    4466788899999999999999999999999999


Q ss_pred             EcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCcc
Q psy17637         90 ATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDG  145 (150)
Q Consensus        90 ~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~~  145 (150)
                      |++++++|+|+.++++||+||+|-+...|++|+||++|.|+.|.++.++++.+.+-
T Consensus       489 cSD~laRGiDv~~v~~VINYd~P~~~ktyVHR~GRTARAgq~G~a~tll~~~~~r~  544 (620)
T KOG0350|consen  489 CSDALARGIDVNDVDNVINYDPPASDKTYVHRAGRTARAGQDGYAITLLDKHEKRL  544 (620)
T ss_pred             ehhhhhcCCcccccceEeecCCCchhhHHHHhhcccccccCCceEEEeeccccchH
Confidence            99999999999999999999999999999999999999999999999999887643

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.87  E-value=3.6e-21  Score=159.03  Aligned_cols=109  Identities=23%  Similarity=0.315  Sum_probs=98.9

Q ss_pred             CCCCeeEEehhhhhHHHHHhhcccc--CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEec
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVK--EYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYD  110 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~  110 (150)
                      ..++++|||++++.++.+++.|...  +.++..+||+|++++|.+++.+|++|+.+|||||+++++|+|+|++++||..+
T Consensus       808 r~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdIierGIDIP~v~~VIi~~  887 (1147)
T PRK10689        808 RGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIER  887 (1147)
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECchhhcccccccCCEEEEec
Confidence            4578999999999999999998765  67899999999999999999999999999999999999999999999999665


Q ss_pred             CC-CChhHHHHhhccccCCCCccEEEEEEecC
Q psy17637        111 LA-RDIDTHTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus       111 ~~-~~~~~~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                      .+ .+...|+|++||+||.|..|.+++++...
T Consensus       888 ad~fglaq~~Qr~GRvGR~g~~g~a~ll~~~~  919 (1147)
T PRK10689        888 ADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  919 (1147)
T ss_pred             CCCCCHHHHHHHhhccCCCCCceEEEEEeCCC
Confidence            54 46788999999999999999999888654

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.86  E-value=1.8e-21  Score=162.53  Aligned_cols=107  Identities=20%  Similarity=0.222  Sum_probs=93.0

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccC---------------------------------ceEEEecCCCCHHHHHHHHHH
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKE---------------------------------YDVLLLHGDMDQSERNSVITK   79 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~---------------------------------~~~~~~~~~~~~~~r~~~~~~   79 (150)
                      ...++||||||+..+|.++..|+...                                 ..+..+||+|++++|..+++.
T Consensus       243 ~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkeeR~~IE~~  322 (1490)
T PRK09751        243 RHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQRAITEQA  322 (1490)
T ss_pred             cCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHHHHHHHHHH
Confidence            45789999999999999998886431                                 125689999999999999999


Q ss_pred             hhcCCceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCC-CccEEEEEEe
Q psy17637         80 FKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAG-NKGVAYTLVT  139 (150)
Q Consensus        80 f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g-~~~~~~~~~~  139 (150)
                      |++|++++||||+.+++|||++.+++||+++.|.+..+|+||+||+||.. ..+.++++..
T Consensus       323 fK~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~~gg~s~gli~p~  383 (1490)
T PRK09751        323 LKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQVGGVSKGLFFPR  383 (1490)
T ss_pred             HHhCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCCCCCccEEEEEeC
Confidence            99999999999999999999999999999999999999999999999963 3345554443

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.86  E-value=6.6e-21  Score=150.91  Aligned_cols=121  Identities=25%  Similarity=0.339  Sum_probs=111.0

Q ss_pred             HHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCC
Q psy17637         20 AGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLD   99 (150)
Q Consensus        20 ~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gid   99 (150)
                      +..+++.+......+.++||||+|++.++.|++.|...++++..+||++++.+|..++..|+.|.+.|+|||+.+++|+|
T Consensus       432 ~~~L~~~L~~~~~~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~rGfd  511 (652)
T PRK05298        432 VDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLD  511 (652)
T ss_pred             HHHHHHHHHHHHhCCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHhCCcc
Confidence            45777778776567889999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCcEEEEecC-----CCChhHHHHhhccccCCCCccEEEEEEecC
Q psy17637        100 IPHIRTVVNYDL-----ARDIDTHTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus       100 i~~~~~vi~~~~-----~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                      +|++++||+++.     |.+..+|+|++||+||. ..|.++.|++..
T Consensus       512 lp~v~lVii~d~eifG~~~~~~~yiqr~GR~gR~-~~G~~i~~~~~~  557 (652)
T PRK05298        512 IPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVILYADKI  557 (652)
T ss_pred             ccCCcEEEEeCCcccccCCCHHHHHHHhccccCC-CCCEEEEEecCC
Confidence            999999998875     78999999999999996 678999998843

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.86  E-value=6.1e-21  Score=150.91  Aligned_cols=123  Identities=20%  Similarity=0.205  Sum_probs=109.7

Q ss_pred             hHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCccc
Q psy17637         18 EFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG   97 (150)
Q Consensus        18 ~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G   97 (150)
                      .+...++..+......+.|+||||+|++.++.+...|...++++..+||.+.+.++..+...++.|  .|+|||+++++|
T Consensus       408 ~K~~ai~~~i~~~~~~~~pvLIft~s~~~se~ls~~L~~~gi~~~~L~a~~~~~E~~ii~~ag~~g--~VlIATdmAgRG  485 (762)
T TIGR03714       408 EKLMATLEDVKEYHETGQPVLLITGSVEMSEIYSELLLREGIPHNLLNAQNAAKEAQIIAEAGQKG--AVTVATSMAGRG  485 (762)
T ss_pred             HHHHHHHHHHHHHhhCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCChHHHHHHHHHcCCCC--eEEEEccccccc
Confidence            345577777776556789999999999999999999999999999999999998888887777666  799999999999


Q ss_pred             CCcc---------CCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         98 LDIP---------HIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        98 idi~---------~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +|++         ++++|+++++|..... .|++||+||.|++|.+++|++.+|.
T Consensus       486 tDI~l~~~v~~~GGL~vIit~~~ps~rid-~qr~GRtGRqG~~G~s~~~is~eD~  539 (762)
T TIGR03714       486 TDIKLGKGVAELGGLAVIGTERMENSRVD-LQLRGRSGRQGDPGSSQFFVSLEDD  539 (762)
T ss_pred             cCCCCCccccccCCeEEEEecCCCCcHHH-HHhhhcccCCCCceeEEEEEccchh
Confidence            9999         9999999999988766 9999999999999999999988654

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.

>PRK02362 ski2-like helicase; Provisional

Probab=99.86  E-value=2.7e-21  Score=155.37  Aligned_cols=110  Identities=24%  Similarity=0.354  Sum_probs=96.4

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhcccc------------------------------------CceEEEecCCCCHHHHHH
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVK------------------------------------EYDVLLLHGDMDQSERNS   75 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~------------------------------------~~~~~~~~~~~~~~~r~~   75 (150)
                      ....++||||+|++.++.++..|...                                    ...+.++||+|++++|..
T Consensus       241 ~~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hHagl~~~eR~~  320 (737)
T PRK02362        241 EEGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHHAGLSREHREL  320 (737)
T ss_pred             HcCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEeecCCCCHHHHHH
Confidence            35679999999999999888777532                                    125889999999999999


Q ss_pred             HHHHhhcCCceEEEEcCCCcccCCccCCcEEEE----ec-----CCCChhHHHHhhccccCCCCc--cEEEEEEecC
Q psy17637         76 VITKFKRQECRILVATDVAARGLDIPHIRTVVN----YD-----LARDIDTHTHRIGRTGRAGNK--GVAYTLVTDK  141 (150)
Q Consensus        76 ~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~----~~-----~~~~~~~~~q~~GR~~R~g~~--~~~~~~~~~~  141 (150)
                      +++.|++|.++|||||+.+++|+|+|...+||.    |+     .|.+..+|.||+|||||.|.+  |.+++++...
T Consensus       321 ve~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~g~d~~G~~ii~~~~~  397 (737)
T PRK02362        321 VEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLDPYGEAVLLAKSY  397 (737)
T ss_pred             HHHHHHcCCCeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCCCCCCCceEEEEecCc
Confidence            999999999999999999999999999999996    65     588999999999999999864  7888888664

>PRK13766 Hef nuclease; Provisional

Probab=99.85  E-value=1.3e-20  Score=152.35  Aligned_cols=123  Identities=27%  Similarity=0.419  Sum_probs=108.0

Q ss_pred             HHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCC--------CCHHHHHHHHHHhhcCCceEEEEcC
Q psy17637         21 GHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGD--------MDQSERNSVITKFKRQECRILVATD   92 (150)
Q Consensus        21 ~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~--------~~~~~r~~~~~~f~~g~~~vlv~T~   92 (150)
                      ..+++.+... ....++||||++++.++.|++.|...++.+..+||.        |++.+|..+++.|++|+..+||+|+
T Consensus       353 ~~il~~~~~~-~~~~kvlIF~~~~~t~~~L~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~g~~~vLvaT~  431 (773)
T PRK13766        353 REIVKEQLGK-NPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNVLVSTS  431 (773)
T ss_pred             HHHHHHHHhc-CCCCeEEEEeCcHHHHHHHHHHHHhCCCceEEEEccccccccCCCCHHHHHHHHHHHHcCCCCEEEECC
Confidence            3344443332 467899999999999999999998889888899886        9999999999999999999999999


Q ss_pred             CCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCcc
Q psy17637         93 VAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDG  145 (150)
Q Consensus        93 ~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~~  145 (150)
                      ++++|+|+|.+++||+|++|+++..|+||+||+||.| ++.++.++...+.++
T Consensus       432 ~~~eGldi~~~~~VI~yd~~~s~~r~iQR~GR~gR~~-~~~v~~l~~~~t~ee  483 (773)
T PRK13766        432 VAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGRQE-EGRVVVLIAKGTRDE  483 (773)
T ss_pred             hhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccCcCC-CCEEEEEEeCCChHH
Confidence            9999999999999999999999999999999999987 478888888766544

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.85  E-value=1.5e-20  Score=139.98  Aligned_cols=108  Identities=23%  Similarity=0.366  Sum_probs=91.7

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCc--eEEEecCCCCHHHHHH----HHHHhhcCCceEEEEcCCCcccCCccCCcE
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEY--DVLLLHGDMDQSERNS----VITKFKRQECRILVATDVAARGLDIPHIRT  105 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~--~~~~~~~~~~~~~r~~----~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~  105 (150)
                      ....++||||++++.++.++..|...+.  .+..+||++++.+|.+    +++.|++|...+||||+++++|+|++ +++
T Consensus       220 ~~~~~~lVf~~t~~~~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~~~~~GiDi~-~~~  298 (358)
T TIGR01587       220 KKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDIS-ADV  298 (358)
T ss_pred             hCCCeEEEEECCHHHHHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECcchhceeccC-CCE
Confidence            4567999999999999999999987665  5899999999999976    48899999999999999999999995 788


Q ss_pred             EEEecCCCChhHHHHhhccccCCCCcc----EEEEEEecCC
Q psy17637        106 VVNYDLARDIDTHTHRIGRTGRAGNKG----VAYTLVTDKD  142 (150)
Q Consensus       106 vi~~~~~~~~~~~~q~~GR~~R~g~~~----~~~~~~~~~~  142 (150)
                      +|++..|  +++|+||+||+||.|...    .++++....+
T Consensus       299 vi~~~~~--~~~~iqr~GR~gR~g~~~~~~~~~~v~~~~~~  337 (358)
T TIGR01587       299 MITELAP--IDSLIQRLGRLHRYGRKNGENFEVYIITIAPE  337 (358)
T ss_pred             EEEcCCC--HHHHHHHhccccCCCCCCCCCCeEEEEeecCC
Confidence            8887666  789999999999988542    5566655443

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.

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.85  E-value=1.4e-20  Score=148.29  Aligned_cols=123  Identities=21%  Similarity=0.261  Sum_probs=113.7

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccC
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGL   98 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gi   98 (150)
                      +...+++.+......+.|+||||+|.+.++.+...|...+++...+|+.  +.+|+..+..|..+...|+|||+++++|+
T Consensus       390 k~~ai~~~i~~~~~~grpvLV~t~si~~se~ls~~L~~~gi~~~~Lna~--q~~rEa~ii~~ag~~g~VtIATnmAgRGt  467 (745)
T TIGR00963       390 KWKAVVDEIKERHAKGQPVLVGTTSVEKSELLSNLLKERGIPHNVLNAK--NHEREAEIIAQAGRKGAVTIATNMAGRGT  467 (745)
T ss_pred             HHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCeEEeeCC--hHHHHHHHHHhcCCCceEEEEeccccCCc
Confidence            4467888886666789999999999999999999999999999999998  88999999999999999999999999999


Q ss_pred             CccC-------CcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         99 DIPH-------IRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        99 di~~-------~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |++.       ..+||+++.|.|...|.|++||+||.|++|.+.+|++.+|.
T Consensus       468 DI~l~~V~~~GGl~VI~t~~p~s~ri~~q~~GRtGRqG~~G~s~~~ls~eD~  519 (745)
T TIGR00963       468 DIKLEEVKELGGLYVIGTERHESRRIDNQLRGRSGRQGDPGSSRFFLSLEDN  519 (745)
T ss_pred             CCCccchhhcCCcEEEecCCCCcHHHHHHHhccccCCCCCcceEEEEeccHH
Confidence            9987       45999999999999999999999999999999999998764

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.

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.85  E-value=1.5e-20  Score=145.41  Aligned_cols=102  Identities=18%  Similarity=0.200  Sum_probs=95.2

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEc-CCCcccCCccCCcEEEEec
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVAT-DVAARGLDIPHIRTVVNYD  110 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T-~~~~~Gidi~~~~~vi~~~  110 (150)
                      ..+.+++|||.+.++++.|++.|...+.++..+||+|+.++|..+++.|++|+..+||+| +.+++|+|+|++++||++.
T Consensus       342 ~~~~~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLvaT~~~l~eG~Dip~ld~vIl~~  421 (501)
T PHA02558        342 KKGENTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYGVFSTGISIKNLHHVIFAH  421 (501)
T ss_pred             hcCCCEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHhCCCCeEEEEEcceeccccccccccEEEEec
Confidence            356789999999999999999999999999999999999999999999999998999998 8999999999999999999


Q ss_pred             CCCChhHHHHhhccccCCCCccE
Q psy17637        111 LARDIDTHTHRIGRTGRAGNKGV  133 (150)
Q Consensus       111 ~~~~~~~~~q~~GR~~R~g~~~~  133 (150)
                      +++|...|+|++||++|.+..+.
T Consensus       422 p~~s~~~~~QriGR~~R~~~~K~  444 (501)
T PHA02558        422 PSKSKIIVLQSIGRVLRKHGSKS  444 (501)
T ss_pred             CCcchhhhhhhhhccccCCCCCc
Confidence            99999999999999999886543

>KOG0334|consensus

Probab=99.85  E-value=6.7e-21  Score=151.83  Aligned_cols=134  Identities=37%  Similarity=0.504  Sum_probs=121.0

Q ss_pred             eeEEEeecc-hhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCc
Q psy17637          7 VAYTLVTDK-DKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQEC   85 (150)
Q Consensus         7 ~~~~~~~~~-~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~   85 (150)
                      +...+.-.. +.+++..|+..|... ....++||||...+.|+.+...|.+.++.+..+||+.++.+|..++++|+++.+
T Consensus       586 V~q~v~V~~~e~eKf~kL~eLl~e~-~e~~~tiiFv~~qe~~d~l~~~L~~ag~~~~slHGgv~q~dR~sti~dfK~~~~  664 (997)
T KOG0334|consen  586 VTQVVRVCAIENEKFLKLLELLGER-YEDGKTIIFVDKQEKADALLRDLQKAGYNCDSLHGGVDQHDRSSTIEDFKNGVV  664 (997)
T ss_pred             ceEEEEEecCchHHHHHHHHHHHHH-hhcCCEEEEEcCchHHHHHHHHHHhcCcchhhhcCCCchHHHHhHHHHHhccCc
Confidence            333333333 566677888888777 558899999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecC
Q psy17637         86 RILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus        86 ~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                      .+||+|+.+++|+|+..+.+||+|++|...+.|++|.||+||.|+.|.+++|+++.
T Consensus       665 ~LLvaTsvvarGLdv~~l~Lvvnyd~pnh~edyvhR~gRTgragrkg~AvtFi~p~  720 (997)
T KOG0334|consen  665 NLLVATSVVARGLDVKELILVVNYDFPNHYEDYVHRVGRTGRAGRKGAAVTFITPD  720 (997)
T ss_pred             eEEEehhhhhcccccccceEEEEcccchhHHHHHHHhcccccCCccceeEEEeChH
Confidence            99999999999999999999999999999999999999999999999999999984

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.85  E-value=9.8e-21  Score=152.30  Aligned_cols=110  Identities=26%  Similarity=0.409  Sum_probs=100.4

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc---cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEe
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV---KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNY  109 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~  109 (150)
                      ..+++|||+++..+++.+++.|..   .++.+.++||+|++++|.++++.|.+|..+|+|||++++.|+|+|++++||++
T Consensus       208 ~~g~iLVFlpg~~eI~~l~~~L~~~~~~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATnIAErgItIp~V~~VID~  287 (819)
T TIGR01970       208 ETGSILVFLPGQAEIRRVQEQLAERLDSDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDS  287 (819)
T ss_pred             cCCcEEEEECCHHHHHHHHHHHHhhcCCCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecchHhhcccccCceEEEEc
Confidence            357899999999999999999976   47889999999999999999999999999999999999999999999999999


Q ss_pred             cCCC------------------ChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637        110 DLAR------------------DIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus       110 ~~~~------------------~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +.++                  |.+++.||+||+||. .+|.||.++++.+.
T Consensus       288 Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRAGR~-~~G~cyrL~t~~~~  338 (819)
T TIGR01970       288 GLARVARFDPKTGITRLETVRISQASATQRAGRAGRL-EPGVCYRLWSEEQH  338 (819)
T ss_pred             CcccccccccccCCceeeEEEECHHHHHhhhhhcCCC-CCCEEEEeCCHHHH
Confidence            9875                  346789999999999 69999999987654

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.

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.85  E-value=1e-20  Score=149.33  Aligned_cols=118  Identities=19%  Similarity=0.284  Sum_probs=99.8

Q ss_pred             HHHHHHhcc-CCCCCeeEEehhhhhHHHHHhhcccc--CceEEEecCCCCHHHHHHHHHHh-hcCCceEEEEcCCCcccC
Q psy17637         23 LVRNLEGAN-QEVPPALMNLAMQLNAEELANSLTVK--EYDVLLLHGDMDQSERNSVITKF-KRQECRILVATDVAARGL   98 (150)
Q Consensus        23 ll~~l~~~~-~~~~~~ivf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f-~~g~~~vlv~T~~~~~Gi   98 (150)
                      ++..+.... ....++|||+++++.++.+++.|...  ++.+.++||+|++.  ++.+++| ++|+.+|||||+.+++|+
T Consensus       383 ~l~~L~~~~~~~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~gk~kILVATdIAERGI  460 (675)
T PHA02653        383 IVTALKKYTPPKGSSGIVFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVPNI--DEILEKVYSSKNPSIIISTPYLESSV  460 (675)
T ss_pred             HHHHHHHhhcccCCcEEEEECcHHHHHHHHHHHHhhcCCceEEeccCCcCHH--HHHHHHHhccCceeEEeccChhhccc
Confidence            444444321 24568999999999999999999876  68999999999975  4666777 689999999999999999


Q ss_pred             CccCCcEEEEec---CCC---------ChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         99 DIPHIRTVVNYD---LAR---------DIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        99 di~~~~~vi~~~---~~~---------~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |+|++++||+++   .|.         |.++|.||+||+||. .+|.|+.|+++.+.
T Consensus       461 DIp~V~~VID~G~~k~p~~~~g~~~~iSkasa~QRaGRAGR~-~~G~c~rLyt~~~~  516 (675)
T PHA02653        461 TIRNATHVYDTGRVYVPEPFGGKEMFISKSMRTQRKGRVGRV-SPGTYVYFYDLDLL  516 (675)
T ss_pred             cccCeeEEEECCCccCCCcccCcccccCHHHHHHhccCcCCC-CCCeEEEEECHHHh
Confidence            999999999998   554         888999999999999 68999999987653

>KOG4284|consensus

Probab=99.85  E-value=5.8e-21  Score=146.45  Aligned_cols=112  Identities=37%  Similarity=0.512  Sum_probs=107.0

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDL  111 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~  111 (150)
                      -+..++||||+....|+-++..|...|+.+.++.|.|++++|..+++.++.-..+|||+|+..++|||-+++++|||.|+
T Consensus       270 ipy~QAlVF~~~~sra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~lr~f~~rILVsTDLtaRGIDa~~vNLVVNiD~  349 (980)
T KOG4284|consen  270 IPYVQALVFCDQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQLRAFRVRILVSTDLTARGIDADNVNLVVNIDA  349 (980)
T ss_pred             CchHHHHhhhhhhhhhhHHHHHhhccCCCeEEeccccchhHHHHHHHHhhhceEEEEEecchhhccCCccccceEEecCC
Confidence            47789999999999999999999999999999999999999999999999988999999999999999999999999999


Q ss_pred             CCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637        112 ARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus       112 ~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |-+...|.+|+|||||.|..|..++|+.....
T Consensus       350 p~d~eTY~HRIGRAgRFG~~G~aVT~~~~~~e  381 (980)
T KOG4284|consen  350 PADEETYFHRIGRAGRFGAHGAAVTLLEDERE  381 (980)
T ss_pred             CcchHHHHHHhhhcccccccceeEEEeccchh
Confidence            99999999999999999999999998876655

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.84  E-value=3.5e-20  Score=147.08  Aligned_cols=125  Identities=19%  Similarity=0.301  Sum_probs=112.5

Q ss_pred             hhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcc
Q psy17637         17 KEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAAR   96 (150)
Q Consensus        17 ~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~   96 (150)
                      ..+...+++.+......+.|+||||+|++.++.++..|...+++...+|+.+...++..+...++.|.  |+|||+++++
T Consensus       423 ~~K~~al~~~i~~~~~~g~pvLI~t~si~~se~ls~~L~~~gi~~~~Lna~~~~~Ea~ii~~ag~~g~--VtIATnmAGR  500 (796)
T PRK12906        423 DSKFNAVVKEIKERHAKGQPVLVGTVAIESSERLSHLLDEAGIPHAVLNAKNHAKEAEIIMNAGQRGA--VTIATNMAGR  500 (796)
T ss_pred             HHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHCCCCeeEecCCcHHHHHHHHHhcCCCce--EEEEeccccC
Confidence            34556788888766578999999999999999999999999999999999999888888878777775  9999999999


Q ss_pred             cCCcc---CCc-----EEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         97 GLDIP---HIR-----TVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        97 Gidi~---~~~-----~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |+||+   ++.     +||+++.|.+...|.|++||+||.|++|.+.++++.+|.
T Consensus       501 GtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~GRtGRqG~~G~s~~~~sleD~  555 (796)
T PRK12906        501 GTDIKLGPGVKELGGLAVIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSLEDD  555 (796)
T ss_pred             CCCCCCCcchhhhCCcEEEeeecCCcHHHHHHHhhhhccCCCCcceEEEEeccch
Confidence            99994   788     999999999999999999999999999999999998854

>KOG0352|consensus

Probab=99.83  E-value=8.2e-21  Score=139.95  Aligned_cols=112  Identities=21%  Similarity=0.356  Sum_probs=107.1

Q ss_pred             CCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCCC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLAR  113 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~  113 (150)
                      .+..||||.|++.||.++-.|...|+.+..||+|+...+|.++-+.|.+++..|+++|..+++|+|-|++.+||++++|.
T Consensus       255 ~GCGIVYCRTR~~cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~~PvI~AT~SFGMGVDKp~VRFViHW~~~q  334 (641)
T KOG0352|consen  255 TGCGIVYCRTRNECEQVAIMLEIAGIPAMAYHAGLKKKERTEVQEKWMNNEIPVIAATVSFGMGVDKPDVRFVIHWSPSQ  334 (641)
T ss_pred             CcceEEEeccHHHHHHHHHHhhhcCcchHHHhcccccchhHHHHHHHhcCCCCEEEEEeccccccCCcceeEEEecCchh
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ChhHHHHhhccccCCCCccEEEEEEecCCCcc
Q psy17637        114 DIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDG  145 (150)
Q Consensus       114 ~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~~  145 (150)
                      ++..|.|..||+||.|.+++|-+++..+|.+.
T Consensus       335 n~AgYYQESGRAGRDGk~SyCRLYYsR~D~~~  366 (641)
T KOG0352|consen  335 NLAGYYQESGRAGRDGKRSYCRLYYSRQDKNA  366 (641)
T ss_pred             hhHHHHHhccccccCCCccceeeeecccchHH
Confidence            99999999999999999999999998877653

>KOG0346|consensus

Probab=99.83  E-value=2.4e-20  Score=137.58  Aligned_cols=139  Identities=24%  Similarity=0.331  Sum_probs=118.4

Q ss_pred             cCeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC
Q psy17637          5 KGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE   84 (150)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~   84 (150)
                      ..+.++.+.+.+.++...+...+. ...-.++.|||+||.+.|-.|.-.|..-|++.+.+.|+||.+.|..++++|..|-
T Consensus       240 dqL~Qy~v~cse~DKflllyallK-L~LI~gKsliFVNtIdr~YrLkLfLeqFGiksciLNseLP~NSR~Hii~QFNkG~  318 (569)
T KOG0346|consen  240 DQLTQYQVKCSEEDKFLLLYALLK-LRLIRGKSLIFVNTIDRCYRLKLFLEQFGIKSCILNSELPANSRCHIIEQFNKGL  318 (569)
T ss_pred             ccceEEEEEeccchhHHHHHHHHH-HHHhcCceEEEEechhhhHHHHHHHHHhCcHhhhhcccccccchhhHHHHhhCcc
Confidence            445555655656555555554443 3246779999999999999999999888999999999999999999999999999


Q ss_pred             ceEEEEcC-----------------------------------CCcccCCccCCcEEEEecCCCChhHHHHhhccccCCC
Q psy17637         85 CRILVATD-----------------------------------VAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAG  129 (150)
Q Consensus        85 ~~vlv~T~-----------------------------------~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g  129 (150)
                      .+++|||+                                   -.++|||+..+++|+|||+|.+..+|++|+||++|.+
T Consensus       319 YdivIAtD~s~~~~~~eee~kgk~~e~~~kndkkskkK~D~E~GVsRGIDF~~V~~VlNFD~P~t~~sYIHRvGRTaRg~  398 (569)
T KOG0346|consen  319 YDIVIATDDSADGDKLEEEVKGKSDEKNPKNDKKSKKKLDKESGVSRGIDFHHVSNVLNFDFPETVTSYIHRVGRTARGN  398 (569)
T ss_pred             eeEEEEccCccchhhhhccccccccccCCCCccccccccCchhchhccccchheeeeeecCCCCchHHHHHhccccccCC
Confidence            99999998                                   1357999999999999999999999999999999999


Q ss_pred             CccEEEEEEecCCCc
Q psy17637        130 NKGVAYTLVTDKDKD  144 (150)
Q Consensus       130 ~~~~~~~~~~~~~~~  144 (150)
                      ++|.++.|+.+.+..
T Consensus       399 n~GtalSfv~P~e~~  413 (569)
T KOG0346|consen  399 NKGTALSFVSPKEEF  413 (569)
T ss_pred             CCCceEEEecchHHh
Confidence            999999999876543

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.83  E-value=3.3e-20  Score=149.40  Aligned_cols=110  Identities=25%  Similarity=0.341  Sum_probs=100.3

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc---cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEe
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV---KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNY  109 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~  109 (150)
                      ..+++|||+++...++.+++.|..   .++.+..+||+|+++++.+++..|.+|..+|+|||+.++.|+|+|++++||++
T Consensus       211 ~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V~~VID~  290 (812)
T PRK11664        211 ESGSLLLFLPGVGEIQRVQEQLASRVASDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDS  290 (812)
T ss_pred             CCCCEEEEcCCHHHHHHHHHHHHHhccCCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecchHHhcccccCceEEEEC
Confidence            467899999999999999999986   57889999999999999999999999999999999999999999999999998


Q ss_pred             cCCC------------------ChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637        110 DLAR------------------DIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus       110 ~~~~------------------~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +.++                  |.++|.||+||+||. .+|.||.++++.+.
T Consensus       291 Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRaGR~-~~G~cyrL~t~~~~  341 (812)
T PRK11664        291 GLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRL-EPGICLHLYSKEQA  341 (812)
T ss_pred             CCcccccccccCCcceeEEEeechhhhhhhccccCCC-CCcEEEEecCHHHH
Confidence            8765                  446899999999999 58999999987644

>KOG0354|consensus

Probab=99.82  E-value=2.1e-19  Score=140.60  Aligned_cols=107  Identities=30%  Similarity=0.381  Sum_probs=94.7

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccc---cCceEEEecC--------CCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCc
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTV---KEYDVLLLHG--------DMDQSERNSVITKFKRQECRILVATDVAARGLDI  100 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~---~~~~~~~~~~--------~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi  100 (150)
                      .+..++||||.+++.++.|..+|..   .++++..+-|        +|++.++++++++|++|+++|||||+++++|+|+
T Consensus       411 ~~dsR~IIFve~R~sa~~l~~~l~~~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G~~NvLVATSV~EEGLDI  490 (746)
T KOG0354|consen  411 NPDSRTIIFVETRESALALKKWLLQLHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRDGEINVLVATSVAEEGLDI  490 (746)
T ss_pred             CCCccEEEEEehHHHHHHHHHHHHhhhhcccccceeeeccccccccccCHHHHHHHHHHHhCCCccEEEEecchhccCCc
Confidence            6788999999999999999999872   2445444444        6999999999999999999999999999999999


Q ss_pred             cCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEec
Q psy17637        101 PHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTD  140 (150)
Q Consensus       101 ~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~  140 (150)
                      +.|+.||.||...++-..+||+|| ||.. .|.++++++.
T Consensus       491 ~ec~lVIcYd~~snpIrmIQrrGR-gRa~-ns~~vll~t~  528 (746)
T KOG0354|consen  491 GECNLVICYDYSSNPIRMVQRRGR-GRAR-NSKCVLLTTG  528 (746)
T ss_pred             ccccEEEEecCCccHHHHHHHhcc-cccc-CCeEEEEEcc
Confidence            999999999999999999999999 9984 6788888773

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.82  E-value=1.1e-19  Score=107.67  Aligned_cols=81  Identities=46%  Similarity=0.711  Sum_probs=76.2

Q ss_pred             HHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCC
Q psy17637         49 ELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRA  128 (150)
Q Consensus        49 ~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~  128 (150)
                      .+++.|...++.+..+||++++++|..+++.|+++...+|++|+++++|+|+|.+++||++++|++...|.|++||++|.
T Consensus         2 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gi~~~~~~~vi~~~~~~~~~~~~Q~~gR~~R~   81 (82)
T smart00490        2 ELAELLKELGIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRA   81 (82)
T ss_pred             HHHHHHHHCCCeEEEEECCCCHHHHHHHHHHHHcCCCeEEEECChhhCCcChhcCCEEEEeCCCCCHHHHHHhhcccccC
Confidence            45667777789999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q psy17637        129 G  129 (150)
Q Consensus       129 g  129 (150)
                      |
T Consensus        82 g   82 (82)
T smart00490       82 G   82 (82)
T ss_pred             C
Confidence            5

>PRK00254 ski2-like helicase; Provisional

Probab=99.81  E-value=8.6e-20  Score=146.43  Aligned_cols=110  Identities=22%  Similarity=0.352  Sum_probs=92.0

Q ss_pred             CCCCeeEEehhhhhHHHHHhhcccc---------------------------------CceEEEecCCCCHHHHHHHHHH
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVK---------------------------------EYDVLLLHGDMDQSERNSVITK   79 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~---------------------------------~~~~~~~~~~~~~~~r~~~~~~   79 (150)
                      ...++||||+|++.++.++..|...                                 ...+.++||+|++++|..+++.
T Consensus       237 ~~~~vLVF~~sr~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl~~~eR~~ve~~  316 (720)
T PRK00254        237 KGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGLGRTERVLIEDA  316 (720)
T ss_pred             hCCCEEEEEcChHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCCCCHHHHHHHHHH
Confidence            4678999999999998777655311                                 1248999999999999999999


Q ss_pred             hhcCCceEEEEcCCCcccCCccCCcEEEE-------ecCCC-ChhHHHHhhccccCCC--CccEEEEEEecCC
Q psy17637         80 FKRQECRILVATDVAARGLDIPHIRTVVN-------YDLAR-DIDTHTHRIGRTGRAG--NKGVAYTLVTDKD  142 (150)
Q Consensus        80 f~~g~~~vlv~T~~~~~Gidi~~~~~vi~-------~~~~~-~~~~~~q~~GR~~R~g--~~~~~~~~~~~~~  142 (150)
                      |++|.++|||||+.+++|+|+|...+||.       ++.|. +..+|.||+|||||.|  ..|.++++++..+
T Consensus       317 F~~G~i~VLvaT~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR~~~d~~G~~ii~~~~~~  389 (720)
T PRK00254        317 FREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEE  389 (720)
T ss_pred             HHCCCCeEEEeCcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhhccCCCCcCCCceEEEEecCcc
Confidence            99999999999999999999999999984       44443 5779999999999976  4578888887644

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

Probab=99.81  E-value=3e-19  Score=142.04  Aligned_cols=119  Identities=24%  Similarity=0.314  Sum_probs=104.5

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccC-ceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCc
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKE-YDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDI  100 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi  100 (150)
                      .++..+.+.-+....++||+||+..+|.++..|+..+ ..+..+||.++.+.|..+.++|++|+++++|||+.++.|||+
T Consensus       241 ~~~~~i~~~v~~~~ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TSSLELGIDi  320 (814)
T COG1201         241 ALYERIAELVKKHRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELGIDI  320 (814)
T ss_pred             HHHHHHHHHHhhcCcEEEEEeChHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcCCceEEEEccchhhcccc
Confidence            3444444444456699999999999999999998876 789999999999999999999999999999999999999999


Q ss_pred             cCCcEEEEecCCCChhHHHHhhccccC-CCCccEEEEEEec
Q psy17637        101 PHIRTVVNYDLARDIDTHTHRIGRTGR-AGNKGVAYTLVTD  140 (150)
Q Consensus       101 ~~~~~vi~~~~~~~~~~~~q~~GR~~R-~g~~~~~~~~~~~  140 (150)
                      .+++.||+++.|.+.+.++||+||+|+ .+..+..+++..+
T Consensus       321 G~vdlVIq~~SP~sV~r~lQRiGRsgHr~~~~Skg~ii~~~  361 (814)
T COG1201         321 GDIDLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKGIIIAED  361 (814)
T ss_pred             CCceEEEEeCCcHHHHHHhHhccccccccCCcccEEEEecC
Confidence            999999999999999999999999996 4455677777665

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.81  E-value=3.3e-19  Score=140.97  Aligned_cols=110  Identities=17%  Similarity=0.277  Sum_probs=97.0

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcC-CceEEEEcCCCcccCCccCCcEEEEecC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQ-ECRILVATDVAARGLDIPHIRTVVNYDL  111 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~vlv~T~~~~~Gidi~~~~~vi~~~~  111 (150)
                      .+.++||||.+.+.++.++..|.     +..+||.+++.+|.++++.|+.| .+++||+|+++.+|+|+|++++||++++
T Consensus       495 ~g~kiLVF~~~~~~l~~~a~~L~-----~~~I~G~ts~~ER~~il~~Fr~~~~i~vLv~SkVgdeGIDlP~a~vvI~~s~  569 (732)
T TIGR00603       495 RGDKIIVFSDNVFALKEYAIKLG-----KPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTSIDLPEANVLIQISS  569 (732)
T ss_pred             cCCeEEEEeCCHHHHHHHHHHcC-----CceEECCCCHHHHHHHHHHHHhCCCccEEEEecccccccCCCCCCEEEEeCC
Confidence            67899999999999999999884     35689999999999999999875 7799999999999999999999999998


Q ss_pred             C-CChhHHHHhhccccCCCCcc-------EEEEEEecCCCcccc
Q psy17637        112 A-RDIDTHTHRIGRTGRAGNKG-------VAYTLVTDKDKDGEL  147 (150)
Q Consensus       112 ~-~~~~~~~q~~GR~~R~g~~~-------~~~~~~~~~~~~~~~  147 (150)
                      | .|...|+||+||++|.+..+       ..|.|++.++.+++.
T Consensus       570 ~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~dT~E~~~  613 (732)
T TIGR00603       570 HYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQEMYY  613 (732)
T ss_pred             CCCCHHHHHHHhcccccCCCCCccccccceEEEEecCCchHHHH
Confidence            7 59999999999999987543       448888887766554

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).

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

Probab=99.81  E-value=5.7e-19  Score=141.09  Aligned_cols=102  Identities=20%  Similarity=0.289  Sum_probs=87.5

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHH-----HHHHHhhc----CC-------ceEEEEcCCCcc
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERN-----SVITKFKR----QE-------CRILVATDVAAR   96 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~-----~~~~~f~~----g~-------~~vlv~T~~~~~   96 (150)
                      ...++||||||++.++.+++.|...++  ..+||.|++.+|.     ++++.|+.    |.       ..|||||+++++
T Consensus       271 ~g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~q~dR~~~~~~~il~~Fk~~~~~g~~~~~~~g~~ILVATdVaer  348 (844)
T TIGR02621       271 SGGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLRGAERDDLVKKEIFNRFLPQMLSGSRARPQQGTVYLVCTSAGEV  348 (844)
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCCHHHHhhHHHHHHHHHHhccccccccccccccceEEeccchhhh
Confidence            567899999999999999999988776  8999999999999     78899987    43       579999999999


Q ss_pred             cCCccCCcEEEEecCCCChhHHHHhhccccCCCCcc-EEEEEEe
Q psy17637         97 GLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKG-VAYTLVT  139 (150)
Q Consensus        97 Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~-~~~~~~~  139 (150)
                      |+|++. ++||++..|  .++|+||+||+||.|+.+ ..+.++.
T Consensus       349 GLDId~-d~VI~d~aP--~esyIQRiGRtgR~G~~~~~~i~vv~  389 (844)
T TIGR02621       349 GVNISA-DHLVCDLAP--FESMQQRFGRVNRFGELQACQIAVVH  389 (844)
T ss_pred             cccCCc-ceEEECCCC--HHHHHHHhcccCCCCCCCCceEEEEe
Confidence            999986 888887666  699999999999999753 3344443

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.

>PRK01172 ski2-like helicase; Provisional

Probab=99.81  E-value=1.9e-19  Score=143.67  Aligned_cols=110  Identities=24%  Similarity=0.366  Sum_probs=90.6

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhcccc-------------------------CceEEEecCCCCHHHHHHHHHHhhcCCce
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVK-------------------------EYDVLLLHGDMDQSERNSVITKFKRQECR   86 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~-------------------------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~   86 (150)
                      ...+++||||++++.++.++..|...                         ...+.++||+|++++|..+++.|++|.++
T Consensus       234 ~~~~~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~~f~~g~i~  313 (674)
T PRK01172        234 NDGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIK  313 (674)
T ss_pred             hCCCcEEEEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHHHHHHHHcCCCe
Confidence            45679999999999999998877532                         12478899999999999999999999999


Q ss_pred             EEEEcCCCcccCCccCCcEEEEecC---------CCChhHHHHhhccccCCCC--ccEEEEEEecCC
Q psy17637         87 ILVATDVAARGLDIPHIRTVVNYDL---------ARDIDTHTHRIGRTGRAGN--KGVAYTLVTDKD  142 (150)
Q Consensus        87 vlv~T~~~~~Gidi~~~~~vi~~~~---------~~~~~~~~q~~GR~~R~g~--~~~~~~~~~~~~  142 (150)
                      |||||+.+++|+|+|...+|| .+.         |.+..+|.||+|||||.|.  .|.+++++...+
T Consensus       314 VLvaT~~la~Gvnipa~~VII-~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g~d~~g~~~i~~~~~~  379 (674)
T PRK01172        314 VIVATPTLAAGVNLPARLVIV-RDITRYGNGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAASPA  379 (674)
T ss_pred             EEEecchhhccCCCcceEEEE-cCceEeCCCCceeCCHHHHHHHhhcCCCCCCCCcceEEEEecCcc
Confidence            999999999999999865444 333         4588899999999999984  456777765443

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.80  E-value=3.5e-19  Score=142.87  Aligned_cols=125  Identities=25%  Similarity=0.307  Sum_probs=112.2

Q ss_pred             hHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCccc
Q psy17637         18 EFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG   97 (150)
Q Consensus        18 ~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G   97 (150)
                      .+...|++.+......+.|+||||+|++.++.|+..|...+++...+|+  .+.+|+..+..|..+...|+|||+++++|
T Consensus       582 eK~~Ali~~I~~~~~~grpVLIft~Sve~sE~Ls~~L~~~gI~h~vLna--kq~~REa~Iia~AG~~g~VtIATNMAGRG  659 (1025)
T PRK12900        582 EKYNAIVLKVEELQKKGQPVLVGTASVEVSETLSRMLRAKRIAHNVLNA--KQHDREAEIVAEAGQKGAVTIATNMAGRG  659 (1025)
T ss_pred             HHHHHHHHHHHHHhhCCCCEEEEeCcHHHHHHHHHHHHHcCCCceeecC--CHHHhHHHHHHhcCCCCeEEEeccCcCCC
Confidence            4556788888766568899999999999999999999999999999997  48899999999999999999999999999


Q ss_pred             CCcc---CCc-----EEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCc
Q psy17637         98 LDIP---HIR-----TVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD  144 (150)
Q Consensus        98 idi~---~~~-----~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~  144 (150)
                      +||+   .+.     +||....|.+...|.|++||+||.|.+|.+.+|++.+|..
T Consensus       660 tDIkl~~~V~~vGGL~VIgterhes~Rid~Ql~GRtGRqGdpGsS~ffvSleD~L  714 (1025)
T PRK12900        660 TDIKLGEGVRELGGLFILGSERHESRRIDRQLRGRAGRQGDPGESVFYVSLEDEL  714 (1025)
T ss_pred             CCcCCccchhhhCCceeeCCCCCchHHHHHHHhhhhhcCCCCcceEEEechhHHH
Confidence            9998   443     4589999999999999999999999999999999987654

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

Probab=99.80  E-value=2.9e-19  Score=135.83  Aligned_cols=109  Identities=26%  Similarity=0.379  Sum_probs=96.8

Q ss_pred             CCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEE---ec
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVN---YD  110 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~---~~  110 (150)
                      .+++|||++|+..|.+++..|..+|+++.+||+||+..+|+.+...|.++++.++|+|-+++.|+|+|.-.+|+-   .+
T Consensus       440 rGQtIVFT~SRrr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVTTAAL~AGVDFPASQVIFEsLaMG  519 (830)
T COG1202         440 RGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAGVDFPASQVIFESLAMG  519 (830)
T ss_pred             CCceEEEecchhhHHHHHHHhhcCCcccccccCCCcHHHHHHHHHHHhcCCcceEeehhhhhcCCCCchHHHHHHHHHcc
Confidence            478999999999999999999999999999999999999999999999999999999999999999997654431   23


Q ss_pred             CCC-ChhHHHHhhccccCCC--CccEEEEEEecCC
Q psy17637        111 LAR-DIDTHTHRIGRTGRAG--NKGVAYTLVTDKD  142 (150)
Q Consensus       111 ~~~-~~~~~~q~~GR~~R~g--~~~~~~~~~~~~~  142 (150)
                      ..| ++.+|.||.|||||++  +.|.+|+++.+..
T Consensus       520 ~~WLs~~EF~QM~GRAGRp~yHdrGkVyllvepg~  554 (830)
T COG1202         520 IEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEPGK  554 (830)
T ss_pred             cccCCHHHHHHHhcccCCCCcccCceEEEEecCCh
Confidence            333 7999999999999988  5688999987653

>KOG0353|consensus

Probab=99.79  E-value=6.3e-19  Score=128.83  Aligned_cols=137  Identities=17%  Similarity=0.282  Sum_probs=120.5

Q ss_pred             CcCeeEEEeec--chhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhh
Q psy17637          4 NKGVAYTLVTD--KDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFK   81 (150)
Q Consensus         4 ~~~~~~~~~~~--~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~   81 (150)
                      ++++.|.+...  .+.+..+.+...+... ..+...||||-+++.+|.++..|+..|+.+..+|+.|.|+++.-+-+.|.
T Consensus       286 r~nl~yev~qkp~n~dd~~edi~k~i~~~-f~gqsgiiyc~sq~d~ekva~alkn~gi~a~~yha~lep~dks~~hq~w~  364 (695)
T KOG0353|consen  286 RPNLKYEVRQKPGNEDDCIEDIAKLIKGD-FAGQSGIIYCFSQKDCEKVAKALKNHGIHAGAYHANLEPEDKSGAHQGWI  364 (695)
T ss_pred             CCCceeEeeeCCCChHHHHHHHHHHhccc-cCCCcceEEEeccccHHHHHHHHHhcCccccccccccCcccccccccccc
Confidence            45666665433  2445666776666655 78899999999999999999999999999999999999999999999999


Q ss_pred             cCCceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHH-----------------------------------------
Q psy17637         82 RQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTH-----------------------------------------  120 (150)
Q Consensus        82 ~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q-----------------------------------------  120 (150)
                      .|+++|+|+|-++++|+|-|++.+||+.++|+|++.|.|                                         
T Consensus       365 a~eiqvivatvafgmgidkpdvrfvihhsl~ksienyyqasarillrmtkqknksdtggstqinilevctnfkiffavfs  444 (695)
T KOG0353|consen  365 AGEIQVIVATVAFGMGIDKPDVRFVIHHSLPKSIENYYQASARILLRMTKQKNKSDTGGSTQINILEVCTNFKIFFAVFS  444 (695)
T ss_pred             ccceEEEEEEeeecccCCCCCeeEEEecccchhHHHHHHHHHHHHHHHhhhcccccCCCcceeehhhhhccceeeeeeec
Confidence            999999999999999999999999999999999999999                                         


Q ss_pred             --hhccccCCCCccEEEEEEecC
Q psy17637        121 --RIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus       121 --~~GR~~R~g~~~~~~~~~~~~  141 (150)
                        ..||+||.+.+..|++++.-.
T Consensus       445 ekesgragrd~~~a~cilyy~~~  467 (695)
T KOG0353|consen  445 EKESGRAGRDDMKADCILYYGFA  467 (695)
T ss_pred             chhccccccCCCcccEEEEechH
Confidence              789999999999999887543

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.76  E-value=2.4e-18  Score=142.26  Aligned_cols=109  Identities=25%  Similarity=0.380  Sum_probs=95.5

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCce---EEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEE
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYD---VLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVN  108 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~---~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~  108 (150)
                      ...+.+|||+++...++.+++.|...++.   +.++||++++++|.++++.  .|..+|+|||++++.|+++|++++||+
T Consensus       284 ~~~GdILVFLpg~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ~~Vf~~--~g~rkIIVATNIAEtSITIpgI~yVID  361 (1294)
T PRK11131        284 EGPGDILIFMSGEREIRDTADALNKLNLRHTEILPLYARLSNSEQNRVFQS--HSGRRIVLATNVAETSLTVPGIKYVID  361 (1294)
T ss_pred             CCCCCEEEEcCCHHHHHHHHHHHHhcCCCcceEeecccCCCHHHHHHHhcc--cCCeeEEEeccHHhhccccCcceEEEE
Confidence            35678999999999999999999876654   7799999999999999876  467899999999999999999999999


Q ss_pred             ecC---------------C---CChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637        109 YDL---------------A---RDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus       109 ~~~---------------~---~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      ++.               |   .|.++|.||+||+||. .+|.||.++++.+.
T Consensus       362 ~Gl~k~~~Yd~~~~~~~Lp~~~iSkasa~QRaGRAGR~-~~G~c~rLyte~d~  413 (1294)
T PRK11131        362 PGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRV-SEGICIRLYSEDDF  413 (1294)
T ss_pred             CCCccccccccccCcccCCeeecCHhhHhhhccccCCC-CCcEEEEeCCHHHH
Confidence            863               3   4668999999999999 58999999997653

>KOG0337|consensus

Probab=99.74  E-value=2.3e-18  Score=126.62  Aligned_cols=131  Identities=33%  Similarity=0.441  Sum_probs=115.7

Q ss_pred             ecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC
Q psy17637         13 TDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD   92 (150)
Q Consensus        13 ~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~   92 (150)
                      ..+..++...|+..+.+. -...+++||+.|..+++.+.+.|...|+....+++.|++..|..-+..|..+...+||.|+
T Consensus       241 ~~~~a~K~aaLl~il~~~-~~~~~t~vf~~tk~hve~~~~ll~~~g~~~s~iysslD~~aRk~~~~~F~~~k~~~lvvTd  319 (529)
T KOG0337|consen  241 RVRKAEKEAALLSILGGR-IKDKQTIVFVATKHHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRDFRGRKTSILVVTD  319 (529)
T ss_pred             eeccHHHHHHHHHHHhcc-ccccceeEEecccchHHHHHHHHHhcCCCccccccccChHhhhhccccccCCccceEEEeh
Confidence            333344444566555554 2356899999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCc
Q psy17637         93 VAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD  144 (150)
Q Consensus        93 ~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~  144 (150)
                      .+.+|+|+|-.+.||+||+|.+...|++|+||+.|.|+.+..|.++...+.-
T Consensus       320 vaaRG~diplldnvinyd~p~~~klFvhRVgr~aragrtg~aYs~V~~~~~~  371 (529)
T KOG0337|consen  320 VAARGLDIPLLDNVINYDFPPDDKLFVHRVGRVARAGRTGRAYSLVASTDDP  371 (529)
T ss_pred             hhhccCCCccccccccccCCCCCceEEEEecchhhccccceEEEEEecccch
Confidence            9999999999999999999999999999999999999999999999887653

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

Probab=99.74  E-value=2.5e-17  Score=127.63  Aligned_cols=137  Identities=25%  Similarity=0.328  Sum_probs=113.1

Q ss_pred             CCcCeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhh--------HHHHHhhcccc--CceEEEecCCCCHHH
Q psy17637          3 GNKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLN--------AEELANSLTVK--EYDVLLLHGDMDQSE   72 (150)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~--------~~~l~~~L~~~--~~~~~~~~~~~~~~~   72 (150)
                      |++.+.-.........   .+++.+.+...++.++.+.|+-.++        ++++++.|...  +.++..+||.|++++
T Consensus       445 GRkpI~T~~i~~~~~~---~v~e~i~~ei~~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~e  521 (677)
T COG1200         445 GRKPITTVVIPHERRP---EVYERIREEIAKGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAE  521 (677)
T ss_pred             CCCceEEEEeccccHH---HHHHHHHHHHHcCCEEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHH
Confidence            5566666665554433   5666776666678899999987665        44566666532  566999999999999


Q ss_pred             HHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCC-CChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637         73 RNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLA-RDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus        73 r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~-~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      +..+++.|++|+++|||||.+++-|+|+|+++++|..+.- ...++..|..||+||-+..++|++++....
T Consensus       522 Kd~vM~~Fk~~e~~ILVaTTVIEVGVdVPnATvMVIe~AERFGLaQLHQLRGRVGRG~~qSyC~Ll~~~~~  592 (677)
T COG1200         522 KDAVMEAFKEGEIDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGDLQSYCVLLYKPPL  592 (677)
T ss_pred             HHHHHHHHHcCCCcEEEEeeEEEecccCCCCeEEEEechhhhhHHHHHHhccccCCCCcceEEEEEeCCCC
Confidence            9999999999999999999999999999999999888776 489999999999999999999999998776

>KOG0349|consensus

Probab=99.73  E-value=1.9e-17  Score=122.72  Aligned_cols=109  Identities=35%  Similarity=0.571  Sum_probs=101.2

Q ss_pred             CCCCeeEEehhhhhHHHHHhhcccc---CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEe
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVK---EYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNY  109 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~---~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~  109 (150)
                      +..++||||.|+..|+.|.+.+..+   .+.++++||+..+.+|+..++.|+.+..+.||||++..+|+|+..+.++|+.
T Consensus       504 ~mdkaiifcrtk~dcDnLer~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~dvkflictdvaargldi~g~p~~inv  583 (725)
T KOG0349|consen  504 AMDKAIIFCRTKQDCDNLERMMNQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITGLPFMINV  583 (725)
T ss_pred             ccCceEEEEeccccchHHHHHHHHcCCccceeEEEecCCChhHHHHHHHhhhhcCeEEEEEehhhhccccccCCceEEEE
Confidence            6789999999999999999999765   4679999999999999999999999999999999999999999999999999


Q ss_pred             cCCCChhHHHHhhccccCCCCccEEEEEEecC
Q psy17637        110 DLARDIDTHTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus       110 ~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                      -+|.....|++|+||+||..+-|.++.++...
T Consensus       584 tlpd~k~nyvhrigrvgraermglaislvat~  615 (725)
T KOG0349|consen  584 TLPDDKTNYVHRIGRVGRAERMGLAISLVATV  615 (725)
T ss_pred             ecCcccchhhhhhhccchhhhcceeEEEeecc
Confidence            99999999999999999998778888887543

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.73  E-value=1.6e-17  Score=137.67  Aligned_cols=108  Identities=25%  Similarity=0.362  Sum_probs=94.1

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccC---ceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEe
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKE---YDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNY  109 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~---~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~  109 (150)
                      ..+.+|||+++..+++.+++.|...+   ..+.++||.|+++++.++++.+  +..+|+|||++++.|+++|++.+||++
T Consensus       278 ~~GdILVFLpg~~EI~~l~~~L~~~~~~~~~VlpLhg~Ls~~eQ~~vf~~~--~~rkIVLATNIAEtSLTIpgV~yVIDs  355 (1283)
T TIGR01967       278 GPGDILIFLPGEREIRDAAEILRKRNLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDT  355 (1283)
T ss_pred             CCCCEEEeCCCHHHHHHHHHHHHhcCCCCcEEEeccCCCCHHHHHHHhCCC--CCceEEEeccHHHhccccCCeeEEEeC
Confidence            45789999999999999999997653   4688999999999999986654  235899999999999999999999998


Q ss_pred             cCC------------------CChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637        110 DLA------------------RDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus       110 ~~~------------------~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +.+                  .|.++|.||.||+||.+ +|.||.++++.+.
T Consensus       356 Gl~r~~~yd~~~~~~~L~~~~ISkasa~QRaGRAGR~~-~G~cyRLyte~~~  406 (1283)
T TIGR01967       356 GTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVA-PGICIRLYSEEDF  406 (1283)
T ss_pred             CCccccccccccCccccCCccCCHHHHHHHhhhhCCCC-CceEEEecCHHHH
Confidence            854                  36789999999999998 8999999987643

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.

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.73  E-value=6.9e-17  Score=132.04  Aligned_cols=114  Identities=18%  Similarity=0.296  Sum_probs=101.8

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcC---CceEEEEcCCCcccCCccCCcEEEE
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQ---ECRILVATDVAARGLDIPHIRTVVN  108 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g---~~~vlv~T~~~~~Gidi~~~~~vi~  108 (150)
                      ..+.++|||+.....++.|...|...++.+..++|+++..+|..+++.|+..   ...+|++|.+++.|+|+..+++||+
T Consensus       485 ~~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLSTrAGGlGINLt~Ad~VIi  564 (1033)
T PLN03142        485 ERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRAGGLGINLATADIVIL  564 (1033)
T ss_pred             hcCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhccccCCceEEEEeccccccCCchhhCCEEEE
Confidence            4678999999999999999999998999999999999999999999999753   2357899999999999999999999


Q ss_pred             ecCCCChhHHHHhhccccCCCCcc--EEEEEEecCCCcc
Q psy17637        109 YDLARDIDTHTHRIGRTGRAGNKG--VAYTLVTDKDKDG  145 (150)
Q Consensus       109 ~~~~~~~~~~~q~~GR~~R~g~~~--~~~~~~~~~~~~~  145 (150)
                      ||++|++....|++||+.|.|+..  .+|.|++....++
T Consensus       565 yD~dWNP~~d~QAidRaHRIGQkk~V~VyRLIt~gTIEE  603 (1033)
T PLN03142        565 YDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEE  603 (1033)
T ss_pred             eCCCCChHHHHHHHHHhhhcCCCceEEEEEEEeCCcHHH
Confidence            999999999999999999999875  4667777765544

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.70  E-value=2e-16  Score=117.93  Aligned_cols=85  Identities=21%  Similarity=0.290  Sum_probs=73.9

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccC--ceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEec
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKE--YDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYD  110 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~--~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~  110 (150)
                      +..++||||+|.+.++.++..|...+  ..+..+||.+++.+|.+.      ++..|||||+++++|+|++.. +|| ++
T Consensus       271 ~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~R~~~------~~~~iLVaTdv~~rGiDi~~~-~vi-~~  342 (357)
T TIGR03158       271 PGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKDRERA------MQFDILLGTSTVDVGVDFKRD-WLI-FS  342 (357)
T ss_pred             CCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHHHHHh------ccCCEEEEecHHhcccCCCCc-eEE-EC
Confidence            56789999999999999999998754  578889999999988754      367899999999999999976 555 45


Q ss_pred             CCCChhHHHHhhcccc
Q psy17637        111 LARDIDTHTHRIGRTG  126 (150)
Q Consensus       111 ~~~~~~~~~q~~GR~~  126 (150)
                       |.+.++|+||+||+|
T Consensus       343 -p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       343 -ARDAAAFWQRLGRLG  357 (357)
T ss_pred             -CCCHHHHhhhcccCC
Confidence             889999999999986

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.

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.70  E-value=4e-16  Score=125.06  Aligned_cols=125  Identities=17%  Similarity=0.230  Sum_probs=111.8

Q ss_pred             hHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCccc
Q psy17637         18 EFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG   97 (150)
Q Consensus        18 ~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G   97 (150)
                      .+...+++.+......+.|+||||+|++.++.++..|...+++...+|+.+.+.++..+.+.|+.|  .|+|||+++++|
T Consensus       428 ~k~~av~~~i~~~~~~g~PVLVgt~Sie~sE~ls~~L~~~gi~h~vLnak~~q~Ea~iia~Ag~~G--~VtIATNmAGRG  505 (896)
T PRK13104        428 DKFQAIIEDVRECGVRKQPVLVGTVSIEASEFLSQLLKKENIKHQVLNAKFHEKEAQIIAEAGRPG--AVTIATNMAGRG  505 (896)
T ss_pred             HHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcCCCeEeecCCCChHHHHHHHhCCCCC--cEEEeccCccCC
Confidence            345578888877777999999999999999999999999999999999999999999999999999  499999999999


Q ss_pred             CCcc-C-------------------------------------CcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEe
Q psy17637         98 LDIP-H-------------------------------------IRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVT  139 (150)
Q Consensus        98 idi~-~-------------------------------------~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~  139 (150)
                      +|+. +                                     ==+||-...+.|...-.|..||+||.|++|.+-+|++
T Consensus       506 tDI~Lggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTerhesrRID~QLrGRaGRQGDPGss~f~lS  585 (896)
T PRK13104        506 TDIVLGGSLAADLANLPADASEQEKEAVKKEWQKRHDEVIAAGGLRIIGSERHESRRIDNQLRGRAGRQGDPGSSRFYLS  585 (896)
T ss_pred             cceecCCchhhhhhccccchhhHHHHHHHHHhhhhhhHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEE
Confidence            9984 1                                     1178888889999999999999999999999999999


Q ss_pred             cCCCc
Q psy17637        140 DKDKD  144 (150)
Q Consensus       140 ~~~~~  144 (150)
                      -+|..
T Consensus       586 leD~l  590 (896)
T PRK13104        586 LEDNL  590 (896)
T ss_pred             cCcHH
Confidence            87653

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.69  E-value=4.8e-16  Score=124.23  Aligned_cols=124  Identities=20%  Similarity=0.240  Sum_probs=110.7

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccC
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGL   98 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gi   98 (150)
                      +...+++.+......+.|+||||+|++.++.++..|...++++..+|+.  +.+|+..+..|+.+...|+|||+++++|+
T Consensus       415 K~~aI~~~I~~~~~~grpVLIft~Si~~se~Ls~~L~~~gi~~~vLnak--q~eREa~Iia~Ag~~g~VtIATNmAGRGt  492 (830)
T PRK12904        415 KFDAVVEDIKERHKKGQPVLVGTVSIEKSELLSKLLKKAGIPHNVLNAK--NHEREAEIIAQAGRPGAVTIATNMAGRGT  492 (830)
T ss_pred             HHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCceEeccCc--hHHHHHHHHHhcCCCceEEEecccccCCc
Confidence            4557788886654678899999999999999999999999999999996  88999999999999999999999999999


Q ss_pred             CccCC--------------------------------------cEEEEecCCCChhHHHHhhccccCCCCccEEEEEEec
Q psy17637         99 DIPHI--------------------------------------RTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTD  140 (150)
Q Consensus        99 di~~~--------------------------------------~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~  140 (150)
                      |++--                                      =+||-...|.|...-.|..||+||+|++|.+-+|++-
T Consensus       493 DI~LgGn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~GGLhVigTerhesrRid~QlrGRagRQGdpGss~f~lSl  572 (830)
T PRK12904        493 DIKLGGNPEMLAAALLEEETEEQIAKIKAEWQEEHEEVLEAGGLHVIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSL  572 (830)
T ss_pred             CccCCCchhhhhhhhhhhhhhHHHHHHHHHHhhhhhhHHHcCCCEEEecccCchHHHHHHhhcccccCCCCCceeEEEEc
Confidence            98632                                      2788888999999999999999999999999999998


Q ss_pred             CCCc
Q psy17637        141 KDKD  144 (150)
Q Consensus       141 ~~~~  144 (150)
                      +|..
T Consensus       573 eD~l  576 (830)
T PRK12904        573 EDDL  576 (830)
T ss_pred             CcHH
Confidence            7653

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

Probab=99.69  E-value=8.6e-16  Score=124.90  Aligned_cols=133  Identities=23%  Similarity=0.293  Sum_probs=110.6

Q ss_pred             CeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhcccc--CceEEEecCCCCHHHHHHHHHHhhcC
Q psy17637          6 GVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVK--EYDVLLLHGDMDQSERNSVITKFKRQ   83 (150)
Q Consensus         6 ~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g   83 (150)
                      .+.-++.+..+.-.-+.|+.++    ..++++-...|..+..+.+++.|...  ..++.+.||.|+..+-++++..|.+|
T Consensus       779 pV~T~V~~~d~~~ireAI~REl----~RgGQvfYv~NrV~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F~~g  854 (1139)
T COG1197         779 PVKTFVSEYDDLLIREAILREL----LRGGQVFYVHNRVESIEKKAERLRELVPEARIAVAHGQMRERELEEVMLDFYNG  854 (1139)
T ss_pred             ceEEEEecCChHHHHHHHHHHH----hcCCEEEEEecchhhHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHHHHHHcC
Confidence            3444445555554444555555    45688888889999999998888764  55789999999999999999999999


Q ss_pred             CceEEEEcCCCcccCCccCCcEEEEecCCC-ChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637         84 ECRILVATDVAARGLDIPHIRTVVNYDLAR-DIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus        84 ~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~-~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      +.+|||||..++.|+|+|++|.+|..+... ..+++.|..||+||..+.+++|+++....
T Consensus       855 ~~dVLv~TTIIEtGIDIPnANTiIIe~AD~fGLsQLyQLRGRVGRS~~~AYAYfl~p~~k  914 (1139)
T COG1197         855 EYDVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSNKQAYAYFLYPPQK  914 (1139)
T ss_pred             CCCEEEEeeeeecCcCCCCCceEEEeccccccHHHHHHhccccCCccceEEEEEeecCcc
Confidence            999999999999999999999988776654 89999999999999999999999998653

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

Probab=99.68  E-value=2.1e-15  Score=115.20  Aligned_cols=95  Identities=21%  Similarity=0.322  Sum_probs=91.3

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLA  112 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~  112 (150)
                      ...+++|||.+.+++++++..+...+. +..+++..+..+|..+++.|+.|.+.+||++.++.+|+|+|+++++|...++
T Consensus       282 ~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~~fr~g~~~~lv~~~vl~EGvDiP~~~~~i~~~~t  360 (442)
T COG1061         282 RGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPT  360 (442)
T ss_pred             CCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCCHHHHHHHHHHHHcCCCCEEEEeeeccceecCCCCcEEEEeCCC
Confidence            567999999999999999999998888 8899999999999999999999999999999999999999999999999999


Q ss_pred             CChhHHHHhhccccCC
Q psy17637        113 RDIDTHTHRIGRTGRA  128 (150)
Q Consensus       113 ~~~~~~~q~~GR~~R~  128 (150)
                      .|...|.||+||..|.
T Consensus       361 ~S~~~~~Q~lGR~LR~  376 (442)
T COG1061         361 GSRRLFIQRLGRGLRP  376 (442)
T ss_pred             CcHHHHHHHhhhhccC
Confidence            9999999999999994

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.67  E-value=6.9e-16  Score=123.56  Aligned_cols=125  Identities=18%  Similarity=0.249  Sum_probs=112.5

Q ss_pred             hHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCccc
Q psy17637         18 EFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG   97 (150)
Q Consensus        18 ~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G   97 (150)
                      ++...+++.+......+.|+||||+|.+.++.++..|...+++...+|+.+++.++..+.+.|+.|.  |+|||+++++|
T Consensus       433 ~K~~Aii~ei~~~~~~GrpVLV~t~sv~~se~ls~~L~~~gi~~~vLnak~~~~Ea~ii~~Ag~~G~--VtIATnmAGRG  510 (908)
T PRK13107        433 EKYQAIIKDIKDCRERGQPVLVGTVSIEQSELLARLMVKEKIPHEVLNAKFHEREAEIVAQAGRTGA--VTIATNMAGRG  510 (908)
T ss_pred             HHHHHHHHHHHHHHHcCCCEEEEeCcHHHHHHHHHHHHHCCCCeEeccCcccHHHHHHHHhCCCCCc--EEEecCCcCCC
Confidence            3445788888877788999999999999999999999999999999999999999999999999997  99999999999


Q ss_pred             CCccC-------------------------------------CcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEec
Q psy17637         98 LDIPH-------------------------------------IRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTD  140 (150)
Q Consensus        98 idi~~-------------------------------------~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~  140 (150)
                      +|+.=                                     ==+||-...+.|...-.|..||+||.|++|.+-+|++-
T Consensus       511 TDIkLggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTerheSrRID~QLrGRaGRQGDPGss~f~lSl  590 (908)
T PRK13107        511 TDIVLGGNWNMEIEALENPTAEQKAKIKADWQIRHDEVVAAGGLHILGTERHESRRIDNQLRGRAGRQGDAGSSRFYLSM  590 (908)
T ss_pred             cceecCCchHHhhhhhcchhhHHHHHHHHHHHhhHHHHHHcCCCEEEecccCchHHHHhhhhcccccCCCCCceeEEEEe
Confidence            99851                                     12788888999999999999999999999999999998


Q ss_pred             CCCc
Q psy17637        141 KDKD  144 (150)
Q Consensus       141 ~~~~  144 (150)
                      +|..
T Consensus       591 ED~L  594 (908)
T PRK13107        591 EDSL  594 (908)
T ss_pred             CcHH
Confidence            7653

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

Probab=99.66  E-value=7.7e-16  Score=116.45  Aligned_cols=122  Identities=23%  Similarity=0.320  Sum_probs=112.2

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccC
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGL   98 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gi   98 (150)
                      .+..|+..+........+++|-+-|++.+|.|.++|.+.|+++.++|++...-+|.++++..+.|.+.|||+.+.+.+|+
T Consensus       431 QvdDL~~EI~~r~~~~eRvLVTtLTKkmAEdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLLREGL  510 (663)
T COG0556         431 QVDDLLSEIRKRVAKNERVLVTTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGL  510 (663)
T ss_pred             cHHHHHHHHHHHHhcCCeEEEEeehHHHHHHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhhhccC
Confidence            46688899988767889999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccCCcEEEEecCCC-----ChhHHHHhhccccCCCCccEEEEEEecC
Q psy17637         99 DIPHIRTVVNYDLAR-----DIDTHTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus        99 di~~~~~vi~~~~~~-----~~~~~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                      |+|.+++|..+|..+     |..+++|-+|||.|.- .|.++.+.+.-
T Consensus       511 DiPEVsLVAIlDADKeGFLRse~SLIQtIGRAARN~-~GkvIlYAD~i  557 (663)
T COG0556         511 DLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNV-NGKVILYADKI  557 (663)
T ss_pred             CCcceeEEEEeecCccccccccchHHHHHHHHhhcc-CCeEEEEchhh
Confidence            999999999887765     8999999999999985 68888887654

>PRK09694 helicase Cas3; Provisional

Probab=99.64  E-value=1.6e-15  Score=122.92  Aligned_cols=106  Identities=25%  Similarity=0.348  Sum_probs=88.3

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccC---ceEEEecCCCCHHHH----HHHHHHh-hcCC---ceEEEE
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKE---YDVLLLHGDMDQSER----NSVITKF-KRQE---CRILVA   90 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~---~~~~~~~~~~~~~~r----~~~~~~f-~~g~---~~vlv~   90 (150)
                      .+++.+.+....+.+++|||||++.++++++.|+..+   ..+..+|+.+++.+|    +++++.| ++|+   ..|||+
T Consensus       548 ~~l~~i~~~~~~g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVa  627 (878)
T PRK09694        548 TLLQRMIAAANAGAQVCLICNLVDDAQKLYQRLKELNNTQVDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILVA  627 (878)
T ss_pred             HHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHhhCCCCceEEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEE
Confidence            4555555443567889999999999999999998654   579999999999999    4567788 6665   379999


Q ss_pred             cCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCC
Q psy17637         91 TDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGN  130 (150)
Q Consensus        91 T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~  130 (150)
                      |++++.|+|+ +++++|....|  .+.++||+||++|.+.
T Consensus       628 TQViE~GLDI-d~DvlItdlaP--idsLiQRaGR~~R~~~  664 (878)
T PRK09694        628 TQVVEQSLDL-DFDWLITQLCP--VDLLFQRLGRLHRHHR  664 (878)
T ss_pred             Ccchhheeec-CCCeEEECCCC--HHHHHHHHhccCCCCC
Confidence            9999999999 57988887777  7899999999999875

>PRK14701 reverse gyrase; Provisional

Probab=99.64  E-value=1.8e-15  Score=128.61  Aligned_cols=120  Identities=19%  Similarity=0.264  Sum_probs=95.4

Q ss_pred             CeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhh---HHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhc
Q psy17637          6 GVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLN---AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKR   82 (150)
Q Consensus         6 ~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~---~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~   82 (150)
                      ++...+.......+ ..++..+...   +.++||||++++.   ++++++.|...|+++..+||+     |...++.|++
T Consensus       306 ~i~~~yi~~~~~~k-~~L~~ll~~~---g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~~-----R~~~l~~F~~  376 (1638)
T PRK14701        306 NIVDVYLNPEKIIK-EHVRELLKKL---GKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAK-----NKKGFDLFEE  376 (1638)
T ss_pred             CcEEEEEECCHHHH-HHHHHHHHhC---CCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecch-----HHHHHHHHHc
Confidence            44444443332222 3555555443   4689999999875   589999999999999999995     8899999999


Q ss_pred             CCceEEEEc----CCCcccCCccC-CcEEEEecCCC---ChhHHHHhh-------------ccccCCCCccEE
Q psy17637         83 QECRILVAT----DVAARGLDIPH-IRTVVNYDLAR---DIDTHTHRI-------------GRTGRAGNKGVA  134 (150)
Q Consensus        83 g~~~vlv~T----~~~~~Gidi~~-~~~vi~~~~~~---~~~~~~q~~-------------GR~~R~g~~~~~  134 (150)
                      |+.+|||||    +.+++|+|+|+ +.+|||+++|+   +++.|.|..             ||++|.|.+..+
T Consensus       377 G~~~VLVaT~s~~gvaaRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~~~~~~~~~~~~~~~~~a~~~g~~~~~  449 (1638)
T PRK14701        377 GEIDYLIGVATYYGTLVRGLDLPERIRFAVFYGVPKFRFRVDLEDPTIYRILGLLSEILKIEEELKEGIPIEG  449 (1638)
T ss_pred             CCCCEEEEecCCCCeeEecCccCCccCEEEEeCCCCCCcchhhcccchhhhhcchHHHHHhhhhcccCCcchh
Confidence            999999999    48899999998 99999999999   888777765             999999876444

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.63  E-value=3e-15  Score=120.00  Aligned_cols=122  Identities=24%  Similarity=0.344  Sum_probs=97.4

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccc---------------------c----------------CceEEEe
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLNAEELANSLTV---------------------K----------------EYDVLLL   64 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~---------------------~----------------~~~~~~~   64 (150)
                      .++..+........+++|||++++.+...+.+|..                     .                ...++++
T Consensus       241 ~~~~~v~~~~~~~~qvLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafH  320 (766)
T COG1204         241 LALELVLESLAEGGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFH  320 (766)
T ss_pred             HHHHHHHHHHhcCCeEEEEEecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCcccc
Confidence            45555555556788999999999998888887762                     0                0126889


Q ss_pred             cCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEE----Eec-----CCCChhHHHHhhccccCCCC--ccE
Q psy17637         65 HGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV----NYD-----LARDIDTHTHRIGRTGRAGN--KGV  133 (150)
Q Consensus        65 ~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi----~~~-----~~~~~~~~~q~~GR~~R~g~--~~~  133 (150)
                      |++++.++|.-+.+.|+.|.++||+||+.+.+|+|+|.-..||    .|+     .+-+.-++.||.|||||+|-  .|.
T Consensus       321 hAGL~~~~R~~vE~~Fr~g~ikVlv~TpTLA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~dv~QM~GRAGRPg~d~~G~  400 (766)
T COG1204         321 HAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPGYDDYGE  400 (766)
T ss_pred             ccCCCHHHHHHHHHHHhcCCceEEEechHHhhhcCCcceEEEEeeeEEEcCCCCeEECchhhHhhccCcCCCCCcCCCCc
Confidence            9999999999999999999999999999999999999877776    466     44578899999999999994  355


Q ss_pred             EEEEEecCCC
Q psy17637        134 AYTLVTDKDK  143 (150)
Q Consensus       134 ~~~~~~~~~~  143 (150)
                      .+.+.+..+.
T Consensus       401 ~~i~~~~~~~  410 (766)
T COG1204         401 AIILATSHDE  410 (766)
T ss_pred             EEEEecCccc
Confidence            6666644433

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

Probab=99.59  E-value=2.4e-14  Score=103.48  Aligned_cols=115  Identities=21%  Similarity=0.298  Sum_probs=94.8

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhhHHHHHhhcccc--CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCC
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVK--EYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLD   99 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gid   99 (150)
                      .|...+....+.+.|++||+++.+..+.+++.|+..  ...++.+|+.  ...|.+.+++|++|++.+|++|..+++|+.
T Consensus       293 kl~~~lekq~~~~~P~liF~p~I~~~eq~a~~lk~~~~~~~i~~Vhs~--d~~R~EkV~~fR~G~~~lLiTTTILERGVT  370 (441)
T COG4098         293 KLKRWLEKQRKTGRPVLIFFPEIETMEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDGKITLLITTTILERGVT  370 (441)
T ss_pred             HHHHHHHHHHhcCCcEEEEecchHHHHHHHHHHHhhCCccceeeeecc--CccHHHHHHHHHcCceEEEEEeehhhcccc
Confidence            677788877778899999999999999999999543  3456788887  557889999999999999999999999999


Q ss_pred             ccCCcEEEEecCC--CChhHHHHhhccccCCCC--ccEEEEEE
Q psy17637        100 IPHIRTVVNYDLA--RDIDTHTHRIGRTGRAGN--KGVAYTLV  138 (150)
Q Consensus       100 i~~~~~vi~~~~~--~~~~~~~q~~GR~~R~g~--~~~~~~~~  138 (150)
                      +|++++.+.-.-.  .+.+.++|..||+||.-+  .|.++.|-
T Consensus       371 fp~vdV~Vlgaeh~vfTesaLVQIaGRvGRs~~~PtGdv~FFH  413 (441)
T COG4098         371 FPNVDVFVLGAEHRVFTESALVQIAGRVGRSLERPTGDVLFFH  413 (441)
T ss_pred             cccceEEEecCCcccccHHHHHHHhhhccCCCcCCCCcEEEEe
Confidence            9999987653333  689999999999999653  34455444

>TIGR00595 priA primosomal protein N'

Probab=99.59  E-value=9e-15  Score=113.18  Aligned_cols=95  Identities=20%  Similarity=0.339  Sum_probs=75.9

Q ss_pred             HHHHHhhcccc--CceEEEecCCCCHHHH--HHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCCC---------
Q psy17637         47 AEELANSLTVK--EYDVLLLHGDMDQSER--NSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLAR---------  113 (150)
Q Consensus        47 ~~~l~~~L~~~--~~~~~~~~~~~~~~~r--~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~---------  113 (150)
                      .+.+.+.|...  +.++..+|++++...+  +++++.|++|+.+|||+|++++.|+|+|++++|+.++...         
T Consensus       271 te~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~i~kG~d~~~v~lV~vl~aD~~l~~pd~ra  350 (505)
T TIGR00595       271 TEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRA  350 (505)
T ss_pred             HHHHHHHHHhhCCCCcEEEEecccccCccHHHHHHHHHhcCCCCEEEeCcccccCCCCCcccEEEEEcCcccccCcccch
Confidence            35666666544  6789999999887666  8999999999999999999999999999999886444432         


Q ss_pred             ---ChhHHHHhhccccCCCCccEEEEEEecC
Q psy17637        114 ---DIDTHTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus       114 ---~~~~~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                         ....|.|++||+||.+..|.++......
T Consensus       351 ~E~~~~ll~q~~GRagR~~~~g~viiqt~~p  381 (505)
T TIGR00595       351 AERGFQLLTQVAGRAGRAEDPGQVIIQTYNP  381 (505)
T ss_pred             HHHHHHHHHHHHhccCCCCCCCEEEEEeCCC
Confidence               2467899999999998888887655443

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).

>PRK09401 reverse gyrase; Reviewed

Probab=99.59  E-value=8e-15  Score=122.14  Aligned_cols=98  Identities=24%  Similarity=0.288  Sum_probs=83.7

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhh---HHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEE----cCCC
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLN---AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVA----TDVA   94 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~---~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~----T~~~   94 (150)
                      .+...+...   +.++||||++++.   ++.+++.|...|+++..+||+|     .+.+++|++|+++||||    |+.+
T Consensus       319 ~L~~ll~~l---~~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l-----~~~l~~F~~G~~~VLVatas~tdv~  390 (1176)
T PRK09401        319 KLVELVKRL---GDGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF-----ERKFEKFEEGEVDVLVGVASYYGVL  390 (1176)
T ss_pred             HHHHHHHhc---CCCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH-----HHHHHHHHCCCCCEEEEecCCCCce
Confidence            444444433   3589999999777   9999999999999999999999     23459999999999999    6899


Q ss_pred             cccCCccC-CcEEEEecCCC------ChhHHHHhhccccC
Q psy17637         95 ARGLDIPH-IRTVVNYDLAR------DIDTHTHRIGRTGR  127 (150)
Q Consensus        95 ~~Gidi~~-~~~vi~~~~~~------~~~~~~q~~GR~~R  127 (150)
                      ++|+|+|+ +++||||++|+      ....+.+++||+..
T Consensus       391 aRGIDiP~~IryVI~y~vP~~~~~~~~~~~~~~~~~r~~~  430 (1176)
T PRK09401        391 VRGIDLPERIRYAIFYGVPKFKFSLEEELAPPFLLLRLLS  430 (1176)
T ss_pred             eecCCCCcceeEEEEeCCCCEEEeccccccCHHHHHHHHh
Confidence            99999999 89999999998      66788999999853

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

Probab=99.57  E-value=3.5e-14  Score=117.85  Aligned_cols=95  Identities=23%  Similarity=0.350  Sum_probs=82.1

Q ss_pred             CCCeeEEehhhhhHHHHHhhcccc------C---ceEEEecCCCCHHHHHHHHHHhhcCCc-eEEEEcCCCcccCCccCC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVK------E---YDVLLLHGDMDQSERNSVITKFKRQEC-RILVATDVAARGLDIPHI  103 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~------~---~~~~~~~~~~~~~~r~~~~~~f~~g~~-~vlv~T~~~~~Gidi~~~  103 (150)
                      ..++||||.++++++.+++.|...      +   ..+..+||.++  ++.++++.|+++.. .|+|+++++.+|+|+|.+
T Consensus       698 ~~KtiIF~~s~~HA~~i~~~L~~~f~~~~~~~~~~~v~~itg~~~--~~~~li~~Fk~~~~p~IlVsvdmL~TG~DvP~v  775 (1123)
T PRK11448        698 EGKTLIFAATDAHADMVVRLLKEAFKKKYGQVEDDAVIKITGSID--KPDQLIRRFKNERLPNIVVTVDLLTTGIDVPSI  775 (1123)
T ss_pred             CCcEEEEEcCHHHHHHHHHHHHHHHHhhcCCcCccceEEEeCCcc--chHHHHHHHhCCCCCeEEEEecccccCCCcccc
Confidence            479999999999999888876542      2   23566888875  56789999999887 589999999999999999


Q ss_pred             cEEEEecCCCChhHHHHhhccccCCCC
Q psy17637        104 RTVVNYDLARDIDTHTHRIGRTGRAGN  130 (150)
Q Consensus       104 ~~vi~~~~~~~~~~~~q~~GR~~R~g~  130 (150)
                      .+||++.++.|...|.||+||+.|...
T Consensus       776 ~~vVf~rpvkS~~lf~QmIGRgtR~~~  802 (1123)
T PRK11448        776 CNLVFLRRVRSRILYEQMLGRATRLCP  802 (1123)
T ss_pred             cEEEEecCCCCHHHHHHHHhhhccCCc
Confidence            999999999999999999999999754

>KOG0947|consensus

Probab=99.56  E-value=2.9e-14  Score=113.73  Aligned_cols=119  Identities=24%  Similarity=0.322  Sum_probs=96.9

Q ss_pred             HHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCce---------------------------------------
Q psy17637         20 AGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYD---------------------------------------   60 (150)
Q Consensus        20 ~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~---------------------------------------   60 (150)
                      ...++..+...  .--|+||||.+++.|++-+++|...++.                                       
T Consensus       555 ~l~lin~L~k~--~lLP~VvFvFSkkrCde~a~~L~~~nL~~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RG  632 (1248)
T KOG0947|consen  555 WLDLINHLRKK--NLLPVVVFVFSKKRCDEYADYLTNLNLTDSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRG  632 (1248)
T ss_pred             HHHHHHHHhhc--ccCceEEEEEccccHHHHHHHHhccCcccchhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHhhc
Confidence            34666777665  6789999999999999999998642221                                       


Q ss_pred             EEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCCC---------ChhHHHHhhccccCCCC-
Q psy17637         61 VLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLAR---------DIDTHTHRIGRTGRAGN-  130 (150)
Q Consensus        61 ~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~---------~~~~~~q~~GR~~R~g~-  130 (150)
                      ++.+|||+-|-.++-+...|+.|-++||+||..+++|+|.|.-.+|+ .+..+         .+.+|.||.|||||.|= 
T Consensus       633 iaVHH~GlLPivKE~VE~LFqrGlVKVLFATETFAMGVNMPARtvVF-~Sl~KhDG~efR~L~PGEytQMAGRAGRRGlD  711 (1248)
T KOG0947|consen  633 IAVHHGGLLPIVKEVVELLFQRGLVKVLFATETFAMGVNMPARTVVF-SSLRKHDGNEFRELLPGEYTQMAGRAGRRGLD  711 (1248)
T ss_pred             chhhcccchHHHHHHHHHHHhcCceEEEeehhhhhhhcCCCceeEEe-eehhhccCcceeecCChhHHhhhccccccccC
Confidence            78899999999999999999999999999999999999998765555 33332         79999999999999993 


Q ss_pred             -ccEEEEEEecC
Q psy17637        131 -KGVAYTLVTDK  141 (150)
Q Consensus       131 -~~~~~~~~~~~  141 (150)
                       .|.++++....
T Consensus       712 ~tGTVii~~~~~  723 (1248)
T KOG0947|consen  712 ETGTVIIMCKDS  723 (1248)
T ss_pred             cCceEEEEecCC
Confidence             46676666554

>KOG0948|consensus

Probab=99.54  E-value=1.1e-14  Score=113.84  Aligned_cols=121  Identities=17%  Similarity=0.311  Sum_probs=98.2

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCce---------------------------------------EE
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYD---------------------------------------VL   62 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~---------------------------------------~~   62 (150)
                      .++..+...  +..|+|||+.+++.||.++-.+....+.                                       +.
T Consensus       373 kiVkmi~~~--~~~PVIvFSFSkkeCE~~Alqm~kldfN~deEk~~V~~iF~nAi~~LseeDr~LPqie~iLPLL~RGIG  450 (1041)
T KOG0948|consen  373 KIVKMIMER--NYLPVIVFSFSKKECEAYALQMSKLDFNTDEEKELVETIFNNAIDQLSEEDRELPQIENILPLLRRGIG  450 (1041)
T ss_pred             HHHHHHHhh--cCCceEEEEecHhHHHHHHHhhccCcCCChhHHHHHHHHHHHHHHhcChhhccchHHHHHHHHHHhccc
Confidence            556666554  7789999999999999988777542211                                       67


Q ss_pred             EecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCCC---------ChhHHHHhhccccCCC--Cc
Q psy17637         63 LLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLAR---------DIDTHTHRIGRTGRAG--NK  131 (150)
Q Consensus        63 ~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~---------~~~~~~q~~GR~~R~g--~~  131 (150)
                      .+|+|+-|--++.+.-.|++|-+++|.||..++.|+|.|.-++|+- ..-+         +..+|+||.|||||.|  ..
T Consensus       451 IHHsGLLPIlKE~IEILFqEGLvKvLFATETFsiGLNMPAkTVvFT-~~rKfDG~~fRwissGEYIQMSGRAGRRG~Ddr  529 (1041)
T KOG0948|consen  451 IHHSGLLPILKEVIEILFQEGLVKVLFATETFSIGLNMPAKTVVFT-AVRKFDGKKFRWISSGEYIQMSGRAGRRGIDDR  529 (1041)
T ss_pred             cccccchHHHHHHHHHHHhccHHHHHHhhhhhhhccCCcceeEEEe-eccccCCcceeeecccceEEecccccccCCCCC
Confidence            8999999999999999999999999999999999999998665553 3322         7899999999999999  45


Q ss_pred             cEEEEEEecCCCcc
Q psy17637        132 GVAYTLVTDKDKDG  145 (150)
Q Consensus       132 ~~~~~~~~~~~~~~  145 (150)
                      |.+++++++.-...
T Consensus       530 GivIlmiDekm~~~  543 (1041)
T KOG0948|consen  530 GIVILMIDEKMEPQ  543 (1041)
T ss_pred             ceEEEEecCcCCHH
Confidence            88888888765543

>KOG0384|consensus

Probab=99.50  E-value=1.5e-13  Score=111.83  Aligned_cols=113  Identities=22%  Similarity=0.320  Sum_probs=104.1

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhc---CCceEEEEcCCCcccCCccCCcEEEE
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKR---QECRILVATDVAARGLDIPHIRTVVN  108 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~---g~~~vlv~T~~~~~Gidi~~~~~vi~  108 (150)
                      ..+.++|||+.....++-|+++|..++++.-.+.|.+..+.|+..+..|..   ..+..|++|.+.+-|||+-.++.||.
T Consensus       697 ~~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AIDhFnap~SddFvFLLSTRAGGLGINLatADTVII  776 (1373)
T KOG0384|consen  697 EGGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPDSDDFVFLLSTRAGGLGINLATADTVII  776 (1373)
T ss_pred             cCCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcchHHHHHHHHhccCCCCCceEEEEecccCcccccccccceEEE
Confidence            357899999999999999999999999999999999999999999999985   34679999999999999999999999


Q ss_pred             ecCCCChhHHHHhhccccCCCCcc--EEEEEEecCCCc
Q psy17637        109 YDLARDIDTHTHRIGRTGRAGNKG--VAYTLVTDKDKD  144 (150)
Q Consensus       109 ~~~~~~~~~~~q~~GR~~R~g~~~--~~~~~~~~~~~~  144 (150)
                      ||..|+|..-+|+..||.|.|+..  .+|.|++...-.
T Consensus       777 FDSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk~TvE  814 (1373)
T KOG0384|consen  777 FDSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTKNTVE  814 (1373)
T ss_pred             eCCCCCcchHHHHHHHHHhhcccceEEEEEEecCCchH
Confidence            999999999999999999999876  468899887544

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

Probab=99.50  E-value=2.3e-13  Score=110.57  Aligned_cols=115  Identities=21%  Similarity=0.311  Sum_probs=99.8

Q ss_pred             CCCCeeEEehhhhhHHHHH----hhccccC----ceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCc
Q psy17637         33 EVPPALMNLAMQLNAEELA----NSLTVKE----YDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIR  104 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~----~~L~~~~----~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~  104 (150)
                      ...++|+|+.+++.++.++    ..+...+    ..+..++++|++++|.++...|+.|++.++++|.+++-|+|+..++
T Consensus       305 ~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~~~g~~~~~~st~AlelgidiG~ld  384 (851)
T COG1205         305 NGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLD  384 (851)
T ss_pred             cCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHHhcCCccEEecchhhhhceeehhhh
Confidence            5779999999999999886    3333334    5688999999999999999999999999999999999999999999


Q ss_pred             EEEEecCCC-ChhHHHHhhccccCCCCccEEEEEEecCCCcccc
Q psy17637        105 TVVNYDLAR-DIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGEL  147 (150)
Q Consensus       105 ~vi~~~~~~-~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~~~~  147 (150)
                      .||..+.|. +..++.|+.||+||.++.+..+.+...+--+.++
T Consensus       385 avi~~g~P~~s~~~~~Q~~GRaGR~~~~~l~~~v~~~~~~d~yy  428 (851)
T COG1205         385 AVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVVLRSDPLDSYY  428 (851)
T ss_pred             hHhhcCCCCchHHHHHHhhhhccCCCCCceEEEEeCCCccchhh
Confidence            999999999 8999999999999999777777777644444443

>TIGR01054 rgy reverse gyrase

Probab=99.50  E-value=2.4e-13  Score=113.52  Aligned_cols=85  Identities=21%  Similarity=0.339  Sum_probs=74.8

Q ss_pred             HHHHHHHhccCCCCCeeEEehhh---hhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEc----CCC
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQ---LNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVAT----DVA   94 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~---~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T----~~~   94 (150)
                      .+++.+...   ..++||||+++   +.++++++.|...|+++..+||+++    ++.++.|++|+++|||||    +.+
T Consensus       317 ~L~~ll~~l---~~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~----~~~l~~Fr~G~~~vLVata~~tdv~  389 (1171)
T TIGR01054       317 TLLEIVKKL---GTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKP----KEDYEKFAEGEIDVLIGVASYYGTL  389 (1171)
T ss_pred             HHHHHHHHc---CCCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCC----HHHHHHHHcCCCCEEEEeccccCcc
Confidence            444444433   35899999999   9999999999999999999999997    378999999999999994    899


Q ss_pred             cccCCccC-CcEEEEecCCC
Q psy17637         95 ARGLDIPH-IRTVVNYDLAR  113 (150)
Q Consensus        95 ~~Gidi~~-~~~vi~~~~~~  113 (150)
                      ++|+|+|+ +++||||++|+
T Consensus       390 aRGIDip~~V~~vI~~~~P~  409 (1171)
T TIGR01054       390 VRGLDLPERVRYAVFLGVPK  409 (1171)
T ss_pred             cccCCCCccccEEEEECCCC
Confidence            99999999 89999999997

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.

>KOG4150|consensus

Probab=99.49  E-value=1.1e-13  Score=105.91  Aligned_cols=115  Identities=15%  Similarity=0.130  Sum_probs=96.6

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc----cC----ceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCc
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV----KE----YDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIR  104 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~----~~----~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~  104 (150)
                      ..-++|.||.+++.||.+....++    -+    -.+..+.||...++|.++...+-.|.+.-+|+|++++.|+|+..++
T Consensus       524 ~~~R~IAFC~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~L~giIaTNALELGIDIG~LD  603 (1034)
T KOG4150|consen  524 HGLRCIAFCPSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGGKLCGIIATNALELGIDIGHLD  603 (1034)
T ss_pred             cCCcEEEeccHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCCeeeEEEecchhhhccccccce
Confidence            467999999999999876554332    11    1245678999999999999999999999999999999999999999


Q ss_pred             EEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCcccc
Q psy17637        105 TVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGEL  147 (150)
Q Consensus       105 ~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~~~~  147 (150)
                      .|++.++|.|++.+.|..||+||..+++..+.++...--++++
T Consensus       604 AVl~~GFP~S~aNl~QQ~GRAGRRNk~SLavyva~~~PVDQ~Y  646 (1034)
T KOG4150|consen  604 AVLHLGFPGSIANLWQQAGRAGRRNKPSLAVYVAFLGPVDQYY  646 (1034)
T ss_pred             eEEEccCchhHHHHHHHhccccccCCCceEEEEEeccchhhHh
Confidence            9999999999999999999999998888777777655444443

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.49  E-value=3.5e-13  Score=107.69  Aligned_cols=96  Identities=26%  Similarity=0.375  Sum_probs=77.2

Q ss_pred             HHHHHhhcccc--CceEEEecCCCC--HHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCC--CC------
Q psy17637         47 AEELANSLTVK--EYDVLLLHGDMD--QSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLA--RD------  114 (150)
Q Consensus        47 ~~~l~~~L~~~--~~~~~~~~~~~~--~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~--~~------  114 (150)
                      ++.+.+.|...  +.++..+|++++  .++++++++.|++|+..|||+|++++.|+|+|++++|+.++.+  .+      
T Consensus       439 ~e~~~e~l~~~fp~~~v~~~~~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~iakG~d~p~v~lV~il~aD~~l~~pdfra  518 (679)
T PRK05580        439 TERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDFRA  518 (679)
T ss_pred             HHHHHHHHHHhCCCCcEEEEeccccccchhHHHHHHHHhcCCCCEEEEChhhccCCCCCCcCEEEEEcCchhccCCccch
Confidence            45566666543  677899999986  4678999999999999999999999999999999998655443  22      


Q ss_pred             ----hhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637        115 ----IDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus       115 ----~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                          ...|.|++||+||.+..|.++......+
T Consensus       519 ~Er~~~~l~q~~GRagR~~~~g~viiqT~~p~  550 (679)
T PRK05580        519 SERTFQLLTQVAGRAGRAEKPGEVLIQTYHPE  550 (679)
T ss_pred             HHHHHHHHHHHHhhccCCCCCCEEEEEeCCCC
Confidence                3568999999999888888887665543

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

Probab=99.41  E-value=1e-12  Score=105.91  Aligned_cols=112  Identities=29%  Similarity=0.420  Sum_probs=98.2

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEE
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV  107 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi  107 (150)
                      +..+.+|||.+..++.+.+++.|.+    ....+.++||.++.+++.++++--..|.-+|+++|++++.++.||++.+||
T Consensus       257 ~~~GdILvFLpG~~EI~~~~~~L~~~~l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATNIAETSLTI~gIr~VI  336 (845)
T COG1643         257 EGSGSILVFLPGQREIERTAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYVI  336 (845)
T ss_pred             CCCCCEEEECCcHHHHHHHHHHHHhccccCCcEEeeccccCCHHHHHhhcCCCCCCcceEEEEccccccceeeCCeEEEe
Confidence            4678999999999999999999887    457899999999999999998888888667999999999999999999999


Q ss_pred             EecCC------------------CChhHHHHhhccccCCCCccEEEEEEecCCCc
Q psy17637        108 NYDLA------------------RDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD  144 (150)
Q Consensus       108 ~~~~~------------------~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~  144 (150)
                      +.+.-                  .|.++..||.|||||.+ +|.||-++++++..
T Consensus       337 DsG~ak~~~y~~~~g~~~L~~~~ISqAsA~QRaGRAGR~~-pGicyRLyse~~~~  390 (845)
T COG1643         337 DSGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGRTG-PGICYRLYSEEDFL  390 (845)
T ss_pred             cCCcccccccccccCceeeeEEEechhhhhhhccccccCC-CceEEEecCHHHHH
Confidence            75543                  37888899999999996 89999999975443

>KOG0387|consensus

Probab=99.40  E-value=2.1e-12  Score=101.64  Aligned_cols=131  Identities=21%  Similarity=0.282  Sum_probs=111.4

Q ss_pred             hhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhcc-ccCceEEEecCCCCHHHHHHHHHHhhcCCc--eEEEEcC
Q psy17637         16 DKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLT-VKEYDVLLLHGDMDQSERNSVITKFKRQEC--RILVATD   92 (150)
Q Consensus        16 ~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~-~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~--~vlv~T~   92 (150)
                      ..-+++.+...|......+.++++|+.++...+.|...|. ..++.++.+.|..+...|..+++.|.+++.  -.|++|.
T Consensus       528 ~sGKm~vl~~ll~~W~kqg~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~~~~R~~lVd~Fne~~s~~VFLLTTr  607 (923)
T KOG0387|consen  528 RSGKMKVLAKLLKDWKKQGDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTPAALRQKLVDRFNEDESIFVFLLTTR  607 (923)
T ss_pred             hcchHHHHHHHHHHHhhCCCEEEEehhHHHHHHHHHHHHHhcCCceEEEecCCCccchhhHHHHhhcCCCceEEEEEEec
Confidence            3334555555555555567899999999999999999888 689999999999999999999999998765  4779999


Q ss_pred             CCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCcc--EEEEEEecCCCccc
Q psy17637         93 VAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKG--VAYTLVTDKDKDGE  146 (150)
Q Consensus        93 ~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~--~~~~~~~~~~~~~~  146 (150)
                      +.+.|+|+..++-||.|||.|+|+.-.|+.-|+.|.|+..  .+|.|++....++.
T Consensus       608 vGGLGlNLTgAnRVIIfDPdWNPStD~QAreRawRiGQkkdV~VYRL~t~gTIEEk  663 (923)
T KOG0387|consen  608 VGGLGLNLTGANRVIIFDPDWNPSTDNQARERAWRIGQKKDVVVYRLMTAGTIEEK  663 (923)
T ss_pred             ccccccccccCceEEEECCCCCCccchHHHHHHHhhcCccceEEEEEecCCcHHHH
Confidence            9999999999999999999999999999999999999876  46777877665443

>KOG0390|consensus

Probab=99.40  E-value=5.7e-12  Score=100.23  Aligned_cols=110  Identities=16%  Similarity=0.306  Sum_probs=88.3

Q ss_pred             CeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCc---eEEEEcCCCcccCCccCCcEEEEecCC
Q psy17637         36 PALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQEC---RILVATDVAARGLDIPHIRTVVNYDLA  112 (150)
Q Consensus        36 ~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~---~vlv~T~~~~~Gidi~~~~~vi~~~~~  112 (150)
                      .+++..+-+...+-+...+.-.|+.+..+||.|+..+|+.+++.|.+...   -.|.+|.++++|+++-+++.||.||++
T Consensus       597 ~~v~Isny~~tldl~e~~~~~~g~~~~rLdG~~~~~qRq~~vd~FN~p~~~~~vfLlSsKAgg~GinLiGAsRlil~D~d  676 (776)
T KOG0390|consen  597 KSVLISNYTQTLDLFEQLCRWRGYEVLRLDGKTSIKQRQKLVDTFNDPESPSFVFLLSSKAGGEGLNLIGASRLILFDPD  676 (776)
T ss_pred             EEEEeccHHHHHHHHHHHHhhcCceEEEEcCCCchHHHHHHHHhccCCCCCceEEEEecccccCceeecccceEEEeCCC
Confidence            33333344445555555555569999999999999999999999997543   356777999999999999999999999


Q ss_pred             CChhHHHHhhccccCCCCcc--EEEEEEecCCCcc
Q psy17637        113 RDIDTHTHRIGRTGRAGNKG--VAYTLVTDKDKDG  145 (150)
Q Consensus       113 ~~~~~~~q~~GR~~R~g~~~--~~~~~~~~~~~~~  145 (150)
                      |+|+.-.|+++|+.|.||..  ++|.|++....++
T Consensus       677 WNPa~d~QAmaR~~RdGQKk~v~iYrLlatGtiEE  711 (776)
T KOG0390|consen  677 WNPAVDQQAMARAWRDGQKKPVYIYRLLATGTIEE  711 (776)
T ss_pred             CCchhHHHHHHHhccCCCcceEEEEEeecCCCchH
Confidence            99999999999999999865  5677777665444

>KOG0329|consensus

Probab=99.39  E-value=8.8e-14  Score=97.21  Aligned_cols=103  Identities=36%  Similarity=0.518  Sum_probs=81.7

Q ss_pred             CeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCc
Q psy17637          6 GVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQEC   85 (150)
Q Consensus         6 ~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~   85 (150)
                      |+.++++.-++.++...+.+.+...  ..++++||+.+....                               .|+   .
T Consensus       257 GLqQ~YvkLke~eKNrkl~dLLd~L--eFNQVvIFvKsv~Rl-------------------------------~f~---k  300 (387)
T KOG0329|consen  257 GLQQYYVKLKENEKNRKLNDLLDVL--EFNQVVIFVKSVQRL-------------------------------SFQ---K  300 (387)
T ss_pred             hHHHHHHhhhhhhhhhhhhhhhhhh--hhcceeEeeehhhhh-------------------------------hhh---h
Confidence            3445555556666666666666655  677899999886651                               031   1


Q ss_pred             eEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCcc
Q psy17637         86 RILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDG  145 (150)
Q Consensus        86 ~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~~  145 (150)
                      + +|+|+.+++|+|+..++.++|||.|.+..+|+++.||+||.|..|.++.|++..+...
T Consensus       301 r-~vat~lfgrgmdiervNi~~NYdmp~~~DtYlHrv~rAgrfGtkglaitfvs~e~da~  359 (387)
T KOG0329|consen  301 R-LVATDLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAK  359 (387)
T ss_pred             h-hHHhhhhccccCcccceeeeccCCCCCchHHHHHhhhhhccccccceeehhcchhhHH
Confidence            3 7999999999999999999999999999999999999999999999999998766543

>KOG0385|consensus

Probab=99.39  E-value=4.5e-12  Score=99.67  Aligned_cols=125  Identities=22%  Similarity=0.351  Sum_probs=107.8

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC---ceEEEEcCCCc
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE---CRILVATDVAA   95 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~---~~vlv~T~~~~   95 (150)
                      .+..|+..|.   +.+.++|||+.-....+-|-.++.-+++....+.|.++-++|...++.|....   .-.|++|.+.+
T Consensus       475 vLDkLL~~Lk---~~GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~~eeR~~aI~~fn~~~s~~FiFlLSTRAGG  551 (971)
T KOG0385|consen  475 VLDKLLPKLK---EQGHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTSHEEREDAIEAFNAPPSEKFIFLLSTRAGG  551 (971)
T ss_pred             hHHHHHHHHH---hCCCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCCcHHHHHHHHhcCCCCcceEEEEEeccccc
Confidence            3444444444   46889999999999999999999999999999999999999999999998754   35789999999


Q ss_pred             ccCCccCCcEEEEecCCCChhHHHHhhccccCCCCcc--EEEEEEecCCCccc
Q psy17637         96 RGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKG--VAYTLVTDKDKDGE  146 (150)
Q Consensus        96 ~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~--~~~~~~~~~~~~~~  146 (150)
                      -|||+..+++||.||..|+|..-+|+..||.|.|+..  .++.|++...-++.
T Consensus       552 LGINL~aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~RLitentVEe~  604 (971)
T KOG0385|consen  552 LGINLTAADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVYRLITENTVEEK  604 (971)
T ss_pred             cccccccccEEEEecCCCCchhhhHHHHHHHhhCCcCceEEEEEeccchHHHH
Confidence            9999999999999999999999999999999999876  56777777655443

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=99.38  E-value=5.3e-12  Score=101.13  Aligned_cols=124  Identities=23%  Similarity=0.290  Sum_probs=100.7

Q ss_pred             hHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC-ceEEEEcCCCcc
Q psy17637         18 EFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE-CRILVATDVAAR   96 (150)
Q Consensus        18 ~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~vlv~T~~~~~   96 (150)
                      .+...+++.+......+.|+||.|.|.+..+.|...|...+++...+++.-...+-.-+ .  +.|. -.|.|||+++++
T Consensus       410 ~K~~Aii~ei~~~~~~gqPVLVgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~e~EA~II-a--~AG~~GaVTIATNMAGR  486 (925)
T PRK12903        410 AKWKAVVKEVKRVHKKGQPILIGTAQVEDSETLHELLLEANIPHTVLNAKQNAREAEII-A--KAGQKGAITIATNMAGR  486 (925)
T ss_pred             HHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCceeecccchhhHHHHH-H--hCCCCCeEEEecccccC
Confidence            34557888888777789999999999999999999999999998888886333222222 2  3343 368999999999


Q ss_pred             cCCccCCc--------EEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCc
Q psy17637         97 GLDIPHIR--------TVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD  144 (150)
Q Consensus        97 Gidi~~~~--------~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~  144 (150)
                      |.||.--.        +||....|.|...--|..||+||.|++|.+-+|++-+|..
T Consensus       487 GTDI~Lg~~V~~~GGLhVIgTerheSrRIDnQLrGRaGRQGDpGss~f~lSLeD~L  542 (925)
T PRK12903        487 GTDIKLSKEVLELGGLYVLGTDKAESRRIDNQLRGRSGRQGDVGESRFFISLDDQL  542 (925)
T ss_pred             CcCccCchhHHHcCCcEEEecccCchHHHHHHHhcccccCCCCCcceEEEecchHH
Confidence            99985322        8999999999999999999999999999999999887653

>KOG0950|consensus

Probab=99.37  E-value=1.1e-12  Score=104.78  Aligned_cols=111  Identities=24%  Similarity=0.366  Sum_probs=91.2

Q ss_pred             CCCCeeEEehhhhhHHHHHhhcccc--------------------------------------CceEEEecCCCCHHHHH
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVK--------------------------------------EYDVLLLHGDMDQSERN   74 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~--------------------------------------~~~~~~~~~~~~~~~r~   74 (150)
                      +..++||||++++.|+.++..+...                                      ...++++|.|++.++|+
T Consensus       459 e~~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~~~~ld~Vl~~ti~~GvAyHhaGLT~eER~  538 (1008)
T KOG0950|consen  459 EGSSVLVFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGILDPVLAKTIPYGVAYHHAGLTSEERE  538 (1008)
T ss_pred             cCCeEEEEcCcccchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhhcCCcccchHHheeccccceecccccccchHH
Confidence            4566999999999999877554210                                      12278999999999999


Q ss_pred             HHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecC----CCChhHHHHhhccccCCCC--ccEEEEEEecCCC
Q psy17637         75 SVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDL----ARDIDTHTHRIGRTGRAGN--KGVAYTLVTDKDK  143 (150)
Q Consensus        75 ~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~----~~~~~~~~q~~GR~~R~g~--~~~~~~~~~~~~~  143 (150)
                      .+...|+.|.+.|+++|+.+..|++.|...+++-...    ..+..+|.||+|||||.|-  -|.+++++.+.+.
T Consensus       539 ~iE~afr~g~i~vl~aTSTlaaGVNLPArRVIiraP~~g~~~l~~~~YkQM~GRAGR~gidT~GdsiLI~k~~e~  613 (1008)
T KOG0950|consen  539 IIEAAFREGNIFVLVATSTLAAGVNLPARRVIIRAPYVGREFLTRLEYKQMVGRAGRTGIDTLGDSILIIKSSEK  613 (1008)
T ss_pred             HHHHHHHhcCeEEEEecchhhccCcCCcceeEEeCCccccchhhhhhHHhhhhhhhhcccccCcceEEEeeccch
Confidence            9999999999999999999999999999888774322    2378899999999999984  3678888887764

>KOG0951|consensus

Probab=99.37  E-value=2.8e-12  Score=105.03  Aligned_cols=110  Identities=17%  Similarity=0.273  Sum_probs=89.4

Q ss_pred             HHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccc-------------------------------------cCceEEE
Q psy17637         21 GHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTV-------------------------------------KEYDVLL   63 (150)
Q Consensus        21 ~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~-------------------------------------~~~~~~~   63 (150)
                      +...+++.+. ....++|||+.++++..+.|+.++.                                     ..+.++.
T Consensus       534 e~~yeKVm~~-agk~qVLVFVHsRkET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLpygfaI  612 (1674)
T KOG0951|consen  534 EACYEKVLEH-AGKNQVLVFVHSRKETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLPYGFAI  612 (1674)
T ss_pred             HHHHHHHHHh-CCCCcEEEEEEechHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhhcccee
Confidence            3455566555 4558999999999987776666641                                     0233789


Q ss_pred             ecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEE----EecCCC------ChhHHHHhhccccCCCCc
Q psy17637         64 LHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV----NYDLAR------DIDTHTHRIGRTGRAGNK  131 (150)
Q Consensus        64 ~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi----~~~~~~------~~~~~~q~~GR~~R~g~~  131 (150)
                      +|+||++.+|..+.+.|++|.+++||+|-.+++|+++|..+++|    -|++-+      ++-+.+||.||+||++.+
T Consensus       613 HhAGl~R~dR~~~EdLf~~g~iqvlvstatlawgvnlpahtViikgtqvy~pekg~w~elsp~dv~qmlgragrp~~D  690 (1674)
T KOG0951|consen  613 HHAGLNRKDRELVEDLFADGHIQVLVSTATLAWGVNLPAHTVIIKGTQVYDPEKGRWTELSPLDVMQMLGRAGRPQYD  690 (1674)
T ss_pred             eccCCCcchHHHHHHHHhcCceeEEEeehhhhhhcCCCcceEEecCccccCcccCccccCCHHHHHHHHhhcCCCccC
Confidence            99999999999999999999999999999999999999987777    355543      788999999999998854

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.37  E-value=4.8e-12  Score=102.10  Aligned_cols=115  Identities=29%  Similarity=0.371  Sum_probs=92.4

Q ss_pred             HHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhh----cCCceEEEEcCCCcccC
Q psy17637         23 LVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFK----RQECRILVATDVAARGL   98 (150)
Q Consensus        23 ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~----~g~~~vlv~T~~~~~Gi   98 (150)
                      +...+....+.+.+++|-|||.+.+.+++..|+..+.++..+|+.++..+|.+.++.+.    .+...|+|+|++++.|+
T Consensus       429 ~~~~~~~~~~~~~kvlvI~NTV~~Aie~Y~~Lk~~~~~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQVIEagv  508 (733)
T COG1203         429 LIELISEEVKEGKKVLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGV  508 (733)
T ss_pred             hhhcchhhhccCCcEEEEEecHHHHHHHHHHHHhcCCCEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEeeEEEEEe
Confidence            34444444467899999999999999999999988878999999999999988877544    46678999999999999


Q ss_pred             CccCCcEEEEecCCCChhHHHHhhccccCCC--CccEEEEEEec
Q psy17637         99 DIPHIRTVVNYDLARDIDTHTHRIGRTGRAG--NKGVAYTLVTD  140 (150)
Q Consensus        99 di~~~~~vi~~~~~~~~~~~~q~~GR~~R~g--~~~~~~~~~~~  140 (150)
                      |+. .+++|--  +..+.+.+||.||++|.|  ..+..+++...
T Consensus       509 Did-fd~mITe--~aPidSLIQR~GRv~R~g~~~~~~~~v~~~~  549 (733)
T COG1203         509 DID-FDVLITE--LAPIDSLIQRAGRVNRHGKKENGKIYVYNDE  549 (733)
T ss_pred             ccc-cCeeeec--CCCHHHHHHHHHHHhhcccccCCceeEeecc
Confidence            994 6776633  334888999999999999  45556655543

>KOG0922|consensus

Probab=99.36  E-value=4.5e-12  Score=98.25  Aligned_cols=112  Identities=26%  Similarity=0.351  Sum_probs=97.0

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhcccc--------CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVK--------EYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHI  103 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~--------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~  103 (150)
                      ++.+.+|||....++.+.+++.|.+.        ..-+.++||+++.+++.++...-..|.-+|+++|+.++..+.|+++
T Consensus       256 E~~GDILvFLtGqeEIe~~~~~l~e~~~~~~~~~~~~~lply~aL~~e~Q~rvF~p~p~g~RKvIlsTNIAETSlTI~GI  335 (674)
T KOG0922|consen  256 EPPGDILVFLTGQEEIEAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGKRKVILSTNIAETSLTIDGI  335 (674)
T ss_pred             CCCCCEEEEeCCHHHHHHHHHHHHHHhhhccccCcceeeeecccCCHHHhhccccCCCCCcceEEEEcceeeeeEEecce
Confidence            67789999999999999998888654        1135789999999999999888888888999999999999999999


Q ss_pred             cEEEEecC------------------CCChhHHHHhhccccCCCCccEEEEEEecCCCc
Q psy17637        104 RTVVNYDL------------------ARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD  144 (150)
Q Consensus       104 ~~vi~~~~------------------~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~  144 (150)
                      .+||+.+.                  |-|.++-.||.|||||.| +|.||.++++.+.+
T Consensus       336 ~YVVDsG~vK~~~y~p~~g~~~L~v~~ISkasA~QRaGRAGRt~-pGkcyRLYte~~~~  393 (674)
T KOG0922|consen  336 RYVVDSGFVKQKKYNPRTGLDSLIVVPISKASANQRAGRAGRTG-PGKCYRLYTESAYD  393 (674)
T ss_pred             EEEEcCCceEEEeeccccCccceeEEechHHHHhhhcccCCCCC-CceEEEeeeHHHHh
Confidence            99997443                  347888899999999997 89999999987663

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.34  E-value=2e-11  Score=96.57  Aligned_cols=125  Identities=24%  Similarity=0.290  Sum_probs=101.1

Q ss_pred             hhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcc
Q psy17637         17 KEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAAR   96 (150)
Q Consensus        17 ~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~   96 (150)
                      .++...+++.+......+.|+||.|.+.+..|.+...|...+++...+.+.-...+-.-+-+.=+.  -.|.|||+++++
T Consensus       410 ~~k~~Aii~ei~~~~~~GrPVLVgt~sI~~SE~ls~~L~~~gI~h~vLNAk~~~~EA~IIa~AG~~--gaVTIATNMAGR  487 (764)
T PRK12326        410 AEKNDAIVEHIAEVHETGQPVLVGTHDVAESEELAERLRAAGVPAVVLNAKNDAEEARIIAEAGKY--GAVTVSTQMAGR  487 (764)
T ss_pred             HHHHHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHhCCCcceeeccCchHhHHHHHHhcCCC--CcEEEEecCCCC
Confidence            345667888888777899999999999999999999999999998888887443332222222222  368999999999


Q ss_pred             cCCccC---------------CcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         97 GLDIPH---------------IRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        97 Gidi~~---------------~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |.||.-               ==+||-...+.|...-.|..||+||.|++|.+-+|++-+|.
T Consensus       488 GTDIkLg~~~~~~~~~V~~~GGLhVIgTerheSrRID~QLrGRaGRQGDpGss~f~lSleDd  549 (764)
T PRK12326        488 GTDIRLGGSDEADRDRVAELGGLHVIGTGRHRSERLDNQLRGRAGRQGDPGSSVFFVSLEDD  549 (764)
T ss_pred             ccCeecCCCcccchHHHHHcCCcEEEeccCCchHHHHHHHhcccccCCCCCceeEEEEcchh
Confidence            999851               12789899999999999999999999999999999987765

>KOG0953|consensus

Probab=99.33  E-value=1.4e-11  Score=94.08  Aligned_cols=114  Identities=21%  Similarity=0.376  Sum_probs=88.2

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCce-EEEecCCCCHHHHHHHHHHhhc--CCceEEEEcCCCcccC
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYD-VLLLHGDMDQSERNSVITKFKR--QECRILVATDVAARGL   98 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~~~~~r~~~~~~f~~--g~~~vlv~T~~~~~Gi   98 (150)
                      .++..+.+.  ..+.||| |.+++..-.+...+...+.. +++++|++||+.|..=-..|.+  ++.+|||||++++||+
T Consensus       347 ~~~~sl~nl--k~GDCvV-~FSkk~I~~~k~kIE~~g~~k~aVIYGsLPPeTr~aQA~~FNd~~~e~dvlVAsDAIGMGL  423 (700)
T KOG0953|consen  347 TALGSLSNL--KPGDCVV-AFSKKDIFTVKKKIEKAGNHKCAVIYGSLPPETRLAQAALFNDPSNECDVLVASDAIGMGL  423 (700)
T ss_pred             hhhhhhccC--CCCCeEE-EeehhhHHHHHHHHHHhcCcceEEEecCCCCchhHHHHHHhCCCCCccceEEeeccccccc
Confidence            555566555  4456654 34455566777777766554 9999999999999999999998  7889999999999999


Q ss_pred             CccCCcEEEEecCCC---------ChhHHHHhhccccCCCC---ccEEEEEEe
Q psy17637         99 DIPHIRTVVNYDLAR---------DIDTHTHRIGRTGRAGN---KGVAYTLVT  139 (150)
Q Consensus        99 di~~~~~vi~~~~~~---------~~~~~~q~~GR~~R~g~---~~~~~~~~~  139 (150)
                      |+ +++-||+++..+         +..+..|..|||||.|.   .|.+..+..
T Consensus       424 NL-~IrRiiF~sl~Kysg~e~~~it~sqikQIAGRAGRf~s~~~~G~vTtl~~  475 (700)
T KOG0953|consen  424 NL-NIRRIIFYSLIKYSGRETEDITVSQIKQIAGRAGRFGSKYPQGEVTTLHS  475 (700)
T ss_pred             cc-ceeEEEEeecccCCcccceeccHHHHHHHhhcccccccCCcCceEEEeeH
Confidence            98 888999988764         67788999999999874   245555443

>KOG0391|consensus

Probab=99.33  E-value=2.6e-11  Score=99.00  Aligned_cols=134  Identities=18%  Similarity=0.273  Sum_probs=112.3

Q ss_pred             EeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC--ceEE
Q psy17637         11 LVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE--CRIL   88 (150)
Q Consensus        11 ~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~--~~vl   88 (150)
                      ..++.....+..||+.|.   ..+.++|||+...+.++-|-..|..+|+....+.|...-++|+..+++|....  ++.+
T Consensus      1256 qyDcGKLQtLAiLLqQLk---~eghRvLIfTQMtkmLDVLeqFLnyHgylY~RLDg~t~vEqRQaLmerFNaD~RIfcfI 1332 (1958)
T KOG0391|consen 1256 QYDCGKLQTLAILLQQLK---SEGHRVLIFTQMTKMLDVLEQFLNYHGYLYVRLDGNTSVEQRQALMERFNADRRIFCFI 1332 (1958)
T ss_pred             ecccchHHHHHHHHHHHH---hcCceEEehhHHHHHHHHHHHHHhhcceEEEEecCCccHHHHHHHHHHhcCCCceEEEE
Confidence            334444444444444444   46899999999999999999999999999999999999999999999998754  3677


Q ss_pred             EEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCcc--EEEEEEecCCCcccc
Q psy17637         89 VATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKG--VAYTLVTDKDKDGEL  147 (150)
Q Consensus        89 v~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~--~~~~~~~~~~~~~~~  147 (150)
                      ++|...+-|||+.+.+.||+||..|++..-.|..-||.|.|+..  +.|.|+++...++++
T Consensus      1333 LSTrSggvGiNLtgADTVvFYDsDwNPtMDaQAQDrChRIGqtRDVHIYRLISe~TIEeni 1393 (1958)
T KOG0391|consen 1333 LSTRSGGVGINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQTRDVHIYRLISERTIEENI 1393 (1958)
T ss_pred             EeccCCccccccccCceEEEecCCCCchhhhHHHHHHHhhcCccceEEEEeeccchHHHHH
Confidence            99999999999999999999999999999999999999999754  678888887665543

>KOG0952|consensus

Probab=99.27  E-value=1.7e-11  Score=99.11  Aligned_cols=117  Identities=22%  Similarity=0.288  Sum_probs=88.6

Q ss_pred             HHHHhccCCCCCeeEEehhhhhHHHHHhhcccc----C-------------------ceEEEecCCCCHHHHHHHHHHhh
Q psy17637         25 RNLEGANQEVPPALMNLAMQLNAEELANSLTVK----E-------------------YDVLLLHGDMDQSERNSVITKFK   81 (150)
Q Consensus        25 ~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~----~-------------------~~~~~~~~~~~~~~r~~~~~~f~   81 (150)
                      +++.+....+.+++|||.++...-..++.|...    +                   -.....|+||...+|.-+.+.|.
T Consensus       340 ~kv~e~~~~g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E~~F~  419 (1230)
T KOG0952|consen  340 DKVVEFLQEGHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVEKEFK  419 (1230)
T ss_pred             HHHHHHHHcCCeEEEEEecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHHHHHh
Confidence            333344456789999999988877777777431    0                   12678899999999999999999


Q ss_pred             cCCceEEEEcCCCcccCCccCCcEEE----EecCCC------ChhHHHHhhccccCCCC--ccEEEEEEecC
Q psy17637         82 RQECRILVATDVAARGLDIPHIRTVV----NYDLAR------DIDTHTHRIGRTGRAGN--KGVAYTLVTDK  141 (150)
Q Consensus        82 ~g~~~vlv~T~~~~~Gidi~~~~~vi----~~~~~~------~~~~~~q~~GR~~R~g~--~~~~~~~~~~~  141 (150)
                      .|.++||+||..+.+|+++|.-.++|    .||..+      +.-+.+|..|||||++-  .|.++.+.+.+
T Consensus       420 ~G~i~vL~cTaTLAwGVNLPA~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPqFd~~G~giIiTt~d  491 (1230)
T KOG0952|consen  420 EGHIKVLCCTATLAWGVNLPAYAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDSSGEGIIITTRD  491 (1230)
T ss_pred             cCCceEEEecceeeeccCCcceEEEecCCcccccccCceeeehHHHHHHHHhccCCCCCCCCceEEEEeccc
Confidence            99999999999999999998755555    255444      56777999999999873  34455444433

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=99.25  E-value=4.3e-11  Score=97.35  Aligned_cols=126  Identities=20%  Similarity=0.236  Sum_probs=102.2

Q ss_pred             hHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCccc
Q psy17637         18 EFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG   97 (150)
Q Consensus        18 ~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G   97 (150)
                      ++...+++.+......+.|+||-|.|.+..|.|...|...+++.-.+.+.....+-+-+-+.=+.  -.|.|||+++++|
T Consensus       612 eK~~Aii~ei~~~~~~GrPVLVGT~SVe~SE~lS~~L~~~gI~H~VLNAK~h~~EAeIVA~AG~~--GaVTIATNMAGRG  689 (1112)
T PRK12901        612 EKYNAVIEEITELSEAGRPVLVGTTSVEISELLSRMLKMRKIPHNVLNAKLHQKEAEIVAEAGQP--GTVTIATNMAGRG  689 (1112)
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEeCcHHHHHHHHHHHHHcCCcHHHhhccchhhHHHHHHhcCCC--CcEEEeccCcCCC
Confidence            34568888888887899999999999999999999999999887777776444444333333333  3689999999999


Q ss_pred             CCcc--------CCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCcc
Q psy17637         98 LDIP--------HIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDG  145 (150)
Q Consensus        98 idi~--------~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~~  145 (150)
                      .||.        +==+||-...+.|...-.|..||+||.|++|.+-+|++-+|...
T Consensus       690 TDIkLg~~V~e~GGL~VIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSLEDdLm  745 (1112)
T PRK12901        690 TDIKLSPEVKAAGGLAIIGTERHESRRVDRQLRGRAGRQGDPGSSQFYVSLEDNLM  745 (1112)
T ss_pred             cCcccchhhHHcCCCEEEEccCCCcHHHHHHHhcccccCCCCCcceEEEEcccHHH
Confidence            9985        22378889999999999999999999999999999999876543

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.23  E-value=1.3e-10  Score=94.04  Aligned_cols=125  Identities=20%  Similarity=0.240  Sum_probs=100.7

Q ss_pred             hhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC-ceEEEEcCCCc
Q psy17637         17 KEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE-CRILVATDVAA   95 (150)
Q Consensus        17 ~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~vlv~T~~~~   95 (150)
                      ..+...+++.+......+.|+||-|.+.+..|.++..|...+++...+.+.-...+..-+-+   .|. -.|.|||++++
T Consensus       551 ~~k~~ai~~ei~~~~~~grPvLigt~si~~se~ls~~L~~~gi~h~vLNak~~~~Ea~iia~---AG~~g~VTIATNmAG  627 (970)
T PRK12899        551 REKYHAIVAEIASIHRKGNPILIGTESVEVSEKLSRILRQNRIEHTVLNAKNHAQEAEIIAG---AGKLGAVTVATNMAG  627 (970)
T ss_pred             HHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcCCcceecccchhhhHHHHHHh---cCCCCcEEEeecccc
Confidence            34556788888887788999999999999999999999999999888887633323222222   233 36899999999


Q ss_pred             ccCCccC---C-----cEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCc
Q psy17637         96 RGLDIPH---I-----RTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD  144 (150)
Q Consensus        96 ~Gidi~~---~-----~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~  144 (150)
                      +|.||.-   +     =+||....|.|...-.|..||+||.|++|.+-+|++-+|..
T Consensus       628 RGTDIkl~~~v~~~GGLhVIgTer~es~Rid~Ql~GRagRQGdpGss~f~lSlEDdL  684 (970)
T PRK12899        628 RGTDIKLDEEAVAVGGLYVIGTSRHQSRRIDRQLRGRCARLGDPGAAKFFLSFEDRL  684 (970)
T ss_pred             CCcccccCchHHhcCCcEEEeeccCchHHHHHHHhcccccCCCCCceeEEEEcchHH
Confidence            9999842   1     27888999999999999999999999999999999887653

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.21  E-value=1e-10  Score=94.40  Aligned_cols=124  Identities=19%  Similarity=0.249  Sum_probs=100.3

Q ss_pred             hHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC-ceEEEEcCCCcc
Q psy17637         18 EFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE-CRILVATDVAAR   96 (150)
Q Consensus        18 ~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~vlv~T~~~~~   96 (150)
                      ++...+++.+......+.|+||-|.|.+..|.|...|...+++.-.+.+.-...+-+-+-   +.|. -.|.|||+++++
T Consensus       433 eK~~Ai~~ei~~~~~~GrPVLVGT~SVe~SE~ls~~L~~~gi~h~VLNAk~~~~EA~IIa---~AG~~GaVTIATNMAGR  509 (913)
T PRK13103        433 EKYAAIITDIKECMALGRPVLVGTATIETSEHMSNLLKKEGIEHKVLNAKYHEKEAEIIA---QAGRPGALTIATNMAGR  509 (913)
T ss_pred             HHHHHHHHHHHHHHhCCCCEEEEeCCHHHHHHHHHHHHHcCCcHHHhccccchhHHHHHH---cCCCCCcEEEeccCCCC
Confidence            345688899988878999999999999999999999999998877777764433333332   2343 368999999999


Q ss_pred             cCCcc-------------------------------------CCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEe
Q psy17637         97 GLDIP-------------------------------------HIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVT  139 (150)
Q Consensus        97 Gidi~-------------------------------------~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~  139 (150)
                      |.||.                                     +==+||-...+.|...-.|..||+||.|++|.+-+|++
T Consensus       510 GTDIkLg~n~~~~~~~~~~~~~~~~~~~~~~~~~~~e~V~e~GGLhVIgTerheSrRID~QLrGRaGRQGDPGsS~f~lS  589 (913)
T PRK13103        510 GTDILLGGNWEVEVAALENPTPEQIAQIKADWQKRHQQVIEAGGLHVIASERHESRRIDNQLRGRAGRQGDPGSSRFYLS  589 (913)
T ss_pred             CCCEecCCchHHHHHhhhhhhHHHHHHHHHHHHhHHHHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEE
Confidence            99983                                     11278888999999999999999999999999999999


Q ss_pred             cCCCc
Q psy17637        140 DKDKD  144 (150)
Q Consensus       140 ~~~~~  144 (150)
                      -+|..
T Consensus       590 lED~L  594 (913)
T PRK13103        590 LEDSL  594 (913)
T ss_pred             cCcHH
Confidence            87653

>KOG0392|consensus

Probab=99.20  E-value=1e-10  Score=95.89  Aligned_cols=114  Identities=20%  Similarity=0.318  Sum_probs=97.4

Q ss_pred             CCCeeEEehhhhhHHHHHhhcccc---CceEEEecCCCCHHHHHHHHHHhhcC-CceEE-EEcCCCcccCCccCCcEEEE
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVK---EYDVLLLHGDMDQSERNSVITKFKRQ-ECRIL-VATDVAARGLDIPHIRTVVN  108 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~---~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~vl-v~T~~~~~Gidi~~~~~vi~  108 (150)
                      ..+++|||.-+..++-+-..|...   .+....+.|..++.+|.++.++|.++ .+++| .+|.+.+-|+|+.+++.||+
T Consensus      1340 qHRiLIFcQlK~mlDlVekDL~k~~mpsVtymRLDGSVpp~~R~kiV~~FN~DptIDvLlLTThVGGLGLNLTGADTVVF 1419 (1549)
T KOG0392|consen 1340 QHRILIFCQLKSMLDLVEKDLFKKYMPSVTYMRLDGSVPPGDRQKIVERFNEDPTIDVLLLTTHVGGLGLNLTGADTVVF 1419 (1549)
T ss_pred             cceeEEeeeHHHHHHHHHHHHhhhhcCceeEEEecCCCCcHHHHHHHHHhcCCCceeEEEEeeeccccccccCCCceEEE
Confidence            578999999999999888777654   34456899999999999999999998 56665 77799999999999999999


Q ss_pred             ecCCCChhHHHHhhccccCCCCccE--EEEEEecCCCcccc
Q psy17637        109 YDLARDIDTHTHRIGRTGRAGNKGV--AYTLVTDKDKDGEL  147 (150)
Q Consensus       109 ~~~~~~~~~~~q~~GR~~R~g~~~~--~~~~~~~~~~~~~~  147 (150)
                      ++..|+|-.-.|++-||.|.|+...  +|.+++....++.+
T Consensus      1420 vEHDWNPMrDLQAMDRAHRIGQKrvVNVyRlItrGTLEEKV 1460 (1549)
T KOG0392|consen 1420 VEHDWNPMRDLQAMDRAHRIGQKRVVNVYRLITRGTLEEKV 1460 (1549)
T ss_pred             EecCCCchhhHHHHHHHHhhcCceeeeeeeehhcccHHHHH
Confidence            9999999999999999999998654  67777776665544

>KOG0389|consensus

Probab=99.20  E-value=1.9e-10  Score=90.83  Aligned_cols=126  Identities=19%  Similarity=0.263  Sum_probs=108.5

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCc--eEEEEcCCCcccCC
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQEC--RILVATDVAARGLD   99 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~--~vlv~T~~~~~Gid   99 (150)
                      .|-..|......+.++|||..-....+-|-..|...+++...+.|...-.+|+.++..|...+.  -.|++|.+.+.|||
T Consensus       765 ~L~~LLp~~k~~G~RVLiFSQFTqmLDILE~~L~~l~~~ylRLDGsTqV~~RQ~lId~Fn~d~difVFLLSTKAGG~GIN  844 (941)
T KOG0389|consen  765 KLKELLPKIKKKGDRVLIFSQFTQMLDILEVVLDTLGYKYLRLDGSTQVNDRQDLIDEFNTDKDIFVFLLSTKAGGFGIN  844 (941)
T ss_pred             HHHHHHHHHhhcCCEEEEeeHHHHHHHHHHHHHHhcCceEEeecCCccchHHHHHHHhhccCCceEEEEEeeccCcceec
Confidence            3333343333457899999999999999999999999999999999999999999999997653  57899999999999


Q ss_pred             ccCCcEEEEecCCCChhHHHHhhccccCCCCcc--EEEEEEecCCCcccc
Q psy17637        100 IPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKG--VAYTLVTDKDKDGEL  147 (150)
Q Consensus       100 i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~--~~~~~~~~~~~~~~~  147 (150)
                      +..+++||.+|...+|-.-.|+--||.|.|+..  .++.|+++...++.+
T Consensus       845 Lt~An~VIihD~dFNP~dD~QAEDRcHRvGQtkpVtV~rLItk~TIEE~I  894 (941)
T KOG0389|consen  845 LTCANTVIIHDIDFNPYDDKQAEDRCHRVGQTKPVTVYRLITKSTIEEGI  894 (941)
T ss_pred             ccccceEEEeecCCCCcccchhHHHHHhhCCcceeEEEEEEecCcHHHHH
Confidence            999999999999999999999999999999865  578888887665544

>KOG0923|consensus

Probab=99.19  E-value=6.5e-11  Score=92.12  Aligned_cols=108  Identities=23%  Similarity=0.343  Sum_probs=92.4

Q ss_pred             cCCCCCeeEEehhhhhHHHHHhhccc---------cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCcc
Q psy17637         31 NQEVPPALMNLAMQLNAEELANSLTV---------KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIP  101 (150)
Q Consensus        31 ~~~~~~~ivf~~~~~~~~~l~~~L~~---------~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~  101 (150)
                      ..+.+.+|||....+..+...+.|..         ..+-+.++|+.+|.+.+.++.+.--.|--+|++||+.++..+.|+
T Consensus       470 tqp~GDILVFltGQeEIEt~~e~l~~~~~~LGski~eliv~PiYaNLPselQakIFePtP~gaRKVVLATNIAETSlTId  549 (902)
T KOG0923|consen  470 TQPLGDILVFLTGQEEIETVKENLKERCRRLGSKIRELIVLPIYANLPSELQAKIFEPTPPGARKVVLATNIAETSLTID  549 (902)
T ss_pred             ccCCccEEEEeccHHHHHHHHHHHHHHHHHhccccceEEEeeccccCChHHHHhhcCCCCCCceeEEEeecchhhceeec
Confidence            35678999999988887776666643         245588999999999999999888888889999999999999999


Q ss_pred             CCcEEEEecC------------------CCChhHHHHhhccccCCCCccEEEEEEe
Q psy17637        102 HIRTVVNYDL------------------ARDIDTHTHRIGRTGRAGNKGVAYTLVT  139 (150)
Q Consensus       102 ~~~~vi~~~~------------------~~~~~~~~q~~GR~~R~g~~~~~~~~~~  139 (150)
                      ++.+||+-++                  |.|.++-.||.|||||.| +|.|+.+++
T Consensus       550 gI~yViDpGf~K~nsynprtGmesL~v~piSKAsA~QRaGRAGRtg-PGKCfRLYt  604 (902)
T KOG0923|consen  550 GIKYVIDPGFVKQNSYNPRTGMESLLVTPISKASANQRAGRAGRTG-PGKCFRLYT  604 (902)
T ss_pred             CeEEEecCccccccCcCCCcCceeEEEeeechhhhhhhccccCCCC-CCceEEeec
Confidence            9999997444                  337778889999999998 899999998

>KOG0388|consensus

Probab=99.17  E-value=1.3e-10  Score=91.33  Aligned_cols=124  Identities=22%  Similarity=0.364  Sum_probs=107.7

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCc-eEEEEcCCCccc
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQEC-RILVATDVAARG   97 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~-~vlv~T~~~~~G   97 (150)
                      .+..|+..|..   .+.++++|+...+..+.+-++|..+++....+.|.....+|..++..|+..++ -.|++|.+.+.|
T Consensus      1032 ~LDeLL~kLka---egHRvL~yfQMTkM~dl~EdYl~yr~Y~ylRLDGSsk~~dRrd~vrDwQ~sdiFvFLLSTRAGGLG 1108 (1185)
T KOG0388|consen 1032 VLDELLPKLKA---EGHRVLMYFQMTKMIDLIEDYLVYRGYTYLRLDGSSKASDRRDVVRDWQASDIFVFLLSTRAGGLG 1108 (1185)
T ss_pred             eHHHHHHHhhc---CCceEEehhHHHHHHHHHHHHHHhhccceEEecCcchhhHHHHHHhhccCCceEEEEEecccCccc
Confidence            34455555544   58899999999999999999999999999999999999999999999998665 477999999999


Q ss_pred             CCccCCcEEEEecCCCChhHHHHhhccccCCCCcc--EEEEEEecCCCcc
Q psy17637         98 LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKG--VAYTLVTDKDKDG  145 (150)
Q Consensus        98 idi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~--~~~~~~~~~~~~~  145 (150)
                      |++..++.||+|+..|++..-.|.+.||.|.|+..  .+|.+++.+..++
T Consensus      1109 INLTAADTViFYdSDWNPT~D~QAMDRAHRLGQTrdvtvyrl~~rgTvEE 1158 (1185)
T KOG0388|consen 1109 INLTAADTVIFYDSDWNPTADQQAMDRAHRLGQTRDVTVYRLITRGTVEE 1158 (1185)
T ss_pred             ccccccceEEEecCCCCcchhhHHHHHHHhccCccceeeeeecccccHHH
Confidence            99999999999999999999999999999999865  4677777655444

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

Probab=99.12  E-value=2.9e-10  Score=93.06  Aligned_cols=115  Identities=23%  Similarity=0.332  Sum_probs=91.1

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccc----------------------------cCce-------------
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLNAEELANSLTV----------------------------KEYD-------------   60 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~----------------------------~~~~-------------   60 (150)
                      .+++.+...  ...|+|+|+.+++.|+..+..+..                            .+++             
T Consensus       369 ~iv~~l~~~--~~lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~e~~i~~ii~~~i~~L~~ed~~lp~~~~~~~~~L~RG  446 (1041)
T COG4581         369 EIVNKLDKD--NLLPAIVFSFSRRGCEEAAQILSTLDLVLTEEKERAIREIIDHAIGDLAEEDRELPLQILEISALLLRG  446 (1041)
T ss_pred             HHHhhhhhh--cCCceEEEEEchhhHHHHHHHhcccccccCCcHHHHHHHHHHHHHhhcChhhhcCcccHHHHHHHHhhh
Confidence            466666665  678999999999999988777641                            0111             


Q ss_pred             EEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCC---------CChhHHHHhhccccCCCCc
Q psy17637         61 VLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLA---------RDIDTHTHRIGRTGRAGNK  131 (150)
Q Consensus        61 ~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~---------~~~~~~~q~~GR~~R~g~~  131 (150)
                      +..+|++|-|..+..+...|..|-.+|+.+|..++.|+|+|.-++|+ ....         -++.+|.|+.|||||.|-+
T Consensus       447 iavHH~GlLP~~K~~vE~Lfq~GLvkvvFaTeT~s~GiNmPartvv~-~~l~K~dG~~~r~L~~gEy~QmsGRAGRRGlD  525 (1041)
T COG4581         447 IAVHHAGLLPAIKELVEELFQEGLVKVVFATETFAIGINMPARTVVF-TSLSKFDGNGHRWLSPGEYTQMSGRAGRRGLD  525 (1041)
T ss_pred             hhhhccccchHHHHHHHHHHhccceeEEeehhhhhhhcCCcccceee-eeeEEecCCceeecChhHHHHhhhhhcccccc
Confidence            46889999999999999999999999999999999999998755544 3332         2899999999999999954


Q ss_pred             --cEEEEEEe
Q psy17637        132 --GVAYTLVT  139 (150)
Q Consensus       132 --~~~~~~~~  139 (150)
                        |.+++.-.
T Consensus       526 ~~G~vI~~~~  535 (1041)
T COG4581         526 VLGTVIVIEP  535 (1041)
T ss_pred             ccceEEEecC
Confidence              55555533

>KOG0920|consensus

Probab=99.10  E-value=2.5e-10  Score=92.50  Aligned_cols=124  Identities=23%  Similarity=0.366  Sum_probs=103.0

Q ss_pred             hhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhcccc-------CceEEEecCCCCHHHHHHHHHHhhcCCceEE
Q psy17637         16 DKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVK-------EYDVLLLHGDMDQSERNSVITKFKRQECRIL   88 (150)
Q Consensus        16 ~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~-------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vl   88 (150)
                      +...+..++..+... ...+.+|||.+.......+++.|...       ..-+.++|+.|+..+++.+...--.|..+|+
T Consensus       396 d~~Li~~li~~I~~~-~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g~RKII  474 (924)
T KOG0920|consen  396 DYDLIEDLIEYIDER-EFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGTRKII  474 (924)
T ss_pred             cHHHHHHHHHhcccC-CCCceEEEEcCCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCCCcchhh
Confidence            445566777777766 56788999999999999999988532       2568899999999999999988888989999


Q ss_pred             EEcCCCcccCCccCCcEEEEec--------CCC----------ChhHHHHhhccccCCCCccEEEEEEecC
Q psy17637         89 VATDVAARGLDIPHIRTVVNYD--------LAR----------DIDTHTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus        89 v~T~~~~~Gidi~~~~~vi~~~--------~~~----------~~~~~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                      ++|+.++..|.|+++-+||+.+        +..          +.+.-.||.|||||.. +|.||.+++..
T Consensus       475 laTNIAETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~GRAGRv~-~G~cy~L~~~~  544 (924)
T KOG0920|consen  475 LATNIAETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRRGRAGRVR-PGICYHLYTRS  544 (924)
T ss_pred             hhhhhHhhcccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHHhcccccCcc-CCeeEEeechh
Confidence            9999999999999999999744        333          4555679999999984 89999999864

>KOG0924|consensus

Probab=99.09  E-value=1e-10  Score=91.38  Aligned_cols=108  Identities=24%  Similarity=0.350  Sum_probs=90.1

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc--------c--CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV--------K--EYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPH  102 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~--------~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~  102 (150)
                      ..+.+|||....+..|.....+..        .  ++.+.++++.++..-+.++.+....|.-+++|+|+.++..+.+|+
T Consensus       562 ~~GdilIfmtGqediE~t~~~i~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi~g  641 (1042)
T KOG0924|consen  562 PPGDILIFMTGQEDIECTCDIIKEKLEQLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTIPG  641 (1042)
T ss_pred             CCCCEEEecCCCcchhHHHHHHHHHHHhhhcCCCCceEEEeehhhCchhhhhhhcccCCCCceeEEEeccchhhceeecc
Confidence            457899999887765544444322        2  788999999999999999988888888899999999999999999


Q ss_pred             CcEEEEecCC------------------CChhHHHHhhccccCCCCccEEEEEEecC
Q psy17637        103 IRTVVNYDLA------------------RDIDTHTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus       103 ~~~vi~~~~~------------------~~~~~~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                      +.+||+.+..                  .|.+.--||.|||||.| +|.||.++++.
T Consensus       642 I~yVID~Gy~K~kvyn~~~G~D~L~~~pIS~AnA~QRaGRAGRt~-pG~cYRlYTe~  697 (1042)
T KOG0924|consen  642 IRYVIDTGYCKLKVYNPRIGMDALQIVPISQANADQRAGRAGRTG-PGTCYRLYTED  697 (1042)
T ss_pred             eEEEEecCceeeeecccccccceeEEEechhccchhhccccCCCC-Ccceeeehhhh
Confidence            9999975553                  36667789999999997 89999999984

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=99.08  E-value=2.6e-09  Score=86.20  Aligned_cols=79  Identities=22%  Similarity=0.237  Sum_probs=62.1

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCC--HHHHHHHHHHhhcCC-ceEEEEcCCCc
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMD--QSERNSVITKFKRQE-CRILVATDVAA   95 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~--~~~r~~~~~~f~~g~-~~vlv~T~~~~   95 (150)
                      +...+++.+....+.+.|+||-|.|.+..|.+...|...+++...+++.-.  ..+-+ ++..  .|. -.|.|||++++
T Consensus       409 K~~AI~~ei~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~~~~~EA~-IIA~--AG~~G~VTIATNMAG  485 (870)
T CHL00122        409 KWRAIADECLQMHQTGRPILIGTTTIEKSELLSQLLKEYRLPHQLLNAKPENVRRESE-IVAQ--AGRKGSITIATNMAG  485 (870)
T ss_pred             HHHHHHHHHHHHHhcCCCEEEeeCCHHHHHHHHHHHHHcCCccceeeCCCccchhHHH-HHHh--cCCCCcEEEeccccC
Confidence            335788888877788999999999999999999999999999888888632  33333 3322  233 36899999999


Q ss_pred             ccCCc
Q psy17637         96 RGLDI  100 (150)
Q Consensus        96 ~Gidi  100 (150)
                      +|.||
T Consensus       486 RGTDI  490 (870)
T CHL00122        486 RGTDI  490 (870)
T ss_pred             CCcCe
Confidence            99997

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

Probab=99.05  E-value=2e-09  Score=88.35  Aligned_cols=113  Identities=21%  Similarity=0.276  Sum_probs=99.5

Q ss_pred             CCC--CeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcC--CceEEEEcCCCcccCCccCCcEEEE
Q psy17637         33 EVP--PALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQ--ECRILVATDVAARGLDIPHIRTVVN  108 (150)
Q Consensus        33 ~~~--~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g--~~~vlv~T~~~~~Gidi~~~~~vi~  108 (150)
                      .+.  ++++|+......+-+...|...++....++|.++.+.|...+..|.++  ...+++++.+++.|+++...++||+
T Consensus       708 ~~~~~kvlifsq~t~~l~il~~~l~~~~~~~~~ldG~~~~~~r~~~i~~f~~~~~~~v~lls~kagg~glnLt~a~~vi~  787 (866)
T COG0553         708 EGHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVIL  787 (866)
T ss_pred             hcccccEEEEeCcHHHHHHHHHHHHhcCCcEEEEeCCCChhhHHHHHHHhhcCCCCceEEEEecccccceeecccceEEE
Confidence            455  899999999999999999998888899999999999999999999986  3456788899999999999999999


Q ss_pred             ecCCCChhHHHHhhccccCCCCcc--EEEEEEecCCCcc
Q psy17637        109 YDLARDIDTHTHRIGRTGRAGNKG--VAYTLVTDKDKDG  145 (150)
Q Consensus       109 ~~~~~~~~~~~q~~GR~~R~g~~~--~~~~~~~~~~~~~  145 (150)
                      +|+.+++....|+..|+.|.|+..  .++.+++.+...+
T Consensus       788 ~d~~wnp~~~~Qa~dRa~RigQ~~~v~v~r~i~~~tiEe  826 (866)
T COG0553         788 FDPWWNPAVELQAIDRAHRIGQKRPVKVYRLITRGTIEE  826 (866)
T ss_pred             eccccChHHHHHHHHHHHHhcCcceeEEEEeecCCcHHH
Confidence            999999999999999999999765  4667776665433

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

Probab=99.03  E-value=3.1e-09  Score=84.95  Aligned_cols=122  Identities=20%  Similarity=0.318  Sum_probs=90.8

Q ss_pred             HHHHHHHHhccCCCCCeeEEehhhhh------------------------------------------------------
Q psy17637         21 GHLVRNLEGANQEVPPALMNLAMQLN------------------------------------------------------   46 (150)
Q Consensus        21 ~~ll~~l~~~~~~~~~~ivf~~~~~~------------------------------------------------------   46 (150)
                      ..+++.+......+.++|+|.|.+-.                                                      
T Consensus       407 ~~Ll~~i~~~l~~geQ~llflnRRGys~~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L  486 (730)
T COG1198         407 PALLEAIRKTLERGEQVLLFLNRRGYAPLLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSEHL  486 (730)
T ss_pred             HHHHHHHHHHHhcCCeEEEEEccCCccceeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCCee
Confidence            57788887776778888888887654                                                      


Q ss_pred             ------HHHHHhhccc--cCceEEEecCCCCHHH--HHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCCC---
Q psy17637         47 ------AEELANSLTV--KEYDVLLLHGDMDQSE--RNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLAR---  113 (150)
Q Consensus        47 ------~~~l~~~L~~--~~~~~~~~~~~~~~~~--r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~---  113 (150)
                            .|.+.+.|..  .+.++..+.++.+...  -+..+..|..|+.+|||+|+++..|.|+|+++.|...+...   
T Consensus       487 ~~~G~GterieeeL~~~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~  566 (730)
T COG1198         487 RAVGPGTERIEEELKRLFPGARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLG  566 (730)
T ss_pred             EEecccHHHHHHHHHHHCCCCcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhc
Confidence                  3344443332  2556777777765433  46889999999999999999999999999999987655442   


Q ss_pred             ---------ChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637        114 ---------DIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus       114 ---------~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                               ....+.|-.||+||.+.+|.++.-....+
T Consensus       567 ~~DfRA~Er~fqll~QvaGRAgR~~~~G~VvIQT~~P~  604 (730)
T COG1198         567 SPDFRASERTFQLLMQVAGRAGRAGKPGEVVIQTYNPD  604 (730)
T ss_pred             CCCcchHHHHHHHHHHHHhhhccCCCCCeEEEEeCCCC
Confidence                     34455788999999988888777665554

>KOG1000|consensus

Probab=99.00  E-value=2.6e-09  Score=81.08  Aligned_cols=117  Identities=17%  Similarity=0.222  Sum_probs=100.9

Q ss_pred             ccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC-ceE-EEEcCCCcccCCccCCcEEE
Q psy17637         30 ANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE-CRI-LVATDVAARGLDIPHIRTVV  107 (150)
Q Consensus        30 ~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~v-lv~T~~~~~Gidi~~~~~vi  107 (150)
                      ...+..+.+|||......+.+...+.++++....+.|..+...|+...+.|+..+ ..| +++..+++.|+++...+.|+
T Consensus       488 ~d~~~~KflVFaHH~~vLd~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvlsItA~gvGLt~tAa~~VV  567 (689)
T KOG1000|consen  488 PDAPPRKFLVFAHHQIVLDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSITAAGVGLTLTAASVVV  567 (689)
T ss_pred             ccCCCceEEEEehhHHHHHHHHHHHHHcCCCeEEecCCCCchhHHHHHHHhccccceEEEEEEEeecccceeeeccceEE
Confidence            3357889999999999999999999999999999999999999999999999754 333 35558999999999999999


Q ss_pred             EecCCCChhHHHHhhccccCCCCccE--EEEEEecCCCccc
Q psy17637        108 NYDLARDIDTHTHRIGRTGRAGNKGV--AYTLVTDKDKDGE  146 (150)
Q Consensus       108 ~~~~~~~~~~~~q~~GR~~R~g~~~~--~~~~~~~~~~~~~  146 (150)
                      +...+++++-++|.=.|+.|.|+.+.  ++.|+-+...+++
T Consensus       568 FaEL~wnPgvLlQAEDRaHRiGQkssV~v~ylvAKgT~Ddy  608 (689)
T KOG1000|consen  568 FAELHWNPGVLLQAEDRAHRIGQKSSVFVQYLVAKGTADDY  608 (689)
T ss_pred             EEEecCCCceEEechhhhhhccccceeeEEEEEecCchHHH
Confidence            99999999999999999999998764  4556666655554

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

Probab=98.99  E-value=3.9e-09  Score=70.92  Aligned_cols=106  Identities=21%  Similarity=0.253  Sum_probs=72.7

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCc--eEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC--CCcccCCccC--CcEE
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEY--DVLLLHGDMDQSERNSVITKFKRQECRILVATD--VAARGLDIPH--IRTV  106 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~--~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~--~~~~Gidi~~--~~~v  106 (150)
                      ..+.++||++|.+..+.+.+.+.....  ....+..  ......++++.|+.++-.||+++.  .+.+|+|+++  +..|
T Consensus         8 ~~g~~lv~f~Sy~~l~~~~~~~~~~~~~~~~~v~~q--~~~~~~~~l~~~~~~~~~il~~v~~g~~~EGiD~~~~~~r~v   85 (167)
T PF13307_consen    8 VPGGVLVFFPSYRRLEKVYERLKERLEEKGIPVFVQ--GSKSRDELLEEFKRGEGAILLAVAGGSFSEGIDFPGDLLRAV   85 (167)
T ss_dssp             CSSEEEEEESSHHHHHHHHTT-TSS-E-ETSCEEES--TCCHHHHHHHHHCCSSSEEEEEETTSCCGSSS--ECESEEEE
T ss_pred             CCCCEEEEeCCHHHHHHHHHHHHhhcccccceeeec--CcchHHHHHHHHHhccCeEEEEEecccEEEeecCCCchhhee
Confidence            457899999999999999999986642  1122232  255788999999999989999998  9999999984  6788


Q ss_pred             EEecCCCC-h-----------------------------hHHHHhhccccCCCCccEEEEEEec
Q psy17637        107 VNYDLARD-I-----------------------------DTHTHRIGRTGRAGNKGVAYTLVTD  140 (150)
Q Consensus       107 i~~~~~~~-~-----------------------------~~~~q~~GR~~R~g~~~~~~~~~~~  140 (150)
                      |...+|.. +                             ....|.+||+-|..++-.+++++++
T Consensus        86 ii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~llD~  149 (167)
T PF13307_consen   86 IIVGLPFPPPSDPLVQAKREYLDKQGKNPFRDWYLPPAIRKLKQAIGRLIRSEDDYGVIILLDS  149 (167)
T ss_dssp             EEES-----TTCHHHHHHHHHHHHCCTTCHHHHTHHHHHHHHHHHHHCC--STT-EEEEEEESG
T ss_pred             eecCCCCCCCCCHHHHHHHHHHHHHhccchhhHhhHHHHHHHhhhcCcceeccCCcEEEEEEcC
Confidence            88888751 1                             1114899999998876666666654

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

Probab=98.98  E-value=8.1e-09  Score=84.95  Aligned_cols=106  Identities=20%  Similarity=0.248  Sum_probs=79.6

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCc--EE
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIR--TV  106 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~--~v  106 (150)
                      ..++++||++|.+.++.++..|..    .++.  .+..+.. ..|.++++.|+.++..||++|+.+++|+|+|+..  +|
T Consensus       673 ~~g~~LVlftS~~~l~~v~~~L~~~~~~~~~~--~l~q~~~-~~r~~ll~~F~~~~~~iLlgt~sf~EGVD~~g~~l~~v  749 (850)
T TIGR01407       673 TSPKILVLFTSYEMLHMVYDMLNELPEFEGYE--VLAQGIN-GSRAKIKKRFNNGEKAILLGTSSFWEGVDFPGNGLVCL  749 (850)
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHhhhccccCce--EEecCCC-ccHHHHHHHHHhCCCeEEEEcceeecccccCCCceEEE
Confidence            457899999999999999999864    2332  3333333 4788999999999999999999999999998766  56


Q ss_pred             EEecCCCC------------------------------hhHHHHhhccccCCCCccEEEEEEecC
Q psy17637        107 VNYDLARD------------------------------IDTHTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus       107 i~~~~~~~------------------------------~~~~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                      |....|..                              ...+.|.+||.-|..++..++++++..
T Consensus       750 iI~~LPf~~p~dp~~~a~~~~~~~~g~~~f~~~~lP~A~~~l~Qa~GRlIRs~~D~G~v~ilD~R  814 (850)
T TIGR01407       750 VIPRLPFANPKHPLTKKYWQKLEQEGKNPFYDYVLPMAIIRLRQALGRLIRRENDRGSIVILDRR  814 (850)
T ss_pred             EEeCCCCCCCCCHHHHHHHHHHHHhcCCchHHhhHHHHHHHHHHhhccccccCCceEEEEEEccc
Confidence            66665541                              122358999999988666666666543

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.

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

Probab=98.96  E-value=9.2e-09  Score=82.13  Aligned_cols=108  Identities=20%  Similarity=0.324  Sum_probs=81.6

Q ss_pred             HHHHHHHHHh--ccCCCCCeeEEehhhhhHHHHHhhcccc-----CceEEEecCCCCHHHHHHHHHHhhcC-C-ceEEEE
Q psy17637         20 AGHLVRNLEG--ANQEVPPALMNLAMQLNAEELANSLTVK-----EYDVLLLHGDMDQSERNSVITKFKRQ-E-CRILVA   90 (150)
Q Consensus        20 ~~~ll~~l~~--~~~~~~~~ivf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g-~-~~vlv~   90 (150)
                      ...+.+.+..  ......++||||.+..|++.+.+.|.+.     +--+..++|.  .++-+..+..|... . ..|.|+
T Consensus       410 ~r~~~~~l~~~~~g~~~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~~IT~d--~~~~q~~Id~f~~ke~~P~Iait  487 (875)
T COG4096         410 ARELTEYLKRGATGDEIGKTIVFAKNHDHAERIREALVNEYPEYNGRYAMKITGD--AEQAQALIDNFIDKEKYPRIAIT  487 (875)
T ss_pred             HHHHHHHhccccCCCccCceEEEeeCcHHHHHHHHHHHHhCccccCceEEEEecc--chhhHHHHHHHHhcCCCCceEEe
Confidence            3344444444  3233689999999999999999988654     2225566666  34445556666653 2 358888


Q ss_pred             cCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCC
Q psy17637         91 TDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAG  129 (150)
Q Consensus        91 T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g  129 (150)
                      .+++..|+|+|.|-+++++..-.|...|.||+||.-|..
T Consensus       488 vdlL~TGiDvpev~nlVF~r~VrSktkF~QMvGRGTRl~  526 (875)
T COG4096         488 VDLLTTGVDVPEVVNLVFDRKVRSKTKFKQMVGRGTRLC  526 (875)
T ss_pred             hhhhhcCCCchheeeeeehhhhhhHHHHHHHhcCccccC
Confidence            899999999999999999999999999999999988854

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=98.89  E-value=2.6e-08  Score=80.68  Aligned_cols=82  Identities=20%  Similarity=0.231  Sum_probs=63.2

Q ss_pred             hHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHH-HHHHHHhhcCC-ceEEEEcCCCc
Q psy17637         18 EFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSER-NSVITKFKRQE-CRILVATDVAA   95 (150)
Q Consensus        18 ~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r-~~~~~~f~~g~-~~vlv~T~~~~   95 (150)
                      .+...+++.+....+.+.|+||-|.|.+..|.+...|...+++...+++.....++ ..++..  .|. -.|.|||++++
T Consensus       423 ~K~~Ai~~ei~~~~~~GrPVLIgT~SVe~SE~ls~~L~~~gi~h~vLNAk~~~~~~EA~IIa~--AG~~GaVTIATNMAG  500 (939)
T PRK12902        423 AKWRAVANETAEMHKQGRPVLVGTTSVEKSELLSALLQEQGIPHNLLNAKPENVEREAEIVAQ--AGRKGAVTIATNMAG  500 (939)
T ss_pred             HHHHHHHHHHHHHHhCCCCEEEeeCCHHHHHHHHHHHHHcCCchheeeCCCcchHhHHHHHHh--cCCCCcEEEeccCCC
Confidence            34557888888877899999999999999999999999999998888886322222 223332  233 36899999999


Q ss_pred             ccCCcc
Q psy17637         96 RGLDIP  101 (150)
Q Consensus        96 ~Gidi~  101 (150)
                      +|.||.
T Consensus       501 RGTDIk  506 (939)
T PRK12902        501 RGTDII  506 (939)
T ss_pred             CCcCEe
Confidence            999973

>KOG1123|consensus

Probab=98.88  E-value=3.3e-08  Score=75.45  Aligned_cols=132  Identities=15%  Similarity=0.248  Sum_probs=97.5

Q ss_pred             eEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcC-Cce
Q psy17637          8 AYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQ-ECR   86 (150)
Q Consensus         8 ~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~   86 (150)
                      ..+++++..-. ..+.+-.+.+.  .+.++|||....-.+.+.+-+|.+.     +++|..++.+|.++++.|+-. .++
T Consensus       520 lLyvMNP~KFr-aCqfLI~~HE~--RgDKiIVFsDnvfALk~YAikl~Kp-----fIYG~Tsq~ERm~ILqnFq~n~~vN  591 (776)
T KOG1123|consen  520 LLYVMNPNKFR-ACQFLIKFHER--RGDKIIVFSDNVFALKEYAIKLGKP-----FIYGPTSQNERMKILQNFQTNPKVN  591 (776)
T ss_pred             eeeecCcchhH-HHHHHHHHHHh--cCCeEEEEeccHHHHHHHHHHcCCc-----eEECCCchhHHHHHHHhcccCCccc
Confidence            34444444333 33333333333  7889999999988888888877644     689999999999999999864 456


Q ss_pred             EEEEcCCCcccCCccCCcEEEEecCCC-ChhHHHHhhccccCCCC------ccEEEEEEecCCCcccc
Q psy17637         87 ILVATDVAARGLDIPHIRTVVNYDLAR-DIDTHTHRIGRTGRAGN------KGVAYTLVTDKDKDGEL  147 (150)
Q Consensus        87 vlv~T~~~~~Gidi~~~~~vi~~~~~~-~~~~~~q~~GR~~R~g~------~~~~~~~~~~~~~~~~~  147 (150)
                      .+.-+.+....+|+|.++++|..+... |..+-.||.||..|.-+      ....|.+++.+..++++
T Consensus       592 TIFlSKVgDtSiDLPEAnvLIQISSH~GSRRQEAQRLGRILRAKk~~de~fnafFYSLVS~DTqEM~Y  659 (776)
T KOG1123|consen  592 TIFLSKVGDTSIDLPEANVLIQISSHGGSRRQEAQRLGRILRAKKRNDEEFNAFFYSLVSKDTQEMYY  659 (776)
T ss_pred             eEEEeeccCccccCCcccEEEEEcccccchHHHHHHHHHHHHHhhcCccccceeeeeeeecchHHHHh
Confidence            777778888899999999999877764 77888999999988542      23577888877666554

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

Probab=98.85  E-value=4.8e-08  Score=78.50  Aligned_cols=108  Identities=18%  Similarity=0.224  Sum_probs=79.0

Q ss_pred             HHHHHHHHHhccC-CCCCeeEEehhhhhHHHHHhhcccc-----CceEEEecCCCCHH---------------------H
Q psy17637         20 AGHLVRNLEGANQ-EVPPALMNLAMQLNAEELANSLTVK-----EYDVLLLHGDMDQS---------------------E   72 (150)
Q Consensus        20 ~~~ll~~l~~~~~-~~~~~ivf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~---------------------~   72 (150)
                      ...+++.+..... ...+++|||.++++|..+++.|...     +.....+++..+.+                     .
T Consensus       499 a~~i~~h~~~~~~~~~~kamvv~~sr~~a~~~~~~l~~~~~~~~~~~~vv~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~  578 (667)
T TIGR00348       499 AKDIAEHYAKFKELFKFKAMVVAISRYACVEEKNALDEELNEKFEASAIVMTGKESDDAEIRDYNKHIRTKFDKSDGFEI  578 (667)
T ss_pred             HHHHHHHHHHhhhcccCceeEEEecHHHHHHHHHHHHhhcccccCCeeEEecCCccchhHHHHHHHHhccccccchhhhH
Confidence            3344444433211 2589999999999999888876433     23455566553322                     1


Q ss_pred             HHHHHHHhhc-CCceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCC
Q psy17637         73 RNSVITKFKR-QECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRA  128 (150)
Q Consensus        73 r~~~~~~f~~-g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~  128 (150)
                      ...++++|++ +.++|||.++++..|+|.|.+++++...+.++. .++|++||+.|.
T Consensus       579 ~~~~~~~Fk~~~~~~ilIVvdmllTGFDaP~l~tLyldKplk~h-~LlQai~R~nR~  634 (667)
T TIGR00348       579 YYKDLERFKKEENPKLLIVVDMLLTGFDAPILNTLYLDKPLKYH-GLLQAIARTNRI  634 (667)
T ss_pred             HHHHHHHhcCCCCceEEEEEcccccccCCCccceEEEecccccc-HHHHHHHHhccc
Confidence            2468888976 678999999999999999999999988887775 489999999994

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

>KOG0949|consensus

Probab=98.80  E-value=1.2e-08  Score=82.63  Aligned_cols=77  Identities=23%  Similarity=0.336  Sum_probs=62.9

Q ss_pred             EEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecC-CCChhHHHHhhccccCCCCc--cEEEEE
Q psy17637         61 VLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDL-ARDIDTHTHRIGRTGRAGNK--GVAYTL  137 (150)
Q Consensus        61 ~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~-~~~~~~~~q~~GR~~R~g~~--~~~~~~  137 (150)
                      +.++|++|+...|..+.-.|+.|...||++|..++-|||+|--++|+--|. .-++-.|.|+.|||||.|-+  |.++.+
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            578899999999999999999999999999999999999975444443332 24788999999999999943  444443

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

Probab=98.73  E-value=1.9e-07  Score=77.58  Aligned_cols=122  Identities=16%  Similarity=0.169  Sum_probs=85.8

Q ss_pred             HHHHHHHHHhcc-CCCCCeeEEehhhhhHHHHHhhccccCc--eEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcc
Q psy17637         20 AGHLVRNLEGAN-QEVPPALMNLAMQLNAEELANSLTVKEY--DVLLLHGDMDQSERNSVITKFKRQECRILVATDVAAR   96 (150)
Q Consensus        20 ~~~ll~~l~~~~-~~~~~~ivf~~~~~~~~~l~~~L~~~~~--~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~   96 (150)
                      ...+.+.+.... ...++++|+++|.+..+.++..|.....  ....+.-+++...+.++++.|+.++-.||++|..+.+
T Consensus       737 ~~~la~~i~~l~~~~~g~~LVLFtSy~~l~~v~~~l~~~~~~~~~~ll~Qg~~~~~r~~l~~~F~~~~~~iLlG~~sFwE  816 (928)
T PRK08074        737 IEEVAAYIAKIAKATKGRMLVLFTSYEMLKKTYYNLKNEEELEGYVLLAQGVSSGSRARLTKQFQQFDKAILLGTSSFWE  816 (928)
T ss_pred             HHHHHHHHHHHHHhCCCCEEEEECCHHHHHHHHHHHhhcccccCceEEecCCCCCCHHHHHHHHHhcCCeEEEecCcccC
Confidence            344544444332 2567899999999999999999865422  1223333444456789999999988889999999999


Q ss_pred             cCCccC--CcEEEEecCCCC------------------------------hhHHHHhhccccCCCCccEEEEEEecC
Q psy17637         97 GLDIPH--IRTVVNYDLARD------------------------------IDTHTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus        97 Gidi~~--~~~vi~~~~~~~------------------------------~~~~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                      |+|+|+  +.+||....|..                              .-.+.|.+||.-|..++..++++++..
T Consensus       817 GVD~pg~~l~~viI~kLPF~~p~dp~~~a~~~~~~~~g~~~F~~~~lP~A~~~lkQg~GRlIRs~~D~G~v~ilD~R  893 (928)
T PRK08074        817 GIDIPGDELSCLVIVRLPFAPPDQPVMEAKSEWAKEQGENPFQELSLPQAVLRFKQGFGRLIRTETDRGTVFVLDRR  893 (928)
T ss_pred             ccccCCCceEEEEEecCCCCCCCCHHHHHHHHHHHHhCCCchhhhhhHHHHHHHHhhhhhhcccCCceEEEEEecCc
Confidence            999985  467887666641                              122258999999988665566666543

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

Probab=98.68  E-value=5.5e-07  Score=73.92  Aligned_cols=120  Identities=21%  Similarity=0.228  Sum_probs=82.9

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccC
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGL   98 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gi   98 (150)
                      ....+.+.+.......++++|+++|.+..+.+++.|......+ ...|.-.  .+.+++++|+.++..||++|..+.+|+
T Consensus       632 ~~~~~~~~i~~~~~~~g~~LVLFtS~~~l~~v~~~l~~~~~~~-l~Qg~~~--~~~~l~~~F~~~~~~vLlG~~sFwEGV  708 (820)
T PRK07246        632 YAEEIAKRLEELKQLQQPILVLFNSKKHLLAVSDLLDQWQVSH-LAQEKNG--TAYNIKKRFDRGEQQILLGLGSFWEGV  708 (820)
T ss_pred             HHHHHHHHHHHHHhcCCCEEEEECcHHHHHHHHHHHhhcCCcE-EEeCCCc--cHHHHHHHHHcCCCeEEEecchhhCCC
Confidence            3344555443333356899999999999999999886554333 4444211  246689999998889999999999999


Q ss_pred             CccC--CcEEEEecCCCC------------------------------hhHHHHhhccccCCCCccEEEEEEecC
Q psy17637         99 DIPH--IRTVVNYDLARD------------------------------IDTHTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus        99 di~~--~~~vi~~~~~~~------------------------------~~~~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                      |+|+  ...||....|..                              .-.+.|.+||.-|..++..++++++..
T Consensus       709 D~p~~~~~~viI~kLPF~~P~dP~~~a~~~~~~~~g~~~F~~~~lP~A~iklkQg~GRLIRs~~D~Gvv~ilD~R  783 (820)
T PRK07246        709 DFVQADRMIEVITRLPFDNPEDPFVKKMNQYLLQEGKNPFYDYFLPMTILRLKQAIGRTMRREDQKSAVLILDRR  783 (820)
T ss_pred             CCCCCCeEEEEEecCCCCCCCCHHHHHHHHHHHHhCCCchhheeHHHHHHHHHHHhcccccCCCCcEEEEEECCc
Confidence            9973  455565555531                              122359999999987665566666654

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

Probab=98.67  E-value=5.3e-07  Score=72.50  Aligned_cols=105  Identities=23%  Similarity=0.257  Sum_probs=78.8

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCce-EEEecCCCCHHHHHHHHHHhhcCCc-eEEEEcCCCcccCCccC--CcEEEE
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYD-VLLLHGDMDQSERNSVITKFKRQEC-RILVATDVAARGLDIPH--IRTVVN  108 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~~~~~r~~~~~~f~~g~~-~vlv~T~~~~~Gidi~~--~~~vi~  108 (150)
                      ..++++||+++.+.++.+++.+...... ....+|..   .+...++.|..+.- .++|+|..+++|+|+|+  +..||.
T Consensus       478 ~~~~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~~---~~~~~l~~f~~~~~~~~lv~~gsf~EGVD~~g~~l~~vvI  554 (654)
T COG1199         478 SPGGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGED---EREELLEKFKASGEGLILVGGGSFWEGVDFPGDALRLVVI  554 (654)
T ss_pred             cCCCEEEEeccHHHHHHHHHHHhhcCccceeeecCCC---cHHHHHHHHHHhcCCeEEEeeccccCcccCCCCCeeEEEE
Confidence            3448999999999999999999866542 34444543   34478888887655 89999999999999984  467887


Q ss_pred             ecCCC------------------------------ChhHHHHhhccccCCCCccEEEEEEec
Q psy17637        109 YDLAR------------------------------DIDTHTHRIGRTGRAGNKGVAYTLVTD  140 (150)
Q Consensus       109 ~~~~~------------------------------~~~~~~q~~GR~~R~g~~~~~~~~~~~  140 (150)
                      ...|.                              ....+.|.+||+-|.-++..++++++.
T Consensus       555 ~~lPfp~p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~QavGRlIR~~~D~G~ivllD~  616 (654)
T COG1199         555 VGLPFPNPDDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSEDDRGVIVLLDK  616 (654)
T ss_pred             EecCCCCCCCHHHHHHHHHHHHhcCCCceEeehHHHHHHHHHhhccccccCCCceEEEEecc
Confidence            77765                              233446999999997766666666665

>KOG0926|consensus

Probab=98.67  E-value=1.5e-08  Score=80.75  Aligned_cols=83  Identities=30%  Similarity=0.427  Sum_probs=71.8

Q ss_pred             CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCCC------------------ChhHHH
Q psy17637         58 EYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLAR------------------DIDTHT  119 (150)
Q Consensus        58 ~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~------------------~~~~~~  119 (150)
                      .+-+.++++=++.+++.++...--.|.--++|+|++++..+.||++.+||+.+.-+                  |.++--
T Consensus       604 pLyvLPLYSLLs~~~Q~RVF~~~p~g~RLcVVaTNVAETSLTIPgIkYVVD~Gr~K~R~Yd~~TGV~~FeV~wiSkASad  683 (1172)
T KOG0926|consen  604 PLYVLPLYSLLSTEKQMRVFDEVPKGERLCVVATNVAETSLTIPGIKYVVDCGRVKERLYDSKTGVSSFEVDWISKASAD  683 (1172)
T ss_pred             ceEEeehhhhcCHHHhhhhccCCCCCceEEEEeccchhcccccCCeeEEEeccchhhhccccccCceeEEEEeeeccccc
Confidence            44588999999999999999998899988999999999999999999999865543                  445557


Q ss_pred             HhhccccCCCCccEEEEEEecC
Q psy17637        120 HRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus       120 q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                      ||.|||||.| +|+||.+++..
T Consensus       684 QRAGRAGRtg-pGHcYRLYSSA  704 (1172)
T KOG0926|consen  684 QRAGRAGRTG-PGHCYRLYSSA  704 (1172)
T ss_pred             hhccccCCCC-CCceeehhhhH
Confidence            9999999998 89999998753

>KOG1015|consensus

Probab=98.67  E-value=8.8e-08  Score=77.79  Aligned_cols=116  Identities=17%  Similarity=0.200  Sum_probs=96.2

Q ss_pred             HHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccc----------------------cCceEEEecCCCCHHHHHHHHH
Q psy17637         21 GHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTV----------------------KEYDVLLLHGDMDQSERNSVIT   78 (150)
Q Consensus        21 ~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~----------------------~~~~~~~~~~~~~~~~r~~~~~   78 (150)
                      ..|++.|.....-+.++|||..+-..++.+-..|..                      .|.....+.|..+..+|+.+..
T Consensus      1129 iLLleIL~mceeIGDKlLVFSQSL~SLdLIe~fLe~v~r~gk~~~d~~~~~~~eGkW~~GkDyyriDGst~s~~R~k~~~ 1208 (1567)
T KOG1015|consen 1129 ILLLEILRMCEEIGDKLLVFSQSLISLDLIEDFLELVSREGKEDKDKPLIYKGEGKWLRGKDYYRLDGSTTSQSRKKWAE 1208 (1567)
T ss_pred             ehHHHHHHHHHHhcceeEEeecccchhHHHHHHHHhhcccCccccccccccccccceecCCceEEecCcccHHHHHHHHH
Confidence            356666665556789999999998888777666632                      2455788999999999999999


Q ss_pred             HhhcCCc----eEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEE
Q psy17637         79 KFKRQEC----RILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYT  136 (150)
Q Consensus        79 ~f~~g~~----~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~  136 (150)
                      .|.+-..    ..||+|.+.+.|+|+-.++-||.||..|++.--.|.+=|+.|.|+..-||.
T Consensus      1209 ~FNdp~NlRaRl~LISTRAGsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyRfGQtKPvyi 1270 (1567)
T KOG1015|consen 1209 EFNDPTNLRARLFLISTRAGSLGINLVAANRVIIFDASWNPSYDTQSIFRVYRFGQTKPVYI 1270 (1567)
T ss_pred             HhcCcccceeEEEEEeeccCccccceeecceEEEEecccCCccchHHHHHHHhhcCcCceee
Confidence            9987542    488999999999999999999999999999999999999999998765544

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.66  E-value=5.8e-07  Score=72.67  Aligned_cols=120  Identities=20%  Similarity=0.252  Sum_probs=82.3

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhh----cCCceEEEEcCCC
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFK----RQECRILVATDVA   94 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~----~g~~~vlv~T~~~   94 (150)
                      ....+.+.+.......+.++||++|.+..+.++..|....-.....+|..   .+.++++.|+    .++..||++|..+
T Consensus       519 ~~~~~~~~i~~l~~~~gg~LVlFtSy~~l~~v~~~l~~~~~~~ll~Q~~~---~~~~ll~~f~~~~~~~~~~VL~g~~sf  595 (697)
T PRK11747        519 HTAEMAEFLPELLEKHKGSLVLFASRRQMQKVADLLPRDLRLMLLVQGDQ---PRQRLLEKHKKRVDEGEGSVLFGLQSF  595 (697)
T ss_pred             HHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHhcCCcEEEeCCc---hHHHHHHHHHHHhccCCCeEEEEeccc
Confidence            44455555544433455689999999999999998864321234445542   4567776666    4667899999999


Q ss_pred             cccCCccC--CcEEEEecCCCC----h--------------------------hHHHHhhccccCCCCccEEEEEEecC
Q psy17637         95 ARGLDIPH--IRTVVNYDLARD----I--------------------------DTHTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus        95 ~~Gidi~~--~~~vi~~~~~~~----~--------------------------~~~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                      .+|+|+|+  +++||...+|..    +                          -.+.|.+||.-|..++..++++++..
T Consensus       596 ~EGVD~pGd~l~~vII~kLPF~~p~dp~~~ar~~~~~~~g~~~F~~~~lP~A~~kl~Qg~GRlIRs~~D~G~i~ilD~R  674 (697)
T PRK11747        596 AEGLDLPGDYLTQVIITKIPFAVPDSPVEATLAEWLKSRGGNPFMEISVPDASFKLIQAVGRLIRSEQDRGRVTILDRR  674 (697)
T ss_pred             cccccCCCCceEEEEEEcCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhccccccCCceEEEEEEccc
Confidence            99999985  678887766641    1                          12258899999987665566666554

>KOG0386|consensus

Probab=98.63  E-value=1.5e-07  Score=76.62  Aligned_cols=121  Identities=22%  Similarity=0.336  Sum_probs=102.7

Q ss_pred             hHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCc---eEEEEcCCC
Q psy17637         18 EFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQEC---RILVATDVA   94 (150)
Q Consensus        18 ~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~---~vlv~T~~~   94 (150)
                      +.+..++..|..   .+.+++.||....-.+-+-.+|.-.+++...+.|....++|-..+..|.....   ..|.+|.+.
T Consensus       713 ELLDRiLPKLka---tgHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG~TK~~eRg~ll~~FN~Pds~yf~Fllstrag  789 (1157)
T KOG0386|consen  713 ELLDRILPKLKA---TGHRVLLFSQMTRLMDILEDYLQIREYKYLRLDGQTKVEERGDLLEIFNAPDSPYFIFLLSTRAG  789 (1157)
T ss_pred             HHHHhhhHHHHh---cCcchhhHHHHHHHHHHHHHHHhhhhhheeeecCCcchhhHHHHHHHhcCCCCceeeeeeeeccc
Confidence            344444444444   58899999999999999999999999999999999999999999999997554   477999999


Q ss_pred             cccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccE--EEEEEecC
Q psy17637         95 ARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGV--AYTLVTDK  141 (150)
Q Consensus        95 ~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~--~~~~~~~~  141 (150)
                      +.|+|++.++.||.||..|++-...|+..|+.|.|+...  ++.+.+-.
T Consensus       790 glglNlQtadtviifdsdwnp~~d~qaqdrahrigq~~evRv~rl~tv~  838 (1157)
T KOG0386|consen  790 GLGLNLQTADTVIIFDSDWNPHQDLQAQDRAHRIGQKKEVRVLRLITVN  838 (1157)
T ss_pred             ccccchhhcceEEEecCCCCchhHHHHHHHHHHhhchhheeeeeeehhh
Confidence            999999999999999999999999999999999997654  45454443

>KOG4439|consensus

Probab=98.62  E-value=5.5e-07  Score=71.17  Aligned_cols=113  Identities=12%  Similarity=0.145  Sum_probs=91.5

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhc--CCceEE-EEcCCCcccCCccCCcEEEEe
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKR--QECRIL-VATDVAARGLDIPHIRTVVNY  109 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~--g~~~vl-v~T~~~~~Gidi~~~~~vi~~  109 (150)
                      ...+++|...=.....-+...+...|+....+||....++|+.+++.|..  |..+|+ +.-.+.+-|+|+.+.+|+|..
T Consensus       745 skeK~viVSQwtsvLniv~~hi~~~g~~y~si~Gqv~vK~Rq~iv~~FN~~k~~~rVmLlSLtAGGVGLNL~GaNHlilv  824 (901)
T KOG4439|consen  745 SKEKVVIVSQWTSVLNIVRKHIQKGGHIYTSITGQVLVKDRQEIVDEFNQEKGGARVMLLSLTAGGVGLNLIGANHLILV  824 (901)
T ss_pred             ccceeeehhHHHHHHHHHHHHHhhCCeeeeeecCccchhHHHHHHHHHHhccCCceEEEEEEccCcceeeecccceEEEE
Confidence            45566555555556677788888899999999999999999999999975  445666 444899999999999999999


Q ss_pred             cCCCChhHHHHhhccccCCCCccE--EEEEEecCCCcc
Q psy17637        110 DLARDIDTHTHRIGRTGRAGNKGV--AYTLVTDKDKDG  145 (150)
Q Consensus       110 ~~~~~~~~~~q~~GR~~R~g~~~~--~~~~~~~~~~~~  145 (150)
                      |+.|++.--.|++.|..|.|+...  .+.|+..+.-++
T Consensus       825 DlHWNPaLEqQAcDRIYR~GQkK~V~IhR~~~~gTvEq  862 (901)
T KOG4439|consen  825 DLHWNPALEQQACDRIYRMGQKKDVFIHRLMCKGTVEQ  862 (901)
T ss_pred             ecccCHHHHHHHHHHHHHhcccCceEEEEEEecCcHHH
Confidence            999999999999999999998764  455665554443

>COG4889 Predicted helicase [General function prediction only]

Probab=98.61  E-value=4.1e-08  Score=79.22  Aligned_cols=97  Identities=22%  Similarity=0.404  Sum_probs=76.6

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc-------------cCc--eEEEecCCCCHHHHHHHHH---HhhcCCceEEEEcCCC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV-------------KEY--DVLLLHGDMDQSERNSVIT---KFKRQECRILVATDVA   94 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~-------------~~~--~~~~~~~~~~~~~r~~~~~---~f~~g~~~vlv~T~~~   94 (150)
                      +..++|-||.+.+..+.+++.+..             .++  .+..+.|.|+..+|.+.+.   .|...+++||-...++
T Consensus       459 p~~RAIaF~k~I~tSK~i~~sFe~Vve~Y~~Elk~d~~nL~iSi~HvDGtmNal~R~~l~~l~~~~~~neckIlSNaRcL  538 (1518)
T COG4889         459 PMQRAIAFAKDIKTSKQIAESFETVVEAYDEELKKDFKNLKISIDHVDGTMNALERLDLLELKNTFEPNECKILSNARCL  538 (1518)
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEeecccccccHHHHHHHHhccCCCCcchheeeccchhh
Confidence            456789999988876655554421             233  4556668999999865543   3456677888888999


Q ss_pred             cccCCccCCcEEEEecCCCChhHHHHhhccccCCC
Q psy17637         95 ARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAG  129 (150)
Q Consensus        95 ~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g  129 (150)
                      ++|+|+|.++.||++++-.++-+.+|.+||+.|..
T Consensus       539 SEGVDVPaLDsViFf~pr~smVDIVQaVGRVMRKa  573 (1518)
T COG4889         539 SEGVDVPALDSVIFFDPRSSMVDIVQAVGRVMRKA  573 (1518)
T ss_pred             hcCCCccccceEEEecCchhHHHHHHHHHHHHHhC
Confidence            99999999999999999999999999999999965

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

Probab=98.60  E-value=2.5e-07  Score=75.62  Aligned_cols=98  Identities=27%  Similarity=0.446  Sum_probs=77.6

Q ss_pred             cCeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehh---hhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhh
Q psy17637          5 KGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAM---QLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFK   81 (150)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~---~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~   81 (150)
                      .++.-.+..+...+   .++..+...   +.-.|||+++   ++.++++++.|+..|+++..+|++     .++.++.|.
T Consensus       312 RNIvD~y~~~~~~e---~~~elvk~l---G~GgLIfV~~d~G~e~aeel~e~Lr~~Gi~a~~~~a~-----~~~~le~F~  380 (1187)
T COG1110         312 RNIVDIYVESESLE---KVVELVKKL---GDGGLIFVPIDYGREKAEELAEYLRSHGINAELIHAE-----KEEALEDFE  380 (1187)
T ss_pred             hheeeeeccCccHH---HHHHHHHHh---CCCeEEEEEcHHhHHHHHHHHHHHHhcCceEEEeecc-----chhhhhhhc
Confidence            34444455553334   455555444   3468999999   999999999999999999999984     378899999


Q ss_pred             cCCceEEEEc----CCCcccCCcc-CCcEEEEecCCC
Q psy17637         82 RQECRILVAT----DVAARGLDIP-HIRTVVNYDLAR  113 (150)
Q Consensus        82 ~g~~~vlv~T----~~~~~Gidi~-~~~~vi~~~~~~  113 (150)
                      .|++++||+.    ..+.+|+|+| .+.++|+++.|+
T Consensus       381 ~GeidvLVGvAsyYG~lVRGlDLP~rirYaIF~GvPk  417 (1187)
T COG1110         381 EGEVDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVPK  417 (1187)
T ss_pred             cCceeEEEEecccccceeecCCchhheeEEEEecCCc
Confidence            9999999776    4889999998 678999999995

>KOG1002|consensus

Probab=98.56  E-value=7.3e-07  Score=68.26  Aligned_cols=128  Identities=16%  Similarity=0.187  Sum_probs=105.4

Q ss_pred             hhHHHHHHHHHHhcc--CCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC-ce-EEEEcC
Q psy17637         17 KEFAGHLVRNLEGAN--QEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE-CR-ILVATD   92 (150)
Q Consensus        17 ~~~~~~ll~~l~~~~--~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~-vlv~T~   92 (150)
                      ..+++.|.+.+....  ....+.|||..-....+.+...|.+.|+.++-+.|+|++..|...++.|.+.. +. .||+-.
T Consensus       619 STKIEAL~EEl~~l~~rd~t~KsIVFSQFTSmLDLi~~rL~kaGfscVkL~GsMs~~ardatik~F~nd~~c~vfLvSLk  698 (791)
T KOG1002|consen  619 STKIEALVEELYFLRERDRTAKSIVFSQFTSMLDLIEWRLGKAGFSCVKLVGSMSPAARDATIKYFKNDIDCRVFLVSLK  698 (791)
T ss_pred             hhHHHHHHHHHHHHHHcccchhhhhHHHHHHHHHHHHHHhhccCceEEEeccCCChHHHHHHHHHhccCCCeEEEEEEec
Confidence            345556666654332  35678999999999999999999999999999999999999999999999764 34 456668


Q ss_pred             CCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCc--cEEEEEEecCCCc
Q psy17637         93 VAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNK--GVAYTLVTDKDKD  144 (150)
Q Consensus        93 ~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~--~~~~~~~~~~~~~  144 (150)
                      +.+-.+|+..+++|+..||=|+++--.|...|..|.|+.  -.++.|+-+...+
T Consensus       699 AGGVALNLteASqVFmmDPWWNpaVe~Qa~DRiHRIGQ~rPvkvvrf~iEnsiE  752 (791)
T KOG1002|consen  699 AGGVALNLTEASQVFMMDPWWNPAVEWQAQDRIHRIGQYRPVKVVRFCIENSIE  752 (791)
T ss_pred             cCceEeeechhceeEeecccccHHHHhhhhhhHHhhcCccceeEEEeehhccHH
Confidence            998889999999999999999999999999999999974  3677777665443

>KOG0925|consensus

Probab=98.52  E-value=6.6e-07  Score=68.27  Aligned_cols=107  Identities=20%  Similarity=0.296  Sum_probs=80.1

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccc---------cCceEEEecCCCCHHHHHHHHHHhhc---CC--ceEEEEcCCCccc
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTV---------KEYDVLLLHGDMDQSERNSVITKFKR---QE--CRILVATDVAARG   97 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~---------~~~~~~~~~~~~~~~~r~~~~~~f~~---g~--~~vlv~T~~~~~G   97 (150)
                      +..+.++||....++.+..++.+..         ..+++.++|    +.++..+.+-...   |.  -+|+|+|..++..
T Consensus       251 ee~GDilvFLtgeeeIe~aC~~i~re~~~L~~~~g~l~v~PLy----P~~qq~iFep~p~~~~~~~~RkvVvstniaets  326 (699)
T KOG0925|consen  251 EEPGDILVFLTGEEEIEDACRKISREVDNLGPQVGPLKVVPLY----PAQQQRIFEPAPEKRNGAYGRKVVVSTNIAETS  326 (699)
T ss_pred             cCCCCEEEEecCHHHHHHHHHHHHHHHHhhccccCCceEEecC----chhhccccCCCCcccCCCccceEEEEecchhee
Confidence            4578899999999988887777652         145688888    3344444333321   22  2699999999999


Q ss_pred             CCccCCcEEEEecC------------------CCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         98 LDIPHIRTVVNYDL------------------ARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        98 idi~~~~~vi~~~~------------------~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +.++++-+||+-++                  |.|..+-.||.||+||. .+|.|+.++++.-.
T Consensus       327 ltidgiv~VIDpGf~kqkVYNPRIRvesllv~PISkasA~qR~gragrt-~pGkcfrLYte~~~  389 (699)
T KOG0925|consen  327 LTIDGIVFVIDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEEAF  389 (699)
T ss_pred             eeeccEEEEecCchhhhcccCcceeeeeeeeccchHhHHHHHhhhccCC-CCCceEEeecHHhh
Confidence            99999999997443                  44788888999999998 48999999987643

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=98.50  E-value=2.3e-07  Score=74.82  Aligned_cols=123  Identities=20%  Similarity=0.243  Sum_probs=93.8

Q ss_pred             hhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCc-eEEEEcCCCc
Q psy17637         17 KEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQEC-RILVATDVAA   95 (150)
Q Consensus        17 ~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~-~vlv~T~~~~   95 (150)
                      .++...++..+......+.|+||-+.+.+..|.+...|...+++...+...-...+-+.+..   .|.. -|-|+|++++
T Consensus       412 ~~K~~Aiv~~I~~~~~~gqPvLvgT~sie~SE~ls~~L~~~~i~h~VLNAk~h~~EA~Iia~---AG~~gaVTiATNMAG  488 (822)
T COG0653         412 EEKFKAIVEDIKERHEKGQPVLVGTVSIEKSELLSKLLRKAGIPHNVLNAKNHAREAEIIAQ---AGQPGAVTIATNMAG  488 (822)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEcCcceecchhHHHHHHhcCCCceeeccccHHHHHHHHhh---cCCCCcccccccccc
Confidence            45667889999888889999999999999999999999999988777777655333333322   2333 5789999999


Q ss_pred             ccCCccCCc-----------EEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637         96 RGLDIPHIR-----------TVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus        96 ~Gidi~~~~-----------~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      +|.|+.--.           +||-.....|...--|..||+||+|.+|..-.+++-++
T Consensus       489 RGTDIkLg~~~~~V~~lGGL~VIgTERhESRRIDnQLRGRsGRQGDpG~S~F~lSleD  546 (822)
T COG0653         489 RGTDIKLGGNPEFVMELGGLHVIGTERHESRRIDNQLRGRAGRQGDPGSSRFYLSLED  546 (822)
T ss_pred             CCcccccCCCHHHHHHhCCcEEEecccchhhHHHHHhhcccccCCCcchhhhhhhhHH
Confidence            999984111           45555555566666699999999999998877776554

>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=98.43  E-value=8.9e-06  Score=62.12  Aligned_cols=124  Identities=15%  Similarity=0.194  Sum_probs=100.2

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCC--cc
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVA--AR   96 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~--~~   96 (150)
                      +...++-.+.+ ......+|||+++.-.--.|.++|+..++....++...++.+-.+.-..|..|+..+|+.|.-+  =+
T Consensus       286 F~~~iLP~l~~-~~~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~~isRAR~~F~~G~~~iLL~TER~HFfr  364 (442)
T PF06862_consen  286 FTKKILPQLKR-DSKMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNSDISRARSQFFHGRKPILLYTERFHFFR  364 (442)
T ss_pred             HHHHHHHHhhh-ccCCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHHHHHHHHHHHHcCCceEEEEEhHHhhhh
Confidence            44556666663 2477899999999888888999999999999999999999999999999999999999999633  33


Q ss_pred             cCCccCCcEEEEecCCCChhHHHHhhccccCCCC------ccEEEEEEecCCC
Q psy17637         97 GLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGN------KGVAYTLVTDKDK  143 (150)
Q Consensus        97 Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~------~~~~~~~~~~~~~  143 (150)
                      -..+.++.+||+|++|..+.-|...++-......      ...|.++++.-|.
T Consensus       365 Ry~irGi~~viFY~~P~~p~fY~El~n~~~~~~~~~~~~~~~~~~~lysk~D~  417 (442)
T PF06862_consen  365 RYRIRGIRHVIFYGPPENPQFYSELLNMLDESSGGEVDAADATVTVLYSKYDA  417 (442)
T ss_pred             hceecCCcEEEEECCCCChhHHHHHHhhhcccccccccccCceEEEEecHhHH
Confidence            4567899999999999999999887765554432      4578888877654

; GO: 0005634 nucleus

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.41  E-value=7.1e-06  Score=66.66  Aligned_cols=122  Identities=14%  Similarity=0.150  Sum_probs=82.8

Q ss_pred             HHHHHHHHHhccC-CCCCeeEEehhhhhHHHHHhhccccCce------EEEecCCCCHHHHHHHHHHhhc----CCceEE
Q psy17637         20 AGHLVRNLEGANQ-EVPPALMNLAMQLNAEELANSLTVKEYD------VLLLHGDMDQSERNSVITKFKR----QECRIL   88 (150)
Q Consensus        20 ~~~ll~~l~~~~~-~~~~~ivf~~~~~~~~~l~~~L~~~~~~------~~~~~~~~~~~~r~~~~~~f~~----g~~~vl   88 (150)
                      ...+.+.+.+... ..+.++||++|....+.+++.+...+..      ...+..+-...++..+++.|+.    +.-.||
T Consensus       507 ~~~l~~~i~~~~~~~pgg~lvfFpSy~~l~~v~~~~~~~~~~~~i~~~k~i~~E~~~~~~~~~~l~~f~~~~~~~~gavL  586 (705)
T TIGR00604       507 VRNLGELLVEFSKIIPDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKLIFVETKDAQETSDALERYKQAVSEGRGAVL  586 (705)
T ss_pred             HHHHHHHHHHHhhcCCCcEEEEccCHHHHHHHHHHHHhcCHHHHHhcCCCEEEeCCCcchHHHHHHHHHHHHhcCCceEE
Confidence            3444444433322 4578999999999999998887654321      1122222223577889999964    445689


Q ss_pred             EEc--CCCcccCCccC--CcEEEEecCCC-Ch------------------------------hHHHHhhccccCCCCccE
Q psy17637         89 VAT--DVAARGLDIPH--IRTVVNYDLAR-DI------------------------------DTHTHRIGRTGRAGNKGV  133 (150)
Q Consensus        89 v~T--~~~~~Gidi~~--~~~vi~~~~~~-~~------------------------------~~~~q~~GR~~R~g~~~~  133 (150)
                      +++  ..+++|+|+++  +..||..++|. ++                              ....|.+||+-|..++-.
T Consensus       587 ~av~gGk~sEGIDf~~~~~r~ViivGlPf~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~a~~~v~QaiGR~IR~~~D~G  666 (705)
T TIGR00604       587 LSVAGGKVSEGIDFCDDLGRAVIMVGIPYEYTESRILLARLEFLRDQYPIRENQDFYEFDAMRAVNQAIGRVIRHKDDYG  666 (705)
T ss_pred             EEecCCcccCccccCCCCCcEEEEEccCCCCCCCHHHHHHHHHHHhhcCCCccHHHHHHHHHHHHHHHhCccccCcCceE
Confidence            888  89999999985  67898888875 11                              112599999999887666


Q ss_pred             EEEEEecC
Q psy17637        134 AYTLVTDK  141 (150)
Q Consensus       134 ~~~~~~~~  141 (150)
                      ++++++..
T Consensus       667 ~iillD~R  674 (705)
T TIGR00604       667 SIVLLDKR  674 (705)
T ss_pred             EEEEEehh
Confidence            77777654

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).

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=98.30  E-value=1.2e-05  Score=52.53  Aligned_cols=78  Identities=26%  Similarity=0.313  Sum_probs=54.9

Q ss_pred             EecCCCCHHHHHHHHHHhhcCCc-eEEEEcCCCcccCCccC--CcEEEEecCCCC-------------------------
Q psy17637         63 LLHGDMDQSERNSVITKFKRQEC-RILVATDVAARGLDIPH--IRTVVNYDLARD-------------------------  114 (150)
Q Consensus        63 ~~~~~~~~~~r~~~~~~f~~g~~-~vlv~T~~~~~Gidi~~--~~~vi~~~~~~~-------------------------  114 (150)
                      .+..+....+..++++.|+...- .||+++..+++|+|+|+  +..||....|..                         
T Consensus        26 i~~e~~~~~~~~~~l~~f~~~~~~~iL~~~~~~~EGiD~~g~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~  105 (141)
T smart00492       26 LLVQGEDGKETGKLLEKYVEACENAILLATARFSEGVDFPGDYLRAVIIDGLPFPYPDSPILKARLELLRDKGQIRPFDF  105 (141)
T ss_pred             EEEeCCChhHHHHHHHHHHHcCCCEEEEEccceecceecCCCCeeEEEEEecCCCCCCCHHHHHHHHHHHHhCCCCchhH
Confidence            34445556567889999987543 79999977999999985  467887776641                         


Q ss_pred             ------hhHHHHhhccccCCCCccEEEEEEec
Q psy17637        115 ------IDTHTHRIGRTGRAGNKGVAYTLVTD  140 (150)
Q Consensus       115 ------~~~~~q~~GR~~R~g~~~~~~~~~~~  140 (150)
                            .....|.+||+-|..++-.++++++.
T Consensus       106 ~~~~~a~~~l~Qa~GR~iR~~~D~g~i~l~D~  137 (141)
T smart00492      106 VSLPDAMRTLAQCVGRLIRGANDYGVVVIADK  137 (141)
T ss_pred             HHHHHHHHHHHHHhCccccCcCceEEEEEEec
Confidence                  11224889999998766556666543

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=98.22  E-value=1.4e-05  Score=52.35  Aligned_cols=71  Identities=21%  Similarity=0.284  Sum_probs=49.5

Q ss_pred             HHHHHHHHHHhhcCCc---eEEEEcCC--CcccCCccC--CcEEEEecCCCC----h-----------------------
Q psy17637         70 QSERNSVITKFKRQEC---RILVATDV--AARGLDIPH--IRTVVNYDLARD----I-----------------------  115 (150)
Q Consensus        70 ~~~r~~~~~~f~~g~~---~vlv~T~~--~~~Gidi~~--~~~vi~~~~~~~----~-----------------------  115 (150)
                      ..+..++++.|+....   .||+++.-  +++|+|+|+  ++.||..+.|..    +                       
T Consensus        30 ~~~~~~~l~~f~~~~~~~g~iL~~v~~G~~~EGiD~~g~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~  109 (142)
T smart00491       30 SGETEELLEKYSAACEARGALLLAVARGKVSEGIDFPDDLGRAVIIVGIPFPNPDSPILRARLEYLDEKGGIRPFDEVYL  109 (142)
T ss_pred             CchHHHHHHHHHHhcCCCCEEEEEEeCCeeecceecCCCccEEEEEEecCCCCCCCHHHHHHHHHHHHhcCCCcHHHHHH
Confidence            3345788888887543   58877765  999999986  567888777641    1                       


Q ss_pred             ----hHHHHhhccccCCCCccEEEEEEec
Q psy17637        116 ----DTHTHRIGRTGRAGNKGVAYTLVTD  140 (150)
Q Consensus       116 ----~~~~q~~GR~~R~g~~~~~~~~~~~  140 (150)
                          ....|.+||+-|..++-.++++++.
T Consensus       110 ~~a~~~~~Qa~GR~iR~~~D~g~i~l~D~  138 (142)
T smart00491      110 FDAMRALAQAIGRAIRHKNDYGVVVLLDK  138 (142)
T ss_pred             HHHHHHHHHHhCccccCccceEEEEEEec
Confidence                1124899999998766556666654

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

Probab=98.21  E-value=3.6e-05  Score=61.53  Aligned_cols=107  Identities=10%  Similarity=0.097  Sum_probs=78.8

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhc----CCceEEEEcCCCcccCCc--------
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKR----QECRILVATDVAARGLDI--------  100 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~----g~~~vlv~T~~~~~Gidi--------  100 (150)
                      ..++++|-+.+...++.+++.|...--....+.|..+  .+...+++|+.    |...||++|+.+.+|+|+        
T Consensus       469 ~~G~~lvLfTS~~~~~~~~~~l~~~l~~~~l~qg~~~--~~~~l~~~f~~~~~~~~~~vL~gt~sfweGvDv~~~~~~p~  546 (636)
T TIGR03117       469 AQGGTLVLTTAFSHISAIGQLVELGIPAEIVIQSEKN--RLASAEQQFLALYANGIQPVLIAAGGAWTGIDLTHKPVSPD  546 (636)
T ss_pred             cCCCEEEEechHHHHHHHHHHHHhhcCCCEEEeCCCc--cHHHHHHHHHHhhcCCCCcEEEeCCccccccccCCccCCCC
Confidence            5678999999999999999998654323455566543  34567888886    467899999999999999        


Q ss_pred             --cCCcEEEEecCCCCh-------------------------hHHHHhhccccCCCCc--cEEEEEEecC
Q psy17637        101 --PHIRTVVNYDLARDI-------------------------DTHTHRIGRTGRAGNK--GVAYTLVTDK  141 (150)
Q Consensus       101 --~~~~~vi~~~~~~~~-------------------------~~~~q~~GR~~R~g~~--~~~~~~~~~~  141 (150)
                        ..+++||....|+.+                         -.+.|-+||.-|..++  ..++.++++.
T Consensus       547 ~G~~Ls~ViI~kLPF~~~dp~a~~~~~~~~g~~~f~~~p~a~i~lkQg~GRLIR~~~D~~~G~i~ilD~R  616 (636)
T TIGR03117       547 KDNLLTDLIITCAPFGLNRSLSMLKRIRKTSVRPWEIINESLMMLRQGLGRLVRHPDMPQNRRIHMLDGR  616 (636)
T ss_pred             CCCcccEEEEEeCCCCcCChHHHHHHHHhcCCChHhhhHHHHHHHHHhcCceeecCCCcCceEEEEEeCC
Confidence              257888887766421                         1235889999998766  5666666655

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.

>PF13871 Helicase_C_4: Helicase_C-like

Probab=97.87  E-value=8.1e-05  Score=53.73  Aligned_cols=66  Identities=18%  Similarity=0.323  Sum_probs=53.5

Q ss_pred             HHHHHHhhcCCceEEEEcCCCcccCCccCC--------cEEEEecCCCChhHHHHhhccccCCCCcc-EEEEEEe
Q psy17637         74 NSVITKFKRQECRILVATDVAARGLDIPHI--------RTVVNYDLARDIDTHTHRIGRTGRAGNKG-VAYTLVT  139 (150)
Q Consensus        74 ~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~--------~~vi~~~~~~~~~~~~q~~GR~~R~g~~~-~~~~~~~  139 (150)
                      ....+.|.+|+..|+|.+++.+.|+.++.-        .+-|.+.+||+....+|..||+.|.++.. -.|.++.
T Consensus        51 ~~e~~~F~~g~k~v~iis~AgstGiSlHAd~~~~nqr~Rv~i~le~pwsad~aiQ~~GR~hRsnQ~~~P~y~~l~  125 (278)
T PF13871_consen   51 IAEKQAFMDGEKDVAIISDAGSTGISLHADRRVKNQRRRVHITLELPWSADKAIQQFGRTHRSNQVSAPEYRFLV  125 (278)
T ss_pred             HHHHHHHhCCCceEEEEecccccccchhccccCCCCCceEEEEeeCCCCHHHHHHHhccccccccccCCEEEEee
Confidence            355679999999999999999999998632        35678999999999999999999999743 3344443

>KOG1016|consensus

Probab=97.85  E-value=4.8e-05  Score=61.40  Aligned_cols=104  Identities=14%  Similarity=0.241  Sum_probs=84.5

Q ss_pred             CCCeeEEehhhhhHHHHHhhccccCc------------------eEEEecCCCCHHHHHHHHHHhhcCC---ceEEEEcC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVKEY------------------DVLLLHGDMDQSERNSVITKFKRQE---CRILVATD   92 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~~~------------------~~~~~~~~~~~~~r~~~~~~f~~g~---~~vlv~T~   92 (150)
                      +.+.|||......++.+.+.|....+                  ....+.|..+..+|++.+++|.+..   +-+|++|.
T Consensus       719 g~kil~fSq~l~~Ld~ieeil~krq~pc~~gdnG~~aqkW~~n~sy~rldG~t~a~~rekLinqfN~e~~lsWlfllstr  798 (1387)
T KOG1016|consen  719 GEKILIFSQNLTALDMIEEILKKRQIPCKDGDNGCPAQKWEKNRSYLRLDGTTSAADREKLINQFNSEPGLSWLFLLSTR  798 (1387)
T ss_pred             CceEEEeecchhHHHHHHHHHhcccccCCCCCCCCchhhhhhccceecccCCcccchHHHHHHhccCCCCceeeeeehhc
Confidence            56788898887777777777755322                  2456788899999999999998643   35779999


Q ss_pred             CCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEE
Q psy17637         93 VAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTL  137 (150)
Q Consensus        93 ~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~  137 (150)
                      +..-|+++-..+-++.|+..|++.--.|.+-|+.|.|+...|+++
T Consensus       799 ag~lGinLIsanr~~ifda~wnpchdaqavcRvyrYGQ~KpcfvY  843 (1387)
T KOG1016|consen  799 AGSLGINLISANRCIIFDACWNPCHDAQAVCRVYRYGQQKPCFVY  843 (1387)
T ss_pred             cccccceeeccceEEEEEeecCccccchhhhhhhhhcCcCceeEE
Confidence            999999999999999999999999999999999999987655443

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=97.83  E-value=8.7e-05  Score=60.97  Aligned_cols=44  Identities=14%  Similarity=0.111  Sum_probs=31.3

Q ss_pred             ecchhhHHHHHHHHHHhcc------CCCCCeeEEehhhhhHHHHHhhccc
Q psy17637         13 TDKDKEFAGHLVRNLEGAN------QEVPPALMNLAMQLNAEELANSLTV   56 (150)
Q Consensus        13 ~~~~~~~~~~ll~~l~~~~------~~~~~~ivf~~~~~~~~~l~~~L~~   56 (150)
                      .......+..+++.+....      ....++||||+.++.|..|.+.|..
T Consensus       268 e~PKw~~L~eiL~eI~~~~~~~~~~~~~~~iLI~~~d~~T~~qL~~~L~~  317 (814)
T TIGR00596       268 ENPKWEVLTDVLKEISHEMRMTNRLQGPGKVLIMCSDNRTCLQLRDYLTT  317 (814)
T ss_pred             cCCCHHHHHHHHHHHHhHHhhhcccCCCCcEEEEEcchHHHHHHHHHHHh
Confidence            3334455666777766541      3456899999999999999998854

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

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=97.62  E-value=0.00035  Score=58.41  Aligned_cols=90  Identities=18%  Similarity=0.138  Sum_probs=61.5

Q ss_pred             eEEehhhhhHHHHHhhc----cccC--ceEEEecCCCCHHHHHHHHHHh----------------------hc----CCc
Q psy17637         38 LMNLAMQLNAEELANSL----TVKE--YDVLLLHGDMDQSERNSVITKF----------------------KR----QEC   85 (150)
Q Consensus        38 ivf~~~~~~~~~l~~~L----~~~~--~~~~~~~~~~~~~~r~~~~~~f----------------------~~----g~~   85 (150)
                      +|-.++++.+-.++..|    ...+  +.+.+||+..+...|..+.+..                      .+    +..
T Consensus       760 liR~anI~p~V~~A~~L~~~~~~~~~~i~~~~yHSr~~l~~Rs~~E~~Ld~~L~R~~~~~~~~~~~i~~~l~~~~~~~~~  839 (1110)
T TIGR02562       760 LIRVANIDPLIRLAQFLYALLAEEKYQIHLCCYHAQDPLLLRSYIERRLDQLLTRHKPEQLFQDDEIIDLMQNSPALNHL  839 (1110)
T ss_pred             EEEEcCchHHHHHHHHHHhhccccCCceeEEEecccChHHHHHHHHHHHHHHhcccChhhhhchHHHHHHHhcccccCCC
Confidence            44445544444444444    3333  4578899998777776555442                      12    356


Q ss_pred             eEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCC
Q psy17637         86 RILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGN  130 (150)
Q Consensus        86 ~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~  130 (150)
                      .|+|+|++.+-|+|+ +.+++|  .-|.+..+.+|+.||+.|.|.
T Consensus       840 ~i~v~Tqv~E~g~D~-dfd~~~--~~~~~~~sliQ~aGR~~R~~~  881 (1110)
T TIGR02562       840 FIVLATPVEEVGRDH-DYDWAI--ADPSSMRSIIQLAGRVNRHRL  881 (1110)
T ss_pred             eEEEEeeeEEEEecc-cCCeee--eccCcHHHHHHHhhccccccc
Confidence            799999999999998 456555  345578999999999999874

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.

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=97.42  E-value=0.0021  Score=52.38  Aligned_cols=76  Identities=18%  Similarity=0.278  Sum_probs=62.2

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhcc----ccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CCcccCCccCCcEE
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLT----VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VAARGLDIPHIRTV  106 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~----~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~~~Gidi~~~~~v  106 (150)
                      ..+.++++-++|+.-+...++.+.    ..++++..+||+++..++.+.+....+|+..|+|+|. .+...+.+.++.+|
T Consensus       308 ~~g~q~lilaPT~~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~v~~~~l~lv  387 (681)
T PRK10917        308 EAGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLV  387 (681)
T ss_pred             HcCCeEEEEeccHHHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcccchhcccceE
Confidence            356789999999887776655554    4478999999999999999999999999999999996 44445677788876


Q ss_pred             E
Q psy17637        107 V  107 (150)
Q Consensus       107 i  107 (150)
                      |
T Consensus       388 V  388 (681)
T PRK10917        388 I  388 (681)
T ss_pred             E
Confidence            6

>PRK05580 primosome assembly protein PriA; Validated

Probab=97.30  E-value=0.003  Score=51.41  Aligned_cols=75  Identities=17%  Similarity=0.229  Sum_probs=60.8

Q ss_pred             CCCCeeEEehhhhhHHHHHhhcccc-CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEE
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVK-EYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVN  108 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~  108 (150)
                      .+.++||.+++++-+..+++.|... +..+..+||+++..++.+.+.....|+.+|+|+|..... ..+.++.+||.
T Consensus       189 ~g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~-~p~~~l~liVv  264 (679)
T PRK05580        189 QGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF-LPFKNLGLIIV  264 (679)
T ss_pred             cCCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc-ccccCCCEEEE
Confidence            4678999999999999888888754 678999999999999999999999999999999963321 34556666653

>KOG1001|consensus

Probab=97.30  E-value=6.2e-05  Score=60.56  Aligned_cols=100  Identities=18%  Similarity=0.201  Sum_probs=88.9

Q ss_pred             CCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCc-eEE-EEcCCCcccCCccCCcEEEEecCC
Q psy17637         35 PPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQEC-RIL-VATDVAARGLDIPHIRTVVNYDLA  112 (150)
Q Consensus        35 ~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~-~vl-v~T~~~~~Gidi~~~~~vi~~~~~  112 (150)
                      ++++||+.-...++-+...|...+.....+.|.|+...|.+.+..|..+.. .+| ++..+..-|+++-.+++|+..|+=
T Consensus       540 ~kiiifsq~~~~l~l~~~~l~~~~~~~~~~~g~~~~~~r~~s~~~~~~~~~~~vll~Slkag~~glnlt~a~~v~~~d~~  619 (674)
T KOG1001|consen  540 PKIVIFSQLIWGLALVCLRLFFKGFVFLRYDGEMLMKIRTKSFTDFPCDPLVTALLMSLKAGKVGLNLTAASHVLLMDPW  619 (674)
T ss_pred             CceeeehhHHHHHHHhhhhhhhcccccchhhhhhHHHHHHhhhcccccCccHHHHHHHHHHhhhhhchhhhhHHHhhchh
Confidence            499999999999998888888889999999999999999999999996543 344 677999999999999999999999


Q ss_pred             CChhHHHHhhccccCCCCccEE
Q psy17637        113 RDIDTHTHRIGRTGRAGNKGVA  134 (150)
Q Consensus       113 ~~~~~~~q~~GR~~R~g~~~~~  134 (150)
                      +++..--|.+-|+.|.|+...+
T Consensus       620 wnp~~eeQaidR~hrigq~k~v  641 (674)
T KOG1001|consen  620 WNPAVEEQAIDRAHRIGQTKPV  641 (674)
T ss_pred             cChHHHHHHHHHHHHhccccee
Confidence            9999999999999999986644

>TIGR00595 priA primosomal protein N'

Probab=97.27  E-value=0.0018  Score=50.95  Aligned_cols=76  Identities=16%  Similarity=0.187  Sum_probs=61.0

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhcccc-CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEE
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVK-EYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVN  108 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~  108 (150)
                      ..+.++|+.++++.-+..+++.|... +..+..+|++++..+|.+.+.....|+..|+|+|...-. ..++++.+||.
T Consensus        23 ~~g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~~~IVVGTrsalf-~p~~~l~lIIV   99 (505)
T TIGR00595        23 ALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVVIGTRSALF-LPFKNLGLIIV   99 (505)
T ss_pred             HcCCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCCCCEEECChHHHc-CcccCCCEEEE
Confidence            34678999999999988888888754 567889999999999999999999999999999964322 34556676663

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).

>PRK14873 primosome assembly protein PriA; Provisional

Probab=97.21  E-value=0.0032  Score=51.07  Aligned_cols=87  Identities=18%  Similarity=0.168  Sum_probs=66.4

Q ss_pred             HHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccC--ceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccC
Q psy17637         21 GHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKE--YDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGL   98 (150)
Q Consensus        21 ~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~--~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gi   98 (150)
                      +..++.+......++++||.++.......+...|....  ..+..+|+++++.+|.+.+....+|+..|+|+|..... .
T Consensus       175 evyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G~~~IViGtRSAvF-a  253 (665)
T PRK14873        175 RRLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSAVF-A  253 (665)
T ss_pred             HHHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCCCCcEEEEcceeEE-e
Confidence            34445555444567899999999999888888887653  46899999999999999999999999999999954421 3


Q ss_pred             CccCCcEEEE
Q psy17637         99 DIPHIRTVVN  108 (150)
Q Consensus        99 di~~~~~vi~  108 (150)
                      -++++..||.
T Consensus       254 P~~~LgLIIv  263 (665)
T PRK14873        254 PVEDLGLVAI  263 (665)
T ss_pred             ccCCCCEEEE
Confidence            3445555553

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=97.20  E-value=0.0041  Score=50.27  Aligned_cols=76  Identities=17%  Similarity=0.259  Sum_probs=61.7

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhcc----ccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCC-CcccCCccCCcEE
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLT----VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDV-AARGLDIPHIRTV  106 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~----~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~-~~~Gidi~~~~~v  106 (150)
                      ..+.++++-++|+.-+...++.+.    ..++++..+||+++..++...++...+|+..|+|+|.. +...+.+.++.+|
T Consensus       282 ~~g~qvlilaPT~~LA~Q~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~~~~~~~l~lv  361 (630)
T TIGR00643       282 EAGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALV  361 (630)
T ss_pred             HcCCcEEEECCHHHHHHHHHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhccccccccceE
Confidence            356789999999888776665554    34789999999999999999999999999999999954 4445667777776


Q ss_pred             E
Q psy17637        107 V  107 (150)
Q Consensus       107 i  107 (150)
                      |
T Consensus       362 V  362 (630)
T TIGR00643       362 I  362 (630)
T ss_pred             E
Confidence            6

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

Probab=97.15  E-value=0.0037  Score=51.16  Aligned_cols=115  Identities=17%  Similarity=0.203  Sum_probs=79.6

Q ss_pred             chhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCC
Q psy17637         15 KDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVA   94 (150)
Q Consensus        15 ~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~   94 (150)
                      ....+...|...|.    .++++-||++|...++.+++.....+.++..+++.-+..   ++ +.|  ++.+|++-|+++
T Consensus       267 ~~~tF~~~L~~~L~----~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~---dv-~~W--~~~~VviYT~~i  336 (824)
T PF02399_consen  267 DETTFFSELLARLN----AGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLE---DV-ESW--KKYDVVIYTPVI  336 (824)
T ss_pred             chhhHHHHHHHHHh----CCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCcc---cc-ccc--cceeEEEEeceE
Confidence            33445556666664    456788999999999999998888888888888875544   22 223  457899999999


Q ss_pred             cccCCccCCc--EEEEe--cCC--CChhHHHHhhccccCCCCccEEEEEEec
Q psy17637         95 ARGLDIPHIR--TVVNY--DLA--RDIDTHTHRIGRTGRAGNKGVAYTLVTD  140 (150)
Q Consensus        95 ~~Gidi~~~~--~vi~~--~~~--~~~~~~~q~~GR~~R~g~~~~~~~~~~~  140 (150)
                      .-|+++....  -++-|  ...  .++.+..|++||+-... ....+++++.
T Consensus       337 tvG~Sf~~~HF~~~f~yvk~~~~gpd~~s~~Q~lgRvR~l~-~~ei~v~~d~  387 (824)
T PF02399_consen  337 TVGLSFEEKHFDSMFAYVKPMSYGPDMVSVYQMLGRVRSLL-DNEIYVYIDA  387 (824)
T ss_pred             EEEeccchhhceEEEEEecCCCCCCcHHHHHHHHHHHHhhc-cCeEEEEEec
Confidence            9999986443  24433  222  24556899999976554 4556665554

It functions as a docking protein to recruit essential components of the viral replication machinery to viral DNA origins. In the presence of the major DNA-binding protein, it opens dsDNA which leads to a conformational change in the origin that facilitates DNA unwinding and subsequent replication [].; GO: 0003688 DNA replication origin binding, 0005524 ATP binding, 0006260 DNA replication

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

Probab=97.14  E-value=0.0042  Score=49.77  Aligned_cols=76  Identities=18%  Similarity=0.243  Sum_probs=66.5

Q ss_pred             CCCCCeeEEehh----hhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCC-cccCCccCCcEE
Q psy17637         32 QEVPPALMNLAM----QLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVA-ARGLDIPHIRTV  106 (150)
Q Consensus        32 ~~~~~~ivf~~~----~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~-~~Gidi~~~~~v  106 (150)
                      ..+.++.+-++|    +.+.+.+.++|...++.+..++|.+..+.|+++++...+|+++++|+|.++ ...+++.++-+|
T Consensus       309 ~~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd~V~F~~LgLV  388 (677)
T COG1200         309 EAGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQDKVEFHNLGLV  388 (677)
T ss_pred             HcCCeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhhcceeecceeEE
Confidence            567889999999    567778888888889999999999999999999999999999999999765 557888888777


Q ss_pred             E
Q psy17637        107 V  107 (150)
Q Consensus       107 i  107 (150)
                      |
T Consensus       389 I  389 (677)
T COG1200         389 I  389 (677)
T ss_pred             E
Confidence            6

>KOG0951|consensus

Probab=97.12  E-value=0.0032  Score=53.67  Aligned_cols=119  Identities=16%  Similarity=0.164  Sum_probs=83.1

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccc----------------------cCceEEEecCCCCHHHHHHH
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTV----------------------KEYDVLLLHGDMDQSERNSV   76 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~----------------------~~~~~~~~~~~~~~~~r~~~   76 (150)
                      +..-....+.+.....++++||+++++++..++..|..                      ..++...-|.+++..+..-+
T Consensus      1344 m~~~~~~ai~~~a~~~k~~~vf~p~rk~~~~~a~~~~~~s~~~~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~iv 1423 (1674)
T KOG0951|consen 1344 MTKPTYTAIVRHAGNRKPAIVFLPTRKHARLVAVDLVTFSHADEPDYLLSELEECDETLRESLKHGVGHEGLSSNDQEIV 1423 (1674)
T ss_pred             hhhhHHHHHHHHhcCCCCeEEEeccchhhhhhhhccchhhccCcHHHHHHHHhcchHhhhhcccccccccccCcchHHHH
Confidence            44445556666656789999999999988766655432                      11222333889999999999


Q ss_pred             HHHhhcCCceEEEEcCCCcccCCccCCcEEE----EecC------CCChhHHHHhhccccCCCCccEEEEEEecC
Q psy17637         77 ITKFKRQECRILVATDVAARGLDIPHIRTVV----NYDL------ARDIDTHTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus        77 ~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi----~~~~------~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                      -..|..|.+.|+|.... .+|+....--+|+    .||.      +-+.++..|+.|++.|.|   .|+++....
T Consensus      1424 ~~l~e~g~i~v~v~s~~-~~~~~~~~~lVvvmgt~~ydg~e~~~~~y~i~~ll~m~G~a~~~~---k~vi~~~~~ 1494 (1674)
T KOG0951|consen 1424 QQLFEAGAIQVCVMSRD-CYGTKLKAHLVVVMGTQYYDGKEHSYEDYPIAELLQMVGLASGAG---KCVIMCHTP 1494 (1674)
T ss_pred             HHHHhcCcEEEEEEEcc-cccccccceEEEEecceeecccccccccCchhHHHHHhhhhcCCc---cEEEEecCc
Confidence            99999999999988866 7787764333333    2332      336889999999998854   577666554

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

Probab=97.08  E-value=0.0034  Score=52.45  Aligned_cols=70  Identities=14%  Similarity=0.206  Sum_probs=53.8

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhhHHHHHhhcccc----C-ceEEE-ecCCCCHHHHHHHHHHhhcCCceEEEEcCC
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVK----E-YDVLL-LHGDMDQSERNSVITKFKRQECRILVATDV   93 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~----~-~~~~~-~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~   93 (150)
                      .+...+...  .++++++.++|.--+...++.|...    + ..+.. +|+.|+.+++++.+++|.+|..+|||+|+.
T Consensus       115 ~~~sl~~a~--kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~  190 (1187)
T COG1110         115 LLMSLYLAK--KGKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQ  190 (1187)
T ss_pred             HHHHHHHHh--cCCeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHH
Confidence            444444444  6688999999988777777776542    2 43333 999999999999999999999999999953

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=96.99  E-value=0.0069  Score=50.95  Aligned_cols=76  Identities=12%  Similarity=0.173  Sum_probs=62.0

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CCcccCCccCCcEEE
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VAARGLDIPHIRTVV  107 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~~~Gidi~~~~~vi  107 (150)
                      .+.+++|.++|+.-+...++.+..    .++++..++|..+..++.+.++.+..|+..|+|+|. .+...+.+.++.++|
T Consensus       499 ~g~qvlvLvPT~~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll~~~v~f~~L~llV  578 (926)
T TIGR00580       499 DGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLI  578 (926)
T ss_pred             hCCeEEEEeCcHHHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHhhCCCCcccCCEEE
Confidence            457899999999988877766543    467888999999999999999999999999999995 445557777888766


Q ss_pred             E
Q psy17637        108 N  108 (150)
Q Consensus       108 ~  108 (150)
                      .
T Consensus       579 I  579 (926)
T TIGR00580       579 I  579 (926)
T ss_pred             e
Confidence            3

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.

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

Probab=96.97  E-value=0.0025  Score=51.96  Aligned_cols=88  Identities=16%  Similarity=0.209  Sum_probs=66.4

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhcccc-CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCccc
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVK-EYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG   97 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G   97 (150)
                      +.+..++.+......++++||-++-+.-...+...|+.+ +.++..+|+++++.+|.+.+.+..+|+.+|+|+|...- -
T Consensus       230 KTEvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAl-F  308 (730)
T COG1198         230 KTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSAL-F  308 (730)
T ss_pred             HHHHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHHHHHHHhcCCceEEEEechhh-c
Confidence            334555555555556889999999887777777766654 67899999999999999999999999999999995332 2


Q ss_pred             CCccCCcEEE
Q psy17637         98 LDIPHIRTVV  107 (150)
Q Consensus        98 idi~~~~~vi  107 (150)
                      .-++++..||
T Consensus       309 ~Pf~~LGLII  318 (730)
T COG1198         309 LPFKNLGLII  318 (730)
T ss_pred             CchhhccEEE
Confidence            3345666555

>PRK14873 primosome assembly protein PriA; Provisional

Probab=96.94  E-value=0.0075  Score=48.97  Aligned_cols=86  Identities=15%  Similarity=0.144  Sum_probs=53.7

Q ss_pred             hhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCCC--------
Q psy17637         42 AMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLAR--------  113 (150)
Q Consensus        42 ~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~--------  113 (150)
                      .|.+..|+|.+.|.  +.++..+.+       ..+++.|. ++..|||+|+..+.-+. ++++.|+.+|...        
T Consensus       439 Gter~eeeL~~~FP--~~~V~r~d~-------d~~l~~~~-~~~~IlVGTqgaepm~~-g~~~lV~ildaD~~L~~pDfR  507 (665)
T PRK14873        439 GARRTAEELGRAFP--GVPVVTSGG-------DQVVDTVD-AGPALVVATPGAEPRVE-GGYGAALLLDAWALLGRQDLR  507 (665)
T ss_pred             cHHHHHHHHHHHCC--CCCEEEECh-------HHHHHhhc-cCCCEEEECCCCccccc-CCceEEEEEcchhhhcCCCcC
Confidence            33444555666554  444554443       24788897 58999999983222222 4667776555432        


Q ss_pred             ----ChhHHHHhhccccCCCCccEEEEEE
Q psy17637        114 ----DIDTHTHRIGRTGRAGNKGVAYTLV  138 (150)
Q Consensus       114 ----~~~~~~q~~GR~~R~g~~~~~~~~~  138 (150)
                          ....+.|..||+||....|.+++..
T Consensus       508 A~Er~~qll~qvagragr~~~~G~V~iq~  536 (665)
T PRK14873        508 AAEDTLRRWMAAAALVRPRADGGQVVVVA  536 (665)
T ss_pred             hHHHHHHHHHHHHHhhcCCCCCCEEEEEe
Confidence                3444578899999988788887764

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

Probab=96.63  E-value=0.023  Score=48.33  Aligned_cols=77  Identities=6%  Similarity=0.122  Sum_probs=65.3

Q ss_pred             CCCCCeeEEehhh----hhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEc-CCCcccCCccCCcEE
Q psy17637         32 QEVPPALMNLAMQ----LNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVAT-DVAARGLDIPHIRTV  106 (150)
Q Consensus        32 ~~~~~~ivf~~~~----~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T-~~~~~Gidi~~~~~v  106 (150)
                      ..++++.|.++|.    .|-+.+.+.+..-.+++..+.--.+.++...+++...+|+++|+|+| ..++.++.+.++-++
T Consensus       641 ~~GKQVAvLVPTTlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL~kdv~FkdLGLl  720 (1139)
T COG1197         641 MDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVKFKDLGLL  720 (1139)
T ss_pred             cCCCeEEEEcccHHhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHhhCCCcEEecCCeE
Confidence            4578999999994    45566666666668889999999999999999999999999999999 577888888888887


Q ss_pred             EE
Q psy17637        107 VN  108 (150)
Q Consensus       107 i~  108 (150)
                      |.
T Consensus       721 II  722 (1139)
T COG1197         721 II  722 (1139)
T ss_pred             EE
Confidence            63

>KOG0921|consensus

Probab=96.50  E-value=0.003  Score=52.20  Aligned_cols=106  Identities=23%  Similarity=0.353  Sum_probs=81.7

Q ss_pred             CCCCeeEEehhhhhHHHHHhhcccc-------CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcE
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVK-------EYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRT  105 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~-------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~  105 (150)
                      -.+-+++|.+.....-.|..+|...       .+.+...|...+..+..++.+....|..++++.|...+..+.+.++..
T Consensus       642 i~gailvflpgwa~i~~L~~~ll~~~~fg~~~~y~ilp~Hsq~~~~eqrkvf~~~p~gv~kii~stniaetsiTidd~v~  721 (1282)
T KOG0921|consen  642 IDGAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEILPLHSQLTSQEQRKVFEPVPEGVTKIILSTNIAETSITIDDVVY  721 (1282)
T ss_pred             CccceeeecCchHHhhhhhhhhhhhhhhccchhcccccchhhcccHhhhhccCcccccccccccccceeeEeeeecceeE
Confidence            3566899999999998998888654       456889999998888888988888899999999988888888777666


Q ss_pred             EEEecCCC------------------ChhHHHHhhccccCCCCccEEEEEEe
Q psy17637        106 VVNYDLAR------------------DIDTHTHRIGRTGRAGNKGVAYTLVT  139 (150)
Q Consensus       106 vi~~~~~~------------------~~~~~~q~~GR~~R~g~~~~~~~~~~  139 (150)
                      |++.+.-.                  +.....|+.||+||.. +|.+..++.
T Consensus       722 vid~cka~~~~~~s~nn~~~~Atvw~sktn~eqr~gr~grvR-~G~~f~lcs  772 (1282)
T KOG0921|consen  722 VIDSCKAKEKLFTSHNNMTHYATVWASKTNLEQRKGRAGRVR-PGFCFHLCS  772 (1282)
T ss_pred             EEeeeeeeeeeeccccceeeeeeecccccchHhhcccCceec-ccccccccH
Confidence            66432221                  5566689999999873 666666553

>PRK10689 transcription-repair coupling factor; Provisional

Probab=96.40  E-value=0.032  Score=48.10  Aligned_cols=75  Identities=9%  Similarity=0.122  Sum_probs=60.2

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CCcccCCccCCcEEE
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VAARGLDIPHIRTVV  107 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~~~Gidi~~~~~vi  107 (150)
                      .+.+++|-++|+.-+..+++.+..    .++++..++++.+..++.++++....|...|+|+|. .+...+.+.++.++|
T Consensus       648 ~g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~~~v~~~~L~lLV  727 (1147)
T PRK10689        648 NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLI  727 (1147)
T ss_pred             cCCeEEEEeCcHHHHHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHhCCCCHhhCCEEE
Confidence            567899999999988877776653    356788899999999999999999999999999995 444445666777665

>KOG0298|consensus

Probab=96.31  E-value=0.0086  Score=51.06  Aligned_cols=104  Identities=14%  Similarity=0.118  Sum_probs=76.7

Q ss_pred             HHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCC
Q psy17637         24 VRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHI  103 (150)
Q Consensus        24 l~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~  103 (150)
                      +..+... +...++|+|+.=-...+.+...+...+++...--+   -++....+..|.+ -...|+-+...+-|+++-+.
T Consensus      1212 il~iK~k-~~qekvIvfsqws~~ldV~e~~~~~N~I~~~~~~~---t~d~~dc~~~fk~-I~clll~~~~~~~GLNL~eA 1286 (1394)
T KOG0298|consen 1212 ILYIKFK-NEQEKVIVFSQWSVVLDVKELRYLMNLIKKQLDGE---TEDFDDCIICFKS-IDCLLLFVSKGSKGLNLIEA 1286 (1394)
T ss_pred             HHHHhcc-CcCceEEEEEehHHHHHHHHHHHHhhhhHhhhccC---Ccchhhhhhhccc-ceEEEEEeccCcccccHHhh
Confidence            3334333 56678999997777777776666655554332222   2344566777775 33466888999999999999


Q ss_pred             cEEEEecCCCChhHHHHhhccccCCCCcc
Q psy17637        104 RTVVNYDLARDIDTHTHRIGRTGRAGNKG  132 (150)
Q Consensus       104 ~~vi~~~~~~~~~~~~q~~GR~~R~g~~~  132 (150)
                      .+|+..+|..+++.-.|.+||+.|.|+..
T Consensus      1287 ~Hvfl~ePiLN~~~E~QAigRvhRiGQ~~ 1315 (1394)
T KOG0298|consen 1287 THVFLVEPILNPGDEAQAIGRVHRIGQKR 1315 (1394)
T ss_pred             hhhheeccccCchHHHhhhhhhhhccccc
Confidence            99999999999999999999999999754

>PRK14701 reverse gyrase; Provisional

Probab=96.20  E-value=0.064  Score=47.89  Aligned_cols=61  Identities=13%  Similarity=0.276  Sum_probs=52.2

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc------cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV------KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDV   93 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~------~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~   93 (150)
                      ++.+++|.++|++-+..+++.|..      .++.+..+||+++..++.+.++.+.+|+..|||+|+-
T Consensus       121 ~g~~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPg  187 (1638)
T PRK14701        121 KGKKCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQ  187 (1638)
T ss_pred             cCCeEEEEECHHHHHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCc
Confidence            456899999999988888777764      2467889999999999999999999999999999963

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

Probab=96.17  E-value=0.044  Score=43.35  Aligned_cols=87  Identities=24%  Similarity=0.295  Sum_probs=59.3

Q ss_pred             hHHHHHHHHHHhccCCC-CCeeEEehhhhhHHHHHhhccc----c-CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEc
Q psy17637         18 EFAGHLVRNLEGANQEV-PPALMNLAMQLNAEELANSLTV----K-EYDVLLLHGDMDQSERNSVITKFKRQECRILVAT   91 (150)
Q Consensus        18 ~~~~~ll~~l~~~~~~~-~~~ivf~~~~~~~~~l~~~L~~----~-~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T   91 (150)
                      .+..-+++.+....... .++||.++|++-+..+++.+..    . ++.+..++|+++...+...+   +.| .+|+|+|
T Consensus        82 Af~lP~l~~l~~~~~~~~~~aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l---~~~-~~ivVaT  157 (513)
T COG0513          82 AFLLPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEAL---KRG-VDIVVAT  157 (513)
T ss_pred             HHHHHHHHHHhcccccCCCceEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHH---hcC-CCEEEEC
Confidence            34445555554311122 2299999999988877777643    2 57789999999877666444   446 8999999


Q ss_pred             C-----CCccc-CCccCCcEEEE
Q psy17637         92 D-----VAARG-LDIPHIRTVVN  108 (150)
Q Consensus        92 ~-----~~~~G-idi~~~~~vi~  108 (150)
                      +     .+.++ +++..+.++|.
T Consensus       158 PGRllD~i~~~~l~l~~v~~lVl  180 (513)
T COG0513         158 PGRLLDLIKRGKLDLSGVETLVL  180 (513)
T ss_pred             ccHHHHHHHcCCcchhhcCEEEe
Confidence            6     44555 77788887773

>KOG2340|consensus

Probab=96.00  E-value=0.035  Score=43.66  Aligned_cols=110  Identities=16%  Similarity=0.170  Sum_probs=83.3

Q ss_pred             CCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCC--cccCCccCCcEEEEecC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVA--ARGLDIPHIRTVVNYDL  111 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~--~~Gidi~~~~~vi~~~~  111 (150)
                      ...++||.++.-.--.+.+++++..+....++.-.+...-...-..|..|...+|+-|.-+  =+--++.++..||+|.+
T Consensus       552 ~s~~LiyIPSYfDFVRvRNy~K~e~i~F~~i~EYssk~~vsRAR~lF~qgr~~vlLyTER~hffrR~~ikGVk~vVfYqp  631 (698)
T KOG2340|consen  552 ESGILIYIPSYFDFVRVRNYMKKEEISFVMINEYSSKSKVSRARELFFQGRKSVLLYTERAHFFRRYHIKGVKNVVFYQP  631 (698)
T ss_pred             cCceEEEecchhhHHHHHHHhhhhhcchHHHhhhhhHhhhhHHHHHHHhcCceEEEEehhhhhhhhheecceeeEEEecC
Confidence            4457999999887778899999888888888877777666777788999999999999633  34567889999999999


Q ss_pred             CCChhHH---HHhhccccCCC----CccEEEEEEecCCC
Q psy17637        112 ARDIDTH---THRIGRTGRAG----NKGVAYTLVTDKDK  143 (150)
Q Consensus       112 ~~~~~~~---~q~~GR~~R~g----~~~~~~~~~~~~~~  143 (150)
                      |..|.=|   +-+.+|+.-.|    ....|.+++++-|.
T Consensus       632 P~~P~FYsEiinm~~k~~~~gn~d~d~~t~~ilytKyD~  670 (698)
T KOG2340|consen  632 PNNPHFYSEIINMSDKTTSQGNTDLDIFTVRILYTKYDR  670 (698)
T ss_pred             CCCcHHHHHHHhhhhhhhccCCccccceEEEEEeechhh
Confidence            9987655   45555654333    22467777776553

>KOG0701|consensus

Probab=96.00  E-value=0.0028  Score=55.30  Aligned_cols=95  Identities=23%  Similarity=0.329  Sum_probs=73.4

Q ss_pred             CCeeEEehhhhhHHHHHhhccccC-ceEEEecCCCC-----------HHHHHHHHHHhhcCCceEEEEcCCCcccCCccC
Q psy17637         35 PPALMNLAMQLNAEELANSLTVKE-YDVLLLHGDMD-----------QSERNSVITKFKRQECRILVATDVAARGLDIPH  102 (150)
Q Consensus        35 ~~~ivf~~~~~~~~~l~~~L~~~~-~~~~~~~~~~~-----------~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~  102 (150)
                      -..++||+.+..+-.+.+.+.... ..+..+.|.+.           ...+..++..|...++++|++|.++.+|+|++.
T Consensus       293 l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~k~~~~~~~~~~~~vl~~~~~~~ln~L~~~~~~~e~~d~~~  372 (1606)
T KOG0701|consen  293 LSGIIFVDQRYTAYVLLELLREIFSNDPLFVTGASGANLWKSFKNELELRQAEVLRRFHFHELNLLIATSVLEEGVDVPK  372 (1606)
T ss_pred             hhheeecccchHHHHHHHHHHHhhccCcceeeccccCccchhhHHHHHhhhHHHHHHHhhhhhhHHHHHHHHHhhcchhh
Confidence            377899988777666666654321 12233555432           223578889999999999999999999999999


Q ss_pred             CcEEEEecCCCChhHHHHhhccccCCC
Q psy17637        103 IRTVVNYDLARDIDTHTHRIGRTGRAG  129 (150)
Q Consensus       103 ~~~vi~~~~~~~~~~~~q~~GR~~R~g  129 (150)
                      ++.++.++.|....+|+|..||+-+..
T Consensus       373 ~~~~~~~~~~~~~~~~vq~~~r~~~~~  399 (1606)
T KOG0701|consen  373 CNLVVLFDAPTYYRSYVQKKGRARAAD  399 (1606)
T ss_pred             hhhheeccCcchHHHHHHhhcccccch
Confidence            999999999999999999999976543

>KOG1133|consensus

Probab=95.70  E-value=0.4  Score=39.13  Aligned_cols=133  Identities=14%  Similarity=0.143  Sum_probs=81.6

Q ss_pred             CeeEEEeecchhhHHHHHHHHHHhccC-CCCCeeEEehhhhhHHHHHhhccccCce-------EEEecCCCCHHHHHHHH
Q psy17637          6 GVAYTLVTDKDKEFAGHLVRNLEGANQ-EVPPALMNLAMQLNAEELANSLTVKEYD-------VLLLHGDMDQSERNSVI   77 (150)
Q Consensus         6 ~~~~~~~~~~~~~~~~~ll~~l~~~~~-~~~~~ivf~~~~~~~~~l~~~L~~~~~~-------~~~~~~~~~~~~r~~~~   77 (150)
                      .+.+.+........+..|-..+.+... -.+-+++|+++.+....+.+.+...|+-       .+++-..-+   -+.++
T Consensus       600 p~eftf~~R~s~~~l~~l~~~~~nL~~~VPgGvV~FfPSy~yL~~v~k~w~~~gil~ri~~kK~vF~E~k~~---~~dvl  676 (821)
T KOG1133|consen  600 PLEFTFETRESPEMIKDLGSSISNLSNAVPGGVVCFFPSYAYLGQVRKRWEQNGILARIVGKKKVFYEPKDT---VEDVL  676 (821)
T ss_pred             ceEEEeeccCChHHHHHHHHHHHHHHhhCCCcEEEEeccHHHHHHHHHHHHhcchHHHhhccchhhccCccc---HHHHH
Confidence            345555555555555555555444321 2367999999999998888887654332       222222112   24555


Q ss_pred             HHhh----cCCceEEEEc--CCCcccCCcc--CCcEEEEecCCCC--------------------hh------------H
Q psy17637         78 TKFK----RQECRILVAT--DVAARGLDIP--HIRTVVNYDLARD--------------------ID------------T  117 (150)
Q Consensus        78 ~~f~----~g~~~vlv~T--~~~~~Gidi~--~~~~vi~~~~~~~--------------------~~------------~  117 (150)
                      +.+.    .|.-.+|.+.  ..+++|||+.  -+..|+..++|..                    +.            .
T Consensus       677 ~~Ya~a~~~g~GaiLlaVVGGKlSEGINF~D~LgRaVvvVGlPyPN~~s~EL~er~k~l~~k~~~~gagke~yEnlCMkA  756 (821)
T KOG1133|consen  677 EGYAEAAERGRGAILLAVVGGKLSEGINFSDDLGRAVVVVGLPYPNIQSVELQERMKHLDGKLPTPGAGKELYENLCMKA  756 (821)
T ss_pred             HHHHHHhhcCCCeEEEEEeccccccccccccccccEEEEeecCCCCCCCHHHHHHHHHhhhccCCCCchHHHHHHHHHHH
Confidence            5554    3444566555  8999999985  3567777777651                    11            1


Q ss_pred             HHHhhccccCCCCccEEEEEEecC
Q psy17637        118 HTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus       118 ~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                      .-|.+|||-|..++-.++.+++..
T Consensus       757 VNQsIGRAIRH~~DYA~i~LlD~R  780 (821)
T KOG1133|consen  757 VNQSIGRAIRHRKDYASIYLLDKR  780 (821)
T ss_pred             HHHHHHHHHhhhccceeEEEehhh
Confidence            138999999987776777777654

>TIGR01054 rgy reverse gyrase

Probab=95.48  E-value=0.11  Score=45.20  Aligned_cols=60  Identities=13%  Similarity=0.227  Sum_probs=49.0

Q ss_pred             CCCCeeEEehhhhhHHHHHhhcccc----Cce---EEEecCCCCHHHHHHHHHHhhcCCceEEEEcC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVK----EYD---VLLLHGDMDQSERNSVITKFKRQECRILVATD   92 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~----~~~---~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~   92 (150)
                      .+.+++|.++|++-+..+++.+...    ++.   +..+||+++..++...++.+.+|...|+|+|+
T Consensus       120 ~g~~vLIL~PTreLa~Qi~~~l~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp  186 (1171)
T TIGR01054       120 KGKRCYIILPTTLLVIQVAEKISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTT  186 (1171)
T ss_pred             cCCeEEEEeCHHHHHHHHHHHHHHHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            4678999999999888887766542    333   34689999999999999999998899999996

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.

>KOG0347|consensus

Probab=95.42  E-value=0.045  Score=43.28  Aligned_cols=56  Identities=18%  Similarity=0.238  Sum_probs=46.8

Q ss_pred             CCCC--eeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC
Q psy17637         33 EVPP--ALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD   92 (150)
Q Consensus        33 ~~~~--~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~   92 (150)
                      ...+  .||+++|++-+..+.+.|..    .++.+..+.|||....++.+++.    ...|+|||+
T Consensus       260 k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~----~p~IVVATP  321 (731)
T KOG0347|consen  260 KYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQ----RPDIVVATP  321 (731)
T ss_pred             ccCcceeEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhc----CCCEEEecc
Confidence            3445  99999999998888887753    48999999999999888888877    457999996

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=95.06  E-value=0.16  Score=39.50  Aligned_cols=82  Identities=21%  Similarity=0.233  Sum_probs=54.5

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccc-----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC----
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLNAEELANSLTV-----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD----   92 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~-----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~----   92 (150)
                      .++..+... ....+++|.++|++-+..+++.++.     .+..+..++|+.+...+...+.    ....|+|+|.    
T Consensus        61 pil~~l~~~-~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~----~~~~IvV~Tp~rl~  135 (460)
T PRK11776         61 GLLQKLDVK-RFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLE----HGAHIIVGTPGRIL  135 (460)
T ss_pred             HHHHHhhhc-cCCceEEEEeCCHHHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhc----CCCCEEEEChHHHH
Confidence            344444322 2345799999999988887776653     2678889999988766554333    4568999994    


Q ss_pred             -CCc-ccCCccCCcEEEE
Q psy17637         93 -VAA-RGLDIPHIRTVVN  108 (150)
Q Consensus        93 -~~~-~Gidi~~~~~vi~  108 (150)
                       .+. ..+++.++.++|.
T Consensus       136 ~~l~~~~~~l~~l~~lVi  153 (460)
T PRK11776        136 DHLRKGTLDLDALNTLVL  153 (460)
T ss_pred             HHHHcCCccHHHCCEEEE
Confidence             222 3456777777763

>KOG1513|consensus

Probab=94.98  E-value=0.032  Score=45.99  Aligned_cols=55  Identities=22%  Similarity=0.394  Sum_probs=46.9

Q ss_pred             HHHhhcCCceEEEEcCCCcccCCccCCcEE--------EEecCCCChhHHHHhhccccCCCCc
Q psy17637         77 ITKFKRQECRILVATDVAARGLDIPHIRTV--------VNYDLARDIDTHTHRIGRTGRAGNK  131 (150)
Q Consensus        77 ~~~f~~g~~~vlv~T~~~~~Gidi~~~~~v--------i~~~~~~~~~~~~q~~GR~~R~g~~  131 (150)
                      -++|.+|+..|-|-+.+.+-||.++.-.-|        |-+.+|||...-+|..||+.|..+.
T Consensus       850 KqrFM~GeK~vAIISEAaSSGiSLQsDrRv~NqRRRvHiTLELPWSADrAIQQFGRTHRSNQV  912 (1300)
T KOG1513|consen  850 KQRFMDGEKLVAIISEAASSGISLQSDRRVQNQRRRVHITLELPWSADRAIQQFGRTHRSNQV  912 (1300)
T ss_pred             HhhhccccceeeeeehhhccCceeecchhhhhhhheEEEEEECCcchhHHHHHhccccccccc
Confidence            467999999899999999999998755433        5689999999999999999998764

>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=94.85  E-value=0.13  Score=36.69  Aligned_cols=78  Identities=15%  Similarity=0.230  Sum_probs=56.0

Q ss_pred             CceEEEecCCCCHHHHHHHHHHhhcCC----ceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhcccc-CCCCcc
Q psy17637         58 EYDVLLLHGDMDQSERNSVITKFKRQE----CRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTG-RAGNKG  132 (150)
Q Consensus        58 ~~~~~~~~~~~~~~~r~~~~~~f~~g~----~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~-R~g~~~  132 (150)
                      ++.+..+.++.+.+.     -.+.++.    ..|+|+=+.+++|+.++++....+...++....++||.-..| |.|-..
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            688888887654432     3444443    678899999999999999999999999997777777744444 666445


Q ss_pred             EEEEEEec
Q psy17637        133 VAYTLVTD  140 (150)
Q Consensus       133 ~~~~~~~~  140 (150)
                      .|=++.++
T Consensus       185 l~Ri~~~~  192 (239)
T PF10593_consen  185 LCRIYMPE  192 (239)
T ss_pred             ceEEecCH
Confidence            55555543

This domain is found associated with a helicase domain of superfamily type II [].

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=94.73  E-value=0.14  Score=40.05  Aligned_cols=59  Identities=15%  Similarity=0.173  Sum_probs=53.1

Q ss_pred             CCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD   92 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~   92 (150)
                      ...+||.+++++-++.....|...++.+..++++.+..++..++.....+..+++++|+
T Consensus        51 ~~~~lVi~P~~~L~~dq~~~l~~~gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TP  109 (470)
T TIGR00614        51 DGITLVISPLISLMEDQVLQLKASGIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTP  109 (470)
T ss_pred             CCcEEEEecHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            45799999999988888888888899999999999999999999999999999999885

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=94.48  E-value=0.3  Score=39.78  Aligned_cols=80  Identities=24%  Similarity=0.315  Sum_probs=52.1

Q ss_pred             HHHHHHhccCCCCCeeEEehhhhhHHHHHhhccc-----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-----
Q psy17637         23 LVRNLEGANQEVPPALMNLAMQLNAEELANSLTV-----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-----   92 (150)
Q Consensus        23 ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~-----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----   92 (150)
                      ++..+... ....++||.|+|++-+..+++.+..     .++.+..+||+.+.+.+...+   . ....|+|+|.     
T Consensus        64 ll~~l~~~-~~~~~~LIL~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l---~-~~~~IVVgTPgrl~d  138 (629)
T PRK11634         64 LLHNLDPE-LKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRAL---R-QGPQIVVGTPGRLLD  138 (629)
T ss_pred             HHHHhhhc-cCCCeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHh---c-CCCCEEEECHHHHHH
Confidence            34444332 3456899999999988877666543     367889999998765544332   2 3468999994     


Q ss_pred             CCcc-cCCccCCcEEE
Q psy17637         93 VAAR-GLDIPHIRTVV  107 (150)
Q Consensus        93 ~~~~-Gidi~~~~~vi  107 (150)
                      .+.. .+++.++.+||
T Consensus       139 ~l~r~~l~l~~l~~lV  154 (629)
T PRK11634        139 HLKRGTLDLSKLSGLV  154 (629)
T ss_pred             HHHcCCcchhhceEEE
Confidence            2222 35666777666

>cd00268 DEADc DEAD-box helicases

Probab=94.33  E-value=0.56  Score=31.97  Aligned_cols=82  Identities=18%  Similarity=0.256  Sum_probs=51.7

Q ss_pred             HHHHHHHhcc-CCCCCeeEEehhhhhHHHHHhhcc----ccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCC---
Q psy17637         22 HLVRNLEGAN-QEVPPALMNLAMQLNAEELANSLT----VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDV---   93 (150)
Q Consensus        22 ~ll~~l~~~~-~~~~~~ivf~~~~~~~~~l~~~L~----~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~---   93 (150)
                      .++..+.... ....++||.+++++.+...+..+.    ..++.+..++|+.+..+......    +...|+|+|..   
T Consensus        56 ~~l~~~~~~~~~~~~~viii~p~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~iiv~T~~~l~  131 (203)
T cd00268          56 PILEKLDPSPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLK----RGPHIVVATPGRLL  131 (203)
T ss_pred             HHHHHHHhhcccCCceEEEEcCCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhc----CCCCEEEEChHHHH
Confidence            3444444431 245689999999888776655443    34677888999887655543322    55689999942   


Q ss_pred             --C-cccCCccCCcEEE
Q psy17637         94 --A-ARGLDIPHIRTVV  107 (150)
Q Consensus        94 --~-~~Gidi~~~~~vi  107 (150)
                        + ....+++++.++|
T Consensus       132 ~~l~~~~~~~~~l~~lI  148 (203)
T cd00268         132 DLLERGKLDLSKVKYLV  148 (203)
T ss_pred             HHHHcCCCChhhCCEEE
Confidence              1 2224566777766

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

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=93.53  E-value=0.31  Score=39.24  Aligned_cols=59  Identities=8%  Similarity=0.111  Sum_probs=52.3

Q ss_pred             CCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD   92 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~   92 (150)
                      ...++|.++++.-++.-...|...++.+..+|++++..++..++.....|...+++.|+
T Consensus        53 ~g~~lVisPl~sL~~dq~~~l~~~gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tp  111 (591)
T TIGR01389        53 KGLTVVISPLISLMKDQVDQLRAAGVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAP  111 (591)
T ss_pred             CCcEEEEcCCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECh
Confidence            45789999999988888888888899999999999999999999999999999998874

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.

>KOG0339|consensus

Probab=93.45  E-value=0.29  Score=38.66  Aligned_cols=70  Identities=16%  Similarity=0.225  Sum_probs=50.6

Q ss_pred             CCeeEEehhhhhHHHHHhhc----cccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC------CCcccCCccCCc
Q psy17637         35 PPALMNLAMQLNAEELANSL----TVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD------VAARGLDIPHIR  104 (150)
Q Consensus        35 ~~~ivf~~~~~~~~~l~~~L----~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~------~~~~Gidi~~~~  104 (150)
                      +=.+|.|+|++-+..+....    +..++.+..+||+++..++.+-++    -...++|||+      +--.++|+.+++
T Consensus       297 Pi~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk----~g~EivVaTPgRlid~VkmKatn~~rvS  372 (731)
T KOG0339|consen  297 PIGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELK----EGAEIVVATPGRLIDMVKMKATNLSRVS  372 (731)
T ss_pred             CeEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhh----cCCeEEEechHHHHHHHHhhcccceeee
Confidence            34677789999777665444    445899999999999888776655    3358999995      223468888888


Q ss_pred             EEEE
Q psy17637        105 TVVN  108 (150)
Q Consensus       105 ~vi~  108 (150)
                      ++++
T Consensus       373 ~LV~  376 (731)
T KOG0339|consen  373 YLVL  376 (731)
T ss_pred             EEEE
Confidence            7664

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=92.50  E-value=1.2  Score=34.37  Aligned_cols=70  Identities=19%  Similarity=0.246  Sum_probs=47.9

Q ss_pred             CCCeeEEehhhhhHHHHHhhc----cccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCC------CcccCCccCC
Q psy17637         34 VPPALMNLAMQLNAEELANSL----TVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDV------AARGLDIPHI  103 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L----~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~------~~~Gidi~~~  103 (150)
                      ..++||.++|++-+..+++.+    ...++.+..++|+.+...+...+    .+...|+|+|.-      ....++...+
T Consensus        73 ~~~~lil~Pt~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l----~~~~~IlV~Tp~rl~~~~~~~~~~~~~v  148 (434)
T PRK11192         73 PPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVF----SENQDIVVATPGRLLQYIKEENFDCRAV  148 (434)
T ss_pred             CceEEEECCcHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHh----cCCCCEEEEChHHHHHHHHcCCcCcccC
Confidence            357999999999877665543    33478899999998876655443    245689999951      1234556666


Q ss_pred             cEEE
Q psy17637        104 RTVV  107 (150)
Q Consensus       104 ~~vi  107 (150)
                      .+||
T Consensus       149 ~~lV  152 (434)
T PRK11192        149 ETLI  152 (434)
T ss_pred             CEEE
Confidence            7665

>KOG0330|consensus

Probab=92.39  E-value=0.97  Score=34.60  Aligned_cols=87  Identities=23%  Similarity=0.235  Sum_probs=59.8

Q ss_pred             hhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEc
Q psy17637         16 DKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVAT   91 (150)
Q Consensus        16 ~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T   91 (150)
                      .-.++.-+++.|.+. .....++|.++|++-+..+++-+..    -|+.+..+-||++..  .+....++  +..|||||
T Consensus       112 T~afaLPIl~~LL~~-p~~~~~lVLtPtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~--~q~~~L~k--kPhilVaT  186 (476)
T KOG0330|consen  112 TGAFALPILQRLLQE-PKLFFALVLTPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMM--LQANQLSK--KPHILVAT  186 (476)
T ss_pred             hhhhHHHHHHHHHcC-CCCceEEEecCcHHHHHHHHHHHHHhccccCeEEEEEecCchHH--HHHHHhhc--CCCEEEeC
Confidence            344566778888776 4557899999999988877776654    378899999998743  33333443  45789999


Q ss_pred             CC-----C--cccCCccCCcEEE
Q psy17637         92 DV-----A--ARGLDIPHIRTVV  107 (150)
Q Consensus        92 ~~-----~--~~Gidi~~~~~vi  107 (150)
                      .-     +  ..|+.+..+.+.|
T Consensus       187 PGrL~dhl~~Tkgf~le~lk~LV  209 (476)
T KOG0330|consen  187 PGRLWDHLENTKGFSLEQLKFLV  209 (476)
T ss_pred             cHHHHHHHHhccCccHHHhHHHh
Confidence            61     1  4566666666544

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=92.08  E-value=1.7  Score=33.96  Aligned_cols=69  Identities=16%  Similarity=0.207  Sum_probs=47.0

Q ss_pred             CCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCC------CcccCCccCCc
Q psy17637         35 PPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDV------AARGLDIPHIR  104 (150)
Q Consensus        35 ~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~------~~~Gidi~~~~  104 (150)
                      .++||.++|++-+..+.+.+..    .++.+..++|+.+.+.....   + .+...|+|+|.-      ....+++..+.
T Consensus        76 ~~aLil~PtreLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~---l-~~~~~IiV~TP~rL~~~~~~~~~~l~~v~  151 (456)
T PRK10590         76 VRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMK---L-RGGVDVLVATPGRLLDLEHQNAVKLDQVE  151 (456)
T ss_pred             ceEEEEeCcHHHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHHH---H-cCCCcEEEEChHHHHHHHHcCCcccccce
Confidence            3699999999988777665543    36778889999876554322   2 356789999951      13345666777


Q ss_pred             EEE
Q psy17637        105 TVV  107 (150)
Q Consensus       105 ~vi  107 (150)
                      ++|
T Consensus       152 ~lV  154 (456)
T PRK10590        152 ILV  154 (456)
T ss_pred             EEE
Confidence            665

>PF04364 DNA_pol3_chi: DNA polymerase III chi subunit, HolC; InterPro: IPR007459 The DNA polymerase III holoenzyme (2

Probab=92.06  E-value=1.3  Score=28.72  Aligned_cols=93  Identities=20%  Similarity=0.168  Sum_probs=41.8

Q ss_pred             eeEEEeecchh-hHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCc
Q psy17637          7 VAYTLVTDKDK-EFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQEC   85 (150)
Q Consensus         7 ~~~~~~~~~~~-~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~   85 (150)
                      +.|+....... ..+..|+++..   ..+.+++|+|.+.+.++.|-+.|=...-....-|+-...        . .....
T Consensus         4 v~Fy~l~~~~~~~~~c~L~~k~~---~~g~rv~V~~~d~~~a~~lD~~LW~~~~~sFlPH~~~~~--------~-~~~~~   71 (137)
T PF04364_consen    4 VDFYHLSSDDLERFACRLAEKAY---RQGQRVLVLCPDEEQAEALDELLWTFSPDSFLPHGLAGE--------P-PAARQ   71 (137)
T ss_dssp             EEEEE-S----HHHHHHHHHHHH---HTT--EEEE-SSHHHHHHHHHHTTTSSTT----EEETT---------S-STT--
T ss_pred             EEEEEcCCCcHHHHHHHHHHHHH---HcCCeEEEEeCCHHHHHHHHHHHHCCCCCCCCCCcccCC--------C-CCCCC
Confidence            44555555444 44444444444   458899999999999999988884433333344443111        0 11224


Q ss_pred             eEEEEcCCCcccCCccCCcEEEEecCCC
Q psy17637         86 RILVATDVAARGLDIPHIRTVVNYDLAR  113 (150)
Q Consensus        86 ~vlv~T~~~~~Gidi~~~~~vi~~~~~~  113 (150)
                      .|+++++...  ...+..+++||++...
T Consensus        72 PV~i~~~~~~--~~~~~~~vLinL~~~~   97 (137)
T PF04364_consen   72 PVLITWDQEA--NPNNHADVLINLSGEV   97 (137)
T ss_dssp             SEEEE-TTS------S--SEEEE--SS-
T ss_pred             eEEEecCccc--CCCCCCCEEEECCCCC
Confidence            7899886542  1223467888876553

7.7.7 from EC) is the polymerase responsible for the replication of the Escherichia coli chromosome. The holoenzyme is composed of the DNA polymerase III core, the sliding clamp, and the DnaX clamp loading complex. The DnaX complex contains either the tau or gamma product of gene dnax, complexed to delta.delta and to chi psi. Chi forms a 1:1 heterodimer with psi. The chi psi complex functions by increasing the affinity of tau and gamma for delta.delta allowing a functional clamp-loading complex to form at physiological subunit concentrations. Psi is responsible for the interaction with DnaX (gamma/tau), but psi is insoluble unless it is in a complex with chi [].; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3SXU_A 1EM8_C.

>cd01524 RHOD_Pyr_redox Member of the Rhodanese Homology Domain superfamily

Probab=91.24  E-value=0.26  Score=29.13  Aligned_cols=38  Identities=21%  Similarity=0.178  Sum_probs=31.1

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMD   69 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~   69 (150)
                      .+..++++||.+-..+...+..|...|+.+..+.|++.
T Consensus        49 ~~~~~vvl~c~~g~~a~~~a~~L~~~G~~v~~l~GG~~   86 (90)
T cd01524          49 PKDKEIIVYCAVGLRGYIAARILTQNGFKVKNLDGGYK   86 (90)
T ss_pred             CCCCcEEEEcCCChhHHHHHHHHHHCCCCEEEecCCHH
Confidence            45678999998877788888888888888888999874

Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar rhodanese-like domains found C-terminal of the pyridine nucleotide-disulphide oxidoreductase (Pyr-redox) domain and the Pyr-redox dimerization domain.

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

Probab=91.24  E-value=1  Score=39.13  Aligned_cols=59  Identities=12%  Similarity=0.121  Sum_probs=50.1

Q ss_pred             CCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhc--CCceEEEEcC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKR--QECRILVATD   92 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~--g~~~vlv~T~   92 (150)
                      ...+||.+++++-+..-...|...++.+..+.++++..++..+++.+..  |..++|++|+
T Consensus       500 ~GiTLVISPLiSLmqDQV~~L~~~GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTP  560 (1195)
T PLN03137        500 PGITLVISPLVSLIQDQIMNLLQANIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTP  560 (1195)
T ss_pred             CCcEEEEeCHHHHHHHHHHHHHhCCCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEECh
Confidence            3579999999998875555566779999999999999999999998876  8889999995

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=91.18  E-value=1.1  Score=36.47  Aligned_cols=59  Identities=8%  Similarity=0.087  Sum_probs=51.9

Q ss_pred             CCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD   92 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~   92 (150)
                      ...+||.+++++-+......|...++.+..+++..+.++...++.....|...++++|+
T Consensus        65 ~g~tlVisPl~sL~~dqv~~l~~~gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tP  123 (607)
T PRK11057         65 DGLTLVVSPLISLMKDQVDQLLANGVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAP  123 (607)
T ss_pred             CCCEEEEecHHHHHHHHHHHHHHcCCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEECh
Confidence            35799999999988888888888899999999999999998888889999999988873

>PRK09401 reverse gyrase; Reviewed

Probab=91.10  E-value=1.6  Score=38.33  Aligned_cols=60  Identities=20%  Similarity=0.344  Sum_probs=46.0

Q ss_pred             CCCCeeEEehhhhhHHHHHhhcccc----CceEEEe--cCCCCHHHHHHHHHHhhcCCceEEEEcC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVK----EYDVLLL--HGDMDQSERNSVITKFKRQECRILVATD   92 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~----~~~~~~~--~~~~~~~~r~~~~~~f~~g~~~vlv~T~   92 (150)
                      .+.+++|.++|++-+..+++.+...    +..+..+  +++++.+++.+..+.+..+...|+|+|.
T Consensus       122 ~g~~alIL~PTreLa~Qi~~~l~~l~~~~~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp  187 (1176)
T PRK09401        122 KGKKSYIIFPTRLLVEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTS  187 (1176)
T ss_pred             cCCeEEEEeccHHHHHHHHHHHHHHhhhcCceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECH
Confidence            4678999999999888887777643    3344333  4556677888888889888899999995

>KOG0331|consensus

Probab=90.96  E-value=1.4  Score=34.99  Aligned_cols=72  Identities=14%  Similarity=0.169  Sum_probs=51.3

Q ss_pred             CCCCeeEEehhhhhHHHHHhhcccc----CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-----CCccc-CCccC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVK----EYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-----VAARG-LDIPH  102 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~~G-idi~~  102 (150)
                      ..+.+||-++|++-+..+...+.+.    .++..+++|+.+...+..-   .+.| +.|+|+|+     .+..| +++..
T Consensus       164 ~~P~vLVL~PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~~---l~~g-vdiviaTPGRl~d~le~g~~~l~~  239 (519)
T KOG0331|consen  164 DGPIVLVLAPTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRD---LERG-VDVVIATPGRLIDLLEEGSLNLSR  239 (519)
T ss_pred             CCCeEEEEcCcHHHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHHHH---HhcC-CcEEEeCChHHHHHHHcCCccccc
Confidence            3567999999999888777766542    4568899999876555433   3333 58999995     44444 67778


Q ss_pred             CcEEEE
Q psy17637        103 IRTVVN  108 (150)
Q Consensus       103 ~~~vi~  108 (150)
                      +++++.
T Consensus       240 v~ylVL  245 (519)
T KOG0331|consen  240 VTYLVL  245 (519)
T ss_pred             eeEEEe
Confidence            888773

>KOG0383|consensus

Probab=90.89  E-value=0.29  Score=40.03  Aligned_cols=78  Identities=19%  Similarity=0.217  Sum_probs=64.2

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhc---CCceEEEEcCCCc
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKR---QECRILVATDVAA   95 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~---g~~~vlv~T~~~~   95 (150)
                      ++..|...+......+.+++||..-....+-+-..+...+ ....+.|..+..+|+..+..|..   .....|.+|.+.+
T Consensus       616 k~~~l~~~~~~l~~~ghrvl~~~q~~~~ldlled~~~~~~-~~~r~dG~~~~~~rq~ai~~~n~~~~~~~cfllstra~g  694 (696)
T KOG0383|consen  616 KLTLLLKMLKKLKSSGHRVLIFSQMIHMLDLLEDYLTYEG-KYERIDGPITGPERQAAIDRFNAPGSNQFCFLLSTRAGG  694 (696)
T ss_pred             HHHHHHHHHHHHHhcchhhHHHHHHHHHHHHhHHHHhccC-cceeccCCccchhhhhhccccCCCCccceEEEeeccccc
Confidence            4445556666666788999999999999999999998888 88899999999999999999983   3456889998876


Q ss_pred             cc
Q psy17637         96 RG   97 (150)
Q Consensus        96 ~G   97 (150)
                      .|
T Consensus       695 ~g  696 (696)
T KOG0383|consen  695 LG  696 (696)
T ss_pred             CC
Confidence            54

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=90.80  E-value=2.7  Score=33.00  Aligned_cols=71  Identities=21%  Similarity=0.302  Sum_probs=48.4

Q ss_pred             CCCeeEEehhhhhHHHHHhhcc----ccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CC-----cccCCccCC
Q psy17637         34 VPPALMNLAMQLNAEELANSLT----VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VA-----ARGLDIPHI  103 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~----~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~-----~~Gidi~~~  103 (150)
                      ..++||.++|++-+..+++.+.    ..++.+..++|+.+.....   +.+..+...|+|+|. .+     ...+.+.++
T Consensus       162 ~~~aLil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~---~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l  238 (475)
T PRK01297        162 EPRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQL---KQLEARFCDILVATPGRLLDFNQRGEVHLDMV  238 (475)
T ss_pred             CceEEEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHHHH---HHHhCCCCCEEEECHHHHHHHHHcCCcccccC
Confidence            4579999999998877666554    3467888999987654433   344556778999995 22     223455666


Q ss_pred             cEEE
Q psy17637        104 RTVV  107 (150)
Q Consensus       104 ~~vi  107 (150)
                      .+||
T Consensus       239 ~~lV  242 (475)
T PRK01297        239 EVMV  242 (475)
T ss_pred             ceEE
Confidence            6666

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=90.69  E-value=2.5  Score=32.53  Aligned_cols=71  Identities=18%  Similarity=0.181  Sum_probs=47.9

Q ss_pred             CCCeeEEehhhhhHHHHHhhcc----ccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCC-C-----cccCCccCC
Q psy17637         34 VPPALMNLAMQLNAEELANSLT----VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDV-A-----ARGLDIPHI  103 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~----~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~-~-----~~Gidi~~~  103 (150)
                      ..++||.++|++-+..+++.+.    ..++.+..++|+.+.......   +. ....|+|+|.- +     ...+++..+
T Consensus        83 ~~~~lil~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~---l~-~~~~IlV~TP~~l~~~l~~~~~~l~~v  158 (423)
T PRK04837         83 QPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKV---LE-SGVDILIGTTGRLIDYAKQNHINLGAI  158 (423)
T ss_pred             CceEEEECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHH---hc-CCCCEEEECHHHHHHHHHcCCcccccc
Confidence            3579999999998887655443    347888999998776554433   22 34689999961 1     224566677


Q ss_pred             cEEEE
Q psy17637        104 RTVVN  108 (150)
Q Consensus       104 ~~vi~  108 (150)
                      .++|.
T Consensus       159 ~~lVi  163 (423)
T PRK04837        159 QVVVL  163 (423)
T ss_pred             cEEEE
Confidence            77663

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

Probab=90.67  E-value=1.7  Score=36.74  Aligned_cols=76  Identities=21%  Similarity=0.203  Sum_probs=57.4

Q ss_pred             chhhHHHHHHHHHHhccCCCCCeeEEehhhh----hHHHHHhhccccC--ceEEEecCCCCHHHHHHHHHHhhcCCceEE
Q psy17637         15 KDKEFAGHLVRNLEGANQEVPPALMNLAMQL----NAEELANSLTVKE--YDVLLLHGDMDQSERNSVITKFKRQECRIL   88 (150)
Q Consensus        15 ~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~----~~~~l~~~L~~~~--~~~~~~~~~~~~~~r~~~~~~f~~g~~~vl   88 (150)
                      |...++.-+++.+...  +..++|++.+++.    +++.+.+.+...+  +.+..++|+.++++|+    .+..+...||
T Consensus        98 KTe~FllPIld~~l~~--~~a~AL~lYPtnALa~DQ~~rl~~~~~~~~~~v~~~~y~Gdt~~~~r~----~~~~~pp~Il  171 (851)
T COG1205          98 KTESFLLPILDHLLRD--PSARALLLYPTNALANDQAERLRELISDLPGKVTFGRYTGDTPPEERR----AIIRNPPDIL  171 (851)
T ss_pred             hhHHHHHHHHHHHhhC--cCccEEEEechhhhHhhHHHHHHHHHHhCCCcceeeeecCCCChHHHH----HHHhCCCCEE
Confidence            3445666788888776  5568899999955    6777777776655  7899999999998887    5566778999


Q ss_pred             EEc-CCCcc
Q psy17637         89 VAT-DVAAR   96 (150)
Q Consensus        89 v~T-~~~~~   96 (150)
                      +++ +++..
T Consensus       172 lTNpdMLh~  180 (851)
T COG1205         172 LTNPDMLHY  180 (851)
T ss_pred             EeCHHHHHH
Confidence            998 45443

>KOG0338|consensus

Probab=90.42  E-value=2.5  Score=33.71  Aligned_cols=97  Identities=16%  Similarity=0.172  Sum_probs=63.7

Q ss_pred             hHHHHHHHHHHhcc--CCCCCeeEEehhhhhHHHHHhhcc----ccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEc
Q psy17637         18 EFAGHLVRNLEGAN--QEVPPALMNLAMQLNAEELANSLT----VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVAT   91 (150)
Q Consensus        18 ~~~~~ll~~l~~~~--~~~~~~ivf~~~~~~~~~l~~~L~----~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T   91 (150)
                      .++.-++..|..-+  .+.-++||.|+|++-+-.++...+    .-.+.+...-||++-..++.+++.-    ..|+|+|
T Consensus       234 AF~lPiLERLlYrPk~~~~TRVLVL~PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs~----PDIVIAT  309 (691)
T KOG0338|consen  234 AFALPILERLLYRPKKVAATRVLVLVPTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRSR----PDIVIAT  309 (691)
T ss_pred             hhHHHHHHHHhcCcccCcceeEEEEeccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhhC----CCEEEec
Confidence            34445556555432  245689999999996655544432    2368888999999988888776543    5799999


Q ss_pred             C-------CCcccCCccCCcEEEEecCCCChhHH
Q psy17637         92 D-------VAARGLDIPHIRTVVNYDLARDIDTH  118 (150)
Q Consensus        92 ~-------~~~~Gidi~~~~~vi~~~~~~~~~~~  118 (150)
                      +       --+.++++.++.++|.=....-+.+|
T Consensus       310 PGRlIDHlrNs~sf~ldsiEVLvlDEADRMLeeg  343 (691)
T KOG0338|consen  310 PGRLIDHLRNSPSFNLDSIEVLVLDEADRMLEEG  343 (691)
T ss_pred             chhHHHHhccCCCccccceeEEEechHHHHHHHH
Confidence            6       23567777777777754444434443

>cd01523 RHOD_Lact_B Member of the Rhodanese Homology Domain superfamily

Probab=90.33  E-value=0.48  Score=28.53  Aligned_cols=38  Identities=24%  Similarity=0.241  Sum_probs=31.8

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMD   69 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~   69 (150)
                      .+..+++++|.+-..+...+..|...|+.+..+.||+.
T Consensus        59 ~~~~~ivv~C~~G~rs~~aa~~L~~~G~~~~~l~GG~~   96 (100)
T cd01523          59 PDDQEVTVICAKEGSSQFVAELLAERGYDVDYLAGGMK   96 (100)
T ss_pred             CCCCeEEEEcCCCCcHHHHHHHHHHcCceeEEeCCcHH
Confidence            35678999999877888889999988998888888874

This CD includes predicted proteins with rhodanese-like domains found N-terminal of the metallo-beta-lactamase domain.

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=90.30  E-value=1.8  Score=34.90  Aligned_cols=70  Identities=16%  Similarity=0.199  Sum_probs=48.6

Q ss_pred             CCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-----CCcc--cCCccC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-----VAAR--GLDIPH  102 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~~--Gidi~~  102 (150)
                      ..++||.++|++-+..+++.+..    .++.+..++|+.+...+...+.    +...|+|+|.     .+..  .+++..
T Consensus        84 ~~raLIl~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l~----~~~dIiV~TP~rL~~~l~~~~~~~l~~  159 (572)
T PRK04537         84 DPRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQ----QGVDVIIATPGRLIDYVKQHKVVSLHA  159 (572)
T ss_pred             CceEEEEeCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHHh----CCCCEEEECHHHHHHHHHhccccchhh
Confidence            46899999999988877765543    4678899999988776654443    3568999994     2221  245556


Q ss_pred             CcEEE
Q psy17637        103 IRTVV  107 (150)
Q Consensus       103 ~~~vi  107 (150)
                      +.++|
T Consensus       160 v~~lV  164 (572)
T PRK04537        160 CEICV  164 (572)
T ss_pred             eeeeE
Confidence            66555

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

Probab=89.57  E-value=3.2  Score=27.07  Aligned_cols=72  Identities=24%  Similarity=0.322  Sum_probs=47.6

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHH-HHHHHHHHhhcCCceEEEEcC-CC-----cccCCcc
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQS-ERNSVITKFKRQECRILVATD-VA-----ARGLDIP  101 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~-~r~~~~~~f~~g~~~vlv~T~-~~-----~~Gidi~  101 (150)
                      ...++++.+++++-++.....+..    .++.+..++++.+.. +....+    .+...|+|+|. .+     ....++.
T Consensus        43 ~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilv~T~~~l~~~~~~~~~~~~  118 (169)
T PF00270_consen   43 KDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLHGGQSISEDQREVL----SNQADILVTTPEQLLDLISNGKINIS  118 (169)
T ss_dssp             SSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEESTTSCHHHHHHHHH----HTTSSEEEEEHHHHHHHHHTTSSTGT
T ss_pred             CCceEEEEeecccccccccccccccccccccccccccccccccccccccc----cccccccccCcchhhccccccccccc
Confidence            345899999999888877766654    356788899988754 333333    56678999994 22     1223556


Q ss_pred             CCcEEEE
Q psy17637        102 HIRTVVN  108 (150)
Q Consensus       102 ~~~~vi~  108 (150)
                      .+++||.
T Consensus       119 ~~~~iVi  125 (169)
T PF00270_consen  119 RLSLIVI  125 (169)
T ss_dssp             TESEEEE
T ss_pred             cceeecc
Confidence            6777663

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

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

Probab=88.77  E-value=2.1  Score=35.67  Aligned_cols=65  Identities=14%  Similarity=0.110  Sum_probs=46.0

Q ss_pred             HHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhcccc---CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC
Q psy17637         21 GHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVK---EYDVLLLHGDMDQSERNSVITKFKRQECRILVATD   92 (150)
Q Consensus        21 ~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~---~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~   92 (150)
                      .-+++.+.+.  +..++|+.++|++-+......|...   ++.+..++|+.+.+++..+    +. ...|+|+|+
T Consensus        70 LPiL~~l~~~--~~~~aL~l~PtraLa~q~~~~l~~l~~~~i~v~~~~Gdt~~~~r~~i----~~-~~~IivtTP  137 (742)
T TIGR03817        70 LPVLSALADD--PRATALYLAPTKALAADQLRAVRELTLRGVRPATYDGDTPTEERRWA----RE-HARYVLTNP  137 (742)
T ss_pred             HHHHHHHhhC--CCcEEEEEcChHHHHHHHHHHHHHhccCCeEEEEEeCCCCHHHHHHH----hc-CCCEEEECh
Confidence            3445555443  5668999999999888777766543   5778899999987766433    22 358999995

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.

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=88.27  E-value=7  Score=32.23  Aligned_cols=68  Identities=18%  Similarity=0.044  Sum_probs=46.5

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhc----cccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEE
Q psy17637         32 QEVPPALMNLAMQLNAEELANSL----TVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV  106 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L----~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~v  106 (150)
                      ..+.+++|.++|+.-+...++.+    ...|+++.++.|++++.+++...      ...|+++|.. +.|.|.-.-+.+
T Consensus       142 l~G~~v~VvTptreLA~qdae~~~~l~~~lGlsv~~i~gg~~~~~r~~~y------~~dIvygT~~-e~~FDyLrd~~~  213 (656)
T PRK12898        142 LAGLPVHVITVNDYLAERDAELMRPLYEALGLTVGCVVEDQSPDERRAAY------GADITYCTNK-ELVFDYLRDRLA  213 (656)
T ss_pred             hcCCeEEEEcCcHHHHHHHHHHHHHHHhhcCCEEEEEeCCCCHHHHHHHc------CCCEEEECCC-chhhhhcccccc
Confidence            45789999999988776555444    44589999999999877665432      3578888842 336665443433

>smart00450 RHOD Rhodanese Homology Domain

Probab=88.23  E-value=0.47  Score=27.92  Aligned_cols=38  Identities=18%  Similarity=0.198  Sum_probs=31.8

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCce-EEEecCCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYD-VLLLHGDMD   69 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~~   69 (150)
                      .+..++|+||.+-..+..++..|...|++ +..+.|++.
T Consensus        54 ~~~~~iv~~c~~g~~a~~~~~~l~~~G~~~v~~l~GG~~   92 (100)
T smart00450       54 DKDKPVVVYCRSGNRSAKAAWLLRELGFKNVYLLDGGYK   92 (100)
T ss_pred             CCCCeEEEEeCCCcHHHHHHHHHHHcCCCceEEecCCHH
Confidence            45678999999888888899999888887 888888864

An alpha beta fold found duplicated in the Rhodanese protein. The the Cysteine containing enzymatically active version of the domain is also found in the CDC25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and stress proteins such as Senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions with a loss of the cysteine are also seen in Dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases. These are likely to play a role in protein interactions.

>KOG0335|consensus

Probab=87.29  E-value=4.3  Score=32.00  Aligned_cols=70  Identities=23%  Similarity=0.399  Sum_probs=48.7

Q ss_pred             CCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-----CCccc-CCccCC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-----VAARG-LDIPHI  103 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~~G-idi~~~  103 (150)
                      .+.++|..+|++-++.+++.-..    ..+++...+|+.+  .+.+.  .+....+.|+|||.     .+++| +.++++
T Consensus       152 ~P~~lIlapTReL~~Qi~nea~k~~~~s~~~~~~~ygg~~--~~~q~--~~~~~gcdIlvaTpGrL~d~~e~g~i~l~~~  227 (482)
T KOG0335|consen  152 YPRALILAPTRELVDQIYNEARKFSYLSGMKSVVVYGGTD--LGAQL--RFIKRGCDILVATPGRLKDLIERGKISLDNC  227 (482)
T ss_pred             CCceEEEeCcHHHhhHHHHHHHhhcccccceeeeeeCCcc--hhhhh--hhhccCccEEEecCchhhhhhhcceeehhhC
Confidence            47899999999999988876543    3677888888833  22222  34445678999995     45555 556677


Q ss_pred             cEEE
Q psy17637        104 RTVV  107 (150)
Q Consensus       104 ~~vi  107 (150)
                      .+++
T Consensus       228 k~~v  231 (482)
T KOG0335|consen  228 KFLV  231 (482)
T ss_pred             cEEE
Confidence            7655

>cd01529 4RHOD_Repeats Member of the Rhodanese Homology Domain superfamily

Probab=86.98  E-value=1  Score=26.89  Aligned_cols=38  Identities=21%  Similarity=0.098  Sum_probs=29.9

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCc-eEEEecCCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEY-DVLLLHGDMD   69 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~-~~~~~~~~~~   69 (150)
                      .+..++|+||++-..+...+..|...|+ ++..+.|++.
T Consensus        54 ~~~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~l~GG~~   92 (96)
T cd01529          54 GRATRYVLTCDGSLLARFAAQELLALGGKPVALLDGGTS   92 (96)
T ss_pred             CCCCCEEEEeCChHHHHHHHHHHHHcCCCCEEEeCCCHH
Confidence            3567899999987777888888887787 4777888863

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. Only the second and most of the fourth repeats contain the putative catalytic Cys residue. This CD aligns the 1st , 2nd, 3rd, and 4th repeats.

>cd01520 RHOD_YbbB Member of the Rhodanese Homology Domain superfamily

Probab=86.91  E-value=1.3  Score=28.14  Aligned_cols=38  Identities=29%  Similarity=0.298  Sum_probs=29.8

Q ss_pred             CCCCCeeEEeh-hhhhHHHHHhhccccCceEEEecCCCC
Q psy17637         32 QEVPPALMNLA-MQLNAEELANSLTVKEYDVLLLHGDMD   69 (150)
Q Consensus        32 ~~~~~~ivf~~-~~~~~~~l~~~L~~~~~~~~~~~~~~~   69 (150)
                      .+..+++|||. +-..+...+..|...|+.+..+.||+.
T Consensus        84 ~~~~~vvvyC~~~G~rs~~a~~~L~~~G~~v~~L~GG~~  122 (128)
T cd01520          84 ERDPKLLIYCARGGMRSQSLAWLLESLGIDVPLLEGGYK  122 (128)
T ss_pred             CCCCeEEEEeCCCCccHHHHHHHHHHcCCceeEeCCcHH
Confidence            56778999996 455666777777777888889999964

This CD includes several putative ATP /GTP binding proteins including E. coli YbbB.

>PTZ00110 helicase; Provisional

Probab=86.54  E-value=2.8  Score=33.62  Aligned_cols=70  Identities=14%  Similarity=0.179  Sum_probs=46.6

Q ss_pred             CCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-----CCccc-CCccCC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-----VAARG-LDIPHI  103 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~~G-idi~~~  103 (150)
                      ...+||.++|++-+..+.+.+..    .++.+..++|+.+.......   +.. ...|+|+|+     .+..+ +++..+
T Consensus       203 gp~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~~~---l~~-~~~IlVaTPgrL~d~l~~~~~~l~~v  278 (545)
T PTZ00110        203 GPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYA---LRR-GVEILIACPGRLIDFLESNVTNLRRV  278 (545)
T ss_pred             CcEEEEECChHHHHHHHHHHHHHHhcccCccEEEEeCCCCHHHHHHH---HHc-CCCEEEECHHHHHHHHHcCCCChhhC
Confidence            45689999999988877666654    35678888998876554333   233 368999995     23333 456667


Q ss_pred             cEEE
Q psy17637        104 RTVV  107 (150)
Q Consensus       104 ~~vi  107 (150)
                      .+||
T Consensus       279 ~~lV  282 (545)
T PTZ00110        279 TYLV  282 (545)
T ss_pred             cEEE
Confidence            7665

>KOG0389|consensus

Probab=86.43  E-value=7.8  Score=32.61  Aligned_cols=70  Identities=20%  Similarity=0.226  Sum_probs=46.7

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhh---HHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcC--CceEEEEcCCCcc
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLN---AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQ--ECRILVATDVAAR   96 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~---~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g--~~~vlv~T~~~~~   96 (150)
                      ..+..|..... .+|-||.|++---   .-++..++.  .+++..|||.  +.+|+++-..+..+  .++|||+|-.+..
T Consensus       437 aFlayLkq~g~-~gpHLVVvPsSTleNWlrEf~kwCP--sl~Ve~YyGS--q~ER~~lR~~i~~~~~~ydVllTTY~la~  511 (941)
T KOG0389|consen  437 AFLAYLKQIGN-PGPHLVVVPSSTLENWLREFAKWCP--SLKVEPYYGS--QDERRELRERIKKNKDDYDVLLTTYNLAA  511 (941)
T ss_pred             HHHHHHHHcCC-CCCcEEEecchhHHHHHHHHHHhCC--ceEEEeccCc--HHHHHHHHHHHhccCCCccEEEEEeeccc
Confidence            34445555533 5677777766321   224444443  6789999998  78999998888876  6789999954443

>cd01449 TST_Repeat_2 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain

Probab=86.41  E-value=1.3  Score=27.34  Aligned_cols=36  Identities=22%  Similarity=0.250  Sum_probs=29.3

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCce-EEEecCCC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYD-VLLLHGDM   68 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~   68 (150)
                      +..++|+||++-..+..++..|...|++ +..+.|++
T Consensus        77 ~~~~iv~yc~~g~~s~~~~~~l~~~G~~~v~~l~GG~  113 (118)
T cd01449          77 PDKPVIVYCGSGVTACVLLLALELLGYKNVRLYDGSW  113 (118)
T ss_pred             CCCCEEEECCcHHHHHHHHHHHHHcCCCCeeeeCChH
Confidence            5678999999977788888888888874 67777875

TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue.

>cd01534 4RHOD_Repeat_3 Member of the Rhodanese Homology Domain superfamily, repeat 3

Probab=85.93  E-value=0.85  Score=27.17  Aligned_cols=37  Identities=16%  Similarity=0.201  Sum_probs=29.0

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMD   69 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~   69 (150)
                      ...++++||.+-..+...+..|...|+++..+.|++.
T Consensus        55 ~~~~iv~~c~~G~rs~~aa~~L~~~G~~v~~l~GG~~   91 (95)
T cd01534          55 RGARIVLADDDGVRADMTASWLAQMGWEVYVLEGGLA   91 (95)
T ss_pred             CCCeEEEECCCCChHHHHHHHHHHcCCEEEEecCcHH
Confidence            3567999999876777778888888888777888863

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 3rd repeat which does not contain the putative catalytic Cys residue.

>TIGR00696 wecB_tagA_cpsF bacterial polymer biosynthesis proteins, WecB/TagA/CpsF family

Probab=85.92  E-value=7.4  Score=26.43  Aligned_cols=56  Identities=18%  Similarity=0.263  Sum_probs=41.5

Q ss_pred             CCCCeeEEehhhhhHHHHHhhcccc--CceEEEecCCCCHHHHHHHHHHhhcCCceEE
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVK--EYDVLLLHGDMDQSERNSVITKFKRQECRIL   88 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vl   88 (150)
                      .+.++-++-.+...++.+++.|+..  ++.+.-.||..++++...+++..+....++|
T Consensus        47 ~~~~vfllG~~~~v~~~~~~~l~~~yP~l~i~g~~g~f~~~~~~~i~~~I~~s~~dil  104 (177)
T TIGR00696        47 EKLPIFLYGGKPDVLQQLKVKLIKEYPKLKIVGAFGPLEPEERKAALAKIARSGAGIV  104 (177)
T ss_pred             cCCeEEEECCCHHHHHHHHHHHHHHCCCCEEEEECCCCChHHHHHHHHHHHHcCCCEE
Confidence            3456666667778888888888754  6666666999988888888888887665544

The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=85.72  E-value=9.1  Score=32.04  Aligned_cols=55  Identities=18%  Similarity=0.113  Sum_probs=41.6

Q ss_pred             CCCCeeEEehhhhhHHHHHhh----ccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCC
Q psy17637         33 EVPPALMNLAMQLNAEELANS----LTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDV   93 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~----L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~   93 (150)
                      .+.++.|.++|..-+...++.    +...|+++.++.|+++++++.....      ..|+++|..
T Consensus        96 ~G~~V~VvTpt~~LA~qdae~~~~l~~~LGLsv~~i~g~~~~~~r~~~y~------~dIvyGT~~  154 (745)
T TIGR00963        96 TGKGVHVVTVNDYLAQRDAEWMGQVYRFLGLSVGLILSGMSPEERREAYA------CDITYGTNN  154 (745)
T ss_pred             hCCCEEEEcCCHHHHHHHHHHHHHHhccCCCeEEEEeCCCCHHHHHHhcC------CCEEEECCC
Confidence            466899999997766555444    4456899999999999887765542      589999965

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.

>PRK13766 Hef nuclease; Provisional

Probab=85.57  E-value=7.6  Score=32.49  Aligned_cols=76  Identities=13%  Similarity=0.224  Sum_probs=48.7

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCC-C-----cccCCcc
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDV-A-----ARGLDIP  101 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~-~-----~~Gidi~  101 (150)
                      .+..++|+.++++.-++..++.+..    .+.++..++|+.+..+|.....   .  ..|+|+|.- +     ..-+++.
T Consensus        56 ~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~r~~~~~---~--~~iiv~T~~~l~~~l~~~~~~~~  130 (773)
T PRK13766         56 KKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTGEVSPEKRAELWE---K--AKVIVATPQVIENDLIAGRISLE  130 (773)
T ss_pred             hCCCeEEEEeCcHHHHHHHHHHHHHHhCCCCceEEEEeCCCCHHHHHHHHh---C--CCEEEECHHHHHHHHHcCCCChh
Confidence            3567999999998777555444433    2347888999998887765443   2  468888852 2     2234555


Q ss_pred             CCcEEEEecCC
Q psy17637        102 HIRTVVNYDLA  112 (150)
Q Consensus       102 ~~~~vi~~~~~  112 (150)
                      .+++||.=...
T Consensus       131 ~~~liVvDEaH  141 (773)
T PRK13766        131 DVSLLIFDEAH  141 (773)
T ss_pred             hCcEEEEECCc
Confidence            66776644333

>cd01448 TST_Repeat_1 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain

Probab=84.51  E-value=1.6  Score=27.25  Aligned_cols=38  Identities=13%  Similarity=0.025  Sum_probs=29.5

Q ss_pred             CCCCCeeEEehh-hhhHHHHHhhccccCce-EEEecCCCC
Q psy17637         32 QEVPPALMNLAM-QLNAEELANSLTVKEYD-VLLLHGDMD   69 (150)
Q Consensus        32 ~~~~~~ivf~~~-~~~~~~l~~~L~~~~~~-~~~~~~~~~   69 (150)
                      .+..++++||.+ -..+...+..|...|++ +..+.|++.
T Consensus        77 ~~~~~vv~~c~~g~~~a~~~~~~l~~~G~~~v~~l~GG~~  116 (122)
T cd01448          77 SNDDTVVVYDDGGGFFAARAWWTLRYFGHENVRVLDGGLQ  116 (122)
T ss_pred             CCCCEEEEECCCCCccHHHHHHHHHHcCCCCEEEecCCHH
Confidence            356789999988 47777788888888875 778888863

TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it is believed to be involved in protein interaction.

>cd01533 4RHOD_Repeat_2 Member of the Rhodanese Homology Domain superfamily, repeat 2

Probab=84.34  E-value=1.5  Score=26.81  Aligned_cols=37  Identities=22%  Similarity=0.108  Sum_probs=29.1

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCce--EEEecCCCC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYD--VLLLHGDMD   69 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~--~~~~~~~~~   69 (150)
                      +..++++||.+-......+..|...|++  +..+.|+++
T Consensus        65 ~~~~ivv~C~~G~rs~~a~~~L~~~G~~~~v~~l~gG~~  103 (109)
T cd01533          65 PRTPIVVNCAGRTRSIIGAQSLINAGLPNPVAALRNGTQ  103 (109)
T ss_pred             CCCeEEEECCCCchHHHHHHHHHHCCCCcceeEecCCHH
Confidence            4568999998876677778888888884  778889874

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 2nd repeat which does contain the putative catalytic Cys residue.

>cd01518 RHOD_YceA Member of the Rhodanese Homology Domain superfamily

Probab=84.27  E-value=0.82  Score=27.57  Aligned_cols=38  Identities=18%  Similarity=0.213  Sum_probs=28.9

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCce-EEEecCCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYD-VLLLHGDMD   69 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~~   69 (150)
                      .+..+++|||.+-..+...+..|...|+. +..+.||+.
T Consensus        59 ~~~~~ivvyC~~G~rs~~a~~~L~~~G~~~v~~l~GG~~   97 (101)
T cd01518          59 LKGKKVLMYCTGGIRCEKASAYLKERGFKNVYQLKGGIL   97 (101)
T ss_pred             cCCCEEEEECCCchhHHHHHHHHHHhCCcceeeechhHH
Confidence            35668999998866667777788888885 777888863

This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins.

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

Probab=84.19  E-value=3.7  Score=33.28  Aligned_cols=57  Identities=14%  Similarity=0.237  Sum_probs=47.6

Q ss_pred             CCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEc
Q psy17637         35 PPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVAT   91 (150)
Q Consensus        35 ~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T   91 (150)
                      +-+||.++=..-.+.=...|+..|+.+.++++.++.+++..++..+..|.+++|.-+
T Consensus        58 G~TLVVSPLiSLM~DQV~~l~~~Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyis  114 (590)
T COG0514          58 GLTLVVSPLISLMKDQVDQLEAAGIRAAYLNSTLSREERQQVLNQLKSGQLKLLYIS  114 (590)
T ss_pred             CCEEEECchHHHHHHHHHHHHHcCceeehhhcccCHHHHHHHHHHHhcCceeEEEEC
Confidence            467888877766665556677789999999999999999999999999999988444

>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli

Probab=83.86  E-value=9.6  Score=25.60  Aligned_cols=68  Identities=18%  Similarity=0.237  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhcccc--CceEE-EecCCCCHHHHHHHHHHhhcCCceEEE
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVK--EYDVL-LLHGDMDQSERNSVITKFKRQECRILV   89 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~--~~~~~-~~~~~~~~~~r~~~~~~f~~g~~~vlv   89 (150)
                      .+..++.....   .+.++-++-.+.+.++.+++.|+..  ++.+. ..+|.+++++...+++..+....++++
T Consensus        36 l~~~l~~~~~~---~~~~ifllG~~~~~~~~~~~~l~~~yP~l~ivg~~~g~f~~~~~~~i~~~I~~~~pdiv~  106 (172)
T PF03808_consen   36 LFPDLLRRAEQ---RGKRIFLLGGSEEVLEKAAANLRRRYPGLRIVGYHHGYFDEEEEEAIINRINASGPDIVF  106 (172)
T ss_pred             HHHHHHHHHHH---cCCeEEEEeCCHHHHHHHHHHHHHHCCCeEEEEecCCCCChhhHHHHHHHHHHcCCCEEE
Confidence            34444443333   3557777778888889898888776  66666 566778888999999999887666553

Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=83.54  E-value=14  Score=31.70  Aligned_cols=57  Identities=9%  Similarity=-0.041  Sum_probs=45.4

Q ss_pred             CCCCCeeEEehh----hhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCC
Q psy17637         32 QEVPPALMNLAM----QLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVA   94 (150)
Q Consensus        32 ~~~~~~ivf~~~----~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~   94 (150)
                      ..+.++-|.+.+    +..++++...+...|+++.++.+++++++|+.+..      .+|+.+|...
T Consensus       121 l~G~~VhvvT~ndyLA~RD~e~m~~l~~~lGl~v~~i~~~~~~~err~~Y~------~dI~YGT~~e  181 (913)
T PRK13103        121 LSGKGVHVVTVNDYLARRDANWMRPLYEFLGLSVGIVTPFQPPEEKRAAYA------ADITYGTNNE  181 (913)
T ss_pred             HcCCCEEEEeCCHHHHHHHHHHHHHHhcccCCEEEEECCCCCHHHHHHHhc------CCEEEEcccc
Confidence            467788888877    44567777777888999999999999999997766      6788888543

>cd01521 RHOD_PspE2 Member of the Rhodanese Homology Domain superfamily

Probab=83.40  E-value=1.4  Score=27.11  Aligned_cols=38  Identities=16%  Similarity=0.062  Sum_probs=29.4

Q ss_pred             CCCCCeeEEehhhh--hHHHHHhhccccCceEEEecCCCC
Q psy17637         32 QEVPPALMNLAMQL--NAEELANSLTVKEYDVLLLHGDMD   69 (150)
Q Consensus        32 ~~~~~~ivf~~~~~--~~~~l~~~L~~~~~~~~~~~~~~~   69 (150)
                      .+..++++||++..  .+..++..|...|+.+..+.|++.
T Consensus        62 ~~~~~vvvyc~~g~~~~s~~~a~~l~~~G~~v~~l~GG~~  101 (110)
T cd01521          62 DKEKLFVVYCDGPGCNGATKAALKLAELGFPVKEMIGGLD  101 (110)
T ss_pred             CCCCeEEEEECCCCCchHHHHHHHHHHcCCeEEEecCCHH
Confidence            45678999998753  577778888888888888888863

This CD includes the putative rhodanese-like protein, Psp2, of Yersinia pestis biovar Medievalis and other similar uncharacterized proteins.

>cd01526 RHOD_ThiF Member of the Rhodanese Homology Domain superfamily

Probab=83.06  E-value=1.1  Score=28.22  Aligned_cols=37  Identities=11%  Similarity=0.038  Sum_probs=31.0

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCc--eEEEecCCCC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEY--DVLLLHGDMD   69 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~--~~~~~~~~~~   69 (150)
                      ...++++||.+-..+...+..|...|+  .+..+.|++.
T Consensus        71 ~~~~ivv~C~~G~rs~~aa~~L~~~G~~~~v~~l~GG~~  109 (122)
T cd01526          71 KDSPIYVVCRRGNDSQTAVRKLKELGLERFVRDIIGGLK  109 (122)
T ss_pred             CCCcEEEECCCCCcHHHHHHHHHHcCCccceeeecchHH
Confidence            467899999987788888889988888  5888999873

This CD includes several putative molybdopterin synthase sulfurylases including the molybdenum cofactor biosynthetic protein (CnxF) of Aspergillus nidulans and the molybdenum cofactor synthesis protein 3 (MOCS3) of Homo sapiens. These rhodanese-like domains are found C-terminal of the ThiF and MoeZ_MoeB domains.

>PF12683 DUF3798: Protein of unknown function (DUF3798); InterPro: IPR024258 This entry represents functionally uncharacterised proteins that are found in bacteria

Probab=83.02  E-value=2.3  Score=30.88  Aligned_cols=103  Identities=20%  Similarity=0.249  Sum_probs=60.8

Q ss_pred             eEEEeecchhhHHHHHHHHHHhc-cCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCce
Q psy17637          8 AYTLVTDKDKEFAGHLVRNLEGA-NQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECR   86 (150)
Q Consensus         8 ~~~~~~~~~~~~~~~ll~~l~~~-~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~   86 (150)
                      ++...+..-....+..+..+... ..+.-++||++....-.-...+..++....+.++-|.+.  +--.+++..    .+
T Consensus        35 ~h~tyPdnf~~e~EttIskI~~lAdDp~mKaIVv~q~vpGt~~af~kIkekRpDIl~ia~~~~--EDp~~i~~~----aD  108 (275)
T PF12683_consen   35 KHVTYPDNFMSEQETTISKIVSLADDPDMKAIVVSQAVPGTAEAFRKIKEKRPDILLIAGEPH--EDPEVISSA----AD  108 (275)
T ss_dssp             EEEE--TTGGGCHHHHHHHHHGGGG-TTEEEEEEE-SS---HHHHHHHHHH-TTSEEEESS----S-HHHHHHH----SS
T ss_pred             EEEeCCCcccchHHHHHHHHHHhccCCCccEEEEeCCCcchHHHHHHHHhcCCCeEEEcCCCc--CCHHHHhhc----cC
Confidence            34444443233355677777663 346788999999888777777777777667777877743  223333333    46


Q ss_pred             EEEEcCCCcccCCcc------CCcEEEEecCCCChh
Q psy17637         87 ILVATDVAARGLDIP------HIRTVVNYDLARDID  116 (150)
Q Consensus        87 vlv~T~~~~~Gidi~------~~~~vi~~~~~~~~~  116 (150)
                      +.+.++...+|-.++      ++...+++++|..++
T Consensus       109 i~~~~D~~~~G~~i~~~Ak~mGAktFVh~sfprhms  144 (275)
T PF12683_consen  109 IVVNPDEISRGYTIVWAAKKMGAKTFVHYSFPRHMS  144 (275)
T ss_dssp             EEEE--HHHHHHHHHHHHHHTT-S-EEEEEETTGGG
T ss_pred             eEeccchhhccHHHHHHHHHcCCceEEEEechhhcc
Confidence            888899999988774      667899999999766

They are typically between 247 and 417 amino acids in length. Most of the proteins in this entry have an N-terminal lipoprotein attachment site. These proteins have distant similarity to periplasmic ligand binding families suggesting that this family has a similar role.; PDB: 3QI7_A.

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=82.84  E-value=8.7  Score=34.77  Aligned_cols=71  Identities=18%  Similarity=0.251  Sum_probs=49.1

Q ss_pred             CCCeeEEehhhhhHHHHHhhccc----------------cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-----
Q psy17637         34 VPPALMNLAMQLNAEELANSLTV----------------KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-----   92 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~----------------~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----   92 (150)
                      ..++|+.+++++-+..+.+.|+.                .++.+...||+.+.++|.+.++    ....|||+|.     
T Consensus        37 ~~raLYISPLKALa~Dv~~~L~~pl~~i~~~~~~~g~~~~~i~V~vrtGDt~~~eR~rll~----~ppdILVTTPEsL~~  112 (1490)
T PRK09751         37 TSRILYISPIKALGTDVQRNLQIPLKGIADERRRRGETEVNLRVGIRTGDTPAQERSKLTR----NPPDILITTPESLYL  112 (1490)
T ss_pred             CCEEEEEeChHHHHHHHHHHHHHHHHhhhhhhhhcccccCceEEEEEECCCCHHHHHHHhc----CCCCEEEecHHHHHH
Confidence            46799999999877766665531                3678999999999988876433    3468999994     


Q ss_pred             CCc-cc-CCccCCcEEEE
Q psy17637         93 VAA-RG-LDIPHIRTVVN  108 (150)
Q Consensus        93 ~~~-~G-idi~~~~~vi~  108 (150)
                      .+. .+ ..+.++.+||.
T Consensus       113 LLtsk~r~~L~~Vr~VIV  130 (1490)
T PRK09751        113 MLTSRARETLRGVETVII  130 (1490)
T ss_pred             HHhhhhhhhhccCCEEEE
Confidence            111 12 24567777763

>KOG0350|consensus

Probab=82.55  E-value=6.3  Score=31.39  Aligned_cols=88  Identities=19%  Similarity=0.180  Sum_probs=56.6

Q ss_pred             HHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHH-HHHHHHHHhhcCCceEEEEcC---
Q psy17637         21 GHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQS-ERNSVITKFKRQECRILVATD---   92 (150)
Q Consensus        21 ~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~-~r~~~~~~f~~g~~~vlv~T~---   92 (150)
                      .-+++.+-.-.-+.-++||.+++++-+-.++..|..    .|+.+..+.|.-+-+ +..+....-....++|||+|+   
T Consensus       202 iPIVQ~L~~R~v~~LRavVivPtr~L~~QV~~~f~~~~~~tgL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRL  281 (620)
T KOG0350|consen  202 IPIVQLLSSRPVKRLRAVVIVPTRELALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRL  281 (620)
T ss_pred             hHHHHHHccCCccceEEEEEeeHHHHHHHHHHHHHHhccCCceEEEecccccchHHHHHHHhcCCCccccceEEcCchHH
Confidence            346666655445567899999999987777766643    477777777764322 222222222334458999996   


Q ss_pred             ----CCcccCCccCCcEEEE
Q psy17637         93 ----VAARGLDIPHIRTVVN  108 (150)
Q Consensus        93 ----~~~~Gidi~~~~~vi~  108 (150)
                          ....|+++..+.++|.
T Consensus       282 VDHl~~~k~f~Lk~LrfLVI  301 (620)
T KOG0350|consen  282 VDHLNNTKSFDLKHLRFLVI  301 (620)
T ss_pred             HHhccCCCCcchhhceEEEe
Confidence                2256888888887664

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

Probab=82.52  E-value=8.6  Score=30.60  Aligned_cols=80  Identities=19%  Similarity=0.231  Sum_probs=53.6

Q ss_pred             CCCeeEEehhhhh----HHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC------CCcccCCccCC
Q psy17637         34 VPPALMNLAMQLN----AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD------VAARGLDIPHI  103 (150)
Q Consensus        34 ~~~~ivf~~~~~~----~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~------~~~~Gidi~~~  103 (150)
                      ++++|+-.+|+.-    ++.+.+.+.-..-.++.++|..++++|...+..     .+|+|+|+      ..+--+|+.++
T Consensus        58 ~~kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~i~~ltGev~p~~R~~~w~~-----~kVfvaTPQvveNDl~~Grid~~dv  132 (542)
T COG1111          58 GGKVLFLAPTKPLVLQHAEFCRKVTGIPEDEIAALTGEVRPEEREELWAK-----KKVFVATPQVVENDLKAGRIDLDDV  132 (542)
T ss_pred             CCeEEEecCCchHHHHHHHHHHHHhCCChhheeeecCCCChHHHHHHHhh-----CCEEEeccHHHHhHHhcCccChHHc
Confidence            4478888899764    445555554445568899999999999866433     36888985      22333788888


Q ss_pred             cEEEEecCCCChhHH
Q psy17637        104 RTVVNYDLARDIDTH  118 (150)
Q Consensus       104 ~~vi~~~~~~~~~~~  118 (150)
                      .++|+=.......+|
T Consensus       133 ~~lifDEAHRAvGny  147 (542)
T COG1111         133 SLLIFDEAHRAVGNY  147 (542)
T ss_pred             eEEEechhhhccCcc
Confidence            888864444444433

>cd01528 RHOD_2 Member of the Rhodanese Homology Domain superfamily, subgroup 2

Probab=82.37  E-value=1.3  Score=26.60  Aligned_cols=37  Identities=16%  Similarity=0.158  Sum_probs=29.2

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCce-EEEecCCCC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYD-VLLLHGDMD   69 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~~   69 (150)
                      +..++++||++-..+...+..|...|+. +..+.|++.
T Consensus        57 ~~~~vv~~c~~g~rs~~~~~~l~~~G~~~v~~l~GG~~   94 (101)
T cd01528          57 PDKDIVVLCHHGGRSMQVAQWLLRQGFENVYNLQGGID   94 (101)
T ss_pred             CCCeEEEEeCCCchHHHHHHHHHHcCCccEEEecCCHH
Confidence            4678999999877778888888877874 778888864

Subgroup 2 includes uncharacterized putative rhodanese-related domains.

>cd01444 GlpE_ST GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily

Probab=82.27  E-value=2.4  Score=24.97  Aligned_cols=37  Identities=19%  Similarity=0.240  Sum_probs=30.1

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCce-EEEecCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYD-VLLLHGDM   68 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~   68 (150)
                      .+..+++++|.+-..+...+..|...|+. +..+.|++
T Consensus        54 ~~~~~ivv~c~~g~~s~~a~~~l~~~G~~~v~~l~gG~   91 (96)
T cd01444          54 DRDRPVVVYCYHGNSSAQLAQALREAGFTDVRSLAGGF   91 (96)
T ss_pred             CCCCCEEEEeCCCChHHHHHHHHHHcCCceEEEcCCCH
Confidence            46678999999888888888888888874 66777775

Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a catalytically active cysteine.

>cd01447 Polysulfide_ST Polysulfide-sulfurtransferase - Rhodanese Homology Domain

Probab=82.15  E-value=0.89  Score=27.27  Aligned_cols=36  Identities=17%  Similarity=0.157  Sum_probs=28.1

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCce-EEEecCCC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYD-VLLLHGDM   68 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~   68 (150)
                      +..+++|||.+-..+...+..|...|+. +..+.|++
T Consensus        60 ~~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~l~Gg~   96 (103)
T cd01447          60 EDKPFVFYCASGWRSALAGKTLQDMGLKPVYNIEGGF   96 (103)
T ss_pred             CCCeEEEEcCCCCcHHHHHHHHHHcChHHhEeecCcH
Confidence            5678999998866677778888877876 77777875

This domain is believed to serve as a polysulfide binding and transferase domain in anaerobic gram-negative bacteria, functioning in oxidative phosphorylation with polysulfide-sulfur as a terminal electron acceptor. The active site contains the same conserved cysteine that is the catalytic residue in other Rhodanese Homology Domain proteins.

>cd01519 RHOD_HSP67B2 Member of the Rhodanese Homology Domain superfamily

Probab=81.99  E-value=1.2  Score=26.93  Aligned_cols=36  Identities=11%  Similarity=0.058  Sum_probs=28.6

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCce-EEEecCCC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYD-VLLLHGDM   68 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~   68 (150)
                      +..++++||.+-..+...+..|...|++ +..+.|++
T Consensus        65 ~~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~~~Gg~  101 (106)
T cd01519          65 KDKELIFYCKAGVRSKAAAELARSLGYENVGNYPGSW  101 (106)
T ss_pred             CCCeEEEECCCcHHHHHHHHHHHHcCCccceecCCcH
Confidence            4678999999977788888888888875 66677775

This CD includes the heat shock protein 67B2 of Drosophila melanogaster and other similar proteins, many of which are uncharacterized.

>cd01527 RHOD_YgaP Member of the Rhodanese Homology Domain superfamily

Probab=81.68  E-value=1.8  Score=25.81  Aligned_cols=37  Identities=11%  Similarity=0.216  Sum_probs=28.9

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCc-eEEEecCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEY-DVLLLHGDM   68 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~-~~~~~~~~~   68 (150)
                      ....++++||++-..+...+..|...|+ .+..+.|++
T Consensus        52 ~~~~~iv~~c~~g~~s~~~~~~L~~~g~~~v~~l~gG~   89 (99)
T cd01527          52 VGANAIIFHCRSGMRTQQNAERLAAISAGEAYVLEGGL   89 (99)
T ss_pred             CCCCcEEEEeCCCchHHHHHHHHHHcCCccEEEeeCCH
Confidence            3467899999997777888888877666 566788885

This CD includes Escherichia coli YgaP, and similar uncharacterized putative rhodanese-related sulfurtransferases.

>KOG0348|consensus

Probab=81.15  E-value=7.8  Score=31.23  Aligned_cols=101  Identities=16%  Similarity=0.224  Sum_probs=57.4

Q ss_pred             hHHHHHHHHHHhccC-----CCCCeeEEehhhhhHHHHHhhcccc---Cce--EEEecCCCCHHHHHHHHHHhhcCCceE
Q psy17637         18 EFAGHLVRNLEGANQ-----EVPPALMNLAMQLNAEELANSLTVK---EYD--VLLLHGDMDQSERNSVITKFKRQECRI   87 (150)
Q Consensus        18 ~~~~~ll~~l~~~~~-----~~~~~ivf~~~~~~~~~l~~~L~~~---~~~--~~~~~~~~~~~~r~~~~~~f~~g~~~v   87 (150)
                      ..+.-+++.|.....     .+.=++|.++|++-|..+++.+...   -..  ...+-||   +.|..--.+.+.| ++|
T Consensus       190 AYllPiVq~Lq~m~~ki~Rs~G~~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGG---EkkKSEKARLRKG-iNI  265 (708)
T KOG0348|consen  190 AYLLPIVQSLQAMEPKIQRSDGPYALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGG---EKKKSEKARLRKG-INI  265 (708)
T ss_pred             HHHHHHHHHHHhcCccccccCCceEEEEechHHHHHHHHHHHHHHhcCceEEeeceeecc---cccccHHHHHhcC-ceE
Confidence            344456666665532     2445899999999888766655432   211  1223333   2233333455666 799


Q ss_pred             EEEcC-------CCcccCCccCCcEEEE--------ecCCCChhHHHHhh
Q psy17637         88 LVATD-------VAARGLDIPHIRTVVN--------YDLARDIDTHTHRI  122 (150)
Q Consensus        88 lv~T~-------~~~~Gidi~~~~~vi~--------~~~~~~~~~~~q~~  122 (150)
                      ||+|+       .-...+++..+.|+|+        +++-+++...+-.+
T Consensus       266 LIgTPGRLvDHLknT~~i~~s~LRwlVlDEaDrlleLGfekdit~Il~~v  315 (708)
T KOG0348|consen  266 LIGTPGRLVDHLKNTKSIKFSRLRWLVLDEADRLLELGFEKDITQILKAV  315 (708)
T ss_pred             EEcCchHHHHHHhccchheeeeeeEEEecchhHHHhccchhhHHHHHHHH
Confidence            99996       1233456667777774        44445555555444

>cd01532 4RHOD_Repeat_1 Member of the Rhodanese Homology Domain superfamily, repeat 1

Probab=81.11  E-value=1.7  Score=25.71  Aligned_cols=37  Identities=27%  Similarity=0.281  Sum_probs=26.9

Q ss_pred             CCCCeeEEehh--hhhHHHHHhhccccCc-eEEEecCCCC
Q psy17637         33 EVPPALMNLAM--QLNAEELANSLTVKEY-DVLLLHGDMD   69 (150)
Q Consensus        33 ~~~~~ivf~~~--~~~~~~l~~~L~~~~~-~~~~~~~~~~   69 (150)
                      +..++++||.+  +..+...+..|...|+ .+..+.||+.
T Consensus        49 ~~~~ivl~c~~G~~~~s~~aa~~L~~~G~~~v~~l~GG~~   88 (92)
T cd01532          49 RDTPIVVYGEGGGEDLAPRAARRLSELGYTDVALLEGGLQ   88 (92)
T ss_pred             CCCeEEEEeCCCCchHHHHHHHHHHHcCccCEEEccCCHH
Confidence            46689999988  3445677777877776 4677888863

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 1st repeat which does not contain the putative catalytic Cys residue.

>cd06533 Glyco_transf_WecG_TagA The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins

Probab=81.07  E-value=14  Score=24.80  Aligned_cols=67  Identities=16%  Similarity=0.168  Sum_probs=46.2

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhcccc--CceEEE-ecCCCCHHHHHHHHHHhhcCCceEE
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVK--EYDVLL-LHGDMDQSERNSVITKFKRQECRIL   88 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~--~~~~~~-~~~~~~~~~r~~~~~~f~~g~~~vl   88 (150)
                      .+..+++....   .+.++-++-.+.+.++.+.+.|+..  ++.+.- .||.+..++...+++..+....+++
T Consensus        34 l~~~ll~~~~~---~~~~v~llG~~~~~~~~~~~~l~~~yp~l~i~g~~~g~~~~~~~~~i~~~I~~~~pdiv  103 (171)
T cd06533          34 LMPALLELAAQ---KGLRVFLLGAKPEVLEKAAERLRARYPGLKIVGYHHGYFGPEEEEEIIERINASGADIL  103 (171)
T ss_pred             HHHHHHHHHHH---cCCeEEEECCCHHHHHHHHHHHHHHCCCcEEEEecCCCCChhhHHHHHHHHHHcCCCEE
Confidence            33444444433   3567777778888888888887664  666655 7788888887778888887766544

E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common antigen (eca) synthesis. B. subtilis TagA plays a key role in the Wall Teichoic Acid (WTA) biosynthetic pathway, catalyzing the transfer of N-acetylmannosamine to the C4 hydroxyl of a membrane-anchored N-acetylglucosaminyl diphospholipid to make ManNAc-beta-(1,4)-GlcNAc-pp-undecaprenyl. This is the first committed step in this pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan.

>KOG1132|consensus

Probab=81.06  E-value=17  Score=31.01  Aligned_cols=107  Identities=20%  Similarity=0.173  Sum_probs=63.3

Q ss_pred             CCCeeEEehhhhhHHHHHhhcccc-------CceEEEecCCCCHHHHHHHHHHhhcCC--------ceEEEEcCCCcccC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVK-------EYDVLLLHGDMDQSERNSVITKFKRQE--------CRILVATDVAARGL   98 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~-------~~~~~~~~~~~~~~~r~~~~~~f~~g~--------~~vlv~T~~~~~Gi   98 (150)
                      ....|+|.++....+++.......       .++- ++.+--+..+-.+++..|.++.        .-..||-...++|+
T Consensus       561 p~G~L~FfPSY~vmdk~~tfw~~~~~we~~~~vk~-l~vEPr~k~~f~e~m~~y~~~i~~pes~ga~~~aVcRGKVSEGl  639 (945)
T KOG1132|consen  561 PYGLLIFFPSYPVMDKLITFWQNRGLWERMEKVKK-LVVEPRSKSEFTEVMSRYYNAIADPESSGAVFFAVCRGKVSEGL  639 (945)
T ss_pred             ccceEEeccchHHHHHHHHHHHcchHHHHhhcccC-ceeccCCccchHHHHHHHHHHhhCccccceEEEEEecccccCCC
Confidence            445999999998877774444332       1111 2222223333445555554322        23447778999999


Q ss_pred             Ccc--CCcEEEEecCCC-------------------C-------------------hhHHHHhhccccCCCCccEEEEEE
Q psy17637         99 DIP--HIRTVVNYDLAR-------------------D-------------------IDTHTHRIGRTGRAGNKGVAYTLV  138 (150)
Q Consensus        99 di~--~~~~vi~~~~~~-------------------~-------------------~~~~~q~~GR~~R~g~~~~~~~~~  138 (150)
                      |+.  +...||..+.|.                   +                   ....-|.+||+.|..++=..+.++
T Consensus       640 DFsD~~~RaVI~tGlPyP~~~D~~V~lK~~y~D~~~~~~g~~s~~lsg~eWY~~qA~RAvNQAiGRviRHR~D~Gav~l~  719 (945)
T KOG1132|consen  640 DFSDDNGRAVIITGLPYPPVMDPRVKLKKQYLDENSSLKGAKSQLLSGQEWYSQQAYRAVNQAIGRVIRHRNDYGAVILC  719 (945)
T ss_pred             CccccCCceeEEecCCCCCCCCHHHHHHHHhhhhhccccccccccccchHHHHhhHHHHHHHHHHHHHhhhcccceeeEe
Confidence            985  445677766664                   1                   111248999999987665555566


Q ss_pred             ecC
Q psy17637        139 TDK  141 (150)
Q Consensus       139 ~~~  141 (150)
                      +..
T Consensus       720 D~R  722 (945)
T KOG1132|consen  720 DDR  722 (945)
T ss_pred             ech
Confidence            654

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

Probab=80.03  E-value=3.7  Score=35.39  Aligned_cols=48  Identities=25%  Similarity=0.343  Sum_probs=37.8

Q ss_pred             hcCCceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCC
Q psy17637         81 KRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAG  129 (150)
Q Consensus        81 ~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g  129 (150)
                      .....++||.++++-.|.|-|.++.+.. |-|--.-..+|.+.|+.|.-
T Consensus       590 ~~d~~kilIV~dmlLTGFDaP~L~TmYv-DK~Lk~H~L~QAisRtNR~~  637 (962)
T COG0610         590 KDDPLDLLIVVDMLLTGFDAPCLNTLYV-DKPLKYHNLIQAISRTNRVF  637 (962)
T ss_pred             cCCCCCEEEEEccccccCCccccceEEe-ccccccchHHHHHHHhccCC
Confidence            3456789999999999999998887664 44444556799999999954

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	150
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		1e-20
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		9e-20
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		1e-19
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		1e-19
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		1e-19
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		1e-19
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-19
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		2e-19
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-19
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		6e-19
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		2e-18
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		2e-18
3gfp_A	189	Structure Of The C-Terminal Domain Of The Dead-Box		2e-18
3peu_A	188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		2e-18
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		3e-18
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		3e-18
2jgn_A	185	Ddx3 Helicase Domain Length = 185		8e-18
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		9e-18
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		2e-17
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		2e-17
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		2e-17
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		2e-17
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		3e-17
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		2e-16
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		3e-16
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		3e-16
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		3e-16
1t5i_A	172	Crystal Structure Of The C-Terminal Domain Of Uap56		3e-16
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		1e-15
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		3e-15
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		7e-15
4db4_A	256	Mss116p Dead-Box Helicase Domain 2 Bound To A Chima		2e-14
4db2_C	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		2e-14
4db2_A	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		3e-14
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		1e-13
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		2e-13
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		2e-13
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		4e-13
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		5e-13
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		6e-13
3eaq_A	212	Novel Dimerization Motif In The Dead Box Rna Helica		2e-12
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		4e-11
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		6e-11
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		9e-11
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		3e-08
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		6e-08
1gm5_A	780	Structure Of Recg Bound To Three-Way Dna Junction L		8e-07
1wp9_A	494	Crystal Structure Of Pyrococcus Furiosus Hef Helica		2e-05
2eyq_A	1151	Crystal Structure Of Escherichia Coli Transcription		5e-05
2v1x_A	591	Crystal Structure Of Human Recq-Like Dna Helicase L		7e-05
4gl2_A	699	Structural Basis For Dsrna Duplex Backbone Recognit		2e-04

>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain Length = 191

Iteration: 1
 Score = 95.1 bits (235), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 45/116 (38%), Positives = 70/116 (60%)
Query: 23  LVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKR 82
           +V  LE   +  PP L+    + + + +   L +K  + + +HG  DQ ER   I  F+ 
Sbjct: 43  MVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFRE 102
Query: 83  QECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLV 138
            +  +LVATDVA++GLD P I+ V+NYD+  +I+ + HRIGRTG +GN G+A T +
Sbjct: 103 GKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFI 158

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score = 92.4 bits (228), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 46/98 (46%), Positives = 64/98 (65%), Gaps = 1/98 (1%)
Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
           A+ LA+ L+ KE+    +HGD  QS+R   +  FK    ++L+AT VA+RGLDI +I+ V
Sbjct: 313 ADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHV 372
Query: 107 VNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           +NYD+   ID + HRIGRTGR GN G A +   D +KD
Sbjct: 373 INYDMPSKIDDYVHRIGRTGRVGNNGRATSFF-DPEKD 409

>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 = 91.7 bits (226), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 39/84 (46%), Positives = 57/84 (67%)
Query: 59  YDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTH 118
           + V  +HGDM Q ER S++ +F+    R+L++TDV ARGLD+P +  ++NYDL  + + +
Sbjct: 302 FTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELY 361
Query: 119 THRIGRTGRAGNKGVAYTLVTDKD 142
            HRIGR+GR G KGVA   V + D
Sbjct: 362 IHRIGRSGRYGRKGVAINFVKNDD 385

>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The Bacillus Subtilis Yxin Protein Length = 163

Iteration: 1
 Score = 91.7 bits (226), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 45/80 (56%), Positives = 58/80 (72%)
Query: 64  LHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIG 123
           +HG M Q +R  V+ +FKR E R LVATDVAARG+DI +I  V+NYDL  + +++ HR G
Sbjct: 65  IHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTG 124
Query: 124 RTGRAGNKGVAYTLVTDKDK 143
           RTGRAGNKG A + VT  +K
Sbjct: 125 RTGRAGNKGKAISFVTAFEK 144

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 91.7 bits (226), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 39/84 (46%), Positives = 57/84 (67%)
Query: 59  YDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTH 118
           + V  +HGDM Q ER S++ +F+    R+L++TDV ARGLD+P +  ++NYDL  + + +
Sbjct: 301 FTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELY 360
Query: 119 THRIGRTGRAGNKGVAYTLVTDKD 142
            HRIGR+GR G KGVA   V + D
Sbjct: 361 IHRIGRSGRYGRKGVAINFVKNDD 384

>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 = 91.7 bits (226), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 39/84 (46%), Positives = 57/84 (67%)
Query: 59  YDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTH 118
           + V  +HGDM Q ER S++ +F+    R+L++TDV ARGLD+P +  ++NYDL  + + +
Sbjct: 302 FTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELY 361
Query: 119 THRIGRTGRAGNKGVAYTLVTDKD 142
            HRIGR+GR G KGVA   V + D
Sbjct: 362 IHRIGRSGRYGRKGVAINFVKNDD 385

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 91.7 bits (226), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 39/84 (46%), Positives = 57/84 (67%)
Query: 59  YDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTH 118
           + V  +HGDM Q ER S++ +F+    R+L++TDV ARGLD+P +  ++NYDL  + + +
Sbjct: 265 FTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELY 324
Query: 119 THRIGRTGRAGNKGVAYTLVTDKD 142
            HRIGR+GR G KGVA   V + D
Sbjct: 325 IHRIGRSGRYGRKGVAVNFVKNDD 348

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 91.7 bits (226), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 39/84 (46%), Positives = 57/84 (67%)
Query: 59  YDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTH 118
           + V  +HGDM Q ER S++ +F+    R+L++TDV ARGLD+P +  ++NYDL  + + +
Sbjct: 280 FTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELY 339
Query: 119 THRIGRTGRAGNKGVAYTLVTDKD 142
            HRIGR+GR G KGVA   V + D
Sbjct: 340 IHRIGRSGRYGRKGVAINFVKNDD 363

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 91.3 bits (225), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 39/84 (46%), Positives = 57/84 (67%)
Query: 59  YDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTH 118
           + V  +HGDM Q ER S++ +F+    R+L++TDV ARGLD+P +  ++NYDL  + + +
Sbjct: 265 FTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELY 324
Query: 119 THRIGRTGRAGNKGVAYTLVTDKD 142
            HRIGR+GR G KGVA   V + D
Sbjct: 325 IHRIGRSGRYGRKGVAVNFVKNDD 348

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score = 89.7 bits (221), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 41/95 (43%), Positives = 66/95 (69%)
Query: 48  EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
           +ELA+ L    +    +HGD+ QS+R  VI  FK+++ RIL+ATDV +RG+D+  +  V+
Sbjct: 252 KELASXLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVXSRGIDVNDLNCVI 311
Query: 108 NYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
           NY L ++ +++ HRIGRTGRAG KG A +++  ++
Sbjct: 312 NYHLPQNPESYXHRIGRTGRAGKKGKAISIINRRE 346

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 87.8 bits (216), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 46/112 (41%), Positives = 68/112 (60%), Gaps = 6/112 (5%)
Query: 37  ALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAAR 96
           +++ +A +  A  L   L  + ++V +LHGD+   ER+ +I  F+    ++L+ T+V AR
Sbjct: 246 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 305
Query: 97  GLDIPHIRTVVNYDLAR------DIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
           G+DIP +  VVNYDL        D  T+ HRIGRTGR G KGVA + V DK+
Sbjct: 306 GIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKN 357

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 87.8 bits (216), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 46/112 (41%), Positives = 68/112 (60%), Gaps = 6/112 (5%)
Query: 37  ALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAAR 96
           +++ +A +  A  L   L  + ++V +LHGD+   ER+ +I  F+    ++L+ T+V AR
Sbjct: 246 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 305
Query: 97  GLDIPHIRTVVNYDLAR------DIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
           G+DIP +  VVNYDL        D  T+ HRIGRTGR G KGVA + V DK+
Sbjct: 306 GIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKN 357

>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein Dbp5 Length = 189

Iteration: 1
 Score = 87.8 bits (216), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 46/115 (40%), Positives = 69/115 (60%), Gaps = 6/115 (5%)
Query: 34  VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDV 93
           +  +++ +A +  A  L   L  + ++V +LHGD+   ER+ +I  F+    ++L+ T+V
Sbjct: 37  IGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNV 96
Query: 94  AARGLDIPHIRTVVNYDLAR------DIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
            ARG+DIP +  VVNYDL        D  T+ HRIGRTGR G KGVA + V DK+
Sbjct: 97  LARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKN 151

>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1 H337r And Ip6 Length = 188

Iteration: 1
 Score = 87.8 bits (216), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 46/115 (40%), Positives = 69/115 (60%), Gaps = 6/115 (5%)
Query: 34  VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDV 93
           +  +++ +A +  A  L   L  + ++V +LHGD+   ER+ +I  F+    ++L+ T+V
Sbjct: 36  IGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNV 95
Query: 94  AARGLDIPHIRTVVNYDLAR------DIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
            ARG+DIP +  VVNYDL        D  T+ HRIGRTGR G KGVA + V DK+
Sbjct: 96  LARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKN 150

>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p Length = 187

Iteration: 1
 Score = 87.4 bits (215), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 46/115 (40%), Positives = 69/115 (60%), Gaps = 6/115 (5%)
Query: 34  VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDV 93
           +  +++ +A +  A  L   L  + ++V +LHGD+   ER+ +I  F+    ++L+ T+V
Sbjct: 35  IGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNV 94
Query: 94  AARGLDIPHIRTVVNYDLAR------DIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
            ARG+DIP +  VVNYDL        D  T+ HRIGRTGR G KGVA + V DK+
Sbjct: 95  LARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKN 149

>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 = 87.4 bits (215), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 46/94 (48%), Positives = 57/94 (60%)
Query: 49  ELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVN 108
           ELAN L     +   L G+M Q +RN  I +       +LVATDVAARG+DIP +  V N
Sbjct: 45  ELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFN 104
Query: 109 YDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
           +D+ R  DT+ HRIGRT RAG KG A +LV   D
Sbjct: 105 FDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHD 138

>pdb|2JGN|A Chain A, Ddx3 Helicase Domain Length = 185

Iteration: 1
 Score = 85.9 bits (211), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 41/96 (42%), Positives = 62/96 (64%)
Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
           A+ L + L  + Y    +HGD  Q +R   + +F+  +  ILVAT VAARGLDI +++ V
Sbjct: 59  ADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHV 118
Query: 107 VNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
           +N+DL  DI+ + HRIGRTGR GN G+A +   +++
Sbjct: 119 INFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERN 154

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 85.9 bits (211), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 41/96 (42%), Positives = 62/96 (64%)
Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
           A+ L + L  + Y    +HGD  Q +R   + +F+  +  ILVAT VAARGLDI +++ V
Sbjct: 289 ADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHV 348
Query: 107 VNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
           +N+DL  DI+ + HRIGRTGR GN G+A +   +++
Sbjct: 349 INFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERN 384

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 84.7 bits (208), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 50/139 (35%), Positives = 80/139 (57%), Gaps = 9/139 (6%)
Query: 9   YTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDM 68
           Y L + +D++F    + NL GA   +  A++    +  A  LA  L+ + + V LL G+M
Sbjct: 281 YVLCSSRDEKFQA--LCNLYGAI-TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEM 337
Query: 69  DQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDID------THTHRI 122
              +R +VI +F+  + ++LV T+V ARG+D+  +  V+N+DL  D D      T+ HRI
Sbjct: 338 MVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRI 397
Query: 123 GRTGRAGNKGVAYTLVTDK 141
           GRTGR G +G+A  +V  K
Sbjct: 398 GRTGRFGKRGLAVNMVDSK 416

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 84.3 bits (207), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 50/139 (35%), Positives = 80/139 (57%), Gaps = 9/139 (6%)
Query: 9   YTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDM 68
           Y L + +D++F    + NL GA   +  A++    +  A  LA  L+ + + V LL G+M
Sbjct: 260 YVLCSSRDEKFQA--LCNLYGAI-TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEM 316
Query: 69  DQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDID------THTHRI 122
              +R +VI +F+  + ++LV T+V ARG+D+  +  V+N+DL  D D      T+ HRI
Sbjct: 317 MVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRI 376
Query: 123 GRTGRAGNKGVAYTLVTDK 141
           GRTGR G +G+A  +V  K
Sbjct: 377 GRTGRFGKRGLAVNMVDSK 395

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 84.3 bits (207), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 50/139 (35%), Positives = 80/139 (57%), Gaps = 9/139 (6%)
Query: 9   YTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDM 68
           Y L + +D++F    + NL GA   +  A++    +  A  LA  L+ + + V LL G+M
Sbjct: 244 YVLCSSRDEKFQA--LCNLYGAI-TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEM 300
Query: 69  DQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDID------THTHRI 122
              +R +VI +F+  + ++LV T+V ARG+D+  +  V+N+DL  D D      T+ HRI
Sbjct: 301 MVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRI 360
Query: 123 GRTGRAGNKGVAYTLVTDK 141
           GRTGR G +G+A  +V  K
Sbjct: 361 GRTGRFGKRGLAVNMVDSK 379

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 84.3 bits (207), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 50/139 (35%), Positives = 80/139 (57%), Gaps = 9/139 (6%)
Query: 9   YTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDM 68
           Y L + +D++F    + NL GA   +  A++    +  A  LA  L+ + + V LL G+M
Sbjct: 311 YVLCSSRDEKFQA--LCNLYGAIT-IAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEM 367
Query: 69  DQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDID------THTHRI 122
              +R +VI +F+  + ++LV T+V ARG+D+  +  V+N+DL  D D      T+ HRI
Sbjct: 368 MVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRI 427
Query: 123 GRTGRAGNKGVAYTLVTDK 141
           GRTGR G +G+A  +V  K
Sbjct: 428 GRTGRFGKRGLAVNMVDSK 446

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 84.0 bits (206), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 39/78 (50%), Positives = 53/78 (67%)
Query: 64  LHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIG 123
           L GD+ QS RN  I  F+  E  +L+ TDVA+RGLDIP +  V+N+D  +D+ T+ HRIG
Sbjct: 246 LRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIG 305
Query: 124 RTGRAGNKGVAYTLVTDK 141
           RTGR G KG A T + ++
Sbjct: 306 RTGRMGRKGEAITFILNE 323

>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 = 81.3 bits (199), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 48/141 (34%), Positives = 74/141 (52%), Gaps = 6/141 (4%)
Query: 5   KGVA--YTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVL 62
           KGV   Y  VT++ K    + + +    NQ +     N + ++  E LA  ++   Y   
Sbjct: 17  KGVTQYYAYVTERQKVHCLNTLFSRLQINQSI--IFCNSSQRV--ELLAKKISQLGYSCF 72
Query: 63  LLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRI 122
            +H  M Q  RN V   F+   CR LV TD+  RG+DI  +  V+N+D  +  +T+ HRI
Sbjct: 73  YIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRI 132
Query: 123 GRTGRAGNKGVAYTLVTDKDK 143
           GR+GR G+ G+A  L+T  D+
Sbjct: 133 GRSGRFGHLGLAINLITYDDR 153

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 80.9 bits (198), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 39/93 (41%), Positives = 56/93 (60%)
Query: 50  LANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNY 109
           LA  L  + +  + +H  M Q ER S   +FK  + RILVAT++  RG+DI  +    NY
Sbjct: 265 LAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNY 324
Query: 110 DLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
           D+  D DT+ HR+ R GR G KG+A T V+D++
Sbjct: 325 DMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN 357

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 80.9 bits (198), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 39/93 (41%), Positives = 56/93 (60%)
Query: 50  LANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNY 109
           LA  L  + +  + +H  M Q ER S   +FK  + RILVAT++  RG+DI  +    NY
Sbjct: 266 LAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNY 325
Query: 110 DLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
           D+  D DT+ HR+ R GR G KG+A T V+D++
Sbjct: 326 DMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN 358

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 80.9 bits (198), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 39/93 (41%), Positives = 56/93 (60%)
Query: 50  LANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNY 109
           LA  L  + +  + +H  M Q ER S   +FK  + RILVAT++  RG+DI  +    NY
Sbjct: 266 LAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNY 325
Query: 110 DLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
           D+  D DT+ HR+ R GR G KG+A T V+D++
Sbjct: 326 DMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN 358

>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56 Length = 172

Iteration: 1
 Score = 80.5 bits (197), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 39/93 (41%), Positives = 56/93 (60%)
Query: 50  LANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNY 109
           LA  L  + +  + +H  M Q ER S   +FK  + RILVAT++  RG+DI  +    NY
Sbjct: 47  LAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNY 106
Query: 110 DLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
           D+  D DT+ HR+ R GR G KG+A T V+D++
Sbjct: 107 DMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN 139

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 78.6 bits (192), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 37/97 (38%), Positives = 56/97 (57%)
Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
            E LA  +T   Y     H  M Q ERN V  +F++ + R LV +D+  RG+DI  +  V
Sbjct: 271 VELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVV 330
Query: 107 VNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK 143
           +N+D  +  +T+ HRIGR+GR G+ G+A  L+   D+
Sbjct: 331 INFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDR 367

>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25 Rna Helicase Length = 175

Iteration: 1
 Score = 76.3 bits (186), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 38/111 (34%), Positives = 66/111 (59%), Gaps = 6/111 (5%)
Query: 34  VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDV 93
           +  A++    + NA+ L   +    + V LL G++   +R S+I +F+  + ++L+ T+V
Sbjct: 34  IGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNV 93
Query: 94  AARGLDIPHIRTVVNYDLA------RDIDTHTHRIGRTGRAGNKGVAYTLV 138
            ARG+D+  +  VVN+DL        D +T+ HRIGRTGR G KG+A+ ++
Sbjct: 94  CARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMI 144

>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric Rna-Dna Duplex Length = 256

Iteration: 1
 Score = 74.3 bits (181), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 31/83 (37%), Positives = 52/83 (62%)
Query: 57  KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDID 116
           K+  +L  HG + Q++R S++ +FK+ E  ILV TDV ARG+D P++  V+   +  ++ 
Sbjct: 59  KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELA 118
Query: 117 THTHRIGRTGRAGNKGVAYTLVT 139
            + HRIGRT R+G +G +   + 
Sbjct: 119 NYIHRIGRTARSGKEGSSVLFIC 141

>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 74.3 bits (181), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 31/83 (37%), Positives = 52/83 (62%)
Query: 57  KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDID 116
           K+  +L  HG + Q++R S++ +FK+ E  ILV TDV ARG+D P++  V+   +  ++ 
Sbjct: 59  KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELA 118
Query: 117 THTHRIGRTGRAGNKGVAYTLVT 139
            + HRIGRT R+G +G +   + 
Sbjct: 119 NYIHRIGRTARSGKEGSSVLFIC 141

>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 74.3 bits (181), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 31/83 (37%), Positives = 52/83 (62%)
Query: 57  KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDID 116
           K+  +L  HG + Q++R S++ +FK+ E  ILV TDV ARG+D P++  V+   +  ++ 
Sbjct: 59  KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELA 118
Query: 117 THTHRIGRTGRAGNKGVAYTLVT 139
            + HRIGRT R+G +G +   + 
Sbjct: 119 NYIHRIGRTARSGKEGSSVLFIC 141

>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 = 72.0 bits (175), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 31/82 (37%), Positives = 52/82 (63%)
Query: 57  KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDID 116
           K+  +L  HG + Q++R S++ +FK+ E  ILV TDV ARG+D P++  V+   +  ++ 
Sbjct: 314 KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELA 373
Query: 117 THTHRIGRTGRAGNKGVAYTLV 138
            + HRIGRT R+G +G +   +
Sbjct: 374 NYIHRIGRTARSGKEGSSVLFI 395

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 71.6 bits (174), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 31/82 (37%), Positives = 52/82 (63%)
Query: 57  KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDID 116
           K+  +L  HG + Q++R S++ +FK+ E  ILV TDV ARG+D P++  V+   +  ++ 
Sbjct: 365 KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELA 424
Query: 117 THTHRIGRTGRAGNKGVAYTLV 138
            + HRIGRT R+G +G +   +
Sbjct: 425 NYIHRIGRTARSGKEGSSVLFI 446

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 70.9 bits (172), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 31/76 (40%), Positives = 50/76 (65%)
Query: 57  KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDID 116
           K+  +L  HG + Q++R S++ +FK+ E  ILV TDV ARG+D P++  V+   +  ++ 
Sbjct: 314 KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELA 373
Query: 117 THTHRIGRTGRAGNKG 132
            + HRIGRT R+G +G
Sbjct: 374 NYIHRIGRTARSGKEG 389

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 70.1 bits (170), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 40/94 (42%), Positives = 63/94 (67%)
Query: 50  LANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNY 109
           L   +  +++ V  +HGDMDQ ER+ ++ +F+    R+L+ TD+ ARG+D+  +  V+NY
Sbjct: 296 LTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINY 355
Query: 110 DLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK 143
           DL  + + + HRIGR GR G KGVA  +VT++DK
Sbjct: 356 DLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDK 389

>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 = 70.1 bits (170), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 35/84 (41%), Positives = 49/84 (58%)
Query: 37  ALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAAR 96
           A++    +   EE+A  L    +    LHGDM Q ER  V+  F++ E R+LVATDVAAR
Sbjct: 31  AMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAAR 90
Query: 97  GLDIPHIRTVVNYDLARDIDTHTH 120
           GLDIP +  VV+Y +    + + H
Sbjct: 91  GLDIPQVDLVVHYRMPDRAEAYQH 114

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 69.7 bits (169), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 40/94 (42%), Positives = 63/94 (67%)
Query: 50  LANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNY 109
           L   +  +++ V  +HGDMDQ ER+ ++ +F+    R+L+ TD+ ARG+D+  +  V+NY
Sbjct: 270 LTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINY 329
Query: 110 DLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK 143
           DL  + + + HRIGR GR G KGVA  +VT++DK
Sbjct: 330 DLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDK 363

>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 = 68.2 bits (165), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 35/84 (41%), Positives = 49/84 (58%)
Query: 37  ALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAAR 96
           A++    +   EE+A  L    +    LHGD+ Q ER  V+  F++ E R+LVATDVAAR
Sbjct: 34  AMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAAR 93
Query: 97  GLDIPHIRTVVNYDLARDIDTHTH 120
           GLDIP +  VV+Y L    + + H
Sbjct: 94  GLDIPQVDLVVHYRLPDRAEAYQH 117

>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score = 63.5 bits (153), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 45/138 (32%), Positives = 80/138 (57%), Gaps = 1/138 (0%)
Query: 5   KGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLL 64
           +G+    V  +++E+    + +L  +   V  A++    +   EEL   L   ++ V  +
Sbjct: 2   EGIKQFYVNVEEEEYKYECLTDLYDSIS-VTQAVIFCNTRRKVEELTTKLRNDKFTVSAI 60
Query: 65  HGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGR 124
           + D+ Q ER++++ +F+    RIL++TD+ ARG+D+  +  V+NYDL  + + + HRIGR
Sbjct: 61  YSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGR 120
Query: 125 TGRAGNKGVAYTLVTDKD 142
            GR G KGVA   VT++D
Sbjct: 121 GGRFGRKGVAINFVTNED 138

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 63.2 bits (152), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 45/138 (32%), Positives = 80/138 (57%), Gaps = 1/138 (0%)
Query: 5   KGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLL 64
           +G+    V  +++E+    + +L  +   V  A++    +   EEL   L   ++ V  +
Sbjct: 232 EGIKQFYVNVEEEEYKYECLTDLYDSIS-VTQAVIFCNTRRKVEELTTKLRNDKFTVSAI 290
Query: 65  HGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGR 124
           + D+ Q ER++++ +F+    RIL++TD+ ARG+D+  +  V+NYDL  + + + HRIGR
Sbjct: 291 YSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGR 350
Query: 125 TGRAGNKGVAYTLVTDKD 142
            GR G KGVA   VT++D
Sbjct: 351 GGRFGRKGVAINFVTNED 368

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 62.4 bits (150), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 45/138 (32%), Positives = 79/138 (57%), Gaps = 1/138 (0%)
Query: 5   KGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLL 64
           +G+    V  +++E+    + +L  +   V  A++    +   EEL   L   ++ V  +
Sbjct: 231 EGIKQFYVNVEEEEYKYECLTDLYDSIS-VTQAVIFCNTRRKVEELTTKLRNDKFTVSAI 289
Query: 65  HGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGR 124
           + D+ Q ER+++  +F+    RIL++TD+ ARG+D+  +  V+NYDL  + + + HRIGR
Sbjct: 290 YSDLPQQERDTIXKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGR 349
Query: 125 TGRAGNKGVAYTLVTDKD 142
            GR G KGVA   VT++D
Sbjct: 350 GGRFGRKGVAINFVTNED 367

>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core Length = 523

Iteration: 1
 Score = 54.3 bits (129), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 27/82 (32%), Positives = 46/82 (56%)
Query: 48  EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
           E+ A  L  K       H  ++ + R  V  KF+R + +I+VAT     G++ P++R VV
Sbjct: 250 EDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXGINKPNVRFVV 309
Query: 108 NYDLARDIDTHTHRIGRTGRAG 129
           ++D+ R+I+++    GR GR G
Sbjct: 310 HFDIPRNIESYYQETGRAGRDG 331

>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S Length = 523

Iteration: 1
 Score = 53.1 bits (126), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 27/82 (32%), Positives = 46/82 (56%)
Query: 48  EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
           E+ A  L  K       H  ++ + R  V  KF+R + +I+VAT     G++ P++R VV
Sbjct: 250 EDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVV 309
Query: 108 NYDLARDIDTHTHRIGRTGRAG 129
           ++D+ R+I+++    GR GR G
Sbjct: 310 HFDIPRNIESYYQETGRAGRDG 331

>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction Length = 780

Iteration: 1
 Score = 49.3 bits (116), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 37/141 (26%), Positives = 60/141 (42%), Gaps = 22/141 (15%)
Query: 1   RAGNKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYD 60
           R G   + Y L+ + DK      V   E  ++EV P                     E+ 
Sbjct: 577 RGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFP---------------------EFK 615
Query: 61  VLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTH 120
           + L+HG + Q E++ V+ +F      ILV+T V   G+D+P    +V  +  R      H
Sbjct: 616 LGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLH 675
Query: 121 RI-GRTGRAGNKGVAYTLVTD 140
           ++ GR GR G +   + +V D
Sbjct: 676 QLRGRVGRGGQEAYCFLVVGD 696

>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase Domain Length = 494

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/60 (38%), Positives = 32/60 (53%)
Query: 68  MDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGR 127
           + Q E+  ++ +F R E  +LVAT V   GLD+P +  VV Y+          R GRTGR
Sbjct: 403 LSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGR 462

>pdb|2EYQ|A Chain A, Crystal Structure Of Escherichia Coli Transcription-Repair Coupling Factor Length = 1151

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 32/100 (32%), Positives = 49/100 (49%), Gaps = 11/100 (11%)
Query: 43  MQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPH 102
           +Q  AE LA    V E  + + HG M + E   V+  F  Q   +LV T +   G+DIP 
Sbjct: 825 IQKAAERLAE--LVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPT 882
Query: 103 IRTVV-----NYDLARDIDTHTHRIGRTGRAGNKGVAYTL 137
             T++     ++ LA+    H  R GR GR+ ++  A+ L
Sbjct: 883 ANTIIIERADHFGLAQ---LHQLR-GRVGRSHHQAYAWLL 918

>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase Length = 591

Iteration: 1
 Score = 43.1 bits (100), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 20/84 (23%), Positives = 45/84 (53%)
Query: 44  QLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHI 103
           Q ++E++  SL          H +++  ++ +V  K+   E +++VAT     G+D P +
Sbjct: 277 QKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDV 336
Query: 104 RTVVNYDLARDIDTHTHRIGRTGR 127
           R V+++ +++ ++ +    GR GR
Sbjct: 337 RFVIHHSMSKSMENYYQESGRAGR 360

>pdb|4GL2|A Chain A, Structural Basis For Dsrna Duplex Backbone Recognition By Mda5 Length = 699

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/71 (35%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 68  MDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGR 127
           M Q+E+  VI+KF+  +  +L+AT VA  GLDI     V+ Y L   +      +   GR
Sbjct: 448 MTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGL---VTNEIAMVQARGR 504
Query: 128 AGNKGVAYTLV 138
           A      Y LV
Sbjct: 505 ARADESTYVLV 515

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	150
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	1e-47
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	3e-11
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	4e-47
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	1e-13
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	9e-46
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	1e-44
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	8e-44
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	4e-12
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	3e-43
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	5e-43
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	1e-42
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	1e-42
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	1e-42
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	1e-42
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	1e-42
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	1e-42
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	6e-10
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	5e-42
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	1e-41
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	2e-41
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	2e-41
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	3e-41
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	5e-41
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	3e-40
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	3e-40
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	6e-38
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	2e-36
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	2e-35
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	3e-22
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	5e-18
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	4e-10
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	5e-10
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	6e-10
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	9e-10
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	1e-09
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	5e-09
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	1e-08
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	2e-08
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	6e-08
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	6e-08
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	7e-08
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	3e-06
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	4e-06
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	4e-06
1yks_A	440	Genome polyprotein [contains: flavivirin protease	1e-05
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	2e-05
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	3e-05
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	2e-04
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	7e-04

>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 =  158 bits (402), Expect = 1e-47
 Identities = 45/102 (44%), Positives = 64/102 (62%), Gaps = 1/102 (0%)

Query: 46  NAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRT 105
            A+ LA+ L+ KE+    +HGD  QS+R   +  FK    ++L+AT VA+RGLDI +I+ 
Sbjct: 312 GADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKH 371

Query: 106 VVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGEL 147
           V+NYD+   ID + HRIGRTGR GN G A +     +KD  +
Sbjct: 372 VINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFD-PEKDRAI 412

>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 = 58.7 bits (143), Expect = 3e-11
 Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 1/39 (2%)

Query: 1   RAGNKGVAYTLVT-DKDKEFAGHLVRNLEGANQEVPPAL 38
           R GN G A +    +KD+  A  LV+ LEG+ Q VP  L
Sbjct: 393 RVGNNGRATSFFDPEKDRAIAADLVKILEGSGQTVPDFL 431

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  156 bits (397), Expect = 4e-47
 Identities = 41/98 (41%), Positives = 62/98 (63%)

Query: 46  NAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRT 105
            A+ L + L  + Y    +HGD  Q +R   + +F+  +  ILVAT VAARGLDI +++ 
Sbjct: 288 GADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKH 347

Query: 106 VVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK 143
           V+N+DL  DI+ + HRIGRTGR GN G+A +   +++ 
Sbjct: 348 VINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNI 385

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score = 65.6 bits (161), Expect = 1e-13
 Identities = 15/44 (34%), Positives = 23/44 (52%)

Query: 1   RAGNKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQ 44
           R GN G+A +   +++      L+  L  A QEVP  L N+A +
Sbjct: 369 RVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAYE 412

>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 =  143 bits (362), Expect = 1e-44
 Identities = 40/102 (39%), Positives = 57/102 (55%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
              LA  L  + +  + +H  M Q ER S   +FK  + RILVAT++  RG+DI  +   
Sbjct: 44  CIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIA 103

Query: 107 VNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGELR 148
            NYD+  D DT+ HR+ R GR G KG+A T V+D++    L 
Sbjct: 104 FNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILN 145

>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 =  141 bits (358), Expect = 8e-44
 Identities = 41/99 (41%), Positives = 63/99 (63%)

Query: 46  NAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRT 105
            A+ L + L  + Y    +HGD  Q +R   + +F+  +  ILVAT VAARGLDI +++ 
Sbjct: 58  GADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKH 117

Query: 106 VVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           V+N+DL  DI+ + HRIGRTGR GN G+A +   +++ +
Sbjct: 118 VINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNIN 156

>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 = 59.9 bits (146), Expect = 4e-12
 Identities = 15/44 (34%), Positives = 23/44 (52%)

Query: 1   RAGNKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQ 44
           R GN G+A +   +++      L+  L  A QEVP  L N+A +
Sbjct: 139 RVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAYE 182

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score =  139 bits (353), Expect = 3e-43
 Identities = 48/98 (48%), Positives = 63/98 (64%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
             +L + L    Y    +HG M Q +R  V+ +FKR E R LVATDVAARG+DI +I  V
Sbjct: 48  VNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLV 107

Query: 107 VNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           +NYDL  + +++ HR GRTGRAGNKG A + VT  +K 
Sbjct: 108 INYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKR 145

>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 =  145 bits (368), Expect = 5e-43
 Identities = 39/98 (39%), Positives = 62/98 (63%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
            EEL   L   ++ V  ++ D+ Q ER++++ +F+    RIL++TD+ ARG+D+  +  V
Sbjct: 272 VEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLV 331

Query: 107 VNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           +NYDL  + + + HRIGR GR G KGVA   VT++D  
Sbjct: 332 INYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVG 369

>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 =  145 bits (367), Expect = 1e-42
 Identities = 40/97 (41%), Positives = 64/97 (65%)

Query: 48  EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
           + L   +  +++ V  +HGDMDQ ER+ ++ +F+    R+L+ TD+ ARG+D+  +  V+
Sbjct: 294 DWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVI 353

Query: 108 NYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           NYDL  + + + HRIGR GR G KGVA  +VT++DK 
Sbjct: 354 NYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKR 390

>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 =  138 bits (349), Expect = 1e-42
 Identities = 46/98 (46%), Positives = 57/98 (58%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
             ELAN L     +   L G+M Q +RN  I +       +LVATDVAARG+DIP +  V
Sbjct: 43  VHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHV 102

Query: 107 VNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
            N+D+ R  DT+ HRIGRT RAG KG A +LV   D  
Sbjct: 103 FNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHL 140

>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 =  138 bits (349), Expect = 1e-42
 Identities = 36/104 (34%), Positives = 61/104 (58%), Gaps = 6/104 (5%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
           A+ L   +    + V LL G++   +R S+I +F+  + ++L+ T+V ARG+D+  +  V
Sbjct: 47  AKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIV 106

Query: 107 VNYDL------ARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           VN+DL        D +T+ HRIGRTGR G KG+A+ ++   +  
Sbjct: 107 VNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELP 150

>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 =  144 bits (366), Expect = 1e-42
 Identities = 40/96 (41%), Positives = 60/96 (62%)

Query: 48  EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
           + L   +    + V  +HGDM Q ER S++ +F+    R+L++TDV ARGLD+P +  ++
Sbjct: 290 DWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLII 349

Query: 108 NYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK 143
           NYDL  + + + HRIGR+GR G KGVA   V + D 
Sbjct: 350 NYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDI 385

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score =  137 bits (348), Expect = 1e-42
 Identities = 39/98 (39%), Positives = 62/98 (63%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
            EEL   L   ++ V  ++ D+ Q ER++++ +F+    RIL++TD+ ARG+D+  +  V
Sbjct: 43  VEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLV 102

Query: 107 VNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           +NYDL  + + + HRIGR GR G KGVA   VT++D  
Sbjct: 103 INYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVG 140

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score =  138 bits (350), Expect = 1e-42
 Identities = 41/102 (40%), Positives = 63/102 (61%), Gaps = 1/102 (0%)

Query: 46  NAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRT 105
           + + +   L +K  + + +HG  DQ ER   I  F+  +  +LVATDVA++GLD P I+ 
Sbjct: 66  DVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQH 125

Query: 106 VVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGEL 147
           V+NYD+  +I+ + HRIGRTG +GN G+A T +  K  D  +
Sbjct: 126 VINYDMPEEIENYVHRIGRTGCSGNTGIATTFIN-KACDESV 166

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score = 53.8 bits (130), Expect = 6e-10
 Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 1   RAGNKGVAYTLVT-DKDKEFAGHLVRNLEGANQEVPPALMNLAM 43
            +GN G+A T +    D+     L   L  A Q+VPP L  L  
Sbjct: 147 CSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQVLHC 190

>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 =  142 bits (361), Expect = 5e-42
 Identities = 37/98 (37%), Positives = 56/98 (57%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
            E LA  +T   Y     H  M Q ERN V  +F++ + R LV +D+  RG+DI  +  V
Sbjct: 271 VELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVV 330

Query: 107 VNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           +N+D  +  +T+ HRIGR+GR G+ G+A  L+   D+ 
Sbjct: 331 INFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRF 368

>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 =  141 bits (358), Expect = 1e-41
 Identities = 40/103 (38%), Positives = 57/103 (55%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
              LA  L  + +  + +H  M Q ER S   +FK  + RILVAT++  RG+DI  +   
Sbjct: 263 CIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIA 322

Query: 107 VNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGELRS 149
            NYD+  D DT+ HR+ R GR G KG+A T V+D++    L  
Sbjct: 323 FNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILND 365

>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 =  140 bits (355), Expect = 2e-41
 Identities = 41/98 (41%), Positives = 66/98 (67%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
            +ELA+ L    +    +HGD+ QS+R  VI  FK+++ RIL+ATDV +RG+D+  +  V
Sbjct: 251 TKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCV 310

Query: 107 VNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           +NY L ++ +++ HRIGRTGRAG KG A +++  ++  
Sbjct: 311 INYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYK 348

>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 =  141 bits (357), Expect = 2e-41
 Identities = 41/109 (37%), Positives = 63/109 (57%), Gaps = 6/109 (5%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
           A  LA  L+ + + V LL G+M   +R +VI +F+  + ++LV T+V ARG+D+  +  V
Sbjct: 279 ASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVV 338

Query: 107 VNYDL------ARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGELRS 149
           +N+DL        D +T+ HRIGRTGR G +G+A  +V  K     L  
Sbjct: 339 INFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNR 387

>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 =  140 bits (356), Expect = 3e-41
 Identities = 46/110 (41%), Positives = 64/110 (58%), Gaps = 6/110 (5%)

Query: 46  NAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRT 105
            A  L   L  + ++V +LHGD+   ER+ +I  F+    ++L+ T+V ARG+DIP +  
Sbjct: 255 TANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSM 314

Query: 106 VVNYDL------ARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGELRS 149
           VVNYDL        D  T+ HRIGRTGR G KGVA + V DK+    L +
Sbjct: 315 VVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSA 364

>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 =  135 bits (342), Expect = 5e-41
 Identities = 44/98 (44%), Positives = 58/98 (59%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
            EE+A  L    +    LHGD+ Q ER  V+  F++ E R+LVATDVAARGLDIP +  V
Sbjct: 44  TEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLV 103

Query: 107 VNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           V+Y L    + + HR GRTGRAG  G    L   +++ 
Sbjct: 104 VHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERR 141

>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 =  139 bits (353), Expect = 3e-40
 Identities = 41/109 (37%), Positives = 63/109 (57%), Gaps = 6/109 (5%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
           A  LA  L+ + + V LL G+M   +R +VI +F+  + ++LV T+V ARG+D+  +  V
Sbjct: 346 ASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVV 405

Query: 107 VNYDL------ARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGELRS 149
           +N+DL        D +T+ HRIGRTGR G +G+A  +V  K     L  
Sbjct: 406 INFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNR 454

>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 =  136 bits (343), Expect = 3e-40
 Identities = 44/98 (44%), Positives = 58/98 (59%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
            EE+A  L    +    LHGDM Q ER  V+  F++ E R+LVATDVAARGLDIP +  V
Sbjct: 41  TEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLV 100

Query: 107 VNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
           V+Y +    + + HR GRTGRAG  G    L   +++ 
Sbjct: 101 VHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERR 138

>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 =  130 bits (330), Expect = 6e-38
 Identities = 40/94 (42%), Positives = 56/94 (59%), Gaps = 4/94 (4%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
             +L         + + L GD+ QS RN  I  F+  E  +L+ TDVA+RGLDIP +  V
Sbjct: 233 VAKLVRLF----DNAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKV 288

Query: 107 VNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTD 140
           +N+D  +D+ T+ HRIGRTGR G KG A T + +
Sbjct: 289 INFDAPQDLRTYIHRIGRTGRMGRKGEAITFILN 322

>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 =  130 bits (328), Expect = 2e-36
 Identities = 31/96 (32%), Positives = 55/96 (57%)

Query: 49  ELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVN 108
            +  +   K+  +L  HG + Q++R S++ +FK+ E  ILV TDV ARG+D P++  V+ 
Sbjct: 357 SILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQ 416

Query: 109 YDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
             +  ++  + HRIGRT R+G +G +   +   +  
Sbjct: 417 IGVPSELANYIHRIGRTARSGKEGSSVLFICKDELP 452

>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 =  128 bits (322), Expect = 2e-35
 Identities = 32/101 (31%), Positives = 55/101 (54%), Gaps = 3/101 (2%)

Query: 47  AEELANSLTVKE---YDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHI 103
              L + L  +      +L  HG + Q++R S++ +FK+ E  ILV TDV ARG+D P++
Sbjct: 301 TSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNV 360

Query: 104 RTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
             V+   +  ++  + HRIGRT R+G +G +   +   +  
Sbjct: 361 HEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELP 401

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 90.2 bits (224), Expect = 3e-22
 Identities = 21/107 (19%), Positives = 46/107 (42%), Gaps = 14/107 (13%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDV----AARGLDIPH 102
            +EL   L   +++V     + ++         FK  +  IL+          RG+D+P 
Sbjct: 265 GKELYEYLKRFKFNVGETWSEFEK-----NFEDFKVGKINILIGVQAYYGKLTRGVDLPE 319

Query: 103 -IRTVVNYDL--ARDIDTHTHRIGRTGRAGNKGV--AYTLVTDKDKD 144
            I+ V+ +      D+ T+    GR+ R  N  +    +++ ++D++
Sbjct: 320 RIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFEEDEE 366

>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 = 78.7 bits (193), Expect = 5e-18
 Identities = 30/109 (27%), Positives = 44/109 (40%), Gaps = 9/109 (8%)

Query: 47  AEELANSLTVKEYDVLLLHGD--------MDQSERNSVITKFKRQECRILVATDVAARGL 98
           A+++ N L           G         + Q E+  ++ +F R E  +LVAT V   GL
Sbjct: 374 AKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGL 433

Query: 99  DIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGEL 147
           D+P +  VV Y+          R GRTGR    G    L+    +D   
Sbjct: 434 DVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMP-GRVIILMAKGTRDEAY 481

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 55.7 bits (133), Expect = 4e-10
 Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 3/84 (3%)

Query: 67  DMDQSERNSVITKFKRQ-ECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRT 125
            M    +  V+  F+   +  IL+AT VA  G+DI     V+ Y+   ++       GR 
Sbjct: 434 GMTLPAQKCVLEAFRASGDNNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR- 492

Query: 126 GRAGNKGVAYTLVTDKDKDGELRS 149
           GRA +    + L +  D   + ++
Sbjct: 493 GRARD-SKCFLLTSSADVIEKEKA 515

>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 = 55.7 bits (133), Expect = 5e-10
 Identities = 27/83 (32%), Positives = 38/83 (45%), Gaps = 4/83 (4%)

Query: 65  HGDMDQSERNSVITKFKRQE-CRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIG 123
              M    +  V+  FK  +  R+L+AT VA  G+DI     VV Y+ + ++       G
Sbjct: 674 TTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRG 733

Query: 124 RTGRAGNKGVAYTLVTDKDKDGE 146
           R GRA   G    LVT K +  E
Sbjct: 734 R-GRA--AGSKCILVTSKTEVVE 753

>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 = 55.3 bits (132), Expect = 6e-10
 Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 2/87 (2%)

Query: 65  HGDMDQSERNSVITKFKRQE-CRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIG 123
              M    +  V+  FK  +  R+L+AT VA  G+DI     VV Y+ + ++       G
Sbjct: 433 TTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRG 492

Query: 124 RTGRAGNKGVAYTLVTDKDKDGELRSQ 150
           R GRA            +  + E  ++
Sbjct: 493 R-GRAAGSKCILVTSKTEVVENEKCNR 518

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 55.0 bits (131), Expect = 9e-10
 Identities = 20/87 (22%), Positives = 33/87 (37%), Gaps = 2/87 (2%)

Query: 65  HGDMDQSERNSVITKFKRQ-ECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIG 123
           +  M    +  ++  FK   +  IL+AT VA  G+DI     V+ Y+   ++       G
Sbjct: 441 NTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRG 500

Query: 124 RTGRAGNKGVAYTLVTDKDKDGELRSQ 150
           R GRA               + E  + 
Sbjct: 501 R-GRARGSKCFLLTSNAGVIEKEQINM 526

>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 = 54.7 bits (131), Expect = 1e-09
 Identities = 23/107 (21%), Positives = 42/107 (39%), Gaps = 5/107 (4%)

Query: 47  AEELANSLTVKE-YDVLLLHGDMDQSERNSVITKFKRQE--CRILVATDVAARGLDIPHI 103
           A +L   L  +E     + H  M   ER+     F  ++   ++L+ +++ + G +    
Sbjct: 516 ALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFA 575

Query: 104 RTVVNYDLARDIDTHTHRIGRTGRAGNKG--VAYTLVTDKDKDGELR 148
             +V +DL  + D    RIGR  R G       +    +K     L 
Sbjct: 576 SHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQSVLV 622

>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 = 53.1 bits (126), Expect = 5e-09
 Identities = 27/83 (32%), Positives = 38/83 (45%), Gaps = 4/83 (4%)

Query: 65  HGDMDQSERNSVITKFKRQE-CRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIG 123
              M    +  V+  FK  +  R+L+AT VA  G+DI     VV Y+ + ++       G
Sbjct: 674 TTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRG 733

Query: 124 RTGRAGNKGVAYTLVTDKDKDGE 146
           R GRA   G    LVT K +  E
Sbjct: 734 R-GRA--AGSKCILVTSKTEVVE 753

>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 = 51.7 bits (125), Expect = 1e-08
 Identities = 31/96 (32%), Positives = 50/96 (52%), Gaps = 2/96 (2%)

Query: 48  EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVA-ARGLDIPHIRTV 106
           E+ A  L  K       H  ++ + R  V  KF+R + +I+VAT VA   G++ P++R V
Sbjct: 250 EDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVAT-VAFGMGINKPNVRFV 308

Query: 107 VNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD 142
           V++D+ R+I+++    GR GR G    A       D
Sbjct: 309 VHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPAD 344

>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* 4a92_A* 1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A Length = 666

 Score = 51.2 bits (122), Expect = 2e-08
 Identities = 23/116 (19%), Positives = 37/116 (31%), Gaps = 29/116 (25%)

Query: 41  LAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDI 100
              +   +ELA  L+    + +  +  +D S     I         ++VATD    G   
Sbjct: 403 CHSKKKCDELAAKLSGLGINAVAYYRGLDVSV----IPTIGD---VVVVATDALMTGYTG 455

Query: 101 PHIRTVV------------NYDLARDIDTHT---------HRIGRTGRAGNKGVAY 135
               +V+            + D    I+T T          R GRTGR       +
Sbjct: 456 -DFDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGRGRRGIYRF 510

>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 = 49.4 bits (118), Expect = 6e-08
 Identities = 20/94 (21%), Positives = 37/94 (39%), Gaps = 17/94 (18%)

Query: 57  KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDID 116
           K + +  +     + ER  ++  F+    R +V++ V   G+D+P     V       I 
Sbjct: 367 KVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGV-------IM 419

Query: 117 THTH-------RIGRTGRAG-NKGVA--YTLVTD 140
           + +        R+GR  R    K  A  Y L++ 
Sbjct: 420 SGSGSAREYIQRLGRILRPSKGKKEAVLYELISR 453

>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 Length = 780

 Score = 49.5 bits (119), Expect = 6e-08
 Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 4/64 (6%)

Query: 42  AMQL-NAEELANSLTV---KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
            + + +A E+   L+     E+ + L+HG + Q E++ V+ +F      ILV+T V   G
Sbjct: 593 KLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVG 652

Query: 98  LDIP 101
           +D+P
Sbjct: 653 IDVP 656

>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 = 49.2 bits (118), Expect = 7e-08
 Identities = 22/93 (23%), Positives = 47/93 (50%), Gaps = 2/93 (2%)

Query: 46  NAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVA-ARGLDIPHIR 104
           ++E++  SL          H +++  ++ +V  K+   E +++VAT VA   G+D P +R
Sbjct: 279 DSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVAT-VAFGMGIDKPDVR 337

Query: 105 TVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTL 137
            V+++ +++ ++ +    GR GR   K      
Sbjct: 338 FVIHHSMSKSMENYYQESGRAGRDDMKADCILY 370

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4} Length = 510

 Score = 44.5 bits (104), Expect = 3e-06
 Identities = 17/82 (20%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVAT-DVAARGLDIPHIRT 105
            + + + +  +   V  + G++D   RN + T  +  +  I+VA+  V + G+ + ++  
Sbjct: 360 GKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFSTGISVKNLHH 419

Query: 106 VVNYDLARDIDTHTHRIGRTGR 127
           VV     +        IGR  R
Sbjct: 420 VVLAHGVKSKIIVLQTIGRVLR 441

>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 Length = 618

 Score = 44.6 bits (105), Expect = 4e-06
 Identities = 21/129 (16%), Positives = 33/129 (25%), Gaps = 26/129 (20%)

Query: 41  LAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDI 100
           +       ++AN L      V+ L      +E      K K  +   +V TD++  G + 
Sbjct: 362 VPSIKAGNDIANCLRKSGKRVIQLSRKTFDTE----YPKTKLTDWDFVVTTDISEMGANF 417

Query: 101 PHIRTVVNYDLAR------DIDTHT--------------HRIGRTGRAGNKGVAYTLVTD 140
                V++           D                    R GR GR          V  
Sbjct: 418 -RAGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPA-QEDDQYVFS 475

Query: 141 KDKDGELRS 149
            D       
Sbjct: 476 GDPLKNDED 484

>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 = 44.4 bits (105), Expect = 4e-06
 Identities = 27/99 (27%), Positives = 46/99 (46%), Gaps = 13/99 (13%)

Query: 61  VLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTH 120
               H  +   +R  V   F+R   +++VAT   A G+++P  R V+   L R  D ++ 
Sbjct: 299 AAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLP-ARRVIVRSLYR-FDGYSK 356

Query: 121 RI---------GRTGRAG--NKGVAYTLVTDKDKDGELR 148
           RI         GR GR G   +G A  +V  +D++  ++
Sbjct: 357 RIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDREIAVK 395

>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* Length = 440

 Score = 42.9 bits (101), Expect = 1e-05
 Identities = 22/108 (20%), Positives = 41/108 (37%), Gaps = 25/108 (23%)

Query: 48  EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
             +A SL      V++L+    + E        K+++   ++ATD+A  G ++  +  V+
Sbjct: 191 NVMAASLRKAGKSVVVLNRKTFERE----YPTIKQKKPDFILATDIAEMGANLC-VERVL 245

Query: 108 NYDLAR--DIDTHTH-----------------RIGRTGRAGNK-GVAY 135
           +   A    +                      R GR GR  N+ G +Y
Sbjct: 246 DCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSY 293

>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 Length = 451

 Score = 42.1 bits (99), Expect = 2e-05
 Identities = 21/129 (16%), Positives = 33/129 (25%), Gaps = 26/129 (20%)

Query: 41  LAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDI 100
           +       ++AN L      V+ L      +E      K K  +   +V TD++  G + 
Sbjct: 195 VPSIKAGNDIANCLRKSGKRVIQLSRKTFDTE----YPKTKLTDWDFVVTTDISEMGANF 250

Query: 101 PHIRTVVNYDLAR------DIDTHT--------------HRIGRTGRAGNKGVAYTLVTD 140
                V++           D                    R GR GR          V  
Sbjct: 251 R-AGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNP-AQEDDQYVFS 308

Query: 141 KDKDGELRS 149
            D       
Sbjct: 309 GDPLKNDED 317

>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 = 42.1 bits (99), Expect = 3e-05
 Identities = 25/122 (20%), Positives = 43/122 (35%), Gaps = 15/122 (12%)

Query: 38  LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
             +L      E+LA ++      V   H  + + ER  V   F++   + +VAT   + G
Sbjct: 277 ADSLEENPTNEKLAKAI---RGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAG 333

Query: 98  LDIPHIRTVVNYDLA-------RDIDTHTHR--IGRTGRAG--NKGVAYTLVTDKDKDGE 146
           ++ P    V+  D+          I        +GR GR      G    + T  D    
Sbjct: 334 INTP-AFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPREV 392

Query: 147 LR 148
           + 
Sbjct: 393 MN 394

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A Length = 431

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 24/117 (20%), Positives = 37/117 (31%), Gaps = 23/117 (19%)

Query: 48  EELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV 107
            E+   L      VL L+    +SE      K K ++   ++ TD++  G +      V+
Sbjct: 185 AEIGTCLQKAGKKVLYLNRKTFESE----YPKCKSEKWDFVITTDISEMGANF-KADRVI 239

Query: 108 ---------NYDLARDIDTHT--------HRIGRTGRAGNK-GVAYTLVTDKDKDGE 146
                      D    +             R GR GR   K G  Y    +   D E
Sbjct: 240 DPRKTIKPILLDGRVSMQGPIAITPASAAQRRGRIGRNPEKLGDIYAYSGNVSSDNE 296

>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 = 37.7 bits (88), Expect = 7e-04
 Identities = 31/103 (30%), Positives = 48/103 (46%), Gaps = 12/103 (11%)

Query: 48  EELANSLT--VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRT 105
           ++ A  L   V E  + + HG M + E   V+  F  Q   +LV T +   G+DIP   T
Sbjct: 826 QKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANT 885

Query: 106 VVNYD-----LARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK 143
           ++        LA+    H  R GR GR+ ++  A+ L+T   K
Sbjct: 886 IIIERADHFGLAQ---LHQLR-GRVGRSHHQAYAW-LLTPHPK 923

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	150
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	100.0
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	100.0
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.98
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.97
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.97
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.97
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.97
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.97
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.93
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.96
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.95
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.95
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.95
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.95
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.95
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.94
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.94
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.94
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.94
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.94
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.94
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.94
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.92
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.92
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.92
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.91
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.91
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.91
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.91
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.9
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.9
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.9
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.9
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.9
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.89
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.89
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.89
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.88
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.88
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.88
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.88
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.88
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.88
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.87
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.87
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.87
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.87
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.87
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.87
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.87
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.87
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.86
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.86
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.86
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.86
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.86
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.85
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.85
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.85
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.85
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.84
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.84
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.83
3h1t_A	590	Type I site-specific restriction-modification syst	99.83
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.83
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.82
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.78
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.77
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.76
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.54
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.07
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.94
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	98.6
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	98.57
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	98.07
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	97.07
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	96.4
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	95.77
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	95.63
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	94.22
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	94.18
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	93.85
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	93.6
2l82_A	162	Designed protein OR32; structural genomics, northe	93.51
3gk5_A	108	Uncharacterized rhodanese-related protein TVG08686	92.98
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	92.85
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	92.69
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	92.26
3bor_A	237	Human initiation factor 4A-II; translation initiat	91.93
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	91.61
3dmn_A	174	Putative DNA helicase; APC89291.2, lactobacillus p	91.37
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	91.19
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	90.75
3flh_A	124	Uncharacterized protein LP_1913; alpha-beta protei	90.13
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	89.94
3g5j_A	134	Putative ATP/GTP binding protein; N-terminal domai	89.92
3foj_A	100	Uncharacterized protein; protein SSP1007, structur	89.67
3eme_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	89.45
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	89.18
3hix_A	106	ALR3790 protein; rhodanese, rhodanese_3, Q8YQN0, Q	89.17
3iwh_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	89.15
1wv9_A	94	Rhodanese homolog TT1651; CDC25, phosphatase, sulf	89.1
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	88.47
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	88.23
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	88.11
1gmx_A	108	GLPE protein; transferase, rhodanese, sulfurtransf	88.1
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	87.99
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	87.9
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	87.87
1tq1_A	129	AT5G66040, senescence-associated family protein; C	87.44
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	87.36
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	86.87
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	86.31
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	86.21
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	86.15
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	86.13
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	85.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	84.53
2k0z_A	110	Uncharacterized protein HP1203; A/B domain, struct	84.35
3nhv_A	144	BH2092 protein; alpha-beta protein, structural gen	84.08
2fsx_A	148	RV0390, COG0607: rhodanese-related sulfurtransfera	83.94
3ilm_A	141	ALR3790 protein; rhodanese-like, NSR437H, NESG, st	83.66
1vee_A	134	Proline-rich protein family; hypothetical protein,	83.23
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	83.14
1qxn_A	137	SUD, sulfide dehydrogenase; polysulfide-sulfur tra	83.13
2jtq_A	85	Phage shock protein E; solution structure rhodanes	82.31
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	82.16
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	81.95
2hhg_A	139	Hypothetical protein RPA3614; MCSG, structural gen	81.73
3d1p_A	139	Putative thiosulfate sulfurtransferase YOR285W; at	80.85

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=100.00  E-value=6e-32  Score=179.98  Aligned_cols=138  Identities=36%  Similarity=0.523  Sum_probs=124.5

Q ss_pred             CcCeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcC
Q psy17637          4 NKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQ   83 (150)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g   83 (150)
                      ..++.+.+.......+...|...+...  ...++||||++++.++.++..|...++.+..+||+|++.+|..+++.|++|
T Consensus         7 ~~~i~~~~~~~~~~~K~~~L~~ll~~~--~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g   84 (163)
T 2hjv_A            7 TRNIEHAVIQVREENKFSLLKDVLMTE--NPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRG   84 (163)
T ss_dssp             CCCEEEEEEECCGGGHHHHHHHHHHHH--CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             cccceEEEEECChHHHHHHHHHHHHhc--CCCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcC
Confidence            455677776666666666777766654  667999999999999999999999999999999999999999999999999


Q ss_pred             CceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         84 ECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        84 ~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +..|||+|+++++|+|+|++++||++++|+++..|.||+||+||.|+.|.+++|++..+.
T Consensus        85 ~~~vlv~T~~~~~Gld~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~  144 (163)
T 2hjv_A           85 EYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEK  144 (163)
T ss_dssp             SCSEEEECGGGTTTCCCSCCSEEEESSCCSSHHHHHHHTTTSSCTTCCEEEEEEECGGGH
T ss_pred             CCeEEEECChhhcCCchhcCCEEEEeCCCCCHHHHHHhccccCcCCCCceEEEEecHHHH
Confidence            999999999999999999999999999999999999999999999999999999987654

>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=100.00  E-value=2e-32  Score=183.87  Aligned_cols=136  Identities=35%  Similarity=0.491  Sum_probs=122.7

Q ss_pred             cCeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC
Q psy17637          5 KGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE   84 (150)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~   84 (150)
                      .++.+++.......+...|.+.+...  +..++||||++++.++.++..|...++.+..+||+|++.+|..+++.|++|+
T Consensus         4 ~~i~q~~~~~~~~~K~~~L~~ll~~~--~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~   81 (172)
T 1t5i_A            4 HGLQQYYVKLKDNEKNRKLFDLLDVL--EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQ   81 (172)
T ss_dssp             -CCEEEEEECCGGGHHHHHHHHHHHS--CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTS
T ss_pred             CCeEEEEEECChHHHHHHHHHHHHhC--CCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCCC
Confidence            45666666666666667777777665  6679999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637         85 CRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus        85 ~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      ..|||||+++++|+|+|++++||++++|+++..|+||+||+||.|+.|.+++|++..+
T Consensus        82 ~~vLvaT~~~~~Gldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~  139 (172)
T 1t5i_A           82 RRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN  139 (172)
T ss_dssp             CSEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHH
T ss_pred             CcEEEECCchhcCcchhhCCEEEEECCCCCHHHHHHHhcccccCCCCcEEEEEEcChh
Confidence            9999999999999999999999999999999999999999999999999999998654

>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=99.98  E-value=1.7e-31  Score=181.27  Aligned_cols=139  Identities=32%  Similarity=0.543  Sum_probs=111.5

Q ss_pred             CcCeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcC
Q psy17637          4 NKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQ   83 (150)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g   83 (150)
                      .+++.+.+.......+...|++.+... .+..++||||++++.++.++..|...++.+..+||+|++.+|..+++.|++|
T Consensus        17 ~~~i~q~~~~v~~~~K~~~L~~ll~~~-~~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f~~g   95 (185)
T 2jgn_A           17 SENITQKVVWVEESDKRSFLLDLLNAT-GKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSG   95 (185)
T ss_dssp             CTTEEEEEEECCGGGHHHHHHHHHHHC--CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHHHHHHT
T ss_pred             CCCceEEEEEeCcHHHHHHHHHHHHhc-CCCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHHHcC
Confidence            456777776666666667777777664 4678999999999999999999999999999999999999999999999999


Q ss_pred             CceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         84 ECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        84 ~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +..|||||+++++|+|+|++++||++++|+++.+|.|++||+||.|+.|.+++|+++.+.
T Consensus        96 ~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  155 (185)
T 2jgn_A           96 KSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNI  155 (185)
T ss_dssp             SSSEEEEEC------CCCSBSEEEESSCCSSHHHHHHHHTTBCCTTSCEEEEEEECGGGG
T ss_pred             CCeEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHccccCCCCCCcEEEEEEchhhH
Confidence            999999999999999999999999999999999999999999999999999999987654

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=99.97  E-value=2.9e-31  Score=176.94  Aligned_cols=136  Identities=33%  Similarity=0.549  Sum_probs=113.8

Q ss_pred             CeeEEEeecchhh-HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC
Q psy17637          6 GVAYTLVTDKDKE-FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE   84 (150)
Q Consensus         6 ~~~~~~~~~~~~~-~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~   84 (150)
                      ++.+.+....... +...|.+.+...  ...++||||++++.++.++..|...++.+..+||+|++.+|..+++.|++|+
T Consensus         3 ~i~~~~~~~~~~~~K~~~l~~ll~~~--~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~   80 (165)
T 1fuk_A            3 GIKQFYVNVEEEEYKYECLTDLYDSI--SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGS   80 (165)
T ss_dssp             -CEEEEEEEESGGGHHHHHHHHHHHT--TCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTS
T ss_pred             CcEEEEEECCcchhHHHHHHHHHHhC--CCCCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHcCC
Confidence            3444444433333 555666666554  6679999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         85 CRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        85 ~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      ..|||||+++++|+|+|++++||++++|+++.+|.||+||+||.|+.|.+++++++.+.
T Consensus        81 ~~vlv~T~~~~~G~d~~~~~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~  139 (165)
T 1fuk_A           81 SRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDV  139 (165)
T ss_dssp             CSEEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTH
T ss_pred             CEEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEEcchHH
Confidence            99999999999999999999999999999999999999999999999999999987754

>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=99.97  E-value=5.5e-31  Score=177.16  Aligned_cols=137  Identities=29%  Similarity=0.480  Sum_probs=117.1

Q ss_pred             cCeeEEEeecchhh-HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcC
Q psy17637          5 KGVAYTLVTDKDKE-FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQ   83 (150)
Q Consensus         5 ~~~~~~~~~~~~~~-~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g   83 (150)
                      .++.+.+....... +...|...+...  ...++||||++++.++.++..|...++.+..+||+|++.+|..+++.|++|
T Consensus         6 ~~i~q~~~~~~~~~~K~~~L~~ll~~~--~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f~~g   83 (175)
T 2rb4_A            6 NNIRQYYVLCEHRKDKYQALCNIYGSI--TIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDG   83 (175)
T ss_dssp             CCEEEEEEECSSHHHHHHHHHHHHTTS--CCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHTT
T ss_pred             CCceEEEEEcCChHhHHHHHHHHHHhC--CCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcC
Confidence            45666665555433 556666655544  667999999999999999999999999999999999999999999999999


Q ss_pred             CceEEEEcCCCcccCCccCCcEEEEecCC------CChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         84 ECRILVATDVAARGLDIPHIRTVVNYDLA------RDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        84 ~~~vlv~T~~~~~Gidi~~~~~vi~~~~~------~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +..|||||+++++|+|+|++++||++++|      .+..+|+||+||+||.|+.|.++.|++..+.
T Consensus        84 ~~~vLvaT~~~~~Gid~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~  149 (175)
T 2rb4_A           84 KEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDEL  149 (175)
T ss_dssp             SCSEEEECCSCCTTTCCTTEEEEEESSCCC--CCSCCHHHHHHHHCBC----CCEEEEEEECGGGH
T ss_pred             CCeEEEEecchhcCCCcccCCEEEEeCCCCCccccCCHHHHHHHhcccccCCCCceEEEEEccchH
Confidence            99999999999999999999999999999      8999999999999999999999999987653

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.97  E-value=3.2e-31  Score=180.67  Aligned_cols=136  Identities=34%  Similarity=0.551  Sum_probs=118.8

Q ss_pred             cCeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC
Q psy17637          5 KGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE   84 (150)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~   84 (150)
                      .++.+.+.......+...|++.+...   ..++||||++++.++.++..|...++.+..+||+|++.+|..+++.|++|+
T Consensus        28 ~~i~q~~~~~~~~~K~~~L~~~l~~~---~~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~  104 (191)
T 2p6n_A           28 LDVIQEVEYVKEEAKMVYLLECLQKT---PPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGK  104 (191)
T ss_dssp             CCSEEEEEECCGGGHHHHHHHHHTTS---CSCEEEECSCHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHHTS
T ss_pred             cCceEEEEEcChHHHHHHHHHHHHhC---CCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCC
Confidence            45666666555566666777766553   458999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         85 CRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        85 ~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      ..|||+|+++++|+|+|++++||++++|+++..|+||+||+||.|+.|.+++|+++.+.
T Consensus       105 ~~vLvaT~~~~~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~g~~g~~i~l~~~~~~  163 (191)
T 2p6n_A          105 KDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACD  163 (191)
T ss_dssp             CSEEEECHHHHTTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC---CCEEEEEECTTSC
T ss_pred             CEEEEEcCchhcCCCcccCCEEEEeCCCCCHHHHHHHhCccccCCCCcEEEEEEcCchh
Confidence            99999999999999999999999999999999999999999999999999999987643

>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=99.97  E-value=9e-31  Score=181.12  Aligned_cols=128  Identities=38%  Similarity=0.495  Sum_probs=114.2

Q ss_pred             ecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC
Q psy17637         13 TDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD   92 (150)
Q Consensus        13 ~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~   92 (150)
                      ......+...|.+.+...  ...++||||++++.++.++..|...++.+..+||+|++++|..+++.|++|..+|||||+
T Consensus        12 ~~~~~~k~~~l~~ll~~~--~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~   89 (212)
T 3eaq_A           12 PAPVRGRLEVLSDLLYVA--SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATD   89 (212)
T ss_dssp             ECCTTSHHHHHHHHHHHH--CCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECT
T ss_pred             eCCHHHHHHHHHHHHHhC--CCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecC
Confidence            334444455666666554  678999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637         93 VAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus        93 ~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      ++++|+|+|++++||++++|+++..|.||+||+||.|+.|.+++|++..+
T Consensus        90 ~~~~Gidi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~l~~~~~  139 (212)
T 3eaq_A           90 VAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRE  139 (212)
T ss_dssp             TTTCSSSCCCBSEEEESSCCSSHHHHHHHHTTBCCCC--BEEEEEECGGG
T ss_pred             hhhcCCCCccCcEEEECCCCcCHHHHHHHhcccCCCCCCCeEEEEEchhH
Confidence            99999999999999999999999999999999999999999999998765

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=99.97  E-value=8.1e-30  Score=184.35  Aligned_cols=133  Identities=37%  Similarity=0.481  Sum_probs=113.8

Q ss_pred             EEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEE
Q psy17637          9 YTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRIL   88 (150)
Q Consensus         9 ~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vl   88 (150)
                      .++.......+...|.+.+...  ...++||||++++.++.++..|...++.+..+||+|++.+|..+++.|++|..+||
T Consensus         5 ~~~i~~~~~~K~~~L~~ll~~~--~~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vL   82 (300)
T 3i32_A            5 EEAVPAPVRGRLEVLSDLLYVA--SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVL   82 (300)
T ss_dssp             EEEEECCSSSHHHHHHHHHHHH--CCSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHHHHHHTSCCEE
T ss_pred             EEEEECCHHHHHHHHHHHHHhc--CCCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhcCCceEE
Confidence            3334444444555666666554  47899999999999999999999999999999999999999999999999999999


Q ss_pred             EEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         89 VATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        89 v~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |||+++++|+|+|++++||++++|++...|+||+||+||.|+.|.+++|++..+.
T Consensus        83 VaT~va~~Gidi~~v~~VI~~d~p~s~~~y~Qr~GRagR~g~~G~~i~l~~~~e~  137 (300)
T 3i32_A           83 VATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRER  137 (300)
T ss_dssp             EECSTTTCSTTCCCCSEEEESSCCSSTTHHHHHHTCCC-----CEEEEEECSSTH
T ss_pred             EEechhhcCccccceeEEEEcCCCCCHHHHHHHccCcCcCCCCceEEEEeChHHH
Confidence            9999999999999999999999999999999999999999999999999988763

>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=99.93  E-value=1.1e-31  Score=179.77  Aligned_cols=137  Identities=37%  Similarity=0.507  Sum_probs=117.6

Q ss_pred             CeeEEEeecch-hhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC
Q psy17637          6 GVAYTLVTDKD-KEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE   84 (150)
Q Consensus         6 ~~~~~~~~~~~-~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~   84 (150)
                      ++.+.+..... ..+...|.+.+..  ....++||||++++.++.++..|...++.+..+||+|++.+|..+++.|++|+
T Consensus         3 ~i~~~~~~~~~~~~k~~~l~~ll~~--~~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~   80 (170)
T 2yjt_D            3 KIHQWYYRADDLEHKTALLVHLLKQ--PEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGR   80 (170)
Confidence            34444444443 3344455555544  35679999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCc
Q psy17637         85 CRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD  144 (150)
Q Consensus        85 ~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~  144 (150)
                      ..|||||+++++|+|+|++++||++++|+++..|.|++||+||.|+.|.++++++..+..
T Consensus        81 ~~vLvaT~~~~~Gid~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~  140 (170)
T 2yjt_D           81 VNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHL  140 (170)
Confidence            999999999999999999999999999999999999999999999999999998876543

>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=99.96  E-value=3.8e-28  Score=183.61  Aligned_cols=137  Identities=34%  Similarity=0.521  Sum_probs=120.4

Q ss_pred             CeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCc
Q psy17637          6 GVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQEC   85 (150)
Q Consensus         6 ~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~   85 (150)
                      ++...+.......+...+++.+...   ..++||||++++.++.+++.|...++.+..+||++++.+|..+++.|++|+.
T Consensus       275 ~i~~~~~~~~~~~k~~~l~~~l~~~---~~~~lVF~~t~~~a~~l~~~L~~~~~~~~~lhg~~~~~~R~~~l~~F~~g~~  351 (434)
T 2db3_A          275 DVKQTIYEVNKYAKRSKLIEILSEQ---ADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSM  351 (434)
T ss_dssp             TEEEEEEECCGGGHHHHHHHHHHHC---CTTEEEECSSHHHHHHHHHHHHHTTCCEEEESTTSCHHHHHHHHHHHHTSSC
T ss_pred             ccceEEEEeCcHHHHHHHHHHHHhC---CCCEEEEEeCcHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHHHcCCC
Confidence            4444444455555566777777664   2349999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCcc
Q psy17637         86 RILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDG  145 (150)
Q Consensus        86 ~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~~  145 (150)
                      .|||||+++++|+|+|++++||+|++|.+..+|+||+||+||.|+.|.+++|+++.+...
T Consensus       352 ~vLvaT~v~~rGlDi~~v~~VI~~d~p~~~~~y~qriGR~gR~g~~G~a~~~~~~~~~~~  411 (434)
T 2db3_A          352 KVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRA  411 (434)
T ss_dssp             SEEEECGGGTSSCCCTTCCEEEESSCCSSHHHHHHHHTTSSCTTCCEEEEEEECTTTCGG
T ss_pred             cEEEEchhhhCCCCcccCCEEEEECCCCCHHHHHHHhcccccCCCCCEEEEEEeccccHH
Confidence            999999999999999999999999999999999999999999999999999998665443

>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=99.95  E-value=1.9e-27  Score=183.47  Aligned_cols=134  Identities=25%  Similarity=0.404  Sum_probs=118.7

Q ss_pred             cCeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC
Q psy17637          5 KGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE   84 (150)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~   84 (150)
                      +++.+.......  ....+++.+...  +..++||||+|++.++.+++.|...++.+..+||+|++++|..+++.|++|+
T Consensus       211 ~~l~~~v~~~~~--~~~~l~~~l~~~--~~~~~IVf~~sr~~~e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~~~f~~g~  286 (523)
T 1oyw_A          211 PNIRYMLMEKFK--PLDQLMRYVQEQ--RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDD  286 (523)
T ss_dssp             TTEEEEEEECSS--HHHHHHHHHHHT--TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTS
T ss_pred             CceEEEEEeCCC--HHHHHHHHHHhc--CCCcEEEEeCCHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCC
Confidence            445555544332  334677777654  6779999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637         85 CRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus        85 ~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      ..|||||+++++|+|+|++++||++++|+++++|+|++||+||.|.++.++++++..+
T Consensus       287 ~~vlVaT~a~~~GiD~p~v~~VI~~~~p~s~~~y~Qr~GRaGR~g~~~~~~l~~~~~d  344 (523)
T 1oyw_A          287 LQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPAD  344 (523)
T ss_dssp             CSEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHH
T ss_pred             CeEEEEechhhCCCCccCccEEEEECCCCCHHHHHHHhccccCCCCCceEEEEeCHHH
Confidence            9999999999999999999999999999999999999999999999999999997654

>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=99.95  E-value=1.8e-27  Score=185.78  Aligned_cols=137  Identities=19%  Similarity=0.318  Sum_probs=119.5

Q ss_pred             cCeeEEEeecc--hhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhc
Q psy17637          5 KGVAYTLVTDK--DKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKR   82 (150)
Q Consensus         5 ~~~~~~~~~~~--~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~   82 (150)
                      +++.|......  .......+++.+... ....++||||++++.++.+++.|...++.+..+||+|++++|..+++.|++
T Consensus       237 ~nl~~~v~~~~~~~~~~~~~l~~~l~~~-~~~~~~IVf~~sr~~~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~~~F~~  315 (591)
T 2v1x_A          237 PNLYYEVRQKPSNTEDFIEDIVKLINGR-YKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSA  315 (591)
T ss_dssp             TTEEEEEEECCSSHHHHHHHHHHHHTTT-TTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHT
T ss_pred             cccEEEEEeCCCcHHHHHHHHHHHHHHh-ccCCCeEEEeCcHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHc
Confidence            44555544332  234455666666543 467899999999999999999999999999999999999999999999999


Q ss_pred             CCceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637         83 QECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus        83 g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      |+.+|||||+++++|+|+|++++||++++|.+++.|+|++||+||.|.++.++++++..|
T Consensus       316 g~~~VlVAT~a~~~GID~p~V~~VI~~~~p~s~~~y~Qr~GRaGR~G~~g~~i~l~~~~D  375 (591)
T 2v1x_A          316 NEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGD  375 (591)
T ss_dssp             TSSSEEEECTTSCTTCCCSCEEEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHH
T ss_pred             CCCeEEEEechhhcCCCcccccEEEEeCCCCCHHHHHHHhccCCcCCCCceEEEEEChHH
Confidence            999999999999999999999999999999999999999999999999999999987654

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.95  E-value=1.6e-27  Score=178.44  Aligned_cols=138  Identities=33%  Similarity=0.547  Sum_probs=118.0

Q ss_pred             CeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCc
Q psy17637          6 GVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQEC   85 (150)
Q Consensus         6 ~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~   85 (150)
                      ++.+.+.......+...+.+.+... ....++||||++++.++.+++.|...++.+..+||++++++|.++++.|++|+.
T Consensus       249 ~i~~~~~~~~~~~~~~~l~~~l~~~-~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~  327 (417)
T 2i4i_A          249 NITQKVVWVEESDKRSFLLDLLNAT-GKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKS  327 (417)
T ss_dssp             SEEEEEEECCGGGHHHHHHHHHHTC-CTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTSS
T ss_pred             CceEEEEEeccHhHHHHHHHHHHhc-CCCCeEEEEECCHHHHHHHHHHHHHCCCCeeEecCCCCHHHHHHHHHHHHcCCC
Confidence            3444444444444445555555544 567789999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCc
Q psy17637         86 RILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD  144 (150)
Q Consensus        86 ~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~  144 (150)
                      .|||||+++++|+|+|++++||++++|.+...|+||+||+||.|+.|.+++|+++.+..
T Consensus       328 ~vlvaT~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~  386 (417)
T 2i4i_A          328 PILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNIN  386 (417)
T ss_dssp             CEEEECHHHHTTSCCCCEEEEEESSCCSSHHHHHHHHTTBCC--CCEEEEEEECGGGGG
T ss_pred             CEEEECChhhcCCCcccCCEEEEEcCCCCHHHHHHhcCccccCCCCceEEEEEccccHH
Confidence            99999999999999999999999999999999999999999999999999999876543

>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=99.95  E-value=4e-27  Score=174.83  Aligned_cols=135  Identities=34%  Similarity=0.478  Sum_probs=119.2

Q ss_pred             eeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCce
Q psy17637          7 VAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECR   86 (150)
Q Consensus         7 ~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~   86 (150)
                      +...+.......+...+.+.+...  ...++||||++++.++.+++.|...++.+..+||++++++|..+++.|++|+..
T Consensus       225 ~~~~~~~~~~~~~~~~l~~~l~~~--~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~  302 (391)
T 1xti_A          225 LQQYYVKLKDNEKNRKLFDLLDVL--EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRR  302 (391)
T ss_dssp             CEEEEEECCGGGHHHHHHHHHHHS--CCSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTCCS
T ss_pred             ceEEEEEcCchhHHHHHHHHHHhc--CCCcEEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCc
Confidence            344444444444555666666554  678999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         87 ILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        87 vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |||||+++++|+|+|++++||++++|++...|.||+||+||.|+.|.+++++++.+.
T Consensus       303 vlv~T~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  359 (391)
T 1xti_A          303 ILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEND  359 (391)
T ss_dssp             EEEESCCCSSCBCCTTEEEEEESSCCSSHHHHHHHHCBCSSSCCCCEEEEEECSHHH
T ss_pred             EEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHhcccccCCCCceEEEEEEcccch
Confidence            999999999999999999999999999999999999999999999999999987644

>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=99.95  E-value=1.4e-26  Score=172.65  Aligned_cols=135  Identities=29%  Similarity=0.465  Sum_probs=117.1

Q ss_pred             eeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCce
Q psy17637          7 VAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECR   86 (150)
Q Consensus         7 ~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~   86 (150)
                      +...........+...+...+...  ...++||||++++.++.+++.|...++.+..+||+|++++|..+++.|++|+..
T Consensus       233 ~~~~~~~~~~~~k~~~l~~~~~~~--~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~  310 (400)
T 1s2m_A          233 ITQYYAFVEERQKLHCLNTLFSKL--QINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVR  310 (400)
T ss_dssp             EEEEEEECCGGGHHHHHHHHHHHS--CCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSS
T ss_pred             ceeEEEEechhhHHHHHHHHHhhc--CCCcEEEEEecHHHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHHHHHhcCCCc
Confidence            333333333334444454444443  667999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         87 ILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        87 vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |||||+++++|+|+|++++||++++|++...|.||+||+||.|+.|.+++++++.+.
T Consensus       311 vLv~T~~~~~Gidip~~~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~l~~~~~~  367 (400)
T 1s2m_A          311 TLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDR  367 (400)
T ss_dssp             EEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGH
T ss_pred             EEEEcCccccCCCccCCCEEEEeCCCCCHHHHHHhcchhcCCCCCceEEEEeccchH
Confidence            999999999999999999999999999999999999999999999999999988754

>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=99.94  E-value=6.4e-27  Score=175.04  Aligned_cols=123  Identities=34%  Similarity=0.588  Sum_probs=112.5

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccC
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGL   98 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gi   98 (150)
                      +...+.+.+...  ...++||||++++.++.+++.|...++.+..+||++++++|..+++.|++|+..|||+|+++++|+
T Consensus       263 k~~~l~~~~~~~--~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gi  340 (410)
T 2j0s_A          263 KFDTLCDLYDTL--TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGL  340 (410)
T ss_dssp             HHHHHHHHHHHH--TSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSC
T ss_pred             HHHHHHHHHHhc--CCCcEEEEEcCHHHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECChhhCcC
Confidence            444555555444  556899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         99 DIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        99 di~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |+|++++||++++|++...|+||+||+||.|+.|.+++|+++.+.
T Consensus       341 di~~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~  385 (410)
T 2j0s_A          341 DVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDI  385 (410)
T ss_dssp             CCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGH
T ss_pred             CcccCCEEEEECCCCCHHHHHHhcccccCCCCceEEEEEecHHHH
Confidence            999999999999999999999999999999999999999987653

>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=99.94  E-value=6.5e-27  Score=173.56  Aligned_cols=136  Identities=36%  Similarity=0.581  Sum_probs=116.3

Q ss_pred             eeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCce
Q psy17637          7 VAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECR   86 (150)
Q Consensus         7 ~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~   86 (150)
                      +...............++..+... ....++||||++++.++.+++.|...++.+..+||+|++++|.++++.|++|+.+
T Consensus       217 ~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~  295 (395)
T 3pey_A          217 IKQLYMDCKNEADKFDVLTELYGL-MTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSK  295 (395)
T ss_dssp             EEEEEEECSSHHHHHHHHHHHHTT-TTSSEEEEECSCHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCC
T ss_pred             ccEEEEEcCchHHHHHHHHHHHHh-ccCCCEEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHCCCCC
Confidence            333344433333233444455444 3667999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCcccCCccCCcEEEEecCCC------ChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         87 ILVATDVAARGLDIPHIRTVVNYDLAR------DIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        87 vlv~T~~~~~Gidi~~~~~vi~~~~~~------~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |||||+++++|+|+|++++||++++|+      ++..|+||+||+||.|+.+.+++++...+.
T Consensus       296 vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~  358 (395)
T 3pey_A          296 VLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNS  358 (395)
T ss_dssp             EEEECGGGSSSCCCTTEEEEEESSCCBCTTSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHH
T ss_pred             EEEECChhhcCCCcccCCEEEEcCCCCCCcCCCCHHHhhHhccccccCCCCceEEEEEechHH
Confidence            999999999999999999999999999      999999999999999999999999986543

>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=99.94  E-value=7.9e-27  Score=174.20  Aligned_cols=126  Identities=34%  Similarity=0.525  Sum_probs=112.7

Q ss_pred             chhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCC
Q psy17637         15 KDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVA   94 (150)
Q Consensus        15 ~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~   94 (150)
                      ....+...+...+...  ...++||||++++.++.++..|...++.+..+||+|++++|..+++.|++|+.+|||||+++
T Consensus       249 ~~~~~~~~l~~~~~~~--~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~  326 (412)
T 3fht_A          249 SRDEKFQALCNLYGAI--TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVC  326 (412)
T ss_dssp             SHHHHHHHHHHHHHHH--SSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGG
T ss_pred             ChHHHHHHHHHHHhhc--CCCCEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCcc
Confidence            3344455555555544  56799999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCccCCcEEEEecCC------CChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637         95 ARGLDIPHIRTVVNYDLA------RDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus        95 ~~Gidi~~~~~vi~~~~~------~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      ++|+|+|++++||++++|      .+..+|+||+||+||.|+.|.++++++..+
T Consensus       327 ~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~  380 (412)
T 3fht_A          327 ARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH  380 (412)
T ss_dssp             TSSCCCTTEEEEEESSCCBCSSSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHH
T ss_pred             ccCCCccCCCEEEEECCCCCCCCCcchheeecccCcccCCCCCceEEEEEcChh
Confidence            999999999999999999      467899999999999999999999998654

>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=99.94  E-value=4.6e-26  Score=167.50  Aligned_cols=134  Identities=35%  Similarity=0.554  Sum_probs=118.1

Q ss_pred             eeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCce
Q psy17637          7 VAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECR   86 (150)
Q Consensus         7 ~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~   86 (150)
                      +...........+...+...+.   ....++||||++++.++.+++.|...+..+..+||++++++|.++++.|++|+..
T Consensus       214 ~~~~~~~~~~~~~~~~l~~~l~---~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~  290 (367)
T 1hv8_A          214 IEQSYVEVNENERFEALCRLLK---NKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIR  290 (367)
T ss_dssp             SEEEEEECCGGGHHHHHHHHHC---STTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSS
T ss_pred             ceEEEEEeChHHHHHHHHHHHh---cCCCcEEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHcCCCe
Confidence            3334444444455556666554   3677899999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         87 ILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        87 vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |||+|+++++|+|+|++++||++++|+++.+|.|++||+||.|++|.+++++++.+.
T Consensus       291 vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~  347 (367)
T 1hv8_A          291 ILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREY  347 (367)
T ss_dssp             EEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSH
T ss_pred             EEEECChhhcCCCcccCCEEEEecCCCCHHHhhhcccccccCCCccEEEEEEcHHHH
Confidence            999999999999999999999999999999999999999999999999999987654

>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=99.94  E-value=9.2e-27  Score=174.05  Aligned_cols=123  Identities=35%  Similarity=0.634  Sum_probs=98.2

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccC
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGL   98 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gi   98 (150)
                      +...+...+...  ...++||||++++.++.+++.|...++.+..+||+|++++|..+++.|++|+.+|||||+++++|+
T Consensus       267 ~~~~l~~~~~~~--~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gi  344 (414)
T 3eiq_A          267 KLDTLCDLYETL--TITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGI  344 (414)
T ss_dssp             HHHHHHHHHHSS--CCSSCEEECSCHHHHHHHHHHHHTTTCCCEEC---CHHHHHHHHHHHHSCC---CEEECSSCC--C
T ss_pred             HHHHHHHHHHhC--CCCcEEEEeCCHHHHHHHHHHHHhcCCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCccccCC
Confidence            444555555443  667999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         99 DIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        99 di~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |+|++++||++++|.+...|+||+||+||.|+.|.+++++++.+.
T Consensus       345 dip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~  389 (414)
T 3eiq_A          345 DVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDK  389 (414)
T ss_dssp             CGGGCSCEEESSCCSSTHHHHHHSCCC-------CEEEEECSTHH
T ss_pred             CccCCCEEEEeCCCCCHHHhhhhcCcccCCCCCceEEEEEcHHHH
Confidence            999999999999999999999999999999999999999987654

>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=99.94  E-value=2.6e-26  Score=178.16  Aligned_cols=112  Identities=29%  Similarity=0.528  Sum_probs=106.5

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhcccc---CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEE
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVK---EYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVN  108 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~---~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~  108 (150)
                      ....++||||++++.++.++..|...   ++.+..+||+|++.+|..+++.|++|+..|||||+++++|+|+|++++||+
T Consensus       337 ~~~~~~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~GiDip~v~~VI~  416 (563)
T 3i5x_A          337 DSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQ  416 (563)
T ss_dssp             TTCCEEEEECSCHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSCCCTTCCEEEE
T ss_pred             CCCCcEEEEcCcHHHHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcchhhcCCCcccCCEEEE
Confidence            46779999999999999999999876   889999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637        109 YDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus       109 ~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +++|.++.+|+||+||+||.|+.|.+++++++.+.
T Consensus       417 ~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~  451 (563)
T 3i5x_A          417 IGVPSELANYIHRIGRTARSGKEGSSVLFICKDEL  451 (563)
T ss_dssp             ESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGH
T ss_pred             ECCCCchhhhhhhcCccccCCCCceEEEEEchhHH
Confidence            99999999999999999999999999999987653

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.94  E-value=4.3e-26  Score=177.74  Aligned_cols=120  Identities=28%  Similarity=0.535  Sum_probs=109.4

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhhHHHHHhhcccc---CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccC
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVK---EYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGL   98 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~---~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gi   98 (150)
                      .+...+... ....++||||++++.++.++..|...   ++.+..+||+|++.+|.++++.|++|+..|||||+++++|+
T Consensus       277 ~l~~~~~~~-~~~~~~iVF~~t~~~~~~l~~~L~~~~~~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~~~~~Gi  355 (579)
T 3sqw_A          277 HIKKQIKER-DSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGM  355 (579)
T ss_dssp             HHHHHHHHT-TTCCEEEEECSSHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSC
T ss_pred             HHHHHHhhc-CCCCcEEEECCcHHHHHHHHHHHHHhhcCCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcchhhcCC
Confidence            333344332 45779999999999999999999876   88999999999999999999999999999999999999999


Q ss_pred             CccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637         99 DIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus        99 di~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      |+|++++||++++|.++..|+||+||+||.|+.|.+++++++.+
T Consensus       356 Dip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e  399 (579)
T 3sqw_A          356 DFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDE  399 (579)
T ss_dssp             CCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGG
T ss_pred             CcccCCEEEEcCCCCCHHHhhhhccccccCCCCceEEEEEcccH
Confidence            99999999999999999999999999999999999999998765

>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=99.92  E-value=2.1e-25  Score=168.61  Aligned_cols=126  Identities=25%  Similarity=0.364  Sum_probs=110.3

Q ss_pred             HHHHHHHHHhcc--CCCCCeeEEehhhhhHHHHHhhccccCceEEEecC--------CCCHHHHHHHHHHhhcCCceEEE
Q psy17637         20 AGHLVRNLEGAN--QEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHG--------DMDQSERNSVITKFKRQECRILV   89 (150)
Q Consensus        20 ~~~ll~~l~~~~--~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~--------~~~~~~r~~~~~~f~~g~~~vlv   89 (150)
                      ...+.+.+....  ....++||||++++.++.+++.|...++.+..+||        +|++++|.++++.|++|+..|||
T Consensus       345 ~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~~~~vLv  424 (494)
T 1wp9_A          345 MDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLV  424 (494)
T ss_dssp             HHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEE
T ss_pred             HHHHHHHHHHHhccCCCCeEEEEEccHHHHHHHHHHHHHcCCCcEEEeccccccccccCCHHHHHHHHHHHhcCCceEEE
Confidence            344444444421  36789999999999999999999999999999999        99999999999999999999999


Q ss_pred             EcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCccc
Q psy17637         90 ATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGE  146 (150)
Q Consensus        90 ~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~~~  146 (150)
                      +|+++++|+|+|++++||++++|+++..|.|++||+||.|+ +.++.++++.+.++.
T Consensus       425 ~T~~~~~Gldl~~~~~Vi~~d~~~~~~~~~Qr~GR~~R~g~-g~~~~l~~~~t~ee~  480 (494)
T 1wp9_A          425 ATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMP-GRVIILMAKGTRDEA  480 (494)
T ss_dssp             ECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCCC-SEEEEEEETTSHHHH
T ss_pred             ECCccccCCCchhCCEEEEeCCCCCHHHHHHHHhhccCCCC-ceEEEEEecCCHHHH
Confidence            99999999999999999999999999999999999999997 999999998876554

>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=99.92  E-value=1.5e-24  Score=157.90  Aligned_cols=110  Identities=38%  Similarity=0.617  Sum_probs=102.4

Q ss_pred             HHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCC
Q psy17637         24 VRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHI  103 (150)
Q Consensus        24 l~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~  103 (150)
                      +..+..  ....++||||++++.++.+++.|.    .+..+||++++.+|.++++.|++|+..|||||+++++|+|+|++
T Consensus       212 ~~~~~~--~~~~~~lvf~~~~~~~~~l~~~l~----~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~  285 (337)
T 2z0m_A          212 VQALRE--NKDKGVIVFVRTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLV  285 (337)
T ss_dssp             HHHHHT--CCCSSEEEECSCHHHHHHHHTTCT----TEEEECTTSCHHHHHHHHHHHHTTSCSEEEECHHHHTTCCCCCB
T ss_pred             HHHHHh--CCCCcEEEEEcCHHHHHHHHHHhh----hhhhhcCCCCHHHHHHHHHHHHcCCCcEEEEcCccccCCCccCC
Confidence            344444  367899999999999999999987    57889999999999999999999999999999999999999999


Q ss_pred             cEEEEecCCCChhHHHHhhccccCCCCccEEEEEEe
Q psy17637        104 RTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVT  139 (150)
Q Consensus       104 ~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~  139 (150)
                      ++||++++|+++..|.|++||+||.|+.+.+++++.
T Consensus       286 ~~Vi~~~~~~s~~~~~Q~~GR~gR~g~~g~~~~~~~  321 (337)
T 2z0m_A          286 EKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFIL  321 (337)
T ss_dssp             SEEEESSCCSSHHHHHHHHTTBCGGGCCEEEEEEES
T ss_pred             CEEEEecCCCCHHHhhHhcCccccCCCCceEEEEEe
Confidence            999999999999999999999999999999999998

>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=99.92  E-value=9.9e-27  Score=177.54  Aligned_cols=113  Identities=36%  Similarity=0.584  Sum_probs=0.0

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLA  112 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~  112 (150)
                      ...++||||++++.++.++..|...++.+..+||+|++.+|..+++.|++|+.+|||||+++++|+|+|++++||++++|
T Consensus       332 ~~~~~lvF~~s~~~~~~l~~~L~~~~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~~~~~GlDip~v~~VI~~d~p  411 (479)
T 3fmp_B          332 TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLP  411 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cCCceEEEeCcHHHHHHHHHHHHhCCccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEccccccCCccccCCEEEEecCC
Confidence            55789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             C------ChhHHHHhhccccCCCCccEEEEEEecCCCcc
Q psy17637        113 R------DIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDG  145 (150)
Q Consensus       113 ~------~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~~  145 (150)
                      .      +...|+||+||+||.|..|.+++|++..+...
T Consensus       412 ~~~~~~~s~~~~~Qr~GRagR~g~~G~~i~~~~~~~~~~  450 (479)
T 3fmp_B          412 VDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMN  450 (479)
T ss_dssp             ---------------------------------------
T ss_pred             CCCccCCCHHHHHHHhcccccCCCCceEEEEEcCcchHH
Confidence            4      66899999999999999999999998765433

>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=99.91  E-value=1.8e-26  Score=171.42  Aligned_cols=112  Identities=37%  Similarity=0.635  Sum_probs=0.0

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLA  112 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~  112 (150)
                      ...++||||++++.++.+++.|...++.+..+||++++++|..+++.|++|+..|||||+++++|+|+|++++||++++|
T Consensus       258 ~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gldi~~~~~Vi~~~~p  337 (394)
T 1fuu_A          258 SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLP  337 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHHcCCeEEEeeCCCCHHHHHHHHHHHHCCCCcEEEECChhhcCCCcccCCEEEEeCCC
Confidence            56789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CChhHHHHhhccccCCCCccEEEEEEecCCCc
Q psy17637        113 RDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD  144 (150)
Q Consensus       113 ~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~  144 (150)
                      .++..|.||+||+||.|+.|.+++++++.+..
T Consensus       338 ~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~  369 (394)
T 1fuu_A          338 ANKENYIHRIGRGGRFGRKGVAINFVTNEDVG  369 (394)
T ss_dssp             --------------------------------
T ss_pred             CCHHHHHHHcCcccCCCCCceEEEEEchhHHH
Confidence            99999999999999999999999999877543

>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=99.91  E-value=4.2e-25  Score=170.51  Aligned_cols=123  Identities=22%  Similarity=0.276  Sum_probs=64.2

Q ss_pred             HHHHHHHHHHhcc--CCCCCeeEEehhhhhHHHHHhhcccc------------CceEEEecCCCCHHHHHHHHHHhhc-C
Q psy17637         19 FAGHLVRNLEGAN--QEVPPALMNLAMQLNAEELANSLTVK------------EYDVLLLHGDMDQSERNSVITKFKR-Q   83 (150)
Q Consensus        19 ~~~~ll~~l~~~~--~~~~~~ivf~~~~~~~~~l~~~L~~~------------~~~~~~~~~~~~~~~r~~~~~~f~~-g   83 (150)
                      +...|.+.+....  ....++||||++++.++.++..|...            |.....+||+|++++|.++++.|++ |
T Consensus       373 K~~~L~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g  452 (556)
T 4a2p_A          373 KLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSK  452 (556)
T ss_dssp             HHHHHHHHHHHHHHHCTTCCEEEEESSHHHHHHHHHHHTTCSGGGSCCEEC-----------------------------
T ss_pred             HHHHHHHHHHHHhcCCCCceEEEEEccHHHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHhcccC
Confidence            3344555554321  46789999999999999999999765            4556677888999999999999999 9


Q ss_pred             CceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         84 ECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        84 ~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +.+|||||+++++|+|+|++++||+||+|+++..|+||+|| ||. .++.++.|+++.+.
T Consensus       453 ~~~vLvaT~~~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~  510 (556)
T 4a2p_A          453 DNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEV  510 (556)
T ss_dssp             -CCEEEEEC-----------CEEEEETCCSCHHHHHHC----------CCEEEEESCHHH
T ss_pred             ceEEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCcch
Confidence            99999999999999999999999999999999999999999 998 68899999887654

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.91  E-value=2.3e-24  Score=153.90  Aligned_cols=128  Identities=16%  Similarity=0.248  Sum_probs=96.7

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhcccc-CceEEEecCCCCHHHHHHHHHHhhcC-Cce-EEEEcCCCc
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVK-EYDVLLLHGDMDQSERNSVITKFKRQ-ECR-ILVATDVAA   95 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~-vlv~T~~~~   95 (150)
                      ++..+.+.+......+.++||||++...++.+...|... ++.+..+||++++++|..+++.|+++ ... +|++|++++
T Consensus        97 K~~~L~~ll~~~~~~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~st~~~g  176 (271)
T 1z5z_A           97 KMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGG  176 (271)
T ss_dssp             HHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCTTC
T ss_pred             HHHHHHHHHHHHHhCCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEEehhhhc
Confidence            444555555444346789999999999999999999875 89999999999999999999999998 666 789999999


Q ss_pred             ccCCccCCcEEEEecCCCChhHHHHhhccccCCCCcc--EEEEEEecCCCccc
Q psy17637         96 RGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKG--VAYTLVTDKDKDGE  146 (150)
Q Consensus        96 ~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~--~~~~~~~~~~~~~~  146 (150)
                      +|+|++.+++||+||+|+++..|.|++||++|.|+.+  .++.+++....++.
T Consensus       177 ~Glnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R~Gq~~~v~v~~li~~~TiEe~  229 (271)
T 1z5z_A          177 FGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEK  229 (271)
T ss_dssp             CCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETTSHHHH
T ss_pred             CCcCcccCCEEEEECCCCChhHHHHHHHhccccCCCCceEEEEEeeCCCHHHH
Confidence            9999999999999999999999999999999999865  45777777655443

>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=99.90  E-value=8.3e-24  Score=168.06  Aligned_cols=126  Identities=18%  Similarity=0.215  Sum_probs=110.8

Q ss_pred             hhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCc
Q psy17637         16 DKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAA   95 (150)
Q Consensus        16 ~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~   95 (150)
                      ...+...|++.+......+.++||||+|++.++.|+..|...|+++..+||++++.++..+.+.|+.|  .|+|||++++
T Consensus       414 ~~~K~~al~~~i~~~~~~~~pvLVft~s~~~se~Ls~~L~~~gi~~~vLhg~~~~rEr~ii~~ag~~g--~VlIATdmAg  491 (844)
T 1tf5_A          414 MEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKG--AVTIATNMAG  491 (844)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTTSTT--CEEEEETTSS
T ss_pred             HHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCccHHHHHHHHHcCCCC--eEEEeCCccc
Confidence            34456677777765434677999999999999999999999999999999999888887666666655  6999999999


Q ss_pred             ccCCcc--------CCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         96 RGLDIP--------HIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        96 ~Gidi~--------~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +|+|++        +..+||+++.|.+...|.|++||+||.|++|.+++|++.+|.
T Consensus       492 RG~DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr~GRTGRqG~~G~s~~~vs~eD~  547 (844)
T 1tf5_A          492 RGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDE  547 (844)
T ss_dssp             TTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSS
T ss_pred             cCcCccccchhhhcCCcEEEEecCCCCHHHHHhhcCccccCCCCCeEEEEecHHHH
Confidence            999999        788999999999999999999999999999999999998765

>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=99.90  E-value=5.9e-24  Score=168.48  Aligned_cols=104  Identities=28%  Similarity=0.384  Sum_probs=90.0

Q ss_pred             CCCeeEEehhhhhHHHHHhhcccc------CceEEEecCC--------CCHHHHHHHHHHhhcCCceEEEEcCCCcccCC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVK------EYDVLLLHGD--------MDQSERNSVITKFKRQECRILVATDVAARGLD   99 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~------~~~~~~~~~~--------~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gid   99 (150)
                      ..++||||++++.++.+++.|...      |+++..+||+        |++.+|.++++.|++|+.+|||||+++++|+|
T Consensus       400 ~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~~~~~GID  479 (699)
T 4gl2_A          400 SARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLD  479 (699)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEECSCCTTSC
T ss_pred             CCcEEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCc
Confidence            789999999999999999999876      8999999999        99999999999999999999999999999999


Q ss_pred             ccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEec
Q psy17637        100 IPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTD  140 (150)
Q Consensus       100 i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~  140 (150)
                      +|++++||+||+|+|+..|+||+||+||.|   .+++++..
T Consensus       480 ip~v~~VI~~d~p~s~~~~~Qr~GRArr~g---~~~~l~~~  517 (699)
T 4gl2_A          480 IKECNIVIRYGLVTNEIAMVQARGRARADE---STYVLVAH  517 (699)
T ss_dssp             CCSCCCCEEESCCCCHHHHHHHHTTSCSSS---CEEEEEEE
T ss_pred             cccCCEEEEeCCCCCHHHHHHHcCCCCCCC---ceEEEEEe
Confidence            999999999999999999999999977665   34444443

>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=99.90  E-value=1.8e-23  Score=165.00  Aligned_cols=123  Identities=22%  Similarity=0.331  Sum_probs=112.4

Q ss_pred             HHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCC
Q psy17637         20 AGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLD   99 (150)
Q Consensus        20 ~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gid   99 (150)
                      ...++..+......+.++||||+|+..++.+++.|...++++..+||++++.+|.++++.|+.|+..|||||+.+++|+|
T Consensus       431 ~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~GlD  510 (661)
T 2d7d_A          431 IDDLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLD  510 (661)
T ss_dssp             HHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTTCC
T ss_pred             HHHHHHHHHHHHhcCCeEEEEECCHHHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCCcc
Confidence            44666777665456789999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCcEEEEecC-----CCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637        100 IPHIRTVVNYDL-----ARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus       100 i~~~~~vi~~~~-----~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +|++++||+++.     |.+..+|+||+||+||. ..|.+++++++.+.
T Consensus       511 ip~v~lVi~~d~d~~G~p~s~~~~iQr~GRagR~-~~G~~i~~~~~~~~  558 (661)
T 2d7d_A          511 IPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-AEGRVIMYADKITK  558 (661)
T ss_dssp             CTTEEEEEETTTTCCTTTTSHHHHHHHHHTTTTS-TTCEEEEECSSCCH
T ss_pred             cCCCCEEEEeCcccccCCCCHHHHHHHhCcccCC-CCCEEEEEEeCCCH
Confidence            999999999997     89999999999999998 58999999887654

>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=99.90  E-value=1.8e-23  Score=165.08  Aligned_cols=123  Identities=22%  Similarity=0.314  Sum_probs=111.5

Q ss_pred             HHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCC
Q psy17637         20 AGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLD   99 (150)
Q Consensus        20 ~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gid   99 (150)
                      ...++..+......+.++||||+|+..++.+++.|...++++..+||++++.+|.++++.|+.|++.|||||+.+++|+|
T Consensus       425 ~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~GlD  504 (664)
T 1c4o_A          425 ILDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLD  504 (664)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCC
T ss_pred             HHHHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHhcCCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhcCcc
Confidence            44666666655446789999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCcEEEEecC-----CCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637        100 IPHIRTVVNYDL-----ARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus       100 i~~~~~vi~~~~-----~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +|++++||+++.     |.+..+|+|++||+||.+ .|.++++++..+.
T Consensus       505 ip~v~lVI~~d~d~~G~p~s~~~~iQr~GRagR~~-~G~~i~~~~~~~~  552 (664)
T 1c4o_A          505 IPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA-RGEVWLYADRVSE  552 (664)
T ss_dssp             CTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTST-TCEEEEECSSCCH
T ss_pred             CCCCCEEEEeCCcccCCCCCHHHHHHHHCccCcCC-CCEEEEEEcCCCH
Confidence            999999999997     889999999999999996 7899998877643

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.90  E-value=1.6e-24  Score=166.97  Aligned_cols=110  Identities=20%  Similarity=0.308  Sum_probs=78.0

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccC------------ceEEEecCCCCHHHHHHHHHHhhc-CCceEEEEcCCCcccC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKE------------YDVLLLHGDMDQSERNSVITKFKR-QECRILVATDVAARGL   98 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~------------~~~~~~~~~~~~~~r~~~~~~f~~-g~~~vlv~T~~~~~Gi   98 (150)
                      .+..++||||++++.++.++..|...+            .....+||+|++++|.++++.|++ |+.+|||||+++++|+
T Consensus       387 ~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~Gl  466 (555)
T 3tbk_A          387 KPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDNNILIATSVADEGI  466 (555)
T ss_dssp             CTTCCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC--------------------------CCSEEEECCCTTCCE
T ss_pred             CCCceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHhcCCCeeEEEEcchhhcCC
Confidence            356899999999999999999997653            344555679999999999999999 9999999999999999


Q ss_pred             CccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         99 DIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        99 di~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |+|++++||+||+|+++..|+||+|| ||. ..+.++.|+++.+.
T Consensus       467 Dlp~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~  509 (555)
T 3tbk_A          467 DIAECNLVILYEYVGNVIKMIQTRGR-GRA-RDSKCFLLTSSADV  509 (555)
T ss_dssp             ETTSCSEEEEESCCSSCCCEECSSCC-CTT-TSCEEEEEESCHHH
T ss_pred             ccccCCEEEEeCCCCCHHHHHHhcCc-CcC-CCceEEEEEcCCCH
Confidence            99999999999999999999999999 988 78999999887644

>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=99.89  E-value=1.3e-22  Score=159.00  Aligned_cols=127  Identities=21%  Similarity=0.275  Sum_probs=109.3

Q ss_pred             chhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCC
Q psy17637         15 KDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVA   94 (150)
Q Consensus        15 ~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~   94 (150)
                      ....+...++..+......+.|+||||+|++.++.++..|...++++..+||+..+.++..+...++.|  .|+|||+++
T Consensus       455 t~~eK~~al~~~I~~~~~~gqpVLVFt~S~e~sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g--~VtVATdmA  532 (822)
T 3jux_A          455 TQKEKYEKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKG--MVTIATNMA  532 (822)
T ss_dssp             SHHHHHHHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTT--CEEEEETTT
T ss_pred             cHHHHHHHHHHHHHHHhhCCCCEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCC--eEEEEcchh
Confidence            344566688888876545678999999999999999999999999999999996555555555556555  699999999


Q ss_pred             cccCCcc--------CCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         95 ARGLDIP--------HIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        95 ~~Gidi~--------~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      ++|+|++        +..+||+++.|.+...|.|++||+||.|++|.+++|++.+|.
T Consensus       533 gRGtDI~lg~~V~~~GglhVInte~Pes~r~y~qriGRTGRqG~~G~a~~fvsleD~  589 (822)
T 3jux_A          533 GRGTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLEDD  589 (822)
T ss_dssp             TTTCCCCCCTTTTTTTSCEEEESSCCSSHHHHHHHHTTSSCSSCCCEEEEEEETTSH
T ss_pred             hCCcCccCCcchhhcCCCEEEecCCCCCHHHHHHhhCccccCCCCeeEEEEechhHH
Confidence            9999997        667999999999999999999999999999999999998864

>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=99.89  E-value=1.2e-23  Score=169.12  Aligned_cols=123  Identities=22%  Similarity=0.276  Sum_probs=69.4

Q ss_pred             HHHHHHHHHHhc--cCCCCCeeEEehhhhhHHHHHhhcccc------------CceEEEecCCCCHHHHHHHHHHhhc-C
Q psy17637         19 FAGHLVRNLEGA--NQEVPPALMNLAMQLNAEELANSLTVK------------EYDVLLLHGDMDQSERNSVITKFKR-Q   83 (150)
Q Consensus        19 ~~~~ll~~l~~~--~~~~~~~ivf~~~~~~~~~l~~~L~~~------------~~~~~~~~~~~~~~~r~~~~~~f~~-g   83 (150)
                      ++..|.+.+...  ..+..++||||++++.++.++..|...            |.....+||+|++.+|..+++.|++ |
T Consensus       614 K~~~L~~lL~~~~~~~~~~kvLIF~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F~~~g  693 (797)
T 4a2q_A          614 KLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSK  693 (797)
T ss_dssp             HHHHHHHHHHHHHHHCSSCCEEEEESSHHHHHHHHHHHHTCSTTCSCCCEEC----------------------------
T ss_pred             HHHHHHHHHHHHhccCCCCeEEEEECcHHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHhhccC
Confidence            344455555431  146789999999999999999999653            5556777899999999999999999 9


Q ss_pred             CceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         84 ECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        84 ~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +++|||||+++++|+|+|++++||+||+|+++..|+||+|| ||. ..+.++.|++..+.
T Consensus       694 ~~~vLVaT~~~~~GIDlp~v~~VI~yd~p~s~~~~iQr~GR-GR~-~~g~~i~l~~~~~~  751 (797)
T 4a2q_A          694 DNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEV  751 (797)
T ss_dssp             CCSEEEEECC-------CCCSEEEEESCCSCHHHHHTC---------CCCEEEEECCHHH
T ss_pred             CceEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCCcH
Confidence            99999999999999999999999999999999999999999 999 68899999877544

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.89  E-value=7.3e-24  Score=167.89  Aligned_cols=122  Identities=20%  Similarity=0.299  Sum_probs=73.1

Q ss_pred             HHHHHHHHHhc--cCCCCCeeEEehhhhhHHHHHhhccccC----ceEEEe--------cCCCCHHHHHHHHHHhhc-CC
Q psy17637         20 AGHLVRNLEGA--NQEVPPALMNLAMQLNAEELANSLTVKE----YDVLLL--------HGDMDQSERNSVITKFKR-QE   84 (150)
Q Consensus        20 ~~~ll~~l~~~--~~~~~~~ivf~~~~~~~~~l~~~L~~~~----~~~~~~--------~~~~~~~~r~~~~~~f~~-g~   84 (150)
                      ...|.+.+...  ..+..++||||++++.++.+++.|...+    +++..+        ||+|++++|.++++.|++ |+
T Consensus       382 ~~~L~~ll~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~  461 (696)
T 2ykg_A          382 LEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGD  461 (696)
T ss_dssp             HHHHHHHHHHHHTTCTTCCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC-----------------------------C
T ss_pred             HHHHHHHHHHHhccCCCCcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHHhcCC
Confidence            33444444432  1356799999999999999999998876    788888        559999999999999998 99


Q ss_pred             ceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         85 CRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        85 ~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      .+|||||+++++|+|+|++++||+||+|+++.+|+||+|| ||. +.+.++.+++..+.
T Consensus       462 ~~vLVaT~v~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-GR~-~~g~~~~l~~~~~~  518 (696)
T 2ykg_A          462 HNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRA-RGSKCFLLTSNAGV  518 (696)
T ss_dssp             CSCSEEEESSCCC---CCCSEEEEESCC--CCCC-----------CCCEEEEEESCHHH
T ss_pred             ccEEEEechhhcCCcCccCCEEEEeCCCCCHHHHHHhhcc-CcC-CCceEEEEecCCCH
Confidence            9999999999999999999999999999999999999999 998 67888888876543

>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=99.88  E-value=1.3e-22  Score=165.75  Aligned_cols=124  Identities=20%  Similarity=0.282  Sum_probs=108.5

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccc-cCceEEEecCCCCHHHHHHHHHHhhcCC--ceEEEEcCCCc
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTV-KEYDVLLLHGDMDQSERNSVITKFKRQE--CRILVATDVAA   95 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~-~~~~~~~~~~~~~~~~r~~~~~~f~~g~--~~vlv~T~~~~   95 (150)
                      +...+.+.+..  ....++||||++++.++.++..|.. .++++..+||+|++.+|..+++.|++|+  ++|||||++++
T Consensus       490 K~~~L~~ll~~--~~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~~~~~~R~~~l~~F~~g~~~~~vLvaT~v~~  567 (968)
T 3dmq_A          490 RVEWLMGYLTS--HRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGS  567 (968)
T ss_dssp             HHHHHHHHHHH--TSSSCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTTSCTTHHHHHHHHHHSTTSSCEEEECSCCTT
T ss_pred             HHHHHHHHHHh--CCCCCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCcccEEEecchhh
Confidence            44556666655  4778999999999999999999984 5999999999999999999999999998  99999999999


Q ss_pred             ccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccE--EEEEEecCCCc
Q psy17637         96 RGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGV--AYTLVTDKDKD  144 (150)
Q Consensus        96 ~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~--~~~~~~~~~~~  144 (150)
                      +|+|+|++++||++++|+++..|.|++||+||.|+.+.  ++.++.....+
T Consensus       568 ~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~Gq~~~v~v~~~~~~~t~e  618 (968)
T 3dmq_A          568 EGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQ  618 (968)
T ss_dssp             CSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCSSSCSCCEEEEEEETTSHH
T ss_pred             cCCCcccCcEEEEecCCCCHHHHHHHhhccccCCCCceEEEEEecCCChHH
Confidence            99999999999999999999999999999999998774  44445554433

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.88  E-value=2.4e-22  Score=150.66  Aligned_cols=121  Identities=26%  Similarity=0.317  Sum_probs=101.0

Q ss_pred             CeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEE-EecCCCCHHHHHHHHHHhhcCC
Q psy17637          6 GVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVL-LLHGDMDQSERNSVITKFKRQE   84 (150)
Q Consensus         6 ~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~-~~~~~~~~~~r~~~~~~f~~g~   84 (150)
                      ++...+.......   .+.+.+...   ..++||||++++.++.++..|...++.+. .+||.    +|+  ++.|++|+
T Consensus       230 ~i~~~~~~~~~~~---~l~~~l~~~---~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~----~r~--~~~f~~g~  297 (414)
T 3oiy_A          230 NITHVRISSRSKE---KLVELLEIF---RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF----EKN--FEDFKVGK  297 (414)
T ss_dssp             SEEEEEESSCCHH---HHHHHHHHH---CSSEEEEESSHHHHHHHHHHHHHTTCCEEESSSCH----HHH--HHHHHTTS
T ss_pred             cchheeeccCHHH---HHHHHHHHc---CCCEEEEECCHHHHHHHHHHHHHcCCceehhhcCc----chH--HHHHhCCC
Confidence            3444444443333   344444432   37899999999999999999999999998 89985    333  99999999


Q ss_pred             ceEEEE----cCCCcccCCccC-CcEEEEecCC--CChhHHHHhhccccCCC----CccEEEEEE
Q psy17637         85 CRILVA----TDVAARGLDIPH-IRTVVNYDLA--RDIDTHTHRIGRTGRAG----NKGVAYTLV  138 (150)
Q Consensus        85 ~~vlv~----T~~~~~Gidi~~-~~~vi~~~~~--~~~~~~~q~~GR~~R~g----~~~~~~~~~  138 (150)
                      .+||||    |+++++|+|+|+ +++||++++|  .+..+|+||+||+||.|    ..|.+++++
T Consensus       298 ~~vLvat~s~T~~~~~GiDip~~v~~VI~~~~p~~~~~~~y~qr~GR~gR~g~~~~~~g~~i~~~  362 (414)
T 3oiy_A          298 INILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFE  362 (414)
T ss_dssp             CSEEEEECCTTCCCCCCCCCTTTCCEEEEESCCTTTCHHHHHHHHGGGCCEETTEECCEEEEEEC
T ss_pred             CeEEEEecCcCchhhccCccccccCEEEEECCCCCCCHHHHHHHhCccccCCCCCCcceEEEEEE
Confidence            999999    999999999999 9999999999  99999999999999987    468888888

>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=99.88  E-value=2.2e-22  Score=159.74  Aligned_cols=127  Identities=19%  Similarity=0.233  Sum_probs=113.4

Q ss_pred             hhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCc
Q psy17637         16 DKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAA   95 (150)
Q Consensus        16 ~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~   95 (150)
                      ...+...+++.+......+.|+||||+|++.++.|+..|...|+++..+||.+.+.++..+.+.|+.|  .|+|||++++
T Consensus       423 ~~~K~~al~~~i~~~~~~gqpvLVft~sie~se~Ls~~L~~~gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAg  500 (853)
T 2fsf_A          423 EAEKIQAIIEDIKERTAKGQPVLVGTISIEKSELVSNELTKAGIKHNVLNAKFHANEAAIVAQAGYPA--AVTIATNMAG  500 (853)
T ss_dssp             HHHHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHHTTCCCEECCTTCHHHHHHHHHTTTSTT--CEEEEESCCS
T ss_pred             HHHHHHHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEeccccc
Confidence            34566678887766545778999999999999999999999999999999999888888888888887  6999999999


Q ss_pred             ccCCccCC-------------------------------------cEEEEecCCCChhHHHHhhccccCCCCccEEEEEE
Q psy17637         96 RGLDIPHI-------------------------------------RTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLV  138 (150)
Q Consensus        96 ~Gidi~~~-------------------------------------~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~  138 (150)
                      +|+|++..                                     .+||+++.|.+...|.|++||+||.|++|.+.+|+
T Consensus       501 RGtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGl~VI~te~pes~riy~qr~GRTGRqGd~G~s~~fl  580 (853)
T 2fsf_A          501 RGTDIVLGGSWQAEVAALENPTAEQIEKIKADWQVRHDAVLEAGGLHIIGTERHESRRIDNQLRGRSGRQGDAGSSRFYL  580 (853)
T ss_dssp             SCSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHHHHHHHHHHHTTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEE
T ss_pred             CCcCccCCCchHhhhhhcccchhHHHHHHHHHhhhhhhHHHhcCCcEEEEccCCCCHHHHHhhccccccCCCCeeEEEEe
Confidence            99999863                                     59999999999999999999999999999999999


Q ss_pred             ecCCCc
Q psy17637        139 TDKDKD  144 (150)
Q Consensus       139 ~~~~~~  144 (150)
                      +.+|..
T Consensus       581 s~eD~l  586 (853)
T 2fsf_A          581 SMEDAL  586 (853)
T ss_dssp             ETTSGG
T ss_pred             cccHHH
Confidence            987643

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.88  E-value=2.8e-22  Score=164.11  Aligned_cols=120  Identities=19%  Similarity=0.286  Sum_probs=105.7

Q ss_pred             HHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCc---------------------------------------e
Q psy17637         20 AGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEY---------------------------------------D   60 (150)
Q Consensus        20 ~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~---------------------------------------~   60 (150)
                      ...++..+...  ...++||||++++.++.++..|...++                                       .
T Consensus       331 l~~l~~~l~~~--~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~g  408 (1010)
T 2xgj_A          331 IYKIVKMIWKK--KYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRG  408 (1010)
T ss_dssp             HHHHHHHHHHH--TCCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHHHHHHHHHHHHTTSCGGGTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhc--CCCCEEEEECCHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHHhCC
Confidence            34466666554  556899999999999999999976433                                       2


Q ss_pred             EEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEE----ecC----CCChhHHHHhhccccCCCC--
Q psy17637         61 VLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVN----YDL----ARDIDTHTHRIGRTGRAGN--  130 (150)
Q Consensus        61 ~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~----~~~----~~~~~~~~q~~GR~~R~g~--  130 (150)
                      +..+||+|++.+|..+++.|++|.++|||||+++++|+|+|.+++||+    ||.    |.++.+|.||+||+||.|.  
T Consensus       409 I~~~Hggl~~~eR~~ve~~F~~G~ikVLVAT~~la~GIDiP~~~vVI~~~~kfd~~~~rp~s~~~y~Qr~GRAGR~G~d~  488 (1010)
T 2xgj_A          409 IGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDD  488 (1010)
T ss_dssp             EEEESTTSCHHHHHHHHHHHHTTCCSEEEEEGGGGGSTTCCBSEEEESCSEEECSSCEEECCHHHHHHHHTTBCCTTTCS
T ss_pred             eeEECCCCCHHHHHHHHHHHhcCCCcEEEEehHhhccCCCCCceEEEeCCcccCCcCCccCCHHHHhHhhhhcccCCCCC
Confidence            789999999999999999999999999999999999999999999999    998    8899999999999999996  


Q ss_pred             ccEEEEEEecC
Q psy17637        131 KGVAYTLVTDK  141 (150)
Q Consensus       131 ~~~~~~~~~~~  141 (150)
                      .|.+++++++.
T Consensus       489 ~G~vi~l~~~~  499 (1010)
T 2xgj_A          489 RGIVIMMIDEK  499 (1010)
T ss_dssp             SEEEEEEECSC
T ss_pred             ceEEEEEECCC
Confidence            48999999865

>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=99.88  E-value=7.3e-23  Score=166.84  Aligned_cols=123  Identities=22%  Similarity=0.276  Sum_probs=71.0

Q ss_pred             HHHHHHHHHHhcc--CCCCCeeEEehhhhhHHHHHhhcccc------------CceEEEecCCCCHHHHHHHHHHhhc-C
Q psy17637         19 FAGHLVRNLEGAN--QEVPPALMNLAMQLNAEELANSLTVK------------EYDVLLLHGDMDQSERNSVITKFKR-Q   83 (150)
Q Consensus        19 ~~~~ll~~l~~~~--~~~~~~ivf~~~~~~~~~l~~~L~~~------------~~~~~~~~~~~~~~~r~~~~~~f~~-g   83 (150)
                      ++..|.+.+....  ....++||||++++.++.|+..|...            |.....+||+|++.+|.++++.|++ |
T Consensus       614 K~~~L~~lL~~~~~~~~~~rvLIF~~t~~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~Fr~~g  693 (936)
T 4a2w_A          614 KLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSK  693 (936)
T ss_dssp             HHHHHHHHHHHTTTSCTTCCEEEEESSHHHHHHHHHHHHHCSTTSSCCCEEC----------------------------
T ss_pred             HHHHHHHHHHHHhccCCCCeEEEEeCCHHHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHhhccC
Confidence            4445555555431  45789999999999999999999865            5556677899999999999999999 9


Q ss_pred             CceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         84 ECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        84 ~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +++|||||+++++|+|+|++++||+||+|+|+..|+||+|| ||. ..+.++.+++..+.
T Consensus       694 ~~~VLVaT~~~~eGIDlp~v~~VI~yD~p~s~~~~iQr~GR-GR~-~~g~vi~Li~~~t~  751 (936)
T 4a2w_A          694 DNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEV  751 (936)
T ss_dssp             CCSEEEEECC------CCCCSEEEEESCCSCSHHHHCC---------CCCEEEEESCHHH
T ss_pred             CeeEEEEeCchhcCCcchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCCEEEEEEeCCCH
Confidence            99999999999999999999999999999999999999999 998 57888888876543

>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=99.88  E-value=4.9e-23  Score=155.98  Aligned_cols=101  Identities=23%  Similarity=0.296  Sum_probs=86.8

Q ss_pred             CCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEE-----
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVN-----  108 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~-----  108 (150)
                      ..++||||++++.++.+++.|...++++..+||.    +|.++++.|++|+.+|||||+++++|+|+| +++||+     
T Consensus       177 ~~~~lVF~~s~~~a~~l~~~L~~~~~~v~~lhg~----~R~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI~~g~~~  251 (440)
T 1yks_A          177 KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRK----TFEREYPTIKQKKPDFILATDIAEMGANLC-VERVLDCRTAF  251 (440)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSS----SCC--------CCCSEEEESSSTTCCTTCC-CSEEEECCEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHcCCCEEEecch----hHHHHHhhhcCCCceEEEECChhheeeccC-ceEEEeCCccc
Confidence            5799999999999999999999999999999993    688999999999999999999999999999 999986     


Q ss_pred             --------------ecCCCChhHHHHhhccccCC-CCccEEEEEEe
Q psy17637        109 --------------YDLARDIDTHTHRIGRTGRA-GNKGVAYTLVT  139 (150)
Q Consensus       109 --------------~~~~~~~~~~~q~~GR~~R~-g~~~~~~~~~~  139 (150)
                                    ++.|.+.++|+||+||+||. |..|.+++|+.
T Consensus       252 ~pv~~~~~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~g~~~~l~~  297 (440)
T 1yks_A          252 KPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSE  297 (440)
T ss_dssp             EEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECS
T ss_pred             eeeecccccceeeccccccCHHHHHHhccccCCCCCCCceEEEEec
Confidence                          89999999999999999998 67899999974

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.87  E-value=3.4e-22  Score=159.05  Aligned_cols=111  Identities=22%  Similarity=0.311  Sum_probs=95.9

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccC------------------------------------ceEEEecCCCCHHHHHH
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKE------------------------------------YDVLLLHGDMDQSERNS   75 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~------------------------------------~~~~~~~~~~~~~~r~~   75 (150)
                      .+..++||||++++.++.++..|....                                    ..+.++||+|++++|..
T Consensus       250 ~~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~r~~  329 (715)
T 2va8_A          250 SKNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAYHHAGLSKALRDL  329 (715)
T ss_dssp             TTTCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTTTEEEECTTSCHHHHHH
T ss_pred             hcCCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhcCEEEECCCCCHHHHHH
Confidence            356899999999999999998886431                                    24889999999999999


Q ss_pred             HHHHhhcCCceEEEEcCCCcccCCccCCcEEEE----ec-------CCCChhHHHHhhccccCCCC--ccEEEEEEecCC
Q psy17637         76 VITKFKRQECRILVATDVAARGLDIPHIRTVVN----YD-------LARDIDTHTHRIGRTGRAGN--KGVAYTLVTDKD  142 (150)
Q Consensus        76 ~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~----~~-------~~~~~~~~~q~~GR~~R~g~--~~~~~~~~~~~~  142 (150)
                      +++.|++|..+|||||+.+++|+|+|++++||+    |+       .|.+..+|.||+||+||.|.  .|.|+.++++.+
T Consensus       330 v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~  409 (715)
T 2va8_A          330 IEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGRPGFDQIGESIVVVRDKE  409 (715)
T ss_dssp             HHHHHHTTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHHHHTTBCCTTTCSCEEEEEECSCGG
T ss_pred             HHHHHHcCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEeCCch
Confidence            999999999999999999999999999999998    88       89999999999999999983  688999987765

>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=99.87  E-value=3.5e-22  Score=164.77  Aligned_cols=123  Identities=18%  Similarity=0.260  Sum_probs=102.9

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCce--------------------------------------
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYD--------------------------------------   60 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~--------------------------------------   60 (150)
                      ....++..+...  ...++||||++++.++.++..|...++.                                      
T Consensus       428 ~l~~li~~l~~~--~~~~vIVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~  505 (1108)
T 3l9o_A          428 DIYKIVKMIWKK--KYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRR  505 (1108)
T ss_dssp             HHHHHHHHHHHT--TCCCEEEEESCHHHHHHHHHHTCSHHHHCC----CHHHHGGGSCTHHHHHTTCCHHHHHHTHHHHH
T ss_pred             HHHHHHHHHHhc--CCCCEEEEeCcHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHHhhhc
Confidence            344566666554  5679999999999999999998754332                                      


Q ss_pred             -EEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCC--------CChhHHHHhhccccCCC--
Q psy17637         61 -VLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLA--------RDIDTHTHRIGRTGRAG--  129 (150)
Q Consensus        61 -~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~--------~~~~~~~q~~GR~~R~g--  129 (150)
                       +..+||+|++.+|..+++.|++|.++|||||+++++|+|+|++++||+++.|        .++.+|+||+||+||.|  
T Consensus       506 gV~~~Hg~l~~~~R~~v~~~F~~G~ikVLVAT~vla~GIDiP~v~~VI~~~~~~d~~~~r~iS~~eyiQr~GRAGR~G~d  585 (1108)
T 3l9o_A          506 GIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLD  585 (1108)
T ss_dssp             TEEEECSCSCHHHHHHHHHHHHHTCCCEEEEESCCCSCCCC--CEEEESCSEEESSSCEEECCHHHHHHHHHHSCCSSSC
T ss_pred             CeeeecCCCCHHHHHHHHHHHhCCCCeEEEECcHHhcCCCCCCceEEEecCcccCccccccCCHHHHHHhhcccCCCCCC
Confidence             7899999999999999999999999999999999999999999999976653        37788999999999999  


Q ss_pred             CccEEEEEEecCCC
Q psy17637        130 NKGVAYTLVTDKDK  143 (150)
Q Consensus       130 ~~~~~~~~~~~~~~  143 (150)
                      ..|.+++++++...
T Consensus       586 ~~G~~ill~~~~~~  599 (1108)
T 3l9o_A          586 DRGIVIMMIDEKME  599 (1108)
T ss_dssp             SSEEEEEEECCCCC
T ss_pred             CceEEEEEecCCcC
Confidence            57888888877644

>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=99.87  E-value=3e-22  Score=152.06  Aligned_cols=103  Identities=18%  Similarity=0.231  Sum_probs=94.6

Q ss_pred             CCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEec---
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYD---  110 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~---  110 (150)
                      ..++||||++++.++.+++.|...++.+..+|+.+.    .++++.|++|+.+|||||+++++|+|+|+ ++||+++   
T Consensus       188 ~~~~lVF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~----~~~~~~f~~g~~~vLVaT~v~~~GiDip~-~~VI~~~~~~  262 (451)
T 2jlq_A          188 QGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTF----DTEYPKTKLTDWDFVVTTDISEMGANFRA-GRVIDPRRCL  262 (451)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHTTTCCEEEECTTTH----HHHGGGGGSSCCSEEEECGGGGSSCCCCC-SEEEECCEEE
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHcCCeEEECCHHHH----HHHHHhhccCCceEEEECCHHHhCcCCCC-CEEEECCCcc
Confidence            568999999999999999999999999999999864    57899999999999999999999999999 9999998   


Q ss_pred             -----------------CCCChhHHHHhhccccCCCC-ccEEEEEEecC
Q psy17637        111 -----------------LARDIDTHTHRIGRTGRAGN-KGVAYTLVTDK  141 (150)
Q Consensus       111 -----------------~~~~~~~~~q~~GR~~R~g~-~~~~~~~~~~~  141 (150)
                                       .|.+..+|+||+||+||.|. .+.++++...+
T Consensus       263 ~~~~d~~~~~~l~~~~~~p~s~~~y~Qr~GRaGR~g~~~g~~~~~~~~~  311 (451)
T 2jlq_A          263 KPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDP  311 (451)
T ss_dssp             EEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCC
T ss_pred             cccccccccceeeecccccCCHHHHHHhccccCCCCCCCccEEEEeCCc
Confidence                             99999999999999999997 77888776543

>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=99.87  E-value=2.6e-22  Score=152.81  Aligned_cols=120  Identities=17%  Similarity=0.253  Sum_probs=102.2

Q ss_pred             HHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCC
Q psy17637         20 AGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLD   99 (150)
Q Consensus        20 ~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gid   99 (150)
                      ...+.+.+..  ....++||||++.+.++.+++.|.     +..+||+++..+|+++++.|++|+.+|||+|+++++|+|
T Consensus       337 ~~~l~~~l~~--~~~~k~lvF~~~~~~~~~l~~~l~-----~~~~~g~~~~~~R~~~~~~F~~g~~~vLv~T~~~~~Gld  409 (472)
T 2fwr_A          337 IRKLREILER--HRKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGID  409 (472)
T ss_dssp             HHHHHHHHHH--TSSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSC
T ss_pred             HHHHHHHHHh--CCCCcEEEEECCHHHHHHHHHHhC-----cceeeCCCCHHHHHHHHHHHhCCCCCEEEEcCchhcCcc
Confidence            3445555544  467899999999999999999985     457899999999999999999999999999999999999


Q ss_pred             ccCCcEEEEecCCCChhHHHHhhccccCCCCc---cEEEEEEecCCCccc
Q psy17637        100 IPHIRTVVNYDLARDIDTHTHRIGRTGRAGNK---GVAYTLVTDKDKDGE  146 (150)
Q Consensus       100 i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~---~~~~~~~~~~~~~~~  146 (150)
                      +|++++||++++|+++..|.|++||+||.|+.   ..+|.+++....++.
T Consensus       410 lp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~k~~~~i~~lv~~~t~ee~  459 (472)
T 2fwr_A          410 VPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRGTGEVN  459 (472)
T ss_dssp             SCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEECSCC---
T ss_pred             cccCcEEEEECCCCCHHHHHHHHhhccCCCCCCceEEEEEEEeCCCchHH
Confidence            99999999999999999999999999999854   356777777655544

>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=99.87  E-value=3.4e-22  Score=159.21  Aligned_cols=110  Identities=26%  Similarity=0.370  Sum_probs=99.0

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccC---------------------------------ceEEEecCCCCHHHHHHHHHH
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKE---------------------------------YDVLLLHGDMDQSERNSVITK   79 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~---------------------------------~~~~~~~~~~~~~~r~~~~~~   79 (150)
                      +..++||||++++.++.++..|....                                 ..+.++||+|++++|..+++.
T Consensus       236 ~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~~  315 (720)
T 2zj8_A          236 KKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEEN  315 (720)
T ss_dssp             TTCCEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEECTTSCHHHHHHHHHH
T ss_pred             CCCCEEEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeecCCCCHHHHHHHHHH
Confidence            46899999999999999998886431                                 138999999999999999999


Q ss_pred             hhcCCceEEEEcCCCcccCCccCCcEEEE----ec----CCCChhHHHHhhccccCCC--CccEEEEEEecCC
Q psy17637         80 FKRQECRILVATDVAARGLDIPHIRTVVN----YD----LARDIDTHTHRIGRTGRAG--NKGVAYTLVTDKD  142 (150)
Q Consensus        80 f~~g~~~vlv~T~~~~~Gidi~~~~~vi~----~~----~~~~~~~~~q~~GR~~R~g--~~~~~~~~~~~~~  142 (150)
                      |++|.++|||||+.+++|+|+|++++||+    |+    .|.+..+|.||+||+||.|  ..|.++.++++.+
T Consensus       316 f~~g~~~vlvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~  388 (720)
T 2zj8_A          316 FRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDD  388 (720)
T ss_dssp             HHTTSSCEEEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCTTTCSEEEEEEECSSSC
T ss_pred             HHCCCCeEEEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCCCCCCCceEEEEecCcc
Confidence            99999999999999999999999999998    66    5899999999999999998  4688999988776

>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=99.87  E-value=1.7e-21  Score=161.37  Aligned_cols=110  Identities=23%  Similarity=0.305  Sum_probs=102.7

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhcccc--CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEe
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVK--EYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNY  109 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~  109 (150)
                      ..+.+++|||++++.++.+++.|...  +..+..+||+|++.+|+++++.|++|+.+|||||+++++|+|+|++++||++
T Consensus       810 ~~g~qvlvf~~~v~~~~~l~~~L~~~~p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~v~e~GiDip~v~~VIi~  889 (1151)
T 2eyq_A          810 LRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIE  889 (1151)
T ss_dssp             TTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEEET
T ss_pred             hcCCeEEEEECCHHHHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECCcceeeecccCCcEEEEe
Confidence            45689999999999999999999876  7889999999999999999999999999999999999999999999999999


Q ss_pred             cC-CCChhHHHHhhccccCCCCccEEEEEEecC
Q psy17637        110 DL-ARDIDTHTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus       110 ~~-~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                      +. +.++..|.|++||+||.|+.+.+++++...
T Consensus       890 ~~~~~~l~~l~Qr~GRvgR~g~~g~~~ll~~~~  922 (1151)
T 2eyq_A          890 RADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  922 (1151)
T ss_dssp             TTTSSCHHHHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             CCCCCCHHHHHHHHhccCcCCCceEEEEEECCc
Confidence            88 569999999999999999999999988754

>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=99.87  E-value=1.2e-21  Score=155.98  Aligned_cols=126  Identities=20%  Similarity=0.229  Sum_probs=111.6

Q ss_pred             hhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCc
Q psy17637         16 DKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAA   95 (150)
Q Consensus        16 ~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~   95 (150)
                      ...+...+++.+......+.|+||||+|++.++.|+..|...|+++..+||.+.+.++..+.+.|+.|  .|+|||++++
T Consensus       442 ~~~K~~al~~~i~~~~~~gqpvLVft~Sie~sE~Ls~~L~~~Gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAg  519 (922)
T 1nkt_A          442 EEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIAVAGRRG--GVTVATNMAG  519 (922)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHHHHHTTTSTT--CEEEEETTCS
T ss_pred             HHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecchhh
Confidence            34456677787766545678999999999999999999999999999999998888887777888877  6999999999


Q ss_pred             ccCCccCC----------------------------------------------------cEEEEecCCCChhHHHHhhc
Q psy17637         96 RGLDIPHI----------------------------------------------------RTVVNYDLARDIDTHTHRIG  123 (150)
Q Consensus        96 ~Gidi~~~----------------------------------------------------~~vi~~~~~~~~~~~~q~~G  123 (150)
                      +|+|++..                                                    .+||+++.|.+...|.|++|
T Consensus       520 RGtDI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGlhVI~te~pes~riy~qr~G  599 (922)
T 1nkt_A          520 RGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRG  599 (922)
T ss_dssp             TTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHH
T ss_pred             cCccccCCCCHHHHHHHHHhhccccccccchhhHHHHHHHHHHHHHHHHHhhhHHHhcCCcEEEeccCCCCHHHHHHHhc
Confidence            99999864                                                    49999999999999999999


Q ss_pred             cccCCCCccEEEEEEecCCC
Q psy17637        124 RTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus       124 R~~R~g~~~~~~~~~~~~~~  143 (150)
                      |+||.|++|.+.+|++.+|.
T Consensus       600 RTGRqGdpG~s~fflSleD~  619 (922)
T 1nkt_A          600 RSGRQGDPGESRFYLSLGDE  619 (922)
T ss_dssp             TSSGGGCCEEEEEEEETTSH
T ss_pred             ccccCCCCeeEEEEechhHH
Confidence            99999999999999998765

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.87  E-value=1.6e-21  Score=159.52  Aligned_cols=122  Identities=24%  Similarity=0.351  Sum_probs=103.6

Q ss_pred             chhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCc-----------------------------------
Q psy17637         15 KDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEY-----------------------------------   59 (150)
Q Consensus        15 ~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~-----------------------------------   59 (150)
                      ........++..+...  ...++||||++++.++.++..|...++                                   
T Consensus       319 ~~~~~~~~li~~l~~~--~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~  396 (997)
T 4a4z_A          319 PSKKTWPEIVNYLRKR--ELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRS  396 (997)
T ss_dssp             CCTTHHHHHHHHHHHT--TCCSEEEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHH
T ss_pred             cchhHHHHHHHHHHhC--CCCCEEEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHH
Confidence            3344456777777765  667999999999999999999976554                                   


Q ss_pred             ----eEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCCC---------ChhHHHHhhcccc
Q psy17637         60 ----DVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLAR---------DIDTHTHRIGRTG  126 (150)
Q Consensus        60 ----~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~---------~~~~~~q~~GR~~  126 (150)
                          .+..+||+|++.+|..+++.|+.|.++|||||+++++|+|+|+ ..||+++.++         ++.+|.|++||+|
T Consensus       397 ~l~~gi~~~H~gl~~~~R~~v~~~F~~G~~kVLvAT~~~a~GIDiP~-~~VVi~~~~k~dg~~~~~~s~~~y~Qr~GRAG  475 (997)
T 4a4z_A          397 LLERGIAVHHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPT-RTVIFSSIRKHDGNGLRELTPGEFTQMAGRAG  475 (997)
T ss_dssp             HHTTTEEEECTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCC-SEEEESCSEEEETTEEEECCHHHHHHHHGGGC
T ss_pred             HhhcCeeeecCCCCHHHHHHHHHHHHCCCCcEEEEchHhhCCCCCCC-ceEEEeccccccCccCCCCCHHHHhHHhcccc
Confidence                4789999999999999999999999999999999999999999 5566655555         9999999999999


Q ss_pred             CCC--CccEEEEEEe
Q psy17637        127 RAG--NKGVAYTLVT  139 (150)
Q Consensus       127 R~g--~~~~~~~~~~  139 (150)
                      |.|  ..|.+++++.
T Consensus       476 R~G~~~~G~vi~l~~  490 (997)
T 4a4z_A          476 RRGLDSTGTVIVMAY  490 (997)
T ss_dssp             CTTTCSSEEEEEECC
T ss_pred             cCCCCcceEEEEecC
Confidence            998  4567777774

>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=99.86  E-value=5.8e-23  Score=164.44  Aligned_cols=110  Identities=21%  Similarity=0.331  Sum_probs=102.0

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc-----------cCceEEEecCCCCHHHHHHHHHHhh-----cCCceEEEEcCCCcc
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV-----------KEYDVLLLHGDMDQSERNSVITKFK-----RQECRILVATDVAAR   96 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~-----------~~~~~~~~~~~~~~~~r~~~~~~f~-----~g~~~vlv~T~~~~~   96 (150)
                      ..+++||||++++.++.++..|..           .++.+.++||+|++++|.++++.|.     .|..+|||||+++++
T Consensus       302 ~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~iae~  381 (773)
T 2xau_A          302 EAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTNIAET  381 (773)
T ss_dssp             CSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECTHHHH
T ss_pred             CCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCcHHHh
Confidence            578999999999999999999874           5788999999999999999999999     999999999999999


Q ss_pred             cCCccCCcEEEEecC------------------CCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         97 GLDIPHIRTVVNYDL------------------ARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        97 Gidi~~~~~vi~~~~------------------~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |+|+|++++||+++.                  |.+..+|.||+||+||. .+|.|+.|+++.+.
T Consensus       382 GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~-~~G~~~~l~~~~~~  445 (773)
T 2xau_A          382 SLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEEAF  445 (773)
T ss_dssp             TCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSS-SSEEEEESSCHHHH
T ss_pred             CcCcCCeEEEEeCCCccceeeccccCccccccccCCHHHHHhhccccCCC-CCCEEEEEecHHHh
Confidence            999999999999877                  88999999999999999 68999999976544

>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=99.86  E-value=1.7e-22  Score=153.81  Aligned_cols=103  Identities=19%  Similarity=0.235  Sum_probs=93.7

Q ss_pred             CCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEE-----
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVN-----  108 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~-----  108 (150)
                      ..++||||++++.++.+++.|...++.+..+|+.    +|.++++.|++|+.+|||||+++++|+|+|+ ++||+     
T Consensus       190 ~~~~LVF~~s~~~~~~l~~~L~~~g~~v~~lh~~----~R~~~~~~f~~g~~~iLVaT~v~~~GiDip~-~~VI~~G~~~  264 (459)
T 2z83_A          190 AGKTVWFVASVKMGNEIAMCLQRAGKKVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFGA-SRVIDCRKSV  264 (459)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCEEEESTT----CCCCCGGGSSSCCCSEEEESSCC---CCCSC-SEEEECCEEC
T ss_pred             CCCEEEEeCChHHHHHHHHHHHhcCCcEEecCHH----HHHHHHhhccCCCceEEEECChHHhCeecCC-CEEEECCccc
Confidence            5689999999999999999999999999999995    6788999999999999999999999999999 99999     


Q ss_pred             ---------------ecCCCChhHHHHhhccccCCCC-ccEEEEEEecC
Q psy17637        109 ---------------YDLARDIDTHTHRIGRTGRAGN-KGVAYTLVTDK  141 (150)
Q Consensus       109 ---------------~~~~~~~~~~~q~~GR~~R~g~-~~~~~~~~~~~  141 (150)
                                     ++.|.+..+|+||+||+||.|. +|.+++|++..
T Consensus       265 ~~~~~~~~~~~~~~~~d~p~s~~~~~QR~GRaGR~g~~~G~~~~~~~~~  313 (459)
T 2z83_A          265 KPTILEEGEGRVILGNPSPITSASAAQRRGRVGRNPNQVGDEYHYGGAT  313 (459)
T ss_dssp             CEEEECSSSCEEEECSCEECCHHHHHHHHTTSSCCTTCCCEEEEECSCC
T ss_pred             ccccccccccccccccCCCCCHHHHHHhccccCCCCCCCCeEEEEEccc
Confidence                           6799999999999999999997 89999999875

>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=99.86  E-value=5.6e-22  Score=157.58  Aligned_cols=110  Identities=26%  Similarity=0.407  Sum_probs=98.9

Q ss_pred             CCCCeeEEehhhhhHHHHHhhcccc------------------------------CceEEEecCCCCHHHHHHHHHHhhc
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVK------------------------------EYDVLLLHGDMDQSERNSVITKFKR   82 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~------------------------------~~~~~~~~~~~~~~~r~~~~~~f~~   82 (150)
                      +..++||||++++.++.++..|...                              +..+.++||+|++++|..+++.|++
T Consensus       241 ~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~~f~~  320 (702)
T 2p6r_A          241 ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRR  320 (702)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHHHT
T ss_pred             cCCCEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecCCCCHHHHHHHHHHHHC
Confidence            5689999999999999998887642                              1247889999999999999999999


Q ss_pred             CCceEEEEcCCCcccCCccCCcEEEE----ec---CCCChhHHHHhhccccCCC--CccEEEEEEecCC
Q psy17637         83 QECRILVATDVAARGLDIPHIRTVVN----YD---LARDIDTHTHRIGRTGRAG--NKGVAYTLVTDKD  142 (150)
Q Consensus        83 g~~~vlv~T~~~~~Gidi~~~~~vi~----~~---~~~~~~~~~q~~GR~~R~g--~~~~~~~~~~~~~  142 (150)
                      |..+|||||+.+++|+|+|++++||+    ||   .|.+..+|.||+||+||.|  ..|.++.++++.+
T Consensus       321 g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~  389 (702)
T 2p6r_A          321 GNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRD  389 (702)
T ss_dssp             TSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGG
T ss_pred             CCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEecCcc
Confidence            99999999999999999999999998    65   7899999999999999998  4688999988765

>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=99.86  E-value=1.5e-21  Score=149.61  Aligned_cols=127  Identities=16%  Similarity=0.233  Sum_probs=104.4

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhcccc-CceEEEecCCCCHHHHHHHHHHhhcC-Cce-EEEEcCCCc
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVK-EYDVLLLHGDMDQSERNSVITKFKRQ-ECR-ILVATDVAA   95 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g-~~~-vlv~T~~~~   95 (150)
                      ++..+.+.+......+.++||||.+.+.++.+...|... +..+..+||++++++|.++++.|+++ ... +|++|++++
T Consensus       326 K~~~l~~~l~~~~~~~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~~~~  405 (500)
T 1z63_A          326 KMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGG  405 (500)
T ss_dssp             HHHHHHHHHHHHHTTTCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECCCC-
T ss_pred             hHHHHHHHHHHHHccCCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEeccccc
Confidence            344555555554456789999999999999999999875 88999999999999999999999998 454 789999999


Q ss_pred             ccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccE--EEEEEecCCCcc
Q psy17637         96 RGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGV--AYTLVTDKDKDG  145 (150)
Q Consensus        96 ~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~--~~~~~~~~~~~~  145 (150)
                      +|+|++.+++||++++|+++..|.|++||++|.|+.+.  ++.++.....++
T Consensus       406 ~Glnl~~~~~vi~~d~~~~~~~~~Q~~gR~~R~Gq~~~v~v~~lv~~~tiee  457 (500)
T 1z63_A          406 FGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEE  457 (500)
T ss_dssp             CCCCCTTCSEEEESSCCSCC---CHHHHTTTTTTTTSCEEEEEEEETTSHHH
T ss_pred             CCCchhhCCEEEEeCCCCCcchHHHHHHHHHHcCCCCeeEEEEEEeCCCHHH
Confidence            99999999999999999999999999999999997654  566777665443

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.86  E-value=1.2e-21  Score=154.77  Aligned_cols=102  Identities=20%  Similarity=0.241  Sum_probs=95.3

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEE----
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVN----  108 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~----  108 (150)
                      ...++||||++++.++.+++.|...++.+..+||.    +|.++++.|++|+.+|||||+++++|+|+| +++||+    
T Consensus       409 ~~~~~lVF~~s~~~~e~la~~L~~~g~~v~~lHg~----eR~~v~~~F~~g~~~VLVaTdv~e~GIDip-v~~VI~~g~~  483 (673)
T 2wv9_A          409 YAGKTVWFVASVKMSNEIAQCLQRAGKRVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFG-ASRVIDCRKS  483 (673)
T ss_dssp             CCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECSS----SHHHHGGGGGTCCCSEEEECGGGGTTCCCC-CSEEEECCEE
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHhCCCeEEEeChH----HHHHHHHHHHCCCceEEEECchhhcceeeC-CcEEEECCCc
Confidence            46799999999999999999999999999999994    789999999999999999999999999999 999998    


Q ss_pred             ----------------ecCCCChhHHHHhhccccCC-CCccEEEEEEe
Q psy17637        109 ----------------YDLARDIDTHTHRIGRTGRA-GNKGVAYTLVT  139 (150)
Q Consensus       109 ----------------~~~~~~~~~~~q~~GR~~R~-g~~~~~~~~~~  139 (150)
                                      ++.|.+.++|+||+||+||. |+.|.+++|+.
T Consensus       484 ~~p~vi~da~~r~~ll~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~~  531 (673)
T 2wv9_A          484 VKPTILDEGEGRVILSVPSAITSASAAQRRGRVGRNPSQIGDEYHYGG  531 (673)
T ss_dssp             CCEEEECSTTCEEEECCSEECCHHHHHHHHTTSSCCSSCCCEEEEECS
T ss_pred             ccceeeecccccceecccCCCCHHHHHHHhhccCCCCCCCCEEEEEEe
Confidence                            56899999999999999999 68889999974

>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=99.85  E-value=1.7e-21  Score=152.80  Aligned_cols=101  Identities=18%  Similarity=0.211  Sum_probs=93.9

Q ss_pred             CCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEE-------
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV-------  106 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~v-------  106 (150)
                      ..++||||++++.++.+++.|...++++..+||.    +|.++++.|++|+.+|||||+++++|+|+| +++|       
T Consensus       355 ~~~~LVF~~s~~~a~~l~~~L~~~g~~v~~lhg~----~R~~~l~~F~~g~~~VLVaTdv~~rGiDi~-v~~VId~g~~~  429 (618)
T 2whx_A          355 QGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRK----TFDTEYPKTKLTDWDFVVTTDISEMGANFR-AGRVIDPRRCL  429 (618)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHTTCCEEEECTT----THHHHTTHHHHSCCSEEEECGGGGTTCCCC-CSEEEECCEEE
T ss_pred             CCCEEEEECChhHHHHHHHHHHHcCCcEEEEChH----HHHHHHHhhcCCCcEEEEECcHHHcCcccC-ceEEEECccee
Confidence            5689999999999999999999999999999985    678899999999999999999999999997 8887       


Q ss_pred             -------------EEecCCCChhHHHHhhccccCCCC-ccEEEEEEe
Q psy17637        107 -------------VNYDLARDIDTHTHRIGRTGRAGN-KGVAYTLVT  139 (150)
Q Consensus       107 -------------i~~~~~~~~~~~~q~~GR~~R~g~-~~~~~~~~~  139 (150)
                                   ++++.|.+.++|+||+||+||.|. .|.+++|++
T Consensus       430 ~P~~~~~~~~~~~i~~d~P~s~~~yiQR~GRaGR~g~~~G~ai~l~~  476 (618)
T 2whx_A          430 KPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSG  476 (618)
T ss_dssp             EEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECS
T ss_pred             cceecccCCCceEEcccccCCHHHHHHhccccCCCCCCCCeEEEEcc
Confidence                         778889999999999999999975 789999987

>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=99.85  E-value=1.5e-22  Score=161.80  Aligned_cols=119  Identities=24%  Similarity=0.395  Sum_probs=103.5

Q ss_pred             HHHHHHHhccCCCCCeeEEehhh--------hhHHHHHhhccc---cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEE
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQ--------LNAEELANSLTV---KEYDVLLLHGDMDQSERNSVITKFKRQECRILVA   90 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~--------~~~~~l~~~L~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~   90 (150)
                      .+++.+......+.+++|||++.        ..++.+++.|..   .+..+..+||+|++++|..+++.|++|+.+||||
T Consensus       566 ~l~~~i~~~l~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G~~~ILVa  645 (780)
T 1gm5_A          566 EVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVS  645 (780)
T ss_dssp             HHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCC
T ss_pred             HHHHHHHHHHhcCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCCCCeEEEE
Confidence            45566655545678999999865        457888888887   4788999999999999999999999999999999


Q ss_pred             cCCCcccCCccCCcEEEEecCCC-ChhHHHHhhccccCCCCccEEEEEEec
Q psy17637         91 TDVAARGLDIPHIRTVVNYDLAR-DIDTHTHRIGRTGRAGNKGVAYTLVTD  140 (150)
Q Consensus        91 T~~~~~Gidi~~~~~vi~~~~~~-~~~~~~q~~GR~~R~g~~~~~~~~~~~  140 (150)
                      |+++++|+|+|++++||++++|. +...|.|++||+||.|..|.|++++++
T Consensus       646 T~vie~GIDiP~v~~VIi~d~~r~~l~~l~Qr~GRaGR~g~~g~~ill~~~  696 (780)
T 1gm5_A          646 TTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGD  696 (780)
T ss_dssp             SSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCS
T ss_pred             CCCCCccccCCCCCEEEEeCCCCCCHHHHHHHhcccCcCCCCCEEEEEECC
Confidence            99999999999999999999996 789999999999999999999999873

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.85  E-value=1.5e-21  Score=149.96  Aligned_cols=105  Identities=18%  Similarity=0.173  Sum_probs=94.4

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEc-CCCcccCCccCCcEEEEecC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVAT-DVAARGLDIPHIRTVVNYDL  111 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T-~~~~~Gidi~~~~~vi~~~~  111 (150)
                      ...++|||++ .++++.+++.|...+.++..+||+|++++|+++++.|++|+..||||| +++++|+|+|++++||++++
T Consensus       347 ~~~~~ivf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~GiDip~v~~vi~~~~  425 (510)
T 2oca_A          347 DENAFVMFKH-VSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFSTGISVKNLHHVVLAHG  425 (510)
T ss_dssp             TCEEEEEESS-HHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHHSCCCCSEEEEEESSC
T ss_pred             CCCeEEEEec-HHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhcccccccCcEEEEeCC
Confidence            3456677777 788899999999887899999999999999999999999999999999 99999999999999999999


Q ss_pred             CCChhHHHHhhccccCCCCccEEEEEE
Q psy17637        112 ARDIDTHTHRIGRTGRAGNKGVAYTLV  138 (150)
Q Consensus       112 ~~~~~~~~q~~GR~~R~g~~~~~~~~~  138 (150)
                      |+++..|.|++||+||.|+.+..+.++
T Consensus       426 ~~s~~~~~Q~~GR~gR~g~~~~~v~i~  452 (510)
T 2oca_A          426 VKSKIIVLQTIGRVLRKHGSKTIATVW  452 (510)
T ss_dssp             CCSCCHHHHHHHHHHTTTCCCCCCEEE
T ss_pred             CCCHHHHHHHHhcccccCCCCceEEEE
Confidence            999999999999999999766444443

>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=99.85  E-value=1.2e-20  Score=148.72  Aligned_cols=123  Identities=13%  Similarity=0.237  Sum_probs=106.9

Q ss_pred             HHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCc---eEEEEcCCCccc
Q psy17637         21 GHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQEC---RILVATDVAARG   97 (150)
Q Consensus        21 ~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~---~vlv~T~~~~~G   97 (150)
                      ..++..+...  ...++||||+....++.+...|...++.+..+||+++.++|.++++.|+++..   .+|++|.+++.|
T Consensus       405 ~~ll~~~~~~--~~~k~lIFs~~~~~~~~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~v~L~st~a~g~G  482 (644)
T 1z3i_X          405 DYILAMTRTT--TSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCG  482 (644)
T ss_dssp             HHHHHHHHHH--CCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTT
T ss_pred             HHHHHHHhhc--CCCEEEEEEccHHHHHHHHHHHHHCCCCEEEEeCCCCHHHHHHHHHHhcCCCCCcEEEEEecccccCC
Confidence            3444444332  57899999999999999999999999999999999999999999999999875   488999999999


Q ss_pred             CCccCCcEEEEecCCCChhHHHHhhccccCCCCcc--EEEEEEecCCCcc
Q psy17637         98 LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKG--VAYTLVTDKDKDG  145 (150)
Q Consensus        98 idi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~--~~~~~~~~~~~~~  145 (150)
                      +|++.+++||++|+|+++..+.|++||++|.|+..  .+|.+++....++
T Consensus       483 lnl~~a~~Vi~~d~~wnp~~~~Qa~gR~~R~Gq~~~v~v~~lv~~~tiEe  532 (644)
T 1z3i_X          483 LNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIEE  532 (644)
T ss_dssp             CCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETTSHHH
T ss_pred             cccccCCEEEEECCCCCccHHHHHHHhhhhcCCCCceEEEEEEECCCHHH
Confidence            99999999999999999999999999999999765  5666777765444

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.84  E-value=5.6e-21  Score=150.80  Aligned_cols=104  Identities=22%  Similarity=0.407  Sum_probs=95.2

Q ss_pred             CCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhc--CCceEEEEcCCCcccCCccCCcEEEEecC-
Q psy17637         35 PPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKR--QECRILVATDVAARGLDIPHIRTVVNYDL-  111 (150)
Q Consensus        35 ~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~--g~~~vlv~T~~~~~Gidi~~~~~vi~~~~-  111 (150)
                      ...+|||++++.++.+++.|...++.+..+||+|++++|.++++.|+.  |..+|||||+++++|+|+ ++++||+++. 
T Consensus       321 ~g~iIf~~s~~~ie~la~~L~~~g~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~v~~VI~~~~~  399 (677)
T 3rc3_A          321 PGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-SIRRIIFYSLI  399 (677)
T ss_dssp             TTEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-CBSEEEESCSB
T ss_pred             CCCEEEEcCHHHHHHHHHHHHhcCCCeeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-CccEEEECCcc
Confidence            456899999999999999999999999999999999999999999999  889999999999999999 9999999999 


Q ss_pred             -------------CCChhHHHHhhccccCCCCc---cEEEEEEe
Q psy17637        112 -------------ARDIDTHTHRIGRTGRAGNK---GVAYTLVT  139 (150)
Q Consensus       112 -------------~~~~~~~~q~~GR~~R~g~~---~~~~~~~~  139 (150)
                                   |.+.++|.||+||+||.|..   |.++.+..
T Consensus       400 k~~~~~~G~~~~~p~s~~~~~QR~GRAGR~g~~g~~G~v~~l~~  443 (677)
T 3rc3_A          400 KPSINEKGERELEPITTSQALQIAGRAGRFSSRFKEGEVTTMNH  443 (677)
T ss_dssp             C-----------CBCCHHHHHHHHTTBTCTTSSCSSEEEEESST
T ss_pred             ccccccCCccccccCCHHHHHHHhcCCCCCCCCCCCEEEEEEec
Confidence                         77999999999999999954   56655543

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.84  E-value=4.5e-21  Score=144.90  Aligned_cols=101  Identities=18%  Similarity=0.167  Sum_probs=89.4

Q ss_pred             CCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcE--------
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRT--------  105 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~--------  105 (150)
                      ..++||||++++.++.+++.|...+..+..+||+    +|.++++.|++|+.+|||||+++++|+|+| +.+        
T Consensus       171 ~~~~lVF~~~~~~~~~l~~~L~~~~~~v~~lhg~----~r~~~~~~f~~g~~~vLVaT~v~e~GiDip-~~~VI~~g~~~  245 (431)
T 2v6i_A          171 DGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRK----TFESEYPKCKSEKWDFVITTDISEMGANFK-ADRVIDPRKTI  245 (431)
T ss_dssp             SSCEEEECSSHHHHHHHHHHHHHTTCCEEEESTT----THHHHTTHHHHSCCSEEEECGGGGTSCCCC-CSEEEECCEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCc----cHHHHHHhhcCCCCeEEEECchHHcCcccC-CcEEEecCccc
Confidence            5689999999999999999999889999999997    577899999999999999999999999999 544        


Q ss_pred             ---------EEEecCCCChhHHHHhhccccCCCCccEEEEEEe
Q psy17637        106 ---------VVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVT  139 (150)
Q Consensus       106 ---------vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~  139 (150)
                               ||+++.|.+..+|+|++||+||.|..+.+++++.
T Consensus       246 ~~v~d~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~~~~~~~~  288 (431)
T 2v6i_A          246 KPILLDGRVSMQGPIAITPASAAQRRGRIGRNPEKLGDIYAYS  288 (431)
T ss_dssp             EEEEETTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCCEEEEC
T ss_pred             cceecccceeecccccCCHHHHHHhhhccCCCCCCCCeEEEEc
Confidence                     6788999999999999999999986554444443

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.83  E-value=2e-20  Score=150.57  Aligned_cols=127  Identities=21%  Similarity=0.302  Sum_probs=110.1

Q ss_pred             HHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCc---eEEEEcCCCcc
Q psy17637         20 AGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQEC---RILVATDVAAR   96 (150)
Q Consensus        20 ~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~---~vlv~T~~~~~   96 (150)
                      +..|.+.+......+.++||||.....++.|...|...++.+..+||+++..+|..+++.|+++..   .+|++|.+++.
T Consensus       558 ~~~L~~lL~~~~~~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F~~~~~~~~v~LlSt~agg~  637 (800)
T 3mwy_W          558 MVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGL  637 (800)
T ss_dssp             HHHHHHHHHHHTTTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTTSSTTCSCCCEEEEHHHHTT
T ss_pred             HHHHHHHHHHHhhCCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhCCCCCceEEEEecccccC
Confidence            344555555544567899999999999999999999999999999999999999999999998654   48999999999


Q ss_pred             cCCccCCcEEEEecCCCChhHHHHhhccccCCCCcc--EEEEEEecCCCccc
Q psy17637         97 GLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKG--VAYTLVTDKDKDGE  146 (150)
Q Consensus        97 Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~--~~~~~~~~~~~~~~  146 (150)
                      |+|++.+++||++++|+++..+.|++||++|.|+..  .+|.|++....++.
T Consensus       638 GlNL~~a~~VI~~D~~wnp~~~~Qa~gR~~RiGQ~k~V~Vyrlv~~~TiEe~  689 (800)
T 3mwy_W          638 GINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEE  689 (800)
T ss_dssp             TCCCTTCCEEEESSCCSCSHHHHHHHTTTSCSSCCSCEEEEEEEETTSHHHH
T ss_pred             CCCccccceEEEecCCCChhhHHHHHHHHHhcCCCceEEEEEEecCCCHHHH
Confidence            999999999999999999999999999999999765  56777777655443

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.83  E-value=2e-20  Score=146.06  Aligned_cols=98  Identities=18%  Similarity=0.295  Sum_probs=87.5

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCce--------EEEecCCCCHHHHHHHHHHhhcCCce---EEEEcCCCcccCCc
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYD--------VLLLHGDMDQSERNSVITKFKRQECR---ILVATDVAARGLDI  100 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~--------~~~~~~~~~~~~r~~~~~~f~~g~~~---vlv~T~~~~~Gidi  100 (150)
                      .+..++||||+++++++.++..|...+..        +..+||.++ ++|+++++.|++|+..   |||+|+++++|+|+
T Consensus       437 ~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~-~~r~~~l~~F~~~~~~~~~ilvtt~~l~~GiDi  515 (590)
T 3h1t_A          437 DRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEG-KIGKGHLSRFQELETSTPVILTTSQLLTTGVDA  515 (590)
T ss_dssp             CTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTH-HHHHHHHHHHHCTTCCCCCEEEESSTTTTTCCC
T ss_pred             CCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCCh-HHHHHHHHHHhCCCCCCCEEEEECChhhcCccc
Confidence            45689999999999999999999765432        678899875 3799999999998765   88999999999999


Q ss_pred             cCCcEEEEecCCCChhHHHHhhccccCCCC
Q psy17637        101 PHIRTVVNYDLARDIDTHTHRIGRTGRAGN  130 (150)
Q Consensus       101 ~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~  130 (150)
                      |++++||++++|+++..|.|++||++|.+.
T Consensus       516 p~v~~Vi~~~~~~s~~~~~Q~iGR~~R~~~  545 (590)
T 3h1t_A          516 PTCKNVVLARVVNSMSEFKQIVGRGTRLRE  545 (590)
T ss_dssp             TTEEEEEEESCCCCHHHHHHHHTTSCCCBG
T ss_pred             hheeEEEEEecCCChHHHHHHHhhhcccCc
Confidence            999999999999999999999999999875

>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=99.83  E-value=5.7e-21  Score=149.90  Aligned_cols=103  Identities=24%  Similarity=0.365  Sum_probs=91.8

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEE-----
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVV-----  107 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi-----  107 (150)
                      ...++||||++++.++.+++.|...++.+..+||+|++++       |..+..+|||||+++++|+|+| +++||     
T Consensus       395 ~~~~vLVFv~Tr~~ae~la~~L~~~g~~v~~lHG~l~q~e-------r~~~~~~VLVATdVaerGIDId-V~~VI~~Gl~  466 (666)
T 3o8b_A          395 RGGRHLIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSV-------IPTIGDVVVVATDALMTGYTGD-FDSVIDCNTC  466 (666)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHTTTCCEEEECTTSCGGG-------SCSSSCEEEEECTTHHHHCCCC-BSEEEECCEE
T ss_pred             cCCcEEEEeCCHHHHHHHHHHHHhCCCcEEEecCCCCHHH-------HHhCCCcEEEECChHHccCCCC-CcEEEecCcc
Confidence            5679999999999999999999999999999999999864       4556669999999999999997 99988     


Q ss_pred             -----Eec-----------CCCChhHHHHhhccccCCCCccEEEEEEecCCCcc
Q psy17637        108 -----NYD-----------LARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDG  145 (150)
Q Consensus       108 -----~~~-----------~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~~  145 (150)
                           |||           .|.+.++|+||+||+|| |..|. +.|+++.+...
T Consensus       467 ~~~ViNyDydP~~gl~~~~~P~s~~syiQRiGRtGR-g~~G~-i~lvt~~e~~~  518 (666)
T 3o8b_A          467 VTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGR-GRRGI-YRFVTPGERPS  518 (666)
T ss_dssp             EEEEEECCCSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEE-EEESCCCCBCS
T ss_pred             cccccccccccccccccccCcCCHHHHHHHhccCCC-CCCCE-EEEEecchhhc
Confidence                 566           89999999999999999 88888 88888776544

>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=99.82  E-value=5.5e-20  Score=151.41  Aligned_cols=103  Identities=24%  Similarity=0.291  Sum_probs=87.3

Q ss_pred             CCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEE----cCCCcccCCccCC-cEEEE
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVA----TDVAARGLDIPHI-RTVVN  108 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~----T~~~~~Gidi~~~-~~vi~  108 (150)
                      ..++||||++++.++.++..|... +++..+||++     ..+++.|++|+.+||||    |+++++|+|+|++ ++||+
T Consensus       275 ~~~~LVF~~t~~~a~~l~~~L~~~-~~v~~lhg~~-----~~~l~~F~~G~~~VLVaTas~Tdv~~rGIDip~VI~~VI~  348 (1054)
T 1gku_B          275 GTGGIIYARTGEEAEEIYESLKNK-FRIGIVTATK-----KGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVF  348 (1054)
T ss_dssp             CSCEEEEESSHHHHHHHHHTTTTS-SCEEECTTSS-----SHHHHHHHHTSCSEEEEECC------CCSCCTTTCCEEEE
T ss_pred             CCCEEEEEcCHHHHHHHHHHHhhc-cCeeEEeccH-----HHHHHHHHcCCCcEEEEecCCCCeeEeccccCCcccEEEE
Confidence            568999999999999999999988 8999999998     37889999999999999    8999999999995 99999


Q ss_pred             ecCC-----------------------------------------------------------------------CChhH
Q psy17637        109 YDLA-----------------------------------------------------------------------RDIDT  117 (150)
Q Consensus       109 ~~~~-----------------------------------------------------------------------~~~~~  117 (150)
                      +++|                                                                       .+..+
T Consensus       349 ~~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  428 (1054)
T 1gku_B          349 VGCPSFRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVMGKERPQAKDVVVREGEVIFPDLRT  428 (1054)
T ss_dssp             ESCCEEEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCTTTSSCHHHHHHHHHHHHTTSCCSCSSSEEETTEEEEECHHH
T ss_pred             eCCCcccccccccccChHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccceeEeecceecCcHHH
Confidence            9999                                                                       78999


Q ss_pred             HHHhhccccCCCCcc--EEEEEEecCC
Q psy17637        118 HTHRIGRTGRAGNKG--VAYTLVTDKD  142 (150)
Q Consensus       118 ~~q~~GR~~R~g~~~--~~~~~~~~~~  142 (150)
                      |+||+||+||.|..|  .+++++...+
T Consensus       429 yiQr~GRagR~g~~g~~~g~~~~~~~d  455 (1054)
T 1gku_B          429 YIQGSGRTSRLFAGGLTKGASFLLEDD  455 (1054)
T ss_dssp             HHHHHHTTCCEETTEECCEEEEEECSC
T ss_pred             HhhhhchhhhccCCCCceEEEEEEecC
Confidence            999999999977654  3666666554

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.78  E-value=4.9e-19  Score=146.12  Aligned_cols=96  Identities=22%  Similarity=0.281  Sum_probs=78.7

Q ss_pred             CeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEE-EecCCCCHHHHHHHHHHhhcCC
Q psy17637          6 GVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVL-LLHGDMDQSERNSVITKFKRQE   84 (150)
Q Consensus         6 ~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~-~~~~~~~~~~r~~~~~~f~~g~   84 (150)
                      ++...+.......   .+...+...   ..++||||++++.++.++..|...++.+. .+||.     +.+ ++.|++|+
T Consensus       287 ~i~~~~~~~~k~~---~L~~ll~~~---~~~~LVF~~s~~~a~~l~~~L~~~g~~~~~~lhg~-----rr~-l~~F~~G~  354 (1104)
T 4ddu_A          287 NITHVRISSRSKE---KLVELLEIF---RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF-----EKN-FEDFKVGK  354 (1104)
T ss_dssp             CEEEEEESCCCHH---HHHHHHHHH---CSSEEEEESSSHHHHHHHHHHHHTTCCEEESSSSH-----HHH-HHHHHHTS
T ss_pred             CceeEEEecCHHH---HHHHHHHhc---CCCEEEEECcHHHHHHHHHHHHhCCCCeeeEecCc-----HHH-HHHHHCCC
Confidence            4444444443333   344444442   37999999999999999999999999998 99993     555 99999999


Q ss_pred             ceEEEE----cCCCcccCCccC-CcEEEEecCCC
Q psy17637         85 CRILVA----TDVAARGLDIPH-IRTVVNYDLAR  113 (150)
Q Consensus        85 ~~vlv~----T~~~~~Gidi~~-~~~vi~~~~~~  113 (150)
                      .+||||    |+++++|+|+|+ +++||+||+|.
T Consensus       355 ~~VLVatas~TdvlarGIDip~~V~~VI~~d~P~  388 (1104)
T 4ddu_A          355 INILIGVQAYYGKLTRGVDLPERIKYVIFWGTPS  388 (1104)
T ss_dssp             CSEEEEETTTHHHHCCSCCCTTTCCEEEEESCCE
T ss_pred             CCEEEEecCCCCeeEecCcCCCCCCEEEEECCCC
Confidence            999999    999999999999 99999999998

>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=99.77  E-value=5.2e-19  Score=150.65  Aligned_cols=115  Identities=18%  Similarity=0.274  Sum_probs=96.9

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhcccc-------------------------------------CceEEEecCCCCHHHHH
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVK-------------------------------------EYDVLLLHGDMDQSERN   74 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~-------------------------------------~~~~~~~~~~~~~~~r~   74 (150)
                      ....++||||+|++.++.++..|...                                     ...++++||+|++++|.
T Consensus       315 ~~~~~~LVF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~HHagL~~~~R~  394 (1724)
T 4f92_B          315 AGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRT  394 (1724)
T ss_dssp             CSSCCEEEECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEECSSSCTHHHH
T ss_pred             hcCCcEEEECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEEcCCCCHHHHH
Confidence            45679999999999998887766321                                     12378999999999999


Q ss_pred             HHHHHhhcCCceEEEEcCCCcccCCccCCcEEEE----ecC------CCChhHHHHhhccccCCCC--ccEEEEEEecCC
Q psy17637         75 SVITKFKRQECRILVATDVAARGLDIPHIRTVVN----YDL------ARDIDTHTHRIGRTGRAGN--KGVAYTLVTDKD  142 (150)
Q Consensus        75 ~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~----~~~------~~~~~~~~q~~GR~~R~g~--~~~~~~~~~~~~  142 (150)
                      .+.+.|++|.++|||||+.+++|+|+|..++||.    |++      |-+..+|.||+|||||.|.  .|.++++.+..+
T Consensus       395 ~vE~~F~~G~i~vlvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR~g~d~~G~~ii~~~~~~  474 (1724)
T 4f92_B          395 LVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILITSHGE  474 (1724)
T ss_dssp             HHHHHHHTTCCCEEEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHHTTBSCTTTCSCEEEEEEEESTT
T ss_pred             HHHHHHHCCCCeEEEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhhhhccCCCCCCccEEEEEecchh
Confidence            9999999999999999999999999999999884    544      4589999999999999884  578888888776


Q ss_pred             Cccc
Q psy17637        143 KDGE  146 (150)
Q Consensus       143 ~~~~  146 (150)
                      ...+
T Consensus       475 ~~~~  478 (1724)
T 4f92_B          475 LQYY  478 (1724)
T ss_dssp             CCHH
T ss_pred             HHHH
Confidence            5543

>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=99.76  E-value=1.2e-18  Score=148.46  Aligned_cols=112  Identities=16%  Similarity=0.213  Sum_probs=94.8

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhcccc----------------------------------CceEEEecCCCCHHHHHHHH
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVK----------------------------------EYDVLLLHGDMDQSERNSVI   77 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~----------------------------------~~~~~~~~~~~~~~~r~~~~   77 (150)
                      .+..++||||+|++.++.++..|...                                  ...+.++||+|++.+|..++
T Consensus      1153 ~~~~~~lVF~~sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHagL~~~~R~~VE 1232 (1724)
T 4f92_B         1153 SPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMERRLVE 1232 (1724)
T ss_dssp             CSSSCEEEEESSHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECTTSCHHHHHHHH
T ss_pred             cCCCCeeeeCCCHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEECCCCCHHHHHHHH
Confidence            56789999999999998877655210                                  12378999999999999999


Q ss_pred             HHhhcCCceEEEEcCCCcccCCccCCcEEEE----e------cCCCChhHHHHhhccccCCCC--ccEEEEEEecCCC
Q psy17637         78 TKFKRQECRILVATDVAARGLDIPHIRTVVN----Y------DLARDIDTHTHRIGRTGRAGN--KGVAYTLVTDKDK  143 (150)
Q Consensus        78 ~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~----~------~~~~~~~~~~q~~GR~~R~g~--~~~~~~~~~~~~~  143 (150)
                      +.|++|.++|||||+.+++|+|+|...+||.    |      ..|.+..+|.||+|||||.|.  .|.+++++...+.
T Consensus      1233 ~lF~~G~i~VLvaT~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Qm~GRAGR~g~d~~G~avll~~~~~~ 1310 (1724)
T 4f92_B         1233 QLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGSKK 1310 (1724)
T ss_dssp             HHHHHTSBCEEEEEGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHHHHTTBCCTTTCSCEEEEEEEEGGGH
T ss_pred             HHHHCCCCeEEEEChHHHcCCCCCccEEEEecCccccCcccccCCCCHHHHHHhhccccCCCCCCceEEEEEecchHH
Confidence            9999999999999999999999999888883    2      235689999999999999996  5788888876544

>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=99.54  E-value=4.9e-14  Score=115.74  Aligned_cols=105  Identities=15%  Similarity=0.181  Sum_probs=85.0

Q ss_pred             CCCeeEEehhhhhHHHHHhhccccC------------ceE-EEecCC----------C----------CHH---------
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVKE------------YDV-LLLHGD----------M----------DQS---------   71 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~~------------~~~-~~~~~~----------~----------~~~---------   71 (150)
                      +.++||||+++++|..++..|...+            +++ ..+||+          +          ++.         
T Consensus       537 g~kamVf~~S~~~A~~~~~~l~~~~~~~~~~~~~~~~~k~avv~s~~~~~~~~~~G~~~~e~~~~~~~~~~~r~~l~~~I  616 (1038)
T 2w00_A          537 GFNAMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRIATIFSFAANEEQNAIGEISDETFDTSAMDSSAKEFLDAAI  616 (1038)
T ss_dssp             CCEEEEEESSHHHHHHHHHHHHHHHHHHTTTSSSCCCCCEEEECCCCC------CCCCCCCCSCGGGSCHHHHHHHHHHH
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhhhhhhcccccccccCcEEEEEeCCCccccccccccccccccccccchhHHHHHHHHH
Confidence            4579999999999999999987643            444 455542          2          221         


Q ss_pred             --------------------HHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCc
Q psy17637         72 --------------------ERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNK  131 (150)
Q Consensus        72 --------------------~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~  131 (150)
                                          .|..++++|++|+++|||+|+++.+|+|+|.+ +++++|.|.+...|+|++||++|.+..
T Consensus       617 ~dyn~~f~~~~~~~~~~~~~~R~~i~~~Fk~g~i~ILIvvd~lltGfDiP~l-~tlylDkpl~~~~liQaIGRtnR~~~~  695 (1038)
T 2w00_A          617 REYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQDIDLLIVVGMFLTGFDAPTL-NTLFVDKNLRYHGLMQAFSRTNRIYDA  695 (1038)
T ss_dssp             HHHHHHHTCCCCSSHHHHHHHHHHHHHHHHTTSSSEEEESSTTSSSCCCTTE-EEEEEESCCCHHHHHHHHHTTCCCCCT
T ss_pred             HHHHHHhcccccccchhhhHHHHHHHHHHHcCCCeEEEEcchHHhCcCcccc-cEEEEccCCCccceeehhhccCcCCCC
Confidence                                47888999999999999999999999999999 678899999999999999999998753


Q ss_pred             ----cEEEEEEe
Q psy17637        132 ----GVAYTLVT  139 (150)
Q Consensus       132 ----~~~~~~~~  139 (150)
                          |.++.|+.
T Consensus       696 ~K~~G~IVdf~~  707 (1038)
T 2w00_A          696 TKTFGNIVTFRD  707 (1038)
T ss_dssp             TCCSEEEEESSC
T ss_pred             CCCcEEEEEccc
Confidence                45555543

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.07  E-value=7.9e-10  Score=89.02  Aligned_cols=125  Identities=19%  Similarity=0.245  Sum_probs=96.8

Q ss_pred             hhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhcc----------------------------------------
Q psy17637         16 DKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLT----------------------------------------   55 (150)
Q Consensus        16 ~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~----------------------------------------   55 (150)
                      ...+...+++.+......+.|+||+|.|.+..|.|...|.                                        
T Consensus       425 ~~~K~~AIv~eI~~~~~~GqPVLVgT~SIe~SE~LS~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  504 (997)
T 2ipc_A          425 EKGKFYAVVEEIAEKYERGQPVLVGTISIEKSERLSQMLKEPRLYLPRLEMRLELFKKASQKQQGPEWERLRKLLERPAQ  504 (997)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCCEEEECSSHHHHHHHHHHHHCGGGGHHHHHHHHHHHHHHHTTCCSHHHHHHHHHTSSSTT
T ss_pred             HHHHHHHHHHHHHHHHHCCCCEEEEeCCHHHHHHHHHHHhhccccchhhhhhhhhhhhhhhhccccchhhhhhhhhcccc
Confidence            4556678888998877789999999999999999999988                                        


Q ss_pred             ------------------------------------ccCceEEEecCCCCHHHHHHHHHHhhcCC-ceEEEEcCCCcccC
Q psy17637         56 ------------------------------------VKEYDVLLLHGDMDQSERNSVITKFKRQE-CRILVATDVAARGL   98 (150)
Q Consensus        56 ------------------------------------~~~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~vlv~T~~~~~Gi   98 (150)
                                                          ..+++.-.+.+.-...+- +++..  .|. -.|.|||+++++|.
T Consensus       505 ~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gI~H~VLNAK~he~EA-eIIAq--AG~~GaVTIATNMAGRGT  581 (997)
T 2ipc_A          505 LKDEDLAPFEGLIPPKGNLRTAWEGLKRAVHTLAVLRQGIPHQVLNAKHHAREA-EIVAQ--AGRSKTVTIATNMAGRGT  581 (997)
T ss_dssp             CSHHHHSGGGGGCCSSHHHHHHHHHHHHHHHHHHHHHHCCCCCEECSSSHHHHH-HHHHT--TTSTTCEEEECSSTTTTS
T ss_pred             ccccccccccccccccccccccccccchhhhhhHHHHcCCCeeeccccchHHHH-HHHHh--cCCCCeEEEEecccCCCc
Confidence                                                345555666665433332 22222  232 36899999999999


Q ss_pred             CccCC-------------------c-------------------------------------------------------
Q psy17637         99 DIPHI-------------------R-------------------------------------------------------  104 (150)
Q Consensus        99 di~~~-------------------~-------------------------------------------------------  104 (150)
                      ||.--                   .                                                       
T Consensus       582 DIkLggn~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~V~e~GGL  661 (997)
T 2ipc_A          582 DIKLGGNPEYLAAALLEKEGFDRYEWKVELFIKKMVAGKEEEARALAQELGIREELLERIREIREECKQDEERVRALGGL  661 (997)
T ss_dssp             CCCSSCCHHHHHHHTTSSSCSSTTHHHHHHHHHHHHHTCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTTTCCC
T ss_pred             CeecCCCHHHHHHHHHHhhcccccccccccccccccccchhhccccchhhhhhhhHHHHHHHhhhhhhhhhhHHHhcCCe
Confidence            98421                   1                                                       


Q ss_pred             EEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637        105 TVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus       105 ~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +||-...+.|...-.|..||+||.|++|..-+|++-+|.
T Consensus       662 hVIGTeRhESrRIDnQLRGRaGRQGDPGsSrF~LSLeDd  700 (997)
T 2ipc_A          662 FIIGTERHESRRIDNQLRGRAGRQGDPGGSRFYVSFDDD  700 (997)
T ss_dssp             CEEESSCCSSHHHHHHHHHTSSCSSCCCEEEEEEESSSH
T ss_pred             EEEeccCCchHHHHHHHhcccccCCCCCCeEEEEECChH
Confidence            788888999999999999999999999999999987764

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.94  E-value=3.7e-09  Score=81.91  Aligned_cols=102  Identities=15%  Similarity=0.131  Sum_probs=66.1

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEE--EcCCCcccCCccC----CcEE
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILV--ATDVAARGLDIPH----IRTV  106 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv--~T~~~~~Gidi~~----~~~v  106 (150)
                      ..+.++||++|...++.+++.|...   ....+|..  ..+.++++.|+.+. .||+  +|..+++|+|+|+    +++|
T Consensus       383 ~~g~~lvff~S~~~~~~v~~~l~~~---~~~~q~~~--~~~~~~l~~f~~~~-~il~~V~~~~~~EGiD~~~~~~~~~~V  456 (540)
T 2vl7_A          383 SSKSVLVFFPSYEMLESVRIHLSGI---PVIEENKK--TRHEEVLELMKTGK-YLVMLVMRAKESEGVEFREKENLFESL  456 (540)
T ss_dssp             CSSEEEEEESCHHHHHHHHTTCTTS---CEEESTTT--CCHHHHHHHHHTSC-CEEEEEC---------------CEEEE
T ss_pred             CCCCEEEEeCCHHHHHHHHHHhccC---ceEecCCC--CcHHHHHHHHhcCC-eEEEEEecCceecceecCCCcccccEE
Confidence            4568999999999999999998752   24555553  46788999998864 5665  8899999999997    7899


Q ss_pred             EEecCCCCh------------------------------hHHHHhhccccCCCCccEEEEEEec
Q psy17637        107 VNYDLARDI------------------------------DTHTHRIGRTGRAGNKGVAYTLVTD  140 (150)
Q Consensus       107 i~~~~~~~~------------------------------~~~~q~~GR~~R~g~~~~~~~~~~~  140 (150)
                      |+.+.|...                              ..+.|.+||+.|..++..++++++.
T Consensus       457 ii~~lPf~~~~d~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~Q~~GR~iR~~~D~g~v~llD~  520 (540)
T 2vl7_A          457 VLAGLPYPNVSDDMVRKRIERLSKLTGKDEDSIIHDLTAIVIKQTIGRAFRDPNDYVKIYLCDS  520 (540)
T ss_dssp             EEESCCCCCTTSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHCCSTTCCCEEEEESG
T ss_pred             EEECCCCCCCCCHHHHHHHHHHHHhhCCChhHHHHHHHHHHHHHHhCCcccCCCccEEEEEEcc
Confidence            999988521                              1235899999997655555556543

>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=98.60  E-value=4.7e-07  Score=65.65  Aligned_cols=119  Identities=10%  Similarity=0.033  Sum_probs=83.7

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccC
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGL   98 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gi   98 (150)
                      .+..|+..+.+   .+.+++||+...+..+-+-.+|...++....+.|.....+ .+.    .++...+.+.|...+-|+
T Consensus       113 ~L~~LL~~l~~---~~~kVLIfsq~t~~LDilE~~l~~~~~~y~RlDG~~~~~~-~k~----~~~~~~i~Lltsag~~gi  184 (328)
T 3hgt_A          113 VLRDLINLVQE---YETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIKSA-AAA----NDFSCTVHLFSSEGINFT  184 (328)
T ss_dssp             HHHHHHHHHTT---SCEEEEEEECSTHHHHHHHHHHTTSSCEEEESSSCCC------------CCSEEEEEEESSCCCTT
T ss_pred             HHHHHHHHHHh---CCCEEEEEECChhHHHHHHHHHhcCCCceEeCCCCchhhh-hhc----ccCCceEEEEECCCCCCc
Confidence            44455555543   5779999999999999999999999999999999855432 221    234445555577777777


Q ss_pred             C-----ccCCcEEEEecCCCChhHH-HHhhccccCCC--C--ccEEEEEEecCCCcc
Q psy17637         99 D-----IPHIRTVVNYDLARDIDTH-THRIGRTGRAG--N--KGVAYTLVTDKDKDG  145 (150)
Q Consensus        99 d-----i~~~~~vi~~~~~~~~~~~-~q~~GR~~R~g--~--~~~~~~~~~~~~~~~  145 (150)
                      +     ....+.||.||+.+++..- +|++-|+.|.|  +  .-.+|.+++....+.
T Consensus       185 n~~~~nl~~aD~VI~~DsdwNp~~d~iQa~~r~~R~~~gq~k~v~V~RLvt~~TiEh  241 (328)
T 3hgt_A          185 KYPIKSKARFDMLICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAINSIDH  241 (328)
T ss_dssp             TSCCCCCSCCSEEEECSTTCCTTSHHHHHHHCCC---------CCEEEEEETTSHHH
T ss_pred             CcccccCCCCCEEEEECCCCCCCChHHHHHHHHhhhccCCCCcceEEEEeCCCCHHH
Confidence            6     6788999999999999886 89999998874  2  336788887765443

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=98.57  E-value=5.8e-07  Score=70.76  Aligned_cols=104  Identities=15%  Similarity=0.218  Sum_probs=73.1

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEc--CCCcccCCcc--CCcEEEE
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVAT--DVAARGLDIP--HIRTVVN  108 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T--~~~~~Gidi~--~~~~vi~  108 (150)
                      ..+.++||++|....+.+++.|..  +... ...+++..++..+++.|+ ++..||+++  ..+++|+|+|  .+..||.
T Consensus       447 ~~g~~lvlF~Sy~~l~~v~~~l~~--~~~~-~~q~~~~~~~~~ll~~f~-~~~~vL~~v~~gsf~EGiD~~g~~l~~viI  522 (620)
T 4a15_A          447 VKKNTIVYFPSYSLMDRVENRVSF--EHMK-EYRGIDQKELYSMLKKFR-RDHGTIFAVSGGRLSEGINFPGNELEMIIL  522 (620)
T ss_dssp             HCSCEEEEESCHHHHHHHTSSCCS--CCEE-CCTTCCSHHHHHHHHHHT-TSCCEEEEETTSCC--------CCCCEEEE
T ss_pred             CCCCEEEEeCCHHHHHHHHHHHHh--cchh-ccCCCChhHHHHHHHHhc-cCCcEEEEEecCceeccccCCCCceEEEEE
Confidence            456799999999999999999872  2222 555666678999999999 777899997  4999999997  4678998


Q ss_pred             ecCCCCh-----------------------------hHHHHhhccccCCCCccEEEEEEec
Q psy17637        109 YDLARDI-----------------------------DTHTHRIGRTGRAGNKGVAYTLVTD  140 (150)
Q Consensus       109 ~~~~~~~-----------------------------~~~~q~~GR~~R~g~~~~~~~~~~~  140 (150)
                      ...|...                             ....|.+||+-|..++..++++++.
T Consensus       523 ~~lPfp~~~p~~~ar~~~~~~~~g~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD~  583 (620)
T 4a15_A          523 AGLPFPRPDAINRSLFDYYERKYGKGWEYSVVYPTAIKIRQEIGRLIRSAEDTGACVILDK  583 (620)
T ss_dssp             SSCCCCCCCHHHHHHHHHHHHHHSCHHHHHTHHHHHHHHHHHHHTTCCSTTCCEEEEEECG
T ss_pred             EcCCCCCCCHHHHHHHHHHHHhhCCCchHHhHHHHHHHHHHHhCccccCCCceEEEEEEcc
Confidence            8877521                             1125999999998766666666654

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=98.07  E-value=7.6e-05  Score=57.93  Aligned_cols=102  Identities=14%  Similarity=0.138  Sum_probs=70.7

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEc--CCCcccCCcc-----CCcE
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVAT--DVAARGLDIP-----HIRT  105 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T--~~~~~Gidi~-----~~~~  105 (150)
                      ..+.++||++|.+.++.+++.+   +..+..=..+++.   .+.++.|+...-.||+++  ..+++|+|+|     .+..
T Consensus       392 ~~g~~lvlF~Sy~~l~~v~~~~---~~~v~~q~~~~~~---~~~~~~~~~~~~~vl~~v~gg~~~EGiD~~d~~g~~l~~  465 (551)
T 3crv_A          392 AKANVLVVFPSYEIMDRVMSRI---SLPKYVESEDSSV---EDLYSAISANNKVLIGSVGKGKLAEGIELRNNDRSLISD  465 (551)
T ss_dssp             CSSEEEEEESCHHHHHHHHTTC---CSSEEECCSSCCH---HHHHHHTTSSSSCEEEEESSCCSCCSSCCEETTEESEEE
T ss_pred             CCCCEEEEecCHHHHHHHHHhc---CCcEEEcCCCCCH---HHHHHHHHhcCCeEEEEEecceecccccccccCCcceeE
Confidence            4568999999999999999843   3333332234553   556778854344799988  6999999999     4678


Q ss_pred             EEEecCCCC--------------------hh----------HHHHhhccccCCCCccEEEEEEec
Q psy17637        106 VVNYDLARD--------------------ID----------THTHRIGRTGRAGNKGVAYTLVTD  140 (150)
Q Consensus       106 vi~~~~~~~--------------------~~----------~~~q~~GR~~R~g~~~~~~~~~~~  140 (150)
                      ||....|..                    .-          ...|.+||+-|..++..++++++.
T Consensus       466 viI~~lPfp~~dp~~~ar~~~~~~~~g~~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD~  530 (551)
T 3crv_A          466 VVIVGIPYPPPDDYLKILAQRVSLKMNRENEEFLFKIPALVTIKQAIGRAIRDVNDKCNVWLLDK  530 (551)
T ss_dssp             EEEESCCCCCCSHHHHHHHHHTTCCSSTTTHHHHTHHHHHHHHHHHHHTTCCSTTCEEEEEEESG
T ss_pred             EEEEcCCCCCCCHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHhccCccCCCccEEEEEeeh
Confidence            888776641                    10          124899999998766666666654

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=97.07  E-value=0.0034  Score=50.81  Aligned_cols=76  Identities=12%  Similarity=0.158  Sum_probs=61.0

Q ss_pred             CCCCeeEEehhhhhHHHHHhhc----cccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CCcccCCccCCcEEE
Q psy17637         33 EVPPALMNLAMQLNAEELANSL----TVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VAARGLDIPHIRTVV  107 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L----~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~~~Gidi~~~~~vi  107 (150)
                      .+.++++.++++.-+...++.+    ...++++..+||+++..++...++.+.+|...|+|+|. .+...+.+.++.+||
T Consensus       416 ~g~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~~~~~~l~lVV  495 (780)
T 1gm5_A          416 AGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVI  495 (780)
T ss_dssp             HTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEE
T ss_pred             cCCeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhhhhhccCCceEE
Confidence            4578999999988766655544    34478999999999999999999999999999999995 344456777887776


Q ss_pred             E
Q psy17637        108 N  108 (150)
Q Consensus       108 ~  108 (150)
                      .
T Consensus       496 I  496 (780)
T 1gm5_A          496 I  496 (780)
T ss_dssp             E
T ss_pred             e
Confidence            3

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=96.40  E-value=0.016  Score=42.93  Aligned_cols=77  Identities=12%  Similarity=0.169  Sum_probs=61.0

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccc---cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CCc---ccCCccCCc
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTV---KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VAA---RGLDIPHIR  104 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~~---~Gidi~~~~  104 (150)
                      ....++||.+++++-+..+++.+..   .++++..++|+.+..++......+..+...|+|+|. .+.   .-++...+.
T Consensus        62 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~  141 (414)
T 3oiy_A           62 RKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFD  141 (414)
T ss_dssp             TTTCCEEEEESSHHHHHHHHHHHHHHCCSSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHHHTTCCCS
T ss_pred             cCCCEEEEEECCHHHHHHHHHHHHHHccCCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHHhcccccc
Confidence            4677999999999988888887766   578999999999999988888999999899999995 221   123445677


Q ss_pred             EEEE
Q psy17637        105 TVVN  108 (150)
Q Consensus       105 ~vi~  108 (150)
                      +||.
T Consensus       142 ~iVi  145 (414)
T 3oiy_A          142 FVFV  145 (414)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            7663

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=95.77  E-value=0.062  Score=45.39  Aligned_cols=76  Identities=8%  Similarity=0.149  Sum_probs=59.9

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhc----cccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CCcccCCccCCcEE
Q psy17637         32 QEVPPALMNLAMQLNAEELANSL----TVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VAARGLDIPHIRTV  106 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L----~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~~~Gidi~~~~~v  106 (150)
                      ..+.+++|.++|+.-+...++.+    ...++.+..+++..+..++...++.+..|...|+|+|. .+...+.+.++.+|
T Consensus       650 ~~g~~vlvlvPt~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~~~~~~~~l~lv  729 (1151)
T 2eyq_A          650 DNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLL  729 (1151)
T ss_dssp             TTTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEE
T ss_pred             HhCCeEEEEechHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhCCccccccceE
Confidence            35679999999988766555554    34467899999999999999999999999999999995 44445667777766


Q ss_pred             E
Q psy17637        107 V  107 (150)
Q Consensus       107 i  107 (150)
                      |
T Consensus       730 I  730 (1151)
T 2eyq_A          730 I  730 (1151)
T ss_dssp             E
T ss_pred             E
Confidence            5

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=95.63  E-value=0.05  Score=45.73  Aligned_cols=77  Identities=12%  Similarity=0.179  Sum_probs=61.6

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccc---cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CCcc---cCCccCCc
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTV---KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VAAR---GLDIPHIR  104 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~~~---Gidi~~~~  104 (150)
                      ..+.++||.+++++-+..+++.+..   .++.+..+||+++..++...++.+..|...|+|+|. .+..   -++..++.
T Consensus       119 ~~~~~~Lil~PtreLa~Q~~~~l~~l~~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~l~~~~l~  198 (1104)
T 4ddu_A          119 RKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFD  198 (1104)
T ss_dssp             TTTCCEEEEESSHHHHHHHHHHHHTTSCTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHHHHTSCCS
T ss_pred             hcCCeEEEEechHHHHHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHhhcccCcC
Confidence            4677899999999999888888776   567899999999998888888999999899999994 2211   13456777


Q ss_pred             EEEE
Q psy17637        105 TVVN  108 (150)
Q Consensus       105 ~vi~  108 (150)
                      +||.
T Consensus       199 ~lVi  202 (1104)
T 4ddu_A          199 FVFV  202 (1104)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            7764

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=94.22  E-value=0.22  Score=33.30  Aligned_cols=72  Identities=15%  Similarity=0.203  Sum_probs=50.0

Q ss_pred             CCCeeEEehhhhhHHHHHhhcccc-----CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CC-----cccCCccC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVK-----EYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VA-----ARGLDIPH  102 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~-----~~Gidi~~  102 (150)
                      ..++||.+++++-++.+++.+...     ++++..++|+.+......   .+..+...|+|+|. .+     ...+++..
T Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~---~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~  158 (220)
T 1t6n_A           82 QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEE---VLKKNCPHIVVGTPGRILALARNKSLNLKH  158 (220)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHH---HHHHSCCSEEEECHHHHHHHHHTTSSCCTT
T ss_pred             CEEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHH---HHhcCCCCEEEeCHHHHHHHHHhCCCCccc
Confidence            458999999998887776655432     688999999988765543   34456678999994 22     22355667


Q ss_pred             CcEEEE
Q psy17637        103 IRTVVN  108 (150)
Q Consensus       103 ~~~vi~  108 (150)
                      +.++|.
T Consensus       159 ~~~lVi  164 (220)
T 1t6n_A          159 IKHFIL  164 (220)
T ss_dssp             CCEEEE
T ss_pred             CCEEEE
Confidence            777663

>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=94.18  E-value=0.1  Score=40.19  Aligned_cols=59  Identities=10%  Similarity=0.108  Sum_probs=53.3

Q ss_pred             CCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD   92 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~   92 (150)
                      .+.+||.++++.-++.....|...++.+..++++.+..++......+..|...++++|.
T Consensus        65 ~g~~lvi~P~~aL~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tp  123 (523)
T 1oyw_A           65 NGLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAP  123 (523)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECH
T ss_pred             CCCEEEECChHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            35799999999999988888888899999999999999999999999999999999884

>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=93.85  E-value=0.12  Score=40.50  Aligned_cols=59  Identities=14%  Similarity=0.075  Sum_probs=52.0

Q ss_pred             CCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHh--hcCCceEEEEcC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKF--KRQECRILVATD   92 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f--~~g~~~vlv~T~   92 (150)
                      .+.+||.+++++-++.....|...++.+..++|+++..++..++..+  ..+...|+++|.
T Consensus        84 ~g~~lVisP~~~L~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tp  144 (591)
T 2v1x_A           84 DGFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTP  144 (591)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHHTCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECH
T ss_pred             CCcEEEEeCHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEECh
Confidence            45899999999999988888888899999999999999998888888  467789999995

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=93.60  E-value=0.47  Score=32.60  Aligned_cols=82  Identities=13%  Similarity=0.205  Sum_probs=53.3

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CC--
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VA--   94 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~--   94 (150)
                      .++..+... ....++||.+++++-+..+++.+..    .++.+..++|+.+.......+    .+...|+|+|. .+  
T Consensus       100 ~il~~l~~~-~~~~~~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~I~v~Tp~~l~~  174 (249)
T 3ber_A          100 PILNALLET-PQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLAL----AKKPHIIIATPGRLID  174 (249)
T ss_dssp             HHHHHHHHS-CCSSCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHH----HTCCSEEEECHHHHHH
T ss_pred             HHHHHHhcC-CCCceEEEEeCCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHh----cCCCCEEEECHHHHHH
Confidence            344444443 3456799999999988777766543    377889999998765544332    24568999994 21  


Q ss_pred             ----cccCCccCCcEEEE
Q psy17637         95 ----ARGLDIPHIRTVVN  108 (150)
Q Consensus        95 ----~~Gidi~~~~~vi~  108 (150)
                          ..++++..+.++|.
T Consensus       175 ~l~~~~~~~l~~~~~lVi  192 (249)
T 3ber_A          175 HLENTKGFNLRALKYLVM  192 (249)
T ss_dssp             HHHHSTTCCCTTCCEEEE
T ss_pred             HHHcCCCcCccccCEEEE
Confidence                13456667777763

>2l82_A Designed protein OR32; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, de novo protein; NMR {Artificial gene}

Probab=93.51  E-value=0.32  Score=29.39  Aligned_cols=48  Identities=19%  Similarity=0.261  Sum_probs=31.5

Q ss_pred             eeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC
Q psy17637         37 ALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE   84 (150)
Q Consensus        37 ~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~   84 (150)
                      .+||++..+-+.++...++..|..+..++++.+.+.|.+-++.|....
T Consensus         5 fvvfssdpeilkeivreikrqgvrvvllysdqdekrrrerleefekqg   52 (162)
T 2l82_A            5 FVVFSSDPEILKEIVREIKRQGVRVVLLYSDQDEKRRRERLEEFEKQG   52 (162)
T ss_dssp             EEEEESCHHHHHHHHHHHHHTTCEEEEEECCSCHHHHHHHHHHHHTTT
T ss_pred             EEEecCCHHHHHHHHHHHHhCCeEEEEEecCchHHHHHHHHHHHHHcC
Confidence            356666666666666666666777777777766666666666665443

>3gk5_A Uncharacterized rhodanese-related protein TVG0868615; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Thermoplasma volcanium GSS1}

Probab=92.98  E-value=0.12  Score=30.88  Aligned_cols=47  Identities=9%  Similarity=0.019  Sum_probs=36.8

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCC
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMD   69 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~   69 (150)
                      .+.+.+... .+..++++||.+-..+...+..|...|+.+..+.||+.
T Consensus        44 ~l~~~~~~l-~~~~~ivvyC~~G~rs~~aa~~L~~~G~~v~~l~GG~~   90 (108)
T 3gk5_A           44 ELREKWKIL-ERDKKYAVICAHGNRSAAAVEFLSQLGLNIVDVEGGIQ   90 (108)
T ss_dssp             HHHHHGGGS-CTTSCEEEECSSSHHHHHHHHHHHTTTCCEEEETTHHH
T ss_pred             HHHHHHHhC-CCCCeEEEEcCCCcHHHHHHHHHHHcCCCEEEEcCcHH
Confidence            344444444 56678999999988888999999999998899999853

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=92.85  E-value=0.36  Score=32.60  Aligned_cols=72  Identities=15%  Similarity=0.172  Sum_probs=49.3

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhcccc-----CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CC-----cccCCc
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVK-----EYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VA-----ARGLDI  100 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~-----~~Gidi  100 (150)
                      ....++||.+++++-+..+++.+...     ++++..++|+.+..+....+     ....|+|+|. .+     ...+++
T Consensus        90 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~Iiv~Tp~~l~~~~~~~~~~~  164 (230)
T 2oxc_A           90 NLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-----KKCHIAVGSPGRIKQLIELDYLNP  164 (230)
T ss_dssp             SCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT-----TSCSEEEECHHHHHHHHHTTSSCG
T ss_pred             CCCceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc-----cCCCEEEECHHHHHHHHhcCCccc
Confidence            34578999999998887777666532     67889999998876554432     2468999995 22     123456


Q ss_pred             cCCcEEEE
Q psy17637        101 PHIRTVVN  108 (150)
Q Consensus       101 ~~~~~vi~  108 (150)
                      ..+.++|.
T Consensus       165 ~~~~~lVi  172 (230)
T 2oxc_A          165 GSIRLFIL  172 (230)
T ss_dssp             GGCCEEEE
T ss_pred             ccCCEEEe
Confidence            67777663

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=92.69  E-value=0.88  Score=30.91  Aligned_cols=72  Identities=13%  Similarity=0.085  Sum_probs=50.1

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-C----Cc-ccCCccC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-V----AA-RGLDIPH  102 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~----~~-~Gidi~~  102 (150)
                      ...++||.+++++-+..+++.+..    .++.+..++|+.+.......+.   . ...|+|+|. .    +. ...++.+
T Consensus       101 ~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~---~-~~~I~v~Tp~~l~~~l~~~~~~~~~  176 (242)
T 3fe2_A          101 DGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLE---R-GVEICIATPGRLIDFLECGKTNLRR  176 (242)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHH---H-CCSEEEECHHHHHHHHHHTSCCCTT
T ss_pred             CCCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhc---C-CCCEEEECHHHHHHHHHcCCCCccc
Confidence            466799999999988877666543    3788999999988766654433   2 368999994 1    11 2345677


Q ss_pred             CcEEEE
Q psy17637        103 IRTVVN  108 (150)
Q Consensus       103 ~~~vi~  108 (150)
                      +.++|.
T Consensus       177 ~~~lVi  182 (242)
T 3fe2_A          177 TTYLVL  182 (242)
T ss_dssp             CCEEEE
T ss_pred             ccEEEE
Confidence            777763

>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=92.26  E-value=0.56  Score=33.96  Aligned_cols=73  Identities=16%  Similarity=0.220  Sum_probs=50.4

Q ss_pred             CCCCeeEEehhhhhHHHHHhhcccc-----CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CC-----cccCCcc
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVK-----EYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VA-----ARGLDIP  101 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~-----~~Gidi~  101 (150)
                      ...++||.|+++.-++.+++.+...     ++.+..++|+.+.......   +..+...|+|+|. .+     ....+..
T Consensus        75 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~~~~~~iiv~T~~~l~~~~~~~~~~~~  151 (391)
T 1xti_A           75 GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEV---LKKNCPHIVVGTPGRILALARNKSLNLK  151 (391)
T ss_dssp             TCCCEEEECSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHH---HHHSCCSEEEECHHHHHHHHHTTSSCCT
T ss_pred             CCeeEEEECCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHH---HhcCCCCEEEECHHHHHHHHHcCCcccc
Confidence            4568999999998887766655432     7889999999887655443   4456678999994 22     2234556


Q ss_pred             CCcEEEE
Q psy17637        102 HIRTVVN  108 (150)
Q Consensus       102 ~~~~vi~  108 (150)
                      .+.+||.
T Consensus       152 ~~~~vVi  158 (391)
T 1xti_A          152 HIKHFIL  158 (391)
T ss_dssp             TCSEEEE
T ss_pred             ccCEEEE
Confidence            7776663

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=91.93  E-value=0.38  Score=32.68  Aligned_cols=73  Identities=16%  Similarity=0.138  Sum_probs=42.2

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-----CCcc-cCCccC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-----VAAR-GLDIPH  102 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~~-Gidi~~  102 (150)
                      ...++||.+++++-+..+++.+..    .+..+..++|+.+...   ....+..+...|+|+|.     .+.. .++...
T Consensus        97 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~---~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~  173 (237)
T 3bor_A           97 KETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRN---EMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKW  173 (237)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC----------------CCCSEEEECHHHHHHHHHTTSSCSTT
T ss_pred             CCceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHH---HHHHHhcCCCCEEEECHHHHHHHHHhCCcCccc
Confidence            456899999999988877766643    3567788888765332   23345556678999993     2222 245566


Q ss_pred             CcEEEE
Q psy17637        103 IRTVVN  108 (150)
Q Consensus       103 ~~~vi~  108 (150)
                      +.+||.
T Consensus       174 ~~~lVi  179 (237)
T 3bor_A          174 IKMFVL  179 (237)
T ss_dssp             CCEEEE
T ss_pred             CcEEEE
Confidence            777663

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=91.61  E-value=0.79  Score=30.08  Aligned_cols=72  Identities=11%  Similarity=0.150  Sum_probs=47.5

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc----c-CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CC----cc-cCCcc
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV----K-EYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VA----AR-GLDIP  101 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~----~-~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~----~~-Gidi~  101 (150)
                      ...++||.+++++-+..+++.+..    . +..+..++|+.+..+...   .+ .+...|+|+|. .+    .. ..++.
T Consensus        70 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~~-~~~~~i~v~T~~~l~~~~~~~~~~~~  145 (206)
T 1vec_A           70 DNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIM---RL-DDTVHVVIATPGRILDLIKKGVAKVD  145 (206)
T ss_dssp             CSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHH---HT-TSCCSEEEECHHHHHHHHHTTCSCCT
T ss_pred             CCeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHH---hc-CCCCCEEEeCHHHHHHHHHcCCcCcc
Confidence            456899999999887777666543    2 677889999987654432   22 24568999995 21    22 23456


Q ss_pred             CCcEEEE
Q psy17637        102 HIRTVVN  108 (150)
Q Consensus       102 ~~~~vi~  108 (150)
                      .+.++|.
T Consensus       146 ~~~~lVi  152 (206)
T 1vec_A          146 HVQMIVL  152 (206)
T ss_dssp             TCCEEEE
T ss_pred             cCCEEEE
Confidence            7777663

>3dmn_A Putative DNA helicase; APC89291.2, lactobacillus plantarum WCFS1, STR genomics, PSI-2, midwest center for structural genomics; HET: MSE; 1.66A {Lactobacillus plantarum}

Probab=91.37  E-value=1.9  Score=27.87  Aligned_cols=78  Identities=17%  Similarity=0.280  Sum_probs=53.6

Q ss_pred             HHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCC
Q psy17637         20 AGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLD   99 (150)
Q Consensus        20 ~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gid   99 (150)
                      ...+.+.+.........+.|.|.+...+..+.+.|...++.+..+.++-.         .+   ...|.|.|-....|+.
T Consensus        47 ~~~i~~~I~~~~~g~~~iAVL~r~~~~~~~l~~~L~~~gi~~~~l~~~~~---------~~---~~~v~v~t~~~~KGlE  114 (174)
T 3dmn_A           47 VDQVVDQLAMNDSERDTTAIIGKSLAECEALTKALKARGEQVTLIQTENQ---------RL---APGVIVVPSFLAKGLE  114 (174)
T ss_dssp             HHHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHHHTTTCCEEECSSCC----------CC---CSSEEEEEGGGCTTCC
T ss_pred             HHHHHHHHHHhccCCCcEEEEecCHHHHHHHHHHHHHcCCcceeeccccc---------cc---CCCeEEEEccccCCcC
Confidence            44555555432123567889999999999999999888888777765421         12   2368899988889988


Q ss_pred             ccCCcEEEEecCC
Q psy17637        100 IPHIRTVVNYDLA  112 (150)
Q Consensus       100 i~~~~~vi~~~~~  112 (150)
                      +   +.||.+++.
T Consensus       115 f---~~V~~~~~~  124 (174)
T 3dmn_A          115 F---DAVIVWNAN  124 (174)
T ss_dssp             E---EEEEEETCB
T ss_pred             C---CEEEEecCC
Confidence            7   456665543

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=91.19  E-value=0.42  Score=32.15  Aligned_cols=72  Identities=14%  Similarity=0.151  Sum_probs=45.1

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc---cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CC-----cccCCccCC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV---KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VA-----ARGLDIPHI  103 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~---~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~-----~~Gidi~~~  103 (150)
                      ...++||.+++++-+..+++.+..   .++.+..++|+.+.......   +.. ...|+|+|. .+     ....++.++
T Consensus        93 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~-~~~iiv~Tp~~l~~~~~~~~~~~~~~  168 (228)
T 3iuy_A           93 NGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQIED---ISK-GVDIIIATPGRLNDLQMNNSVNLRSI  168 (228)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC------CHHH---HHS-CCSEEEECHHHHHHHHHTTCCCCTTC
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEECCCChHHHHHH---hcC-CCCEEEECHHHHHHHHHcCCcCcccc
Confidence            567899999999988877776654   47788889988765443322   232 368999994 11     224556777


Q ss_pred             cEEEE
Q psy17637        104 RTVVN  108 (150)
Q Consensus       104 ~~vi~  108 (150)
                      .++|.
T Consensus       169 ~~lVi  173 (228)
T 3iuy_A          169 TYLVI  173 (228)
T ss_dssp             CEEEE
T ss_pred             eEEEE
Confidence            77763

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=90.75  E-value=0.97  Score=30.47  Aligned_cols=71  Identities=17%  Similarity=0.155  Sum_probs=45.8

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CC----cc--cCCcc
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VA----AR--GLDIP  101 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~----~~--Gidi~  101 (150)
                      ...++||.+++++-+...++.+..    .++.+..++|+.+.......+     +...|+|+|. .+    ..  ..+..
T Consensus        96 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~iiv~Tp~~l~~~l~~~~~~~~~  170 (236)
T 2pl3_A           96 DGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-----NNINILVCTPGRLLQHMDETVSFHAT  170 (236)
T ss_dssp             GCCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-----TTCSEEEECHHHHHHHHHHCSSCCCT
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-----CCCCEEEECHHHHHHHHHhcCCcccc
Confidence            467899999999888777666654    357888999987654433322     3568999994 22    11  24556


Q ss_pred             CCcEEEE
Q psy17637        102 HIRTVVN  108 (150)
Q Consensus       102 ~~~~vi~  108 (150)
                      .+.++|.
T Consensus       171 ~~~~lVi  177 (236)
T 2pl3_A          171 DLQMLVL  177 (236)
T ss_dssp             TCCEEEE
T ss_pred             cccEEEE
Confidence            7777663

>3flh_A Uncharacterized protein LP_1913; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.00A {Lactobacillus plantarum} PDB: 3fnj_A 3i3u_A

Probab=90.13  E-value=0.2  Score=30.69  Aligned_cols=46  Identities=9%  Similarity=0.034  Sum_probs=35.1

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhh--HHHHHhhccccCceEEEecCCC
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLN--AEELANSLTVKEYDVLLLHGDM   68 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~--~~~l~~~L~~~~~~~~~~~~~~   68 (150)
                      .+...+... .+..++++||.+-..  +...+..|...|+++..+.||+
T Consensus        60 ~l~~~~~~l-~~~~~ivvyC~~g~r~~s~~a~~~L~~~G~~v~~l~GG~  107 (124)
T 3flh_A           60 DLATRIGEL-DPAKTYVVYDWTGGTTLGKTALLVLLSAGFEAYELAGAL  107 (124)
T ss_dssp             HHHHHGGGS-CTTSEEEEECSSSSCSHHHHHHHHHHHHTCEEEEETTHH
T ss_pred             HHHHHHhcC-CCCCeEEEEeCCCCchHHHHHHHHHHHcCCeEEEeCCcH
Confidence            344444444 456789999998776  7888889988899988888985

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=89.94  E-value=2.5  Score=29.15  Aligned_cols=72  Identities=17%  Similarity=0.104  Sum_probs=48.7

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-----CC--cccCCcc
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-----VA--ARGLDIP  101 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~--~~Gidi~  101 (150)
                      ...++||.+++++-++..++.+..    .+..+..++|+.........   +..+ ..|+|+|.     .+  ..++++.
T Consensus       125 ~~~~~lil~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~~~-~~Iiv~Tp~~l~~~~~~~~~~~~~  200 (262)
T 3ly5_A          125 NGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQK---LGNG-INIIVATPGRLLDHMQNTPGFMYK  200 (262)
T ss_dssp             GCCCEEEECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHH---HHHC-CSEEEECHHHHHHHHHHCTTCCCT
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHHH---hcCC-CCEEEEcHHHHHHHHHccCCcccc
Confidence            467899999999888777666643    46778889998876554433   3334 68999993     11  1235667


Q ss_pred             CCcEEEE
Q psy17637        102 HIRTVVN  108 (150)
Q Consensus       102 ~~~~vi~  108 (150)
                      ++.+||.
T Consensus       201 ~l~~lVi  207 (262)
T 3ly5_A          201 NLQCLVI  207 (262)
T ss_dssp             TCCEEEE
T ss_pred             cCCEEEE
Confidence            7777763

>3g5j_A Putative ATP/GTP binding protein; N-terminal domain of ATP/GTP binding protein, PSI, MCSG, STR genomics, protein structure initiative; HET: PGE; 1.76A {Clostridium difficile}

Probab=89.92  E-value=0.18  Score=30.95  Aligned_cols=47  Identities=11%  Similarity=0.075  Sum_probs=34.4

Q ss_pred             HHHHHHHhccCCC-CCeeEEe-hhhhhHHHHHhhccccCceEEEecCCCC
Q psy17637         22 HLVRNLEGANQEV-PPALMNL-AMQLNAEELANSLTVKEYDVLLLHGDMD   69 (150)
Q Consensus        22 ~ll~~l~~~~~~~-~~~ivf~-~~~~~~~~l~~~L~~~~~~~~~~~~~~~   69 (150)
                      .+...+... .+. .++|+|| .+-..+...+..|...|+.+..+.||+.
T Consensus        77 ~~~~~~~~~-~~~~~~ivvyC~~~G~rs~~a~~~L~~~G~~v~~l~GG~~  125 (134)
T 3g5j_A           77 DIYLQAAEL-ALNYDNIVIYCARGGMRSGSIVNLLSSLGVNVYQLEGGYK  125 (134)
T ss_dssp             HHHHHHHHH-HTTCSEEEEECSSSSHHHHHHHHHHHHTTCCCEEETTHHH
T ss_pred             HHHHHHHHh-ccCCCeEEEEECCCChHHHHHHHHHHHcCCceEEEeCcHH
Confidence            344444443 244 7899999 5767777888889888988999999864

>3foj_A Uncharacterized protein; protein SSP1007, structural genomics, PSI-2, protein structure initiative; 1.60A {Staphylococcus saprophyticus subsp}

Probab=89.67  E-value=0.18  Score=29.53  Aligned_cols=37  Identities=8%  Similarity=0.090  Sum_probs=31.9

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDM   68 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~   68 (150)
                      .+..++++||.+-..+...+..|...|+.+..+.||+
T Consensus        54 ~~~~~ivvyC~~g~rs~~a~~~L~~~G~~v~~l~GG~   90 (100)
T 3foj_A           54 NDNETYYIICKAGGRSAQVVQYLEQNGVNAVNVEGGM   90 (100)
T ss_dssp             CTTSEEEEECSSSHHHHHHHHHHHTTTCEEEEETTHH
T ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHCCCCEEEecccH
Confidence            4567899999998888899999998999888999985

>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=89.18  E-value=1.2  Score=32.88  Aligned_cols=71  Identities=17%  Similarity=0.197  Sum_probs=47.0

Q ss_pred             CCCCeeEEehhhhhHHHHHhhcccc-C---ceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CCcc-----cCCccC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVK-E---YDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VAAR-----GLDIPH  102 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~-~---~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~~~-----Gidi~~  102 (150)
                      ...++||.|+++.-++..++.+... +   ..+..+||+....++.....     ...|+|+|. .+..     .+....
T Consensus        51 ~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~-----~~~ivv~T~~~l~~~~~~~~~~~~~  125 (494)
T 1wp9_A           51 YGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWA-----RAKVIVATPQTIENDLLAGRISLED  125 (494)
T ss_dssp             SCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEECSCSCHHHHHHHHH-----HCSEEEECHHHHHHHHHTTSCCTTS
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHHHhCcchhheEEeeCCcchhhhhhhcc-----CCCEEEecHHHHHHHHhcCCcchhh
Confidence            5679999999988776666555443 3   38899999998876654432     247888884 2221     244556


Q ss_pred             CcEEEE
Q psy17637        103 IRTVVN  108 (150)
Q Consensus       103 ~~~vi~  108 (150)
                      .++||.
T Consensus       126 ~~~vIi  131 (494)
T 1wp9_A          126 VSLIVF  131 (494)
T ss_dssp             CSEEEE
T ss_pred             ceEEEE
Confidence            666653

>3hix_A ALR3790 protein; rhodanese, rhodanese_3, Q8YQN0, Q8YQN0_anAsp, NSR437I, NESG, structural genomics, PSI-2, protein structure initiative; 1.92A {Anabaena SP} PDB: 3k9r_A

Probab=89.17  E-value=0.34  Score=28.72  Aligned_cols=37  Identities=16%  Similarity=0.165  Sum_probs=31.1

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCce-EEEecCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYD-VLLLHGDM   68 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~   68 (150)
                      .+..++++||.+-..+...+..|...|+. +..+.||+
T Consensus        50 ~~~~~ivvyc~~g~rs~~a~~~L~~~G~~~v~~l~GG~   87 (106)
T 3hix_A           50 EKSRDIYVYGAGDEQTSQAVNLLRSAGFEHVSELKGGL   87 (106)
T ss_dssp             CTTSCEEEECSSHHHHHHHHHHHHHTTCSCEEECTTHH
T ss_pred             CCCCeEEEEECCCChHHHHHHHHHHcCCcCEEEecCCH
Confidence            45678999999888888899999988985 78888885

>3iwh_A Rhodanese-like domain protein; alpha-beta-alpha sandwich, structural genomics, C structural genomics of infectious diseases, csgid; 2.00A {Staphylococcus aureus subsp} PDB: 3mzz_A

Probab=89.15  E-value=0.18  Score=30.00  Aligned_cols=37  Identities=14%  Similarity=0.151  Sum_probs=31.6

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDM   68 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~   68 (150)
                      .+..++++||.+-..+...+..|...|++...+.||+
T Consensus        54 ~~~~~ivv~C~~G~rS~~aa~~L~~~G~~~~~l~GG~   90 (103)
T 3iwh_A           54 NKNEIYYIVCAGGVRSAKVVEYLEANGIDAVNVEGGM   90 (103)
T ss_dssp             CTTSEEEEECSSSSHHHHHHHHHHTTTCEEEEETTHH
T ss_pred             cCCCeEEEECCCCHHHHHHHHHHHHcCCCEEEecChH
Confidence            4567899999988888888999999999988888885

>1wv9_A Rhodanese homolog TT1651; CDC25, phosphatase, sulfurtransferase, structural genomics, NPPSFA; 2.00A {Thermus thermophilus}

Probab=89.10  E-value=0.24  Score=28.68  Aligned_cols=35  Identities=23%  Similarity=0.334  Sum_probs=30.1

Q ss_pred             CCeeEEehhhhhHHHHHhhccccCceEEEecCCCC
Q psy17637         35 PPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMD   69 (150)
Q Consensus        35 ~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~   69 (150)
                      .++++||.+-..+...+..|...|+++..+.|++.
T Consensus        54 ~~ivvyC~~g~rs~~a~~~L~~~G~~v~~l~GG~~   88 (94)
T 1wv9_A           54 RPLLLVCEKGLLSQVAALYLEAEGYEAMSLEGGLQ   88 (94)
T ss_dssp             SCEEEECSSSHHHHHHHHHHHHHTCCEEEETTGGG
T ss_pred             CCEEEEcCCCChHHHHHHHHHHcCCcEEEEcccHH
Confidence            78999999988888888999888988778888864

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=88.47  E-value=0.51  Score=31.52  Aligned_cols=72  Identities=18%  Similarity=0.196  Sum_probs=41.8

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhcc----ccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CC-----cccCCcc
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLT----VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VA-----ARGLDIP  101 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~----~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~-----~~Gidi~  101 (150)
                      ....++||.++++.-+..+++.+.    ..++.+..++|+.+..+....   +.  ...|+|+|. .+     ....+..
T Consensus        80 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~--~~~iiv~Tp~~l~~~~~~~~~~~~  154 (224)
T 1qde_A           80 VKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEG---LR--DAQIVVGTPGRVFDNIQRRRFRTD  154 (224)
T ss_dssp             CCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC-------------CT--TCSEEEECHHHHHHHHHTTSSCCT
T ss_pred             CCCceEEEEECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhc---CC--CCCEEEECHHHHHHHHHhCCcchh
Confidence            345689999999988776666554    346788899998765443322   22  268999994 21     2234556


Q ss_pred             CCcEEEE
Q psy17637        102 HIRTVVN  108 (150)
Q Consensus       102 ~~~~vi~  108 (150)
                      .+.+||.
T Consensus       155 ~~~~iVi  161 (224)
T 1qde_A          155 KIKMFIL  161 (224)
T ss_dssp             TCCEEEE
T ss_pred             hCcEEEE
Confidence            6776663

>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=88.23  E-value=0.9  Score=38.11  Aligned_cols=73  Identities=11%  Similarity=0.231  Sum_probs=53.4

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc----cCc----eEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CCcccCC-ccC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV----KEY----DVLLLHGDMDQSERNSVITKFKRQECRILVATD-VAARGLD-IPH  102 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~----~~~----~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~~~Gid-i~~  102 (150)
                      .+.++||.++|++-+..+++.+..    .++    .+..++|+.+...+.+..+.+..  ..|+|+|+ .+..-+. +..
T Consensus        98 ~~~~~lil~PtreLa~Q~~~~l~~l~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~--~~IlV~TP~~L~~~l~~L~~  175 (1054)
T 1gku_B           98 KGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRN--FKIVITTTQFLSKHYRELGH  175 (1054)
T ss_dssp             TSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG--CSEEEEEHHHHHHCSTTSCC
T ss_pred             cCCeEEEEeccHHHHHHHHHHHHHHHhhcCCCccceEEEEeCCCChhhHHHHHhhccC--CCEEEEcHHHHHHHHHHhcc
Confidence            567899999999988777666643    355    78999999999888777777776  78999995 2221111 446


Q ss_pred             CcEEE
Q psy17637        103 IRTVV  107 (150)
Q Consensus       103 ~~~vi  107 (150)
                      +.+||
T Consensus       176 l~~lV  180 (1054)
T 1gku_B          176 FDFIF  180 (1054)
T ss_dssp             CSEEE
T ss_pred             CCEEE
Confidence            66666

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=88.11  E-value=1.3  Score=28.96  Aligned_cols=72  Identities=22%  Similarity=0.243  Sum_probs=47.9

Q ss_pred             CCCCeeEEehhhhhHHHHHhhcccc--CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CC----c-ccCCccCCc
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVK--EYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VA----A-RGLDIPHIR  104 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~--~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~----~-~Gidi~~~~  104 (150)
                      ...++||.+++++-+..+++.+...  .+.+..++|+.+.......+.    ....|+|+|. .+    . ..+++..+.
T Consensus        71 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~i~v~T~~~l~~~~~~~~~~~~~~~  146 (207)
T 2gxq_A           71 RKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALL----RGADAVVATPGRALDYLRQGVLDLSRVE  146 (207)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHCTTSCEEEECSSSCSHHHHHHHH----HCCSEEEECHHHHHHHHHHTSSCCTTCS
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHHHhhcceEEEEECCCChHHHHHHhh----CCCCEEEECHHHHHHHHHcCCcchhhce
Confidence            4678999999999888887777644  467888898876544433322    2467999994 11    1 234556777


Q ss_pred             EEEE
Q psy17637        105 TVVN  108 (150)
Q Consensus       105 ~vi~  108 (150)
                      ++|.
T Consensus       147 ~iVi  150 (207)
T 2gxq_A          147 VAVL  150 (207)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            7663

>1gmx_A GLPE protein; transferase, rhodanese, sulfurtransferase, glycerol metabolism; 1.1A {Escherichia coli} SCOP: c.46.1.3 PDB: 1gn0_A

Probab=88.10  E-value=0.43  Score=28.28  Aligned_cols=38  Identities=18%  Similarity=0.242  Sum_probs=31.6

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCce-EEEecCCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYD-VLLLHGDMD   69 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~~   69 (150)
                      .+..++++||.+-..+...+..|...|++ +..+.|++.
T Consensus        56 ~~~~~ivvyc~~g~rs~~a~~~L~~~G~~~v~~l~GG~~   94 (108)
T 1gmx_A           56 DFDTPVMVMCYHGNSSKGAAQYLLQQGYDVVYSIDGGFE   94 (108)
T ss_dssp             CTTSCEEEECSSSSHHHHHHHHHHHHTCSSEEEETTHHH
T ss_pred             CCCCCEEEEcCCCchHHHHHHHHHHcCCceEEEecCCHH
Confidence            46678999999987888889999888885 778889863

>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=87.99  E-value=1.8  Score=31.23  Aligned_cols=70  Identities=19%  Similarity=0.213  Sum_probs=46.7

Q ss_pred             CCCCeeEEehhhhhHHHHHhhcc----ccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CC-----cccCCccC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLT----VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VA-----ARGLDIPH  102 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~----~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~-----~~Gidi~~  102 (150)
                      ...++||.++++.-++..++.+.    ..++.+..++|+.+..+....+.     ...|+|+|. .+     ........
T Consensus        88 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-----~~~i~v~T~~~l~~~~~~~~~~~~~  162 (394)
T 1fuu_A           88 KAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-----DAQIVVGTPGRVFDNIQRRRFRTDK  162 (394)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHHH-----HCSEEEECHHHHHHHHHTTSSCCTT
T ss_pred             CCCCEEEEcCCHHHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhcC-----CCCEEEECHHHHHHHHHhCCcchhh
Confidence            56789999999988776666553    34678899999988766554443     357888883 21     11233455


Q ss_pred             CcEEE
Q psy17637        103 IRTVV  107 (150)
Q Consensus       103 ~~~vi  107 (150)
                      +.+||
T Consensus       163 ~~~vI  167 (394)
T 1fuu_A          163 IKMFI  167 (394)
T ss_dssp             CCEEE
T ss_pred             CcEEE
Confidence            66655

>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=87.90  E-value=1.9  Score=32.14  Aligned_cols=83  Identities=17%  Similarity=0.199  Sum_probs=53.3

Q ss_pred             HHHHHHHhcc----CCCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-
Q psy17637         22 HLVRNLEGAN----QEVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-   92 (150)
Q Consensus        22 ~ll~~l~~~~----~~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-   92 (150)
                      .++..+....    ....++||.++|++-+..+++.+..    .++++..++|+.+.......+   . ....|+|+|. 
T Consensus       113 pil~~l~~~~~~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l---~-~~~~Ivv~Tp~  188 (434)
T 2db3_A          113 PILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECI---T-RGCHVVIATPG  188 (434)
T ss_dssp             HHHHHHHHSCCCCCTTCCSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHHH---T-TCCSEEEECHH
T ss_pred             HHHHHHHhcccccccCCccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHHh---h-cCCCEEEEChH
Confidence            3455554431    2356899999999988877666543    467788999998876554332   2 3468999994 


Q ss_pred             C----Ccc-cCCccCCcEEEE
Q psy17637         93 V----AAR-GLDIPHIRTVVN  108 (150)
Q Consensus        93 ~----~~~-Gidi~~~~~vi~  108 (150)
                      .    +.. .+++..+.++|.
T Consensus       189 ~l~~~l~~~~~~l~~~~~lVl  209 (434)
T 2db3_A          189 RLLDFVDRTFITFEDTRFVVL  209 (434)
T ss_dssp             HHHHHHHTTSCCCTTCCEEEE
T ss_pred             HHHHHHHhCCcccccCCeEEE
Confidence            1    122 245667777663

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=87.87  E-value=1.1  Score=30.35  Aligned_cols=83  Identities=16%  Similarity=0.200  Sum_probs=48.9

Q ss_pred             HHHHHHhccCCCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CC---
Q psy17637         23 LVRNLEGANQEVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VA---   94 (150)
Q Consensus        23 ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~---   94 (150)
                      ++..+......+.++||.+++++-+..+++.+..    .++.+..++|+.....   .......+...|+|+|. .+   
T Consensus        87 ~l~~l~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~I~v~Tp~~l~~~  163 (245)
T 3dkp_A           87 ILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAK---KFGPKSSKKFDILVTTPNRLIYL  163 (245)
T ss_dssp             HHHHHCSCCSSSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEECCCHHHHHHT---TTSTTSCCCCCEEEECHHHHHHH
T ss_pred             HHHHHhhcccCCceEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEecCccHHH---HhhhhhcCCCCEEEECHHHHHHH
Confidence            3444433323566899999999988777766654    3666777776522111   11122245568999993 11   


Q ss_pred             ----cccCCccCCcEEEE
Q psy17637         95 ----ARGLDIPHIRTVVN  108 (150)
Q Consensus        95 ----~~Gidi~~~~~vi~  108 (150)
                          ...+++.++.++|.
T Consensus       164 l~~~~~~~~~~~~~~lVi  181 (245)
T 3dkp_A          164 LKQDPPGIDLASVEWLVV  181 (245)
T ss_dssp             HHSSSCSCCCTTCCEEEE
T ss_pred             HHhCCCCcccccCcEEEE
Confidence                11466777887764

>1tq1_A AT5G66040, senescence-associated family protein; CESG, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} SCOP: c.46.1.3

Probab=87.44  E-value=0.37  Score=29.70  Aligned_cols=38  Identities=8%  Similarity=0.034  Sum_probs=31.4

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCce-EEEecCCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYD-VLLLHGDMD   69 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~~   69 (150)
                      .+..++++||.+-..+...+..|...|++ +..+.|++.
T Consensus        80 ~~~~~ivvyC~~G~rs~~aa~~L~~~G~~~v~~l~GG~~  118 (129)
T 1tq1_A           80 GQSDNIIVGCQSGGRSIKATTDLLHAGFTGVKDIVGGYS  118 (129)
T ss_dssp             CTTSSEEEEESSCSHHHHHHHHHHHHHCCSEEEEECCHH
T ss_pred             CCCCeEEEECCCCcHHHHHHHHHHHcCCCCeEEeCCcHH
Confidence            45678999999988888888888888885 788899863

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=87.36  E-value=3.1  Score=28.23  Aligned_cols=71  Identities=15%  Similarity=0.192  Sum_probs=46.8

Q ss_pred             CCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CC-----cccCCccCC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VA-----ARGLDIPHI  103 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~-----~~Gidi~~~  103 (150)
                      ..++||.+++++-+..+++.+..    .++.+..++|+.+.......   +. ....|+|+|. .+     ...+++..+
T Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~-~~~~Ivv~Tp~~l~~~l~~~~~~~~~~  175 (253)
T 1wrb_A          100 YPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIRE---VQ-MGCHLLVATPGRLVDFIEKNKISLEFC  175 (253)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHH---HS-SCCSEEEECHHHHHHHHHTTSBCCTTC
T ss_pred             CceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHH---hC-CCCCEEEECHHHHHHHHHcCCCChhhC
Confidence            46899999999888777666543    35778889998765544322   22 3468999994 22     123456677


Q ss_pred             cEEEE
Q psy17637        104 RTVVN  108 (150)
Q Consensus       104 ~~vi~  108 (150)
                      .++|.
T Consensus       176 ~~lVi  180 (253)
T 1wrb_A          176 KYIVL  180 (253)
T ss_dssp             CEEEE
T ss_pred             CEEEE
Confidence            77663

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=86.87  E-value=0.88  Score=34.52  Aligned_cols=71  Identities=13%  Similarity=0.171  Sum_probs=45.7

Q ss_pred             CCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CCc----cc-C-CccC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VAA----RG-L-DIPH  102 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~~----~G-i-di~~  102 (150)
                      ..++||.++++.-+...+..+..    .++.+..++|+.+...+...+.    +...|+|+|. .+.    .+ + .+..
T Consensus        52 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~i~v~T~~~l~~~~~~~~~~~~~~  127 (555)
T 3tbk_A           52 KGKVVFFANQIPVYEQQATVFSRYFERLGYNIASISGATSDSVSVQHII----EDNDIIILTPQILVNNLNNGAIPSLSV  127 (555)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHHHTTTCCEEEECTTTGGGSCHHHHH----HHCSEEEECHHHHHHHHHTSSSCCGGG
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHHhccCCcEEEEEcCCCcchhhHHHHh----cCCCEEEECHHHHHHHHhcCccccccc
Confidence            77899999998877766655544    3888999999986544322221    1357899984 221    11 2 4556


Q ss_pred             CcEEEE
Q psy17637        103 IRTVVN  108 (150)
Q Consensus       103 ~~~vi~  108 (150)
                      +.+||.
T Consensus       128 ~~~vVi  133 (555)
T 3tbk_A          128 FTLMIF  133 (555)
T ss_dssp             CSEEEE
T ss_pred             CCEEEE
Confidence            676664

>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=86.31  E-value=1.9  Score=34.91  Aligned_cols=71  Identities=14%  Similarity=0.160  Sum_probs=43.3

Q ss_pred             CCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CCc----cc-C-CccC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VAA----RG-L-DIPH  102 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~~----~G-i-di~~  102 (150)
                      ..++||.|+++.-+...+..+..    .++.+..+||+.+...+...+   . +...|+|+|. .+.    .+ + .+..
T Consensus       296 ~~~~Lvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~---~-~~~~Ivv~Tp~~l~~~l~~~~~~~~~~  371 (797)
T 4a2q_A          296 KAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKV---I-EDSDIIVVTPQILVNSFEDGTLTSLSI  371 (797)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECCC-----CHHHH---H-HTCSEEEECHHHHHHHHHSSSCCCGGG
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHhcccCCceEEEEeCCcchhhhHHHh---h-CCCCEEEEchHHHHHHHHhcccccccc
Confidence            77899999998877766555544    388999999998655443222   1 2467999994 221    11 2 4556


Q ss_pred             CcEEEE
Q psy17637        103 IRTVVN  108 (150)
Q Consensus       103 ~~~vi~  108 (150)
                      +.+||.
T Consensus       372 ~~~iVi  377 (797)
T 4a2q_A          372 FTLMIF  377 (797)
T ss_dssp             CSEEEE
T ss_pred             CCEEEE
Confidence            677663

>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=86.21  E-value=1.4  Score=33.48  Aligned_cols=71  Identities=14%  Similarity=0.161  Sum_probs=43.1

Q ss_pred             CCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CCc----cc-C-CccC
Q psy17637         34 VPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VAA----RG-L-DIPH  102 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~~----~G-i-di~~  102 (150)
                      ..++||.++++.-+...+..+..    .++.+..++|+.+...+...+.   . ...|+|+|. .+.    .+ + .+..
T Consensus        55 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~---~-~~~i~v~T~~~l~~~~~~~~~~~~~~  130 (556)
T 4a2p_A           55 KAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVI---E-DSDIIVVTPQILVNSFEDGTLTSLSI  130 (556)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEECCCC-----CHHHHH---H-HCSEEEECHHHHHHHHHSSSCCCSTT
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEeCCCCcchhHHHhh---C-CCCEEEECHHHHHHHHHhCccccccc
Confidence            67899999998877766655544    3888999999986554432221   1 257899994 222    22 2 4556


Q ss_pred             CcEEEE
Q psy17637        103 IRTVVN  108 (150)
Q Consensus       103 ~~~vi~  108 (150)
                      +++||.
T Consensus       131 ~~~vVi  136 (556)
T 4a2p_A          131 FTLMIF  136 (556)
T ss_dssp             CSEEEE
T ss_pred             CCEEEE
Confidence            676663

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=86.15  E-value=0.56  Score=31.31  Aligned_cols=72  Identities=15%  Similarity=0.124  Sum_probs=44.8

Q ss_pred             CCCCeeEEehhhhhHHHHHhhcccc--------CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-----CCcc-cC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVK--------EYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-----VAAR-GL   98 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~--------~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~~-Gi   98 (150)
                      ...++||.+++++-+..+++.+...        +..+..++|+.+.....   +.+ .....|+|+|.     .+.. .+
T Consensus        71 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~---~~~-~~~~~Iiv~Tp~~l~~~l~~~~~  146 (219)
T 1q0u_A           71 AEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKAL---EKL-NVQPHIVIGTPGRINDFIREQAL  146 (219)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTT---CCC-SSCCSEEEECHHHHHHHHHTTCC
T ss_pred             CCceEEEEcCcHHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHH---HHc-CCCCCEEEeCHHHHHHHHHcCCC
Confidence            4568999999999877776655432        57788889886543221   111 23467999994     1112 34


Q ss_pred             CccCCcEEEE
Q psy17637         99 DIPHIRTVVN  108 (150)
Q Consensus        99 di~~~~~vi~  108 (150)
                      ++..+.++|.
T Consensus       147 ~~~~~~~lVi  156 (219)
T 1q0u_A          147 DVHTAHILVV  156 (219)
T ss_dssp             CGGGCCEEEE
T ss_pred             CcCcceEEEE
Confidence            5566776663

>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=86.13  E-value=3.2  Score=30.07  Aligned_cols=72  Identities=14%  Similarity=0.109  Sum_probs=46.8

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCC-----Cc-ccCCccC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDV-----AA-RGLDIPH  102 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~~-~Gidi~~  102 (150)
                      ...++||.++++.-++..++.+..    .++.+..++|+.........    ..+...|+|+|.-     +. ...++.+
T Consensus        88 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~----~~~~~~Ivv~T~~~l~~~~~~~~~~~~~  163 (400)
T 1s2m_A           88 NKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILR----LNETVHILVGTPGRVLDLASRKVADLSD  163 (400)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHH----TTSCCSEEEECHHHHHHHHHTTCSCCTT
T ss_pred             CCccEEEEcCCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHHH----hcCCCCEEEEchHHHHHHHHhCCccccc
Confidence            456899999998887766665543    36788899998775443221    2345689999941     22 2345566


Q ss_pred             CcEEEE
Q psy17637        103 IRTVVN  108 (150)
Q Consensus       103 ~~~vi~  108 (150)
                      +.+||.
T Consensus       164 ~~~vIi  169 (400)
T 1s2m_A          164 CSLFIM  169 (400)
T ss_dssp             CCEEEE
T ss_pred             CCEEEE
Confidence            777663

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=85.00  E-value=0.88  Score=32.26  Aligned_cols=69  Identities=13%  Similarity=0.071  Sum_probs=44.5

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc-----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCC-C-----c-ccCCc
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV-----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDV-A-----A-RGLDI  100 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~-----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~-~-----~-~Gidi  100 (150)
                      ...++||.++|++-+..++..+..     .++.+..++|+......       ......|+|+|.- +     . ..+++
T Consensus       161 ~~~~~lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~-------~~~~~~IlV~TP~~l~~~l~~~~~~~l  233 (300)
T 3fmo_B          161 KYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG-------QKISEQIVIGTPGTVLDWCSKLKFIDP  233 (300)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTT-------CCCCCSEEEECHHHHHHHHTTTCCCCG
T ss_pred             CCceEEEEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhh-------hcCCCCEEEECHHHHHHHHHhcCCCCh
Confidence            445799999999988876555543     25677777777542111       1334579999952 1     1 24667


Q ss_pred             cCCcEEEE
Q psy17637        101 PHIRTVVN  108 (150)
Q Consensus       101 ~~~~~vi~  108 (150)
                      ..+.++|.
T Consensus       234 ~~l~~lVl  241 (300)
T 3fmo_B          234 KKIKVFVL  241 (300)
T ss_dssp             GGCSEEEE
T ss_pred             hhceEEEE
Confidence            78888774

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=84.53  E-value=6.4  Score=28.57  Aligned_cols=70  Identities=16%  Similarity=0.186  Sum_probs=47.2

Q ss_pred             CCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CC-----cccCCccCCc
Q psy17637         35 PPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VA-----ARGLDIPHIR  104 (150)
Q Consensus        35 ~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~-----~~Gidi~~~~  104 (150)
                      .++||.+++++-+..+++.+..    .++.+..++|+.+..+....   +. ....|+|+|. .+     ...+++..+.
T Consensus       102 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~-~~~~I~v~Tp~~l~~~l~~~~~~~~~~~  177 (417)
T 2i4i_A          102 PISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRD---LE-RGCHLLVATPGRLVDMMERGKIGLDFCK  177 (417)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHHHH---HT-TCCSEEEECHHHHHHHHHTTSBCCTTCC
T ss_pred             ccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHHHH---hh-CCCCEEEEChHHHHHHHHcCCcChhhCc
Confidence            5799999999988877776643    46788999999876554332   22 3468999995 22     1124456667


Q ss_pred             EEEE
Q psy17637        105 TVVN  108 (150)
Q Consensus       105 ~vi~  108 (150)
                      +||.
T Consensus       178 ~iVi  181 (417)
T 2i4i_A          178 YLVL  181 (417)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            6663

>2k0z_A Uncharacterized protein HP1203; A/B domain, structural genomics, unknown function, PSI-2, PR structure initiative; NMR {Helicobacter pylori}

Probab=84.35  E-value=0.77  Score=27.32  Aligned_cols=38  Identities=18%  Similarity=0.203  Sum_probs=31.4

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMD   69 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~   69 (150)
                      .+..++++||.+-..+...+..|...|+....+.|++.
T Consensus        54 ~~~~~ivvyC~~G~rs~~aa~~L~~~G~~~~~l~GG~~   91 (110)
T 2k0z_A           54 HKDKKVLLHCRAGRRALDAAKSMHELGYTPYYLEGNVY   91 (110)
T ss_dssp             CSSSCEEEECSSSHHHHHHHHHHHHTTCCCEEEESCGG
T ss_pred             CCCCEEEEEeCCCchHHHHHHHHHHCCCCEEEecCCHH
Confidence            46678999999988888889999888886677889864

>3nhv_A BH2092 protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 2.50A {Bacillus halodurans} PDB: 3o3w_A

Probab=84.08  E-value=0.45  Score=29.97  Aligned_cols=38  Identities=13%  Similarity=0.050  Sum_probs=31.5

Q ss_pred             CCCCCeeEEehhh--hhHHHHHhhccccCceEEEecCCCC
Q psy17637         32 QEVPPALMNLAMQ--LNAEELANSLTVKEYDVLLLHGDMD   69 (150)
Q Consensus        32 ~~~~~~ivf~~~~--~~~~~l~~~L~~~~~~~~~~~~~~~   69 (150)
                      .+..++|+||.+-  ..+...+..|...|+++..+.||+.
T Consensus        70 ~~~~~ivvyC~~g~~~rs~~aa~~L~~~G~~v~~l~GG~~  109 (144)
T 3nhv_A           70 SKEKVIITYCWGPACNGATKAAAKFAQLGFRVKELIGGIE  109 (144)
T ss_dssp             CTTSEEEEECSCTTCCHHHHHHHHHHHTTCEEEEEESHHH
T ss_pred             CCCCeEEEEECCCCccHHHHHHHHHHHCCCeEEEeCCcHH
Confidence            3567899999987  5788888999999999899999853

>2fsx_A RV0390, COG0607: rhodanese-related sulfurtransferase; RV0390 BR SAD DATA with FBAR, structural genomics, PSI; 1.80A {Mycobacterium tuberculosis}

Probab=83.94  E-value=0.77  Score=28.90  Aligned_cols=38  Identities=11%  Similarity=0.002  Sum_probs=29.9

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCce-EEEecCCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYD-VLLLHGDMD   69 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~~   69 (150)
                      .+..++|+||.+-..+...+..|...|+. +..+.|++.
T Consensus        78 ~~~~~ivvyC~~G~rS~~aa~~L~~~G~~~v~~l~GG~~  116 (148)
T 2fsx_A           78 QHERPVIFLCRSGNRSIGAAEVATEAGITPAYNVLDGFE  116 (148)
T ss_dssp             ---CCEEEECSSSSTHHHHHHHHHHTTCCSEEEETTTTT
T ss_pred             CCCCEEEEEcCCChhHHHHHHHHHHcCCcceEEEcCChh
Confidence            35678999999877788888889888984 888999874

>3ilm_A ALR3790 protein; rhodanese-like, NSR437H, NESG, structural genomics, protein structure initiative, northeast structural genomics consortium; 2.26A {Nostoc SP} PDB: 2kl3_A

Probab=83.66  E-value=0.9  Score=28.46  Aligned_cols=37  Identities=16%  Similarity=0.165  Sum_probs=30.9

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCce-EEEecCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYD-VLLLHGDM   68 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~   68 (150)
                      .+..++++||.+-..+...+..|...|+. +..+.||+
T Consensus        54 ~~~~~ivvyC~~g~rs~~aa~~L~~~G~~~v~~l~GG~   91 (141)
T 3ilm_A           54 EKSRDIYVYGAGDEQTSQAVNLLRSAGFEHVSELKGGL   91 (141)
T ss_dssp             CTTSEEEEECSSHHHHHHHHHHHHHTTCCSEEECTTHH
T ss_pred             CCCCeEEEEECCChHHHHHHHHHHHcCCCCEEEecCHH
Confidence            45678999999888888899999888885 77888885

>1vee_A Proline-rich protein family; hypothetical protein, structural genomics, rhodanese domain, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} PDB: 2dcq_A

Probab=83.23  E-value=1.2  Score=27.51  Aligned_cols=37  Identities=11%  Similarity=0.152  Sum_probs=30.5

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCce-EEEecCCCC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYD-VLLLHGDMD   69 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~~   69 (150)
                      +..++++||.+-......+..|...|+. +..+.|++.
T Consensus        73 ~~~~ivv~C~sG~RS~~aa~~L~~~G~~~v~~l~GG~~  110 (134)
T 1vee_A           73 ENTTLYILDKFDGNSELVAELVALNGFKSAYAIKDGAE  110 (134)
T ss_dssp             GGCEEEEECSSSTTHHHHHHHHHHHTCSEEEECTTTTT
T ss_pred             CCCEEEEEeCCCCcHHHHHHHHHHcCCcceEEecCCcc
Confidence            4678999999987788888888888884 788889974

>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=83.14  E-value=5.5  Score=28.24  Aligned_cols=70  Identities=13%  Similarity=0.165  Sum_probs=46.4

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CCc-----ccCCccC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VAA-----RGLDIPH  102 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~~-----~Gidi~~  102 (150)
                      ...++||.++++.-++.+++.+..    .++.+..++|+.........+.     ...|+|+|. .+.     ..+++..
T Consensus        73 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~-----~~~iiv~T~~~l~~~~~~~~~~~~~  147 (367)
T 1hv8_A           73 NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-----NANIVVGTPGRILDHINRGTLNLKN  147 (367)
T ss_dssp             SSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-----TCSEEEECHHHHHHHHHTTCSCTTS
T ss_pred             CCCcEEEEcCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHhhcC-----CCCEEEecHHHHHHHHHcCCccccc
Confidence            567899999998877776666643    4677888999887655443332     357899984 221     1234556


Q ss_pred             CcEEE
Q psy17637        103 IRTVV  107 (150)
Q Consensus       103 ~~~vi  107 (150)
                      +++||
T Consensus       148 ~~~iI  152 (367)
T 1hv8_A          148 VKYFI  152 (367)
T ss_dssp             CCEEE
T ss_pred             CCEEE
Confidence            66666

>1qxn_A SUD, sulfide dehydrogenase; polysulfide-sulfur transferase, homodimer; NMR {Wolinella succinogenes} SCOP: c.46.1.3

Probab=83.13  E-value=0.58  Score=29.16  Aligned_cols=37  Identities=14%  Similarity=0.155  Sum_probs=31.6

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCc-eEEEecCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEY-DVLLLHGDM   68 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~-~~~~~~~~~   68 (150)
                      .+..++++||.+-..+...+..|...|+ .+..+.||+
T Consensus        80 ~~~~~ivvyC~~G~rS~~aa~~L~~~G~~~v~~l~GG~  117 (137)
T 1qxn_A           80 DPEKPVVVFCKTAARAALAGKTLREYGFKTIYNSEGGM  117 (137)
T ss_dssp             CTTSCEEEECCSSSCHHHHHHHHHHHTCSCEEEESSCH
T ss_pred             CCCCeEEEEcCCCcHHHHHHHHHHHcCCcceEEEcCcH
Confidence            4667899999998888888999988898 488899995

>2jtq_A Phage shock protein E; solution structure rhodanese, stress response, transferase; NMR {Escherichia coli} PDB: 2jtr_A 2jts_A

Probab=82.31  E-value=0.73  Score=25.91  Aligned_cols=37  Identities=11%  Similarity=0.071  Sum_probs=28.5

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCce-EEEecCCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYD-VLLLHGDMD   69 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~~   69 (150)
                      .+..++++||.+-..+...+..|...|++ +..+ |++.
T Consensus        39 ~~~~~ivv~C~~g~rs~~aa~~L~~~G~~~v~~l-GG~~   76 (85)
T 2jtq_A           39 DKNDTVKVYCNAGRQSGQAKEILSEMGYTHVENA-GGLK   76 (85)
T ss_dssp             CTTSEEEEEESSSHHHHHHHHHHHHTTCSSEEEE-EETT
T ss_pred             CCCCcEEEEcCCCchHHHHHHHHHHcCCCCEEec-cCHH
Confidence            35678999999988888889999888875 4455 7753

>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=82.16  E-value=5.3  Score=32.79  Aligned_cols=54  Identities=11%  Similarity=-0.034  Sum_probs=40.1

Q ss_pred             CCCCeeEEehhhhhHHHHHhhcc----ccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLT----VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD   92 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~----~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~   92 (150)
                      .+.+++|.++|++-+...++.+.    ..++++.+++|+++...+....      ...|+|+|+
T Consensus       114 ~g~~vlVltPTreLA~Q~~e~~~~l~~~lgl~v~~i~GG~~~~~r~~~~------~~dIvvgTp  171 (853)
T 2fsf_A          114 TGKGVHVVTVNDYLAQRDAENNRPLFEFLGLTVGINLPGMPAPAKREAY------AADITYGTN  171 (853)
T ss_dssp             TSSCCEEEESSHHHHHHHHHHHHHHHHHTTCCEEECCTTCCHHHHHHHH------HSSEEEEEH
T ss_pred             cCCcEEEEcCCHHHHHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHhc------CCCEEEECC
Confidence            45689999999987765555443    3489999999999986554432      268999995

>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=81.95  E-value=5.6  Score=28.84  Aligned_cols=72  Identities=17%  Similarity=0.166  Sum_probs=47.3

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-----CCcc-cCCccC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-----VAAR-GLDIPH  102 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~~-Gidi~~  102 (150)
                      ...++||.++++.-+..+++.+..    .+..+..++|+......   ...+..+...|+|+|.     .+.. .+....
T Consensus       107 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~  183 (414)
T 3eiq_A          107 KATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAE---VQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKY  183 (414)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHGGGSCCCEEECCCCTTHHHH---HHHHTTTCCSEEEECHHHHHHHHHHTSSCSTT
T ss_pred             CceeEEEEeChHHHHHHHHHHHHHHhcccCceEEEEECCcchHHH---HHHHhcCCCCEEEECHHHHHHHHHcCCccccc
Confidence            567899999999887776666643    36677888888664333   3445556778999994     1111 234455


Q ss_pred             CcEEE
Q psy17637        103 IRTVV  107 (150)
Q Consensus       103 ~~~vi  107 (150)
                      +.+||
T Consensus       184 ~~~vV  188 (414)
T 3eiq_A          184 IKMFV  188 (414)
T ss_dssp             CCEEE
T ss_pred             CcEEE
Confidence            66665

>2hhg_A Hypothetical protein RPA3614; MCSG, structural genomics, rohopseudom palustris, PSI-2, protein structure initiative; 1.20A {Rhodopseudomonas palustris}

Probab=81.73  E-value=0.52  Score=29.23  Aligned_cols=37  Identities=19%  Similarity=0.096  Sum_probs=31.0

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCce-EEEecCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYD-VLLLHGDM   68 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~   68 (150)
                      .+..++++||.+-..+...+..|...|+. +..+.|++
T Consensus        84 ~~~~~ivvyC~~G~rs~~a~~~L~~~G~~~v~~l~GG~  121 (139)
T 2hhg_A           84 QEDKKFVFYCAGGLRSALAAKTAQDMGLKPVAHIEGGF  121 (139)
T ss_dssp             GSSSEEEEECSSSHHHHHHHHHHHHHTCCSEEEETTHH
T ss_pred             CCCCeEEEECCCChHHHHHHHHHHHcCCCCeEEecCCH
Confidence            35678999999988888888899888885 88899985

>3d1p_A Putative thiosulfate sulfurtransferase YOR285W; atomic structure, atomic resolution structure, PSI, MCSG; HET: MSE; 0.98A {Saccharomyces cerevisiae}

Probab=80.85  E-value=0.71  Score=28.63  Aligned_cols=37  Identities=16%  Similarity=0.181  Sum_probs=30.7

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCce-EEEecCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYD-VLLLHGDM   68 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~   68 (150)
                      .+..++++||.+-..+...+..|...|+. +..+.||+
T Consensus        89 ~~~~~ivvyC~~G~rs~~aa~~L~~~G~~~v~~l~GG~  126 (139)
T 3d1p_A           89 DSAKELIFYCASGKRGGEAQKVASSHGYSNTSLYPGSM  126 (139)
T ss_dssp             CTTSEEEEECSSSHHHHHHHHHHHTTTCCSEEECTTHH
T ss_pred             CCCCeEEEECCCCchHHHHHHHHHHcCCCCeEEeCCcH
Confidence            35678999999988888888999888885 78888885

---

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	150
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	3e-29
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	4e-20
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	4e-19
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	3e-04
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	4e-19
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	4e-15
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	6e-15
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	3e-14
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	1e-13
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	2e-13
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	2e-13
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	4e-13
d2p6ra4	201	c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglob	8e-11
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	4e-10
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	3e-09
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	0.002
d1yksa2	299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	1e-07
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	4e-05
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	0.001

>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 =  106 bits (265), Expect = 3e-29
 Identities = 20/116 (17%), Positives = 37/116 (31%), Gaps = 14/116 (12%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSER----------NSVITKFKRQECRILVATDVAAR 96
            +ELA  L     + +  +  +D S               +      +   ++  +    
Sbjct: 49  CDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVT 108

Query: 97  G---LDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGELRS 149
                 +    T+    L +D  + T R GRTGR G  G+   +   +   G   S
Sbjct: 109 QTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVAPGERPSGMFDS 163

>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 = 81.9 bits (201), Expect = 4e-20
 Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 1/80 (1%)

Query: 65  HGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGR 124
              + Q E+  ++ +F R E  +LVAT V   GLD+P +  VV Y+          R GR
Sbjct: 200 DRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGR 259

Query: 125 TGRAGNKGVAYTLVTDKDKD 144
           TGR    G    L+    +D
Sbjct: 260 TGRHM-PGRVIILMAKGTRD 278

>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 = 76.5 bits (187), Expect = 4e-19
 Identities = 44/136 (32%), Positives = 77/136 (56%), Gaps = 3/136 (2%)

Query: 9   YTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDM 68
           Y  V +++ ++   L    +  +  V  A++    +   EEL   L   ++ V  ++ D+
Sbjct: 5   YVNVEEEEYKYE-CLTDLYD--SISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDL 61

Query: 69  DQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRA 128
            Q ER++++ +F+    RIL++TD+ ARG+D+  +  V+NYDL  + + + HRIGR GR 
Sbjct: 62  PQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRF 121

Query: 129 GNKGVAYTLVTDKDKD 144
           G KGVA   VT++D  
Sbjct: 122 GRKGVAINFVTNEDVG 137

>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 = 36.8 bits (84), Expect = 3e-04
 Identities = 13/42 (30%), Positives = 19/42 (45%)

Query: 1   RAGNKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLA 42
           R G KGVA   VT++D      L +      +E+P  +  L 
Sbjct: 120 RFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLL 161

>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 = 78.3 bits (192), Expect = 4e-19
 Identities = 22/103 (21%), Positives = 32/103 (31%), Gaps = 15/103 (14%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVAT----DVAARGLDIPH 102
           AEE+  SL  K          +  + +     KF   E   L+ T        RGLD+P 
Sbjct: 38  AEEIYESLKNK------FRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPE 91

Query: 103 -IRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD 144
            IR  V         +    I        + V       ++ D
Sbjct: 92  RIRFAVFV----GCPSFRVTIEDIDSLSPQMVKLLAYLYRNVD 130

>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 = 66.1 bits (160), Expect = 4e-15
 Identities = 42/135 (31%), Positives = 73/135 (54%), Gaps = 2/135 (1%)

Query: 9   YTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDM 68
           + +  ++++     L    +     +  A++    +   + L   +    + V  +HGDM
Sbjct: 11  FFVAVEREEWKFDTLCDLYD--TLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDM 68

Query: 69  DQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRA 128
            Q ER S++ +F+    R+L++TDV ARGLD+P +  ++NYDL  + + + HRIGR+GR 
Sbjct: 69  PQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRY 128

Query: 129 GNKGVAYTLVTDKDK 143
           G KGVA   V + D 
Sbjct: 129 GRKGVAINFVKNDDI 143

>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 = 65.7 bits (159), Expect = 6e-15
 Identities = 48/136 (35%), Positives = 81/136 (59%), Gaps = 5/136 (3%)

Query: 9   YTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDM 68
           Y  V + ++  A  L R L+    +    L+    + + +ELA+ L    +    +HGD+
Sbjct: 8   YVEVNENERFEA--LCRLLK---NKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDL 62

Query: 69  DQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRA 128
            QS+R  VI  FK+++ RIL+ATDV +RG+D+  +  V+NY L ++ +++ HRIGRTGRA
Sbjct: 63  SQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRA 122

Query: 129 GNKGVAYTLVTDKDKD 144
           G KG A +++  ++  
Sbjct: 123 GKKGKAISIINRREYK 138

>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 = 65.7 bits (159), Expect = 3e-14
 Identities = 18/128 (14%), Positives = 37/128 (28%), Gaps = 23/128 (17%)

Query: 38  LMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARG 97
           +  +       ++A  L      V+ L      SE      K +  +   +V TD++  G
Sbjct: 182 VWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSEY----IKTRTNDWDFVVTTDISEMG 237

Query: 98  LDIP---------HIRTVVNYDLARDIDTHT----------HRIGRTGRAGNKGVAYTLV 138
            +            ++ V+  D    +               R GR GR         + 
Sbjct: 238 ANFKAERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIY 297

Query: 139 TDKDKDGE 146
             +  + +
Sbjct: 298 MGEPLEND 305

>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 = 62.6 bits (151), Expect = 1e-13
 Identities = 17/86 (19%), Positives = 34/86 (39%), Gaps = 3/86 (3%)

Query: 57  KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDID 116
           K + +  +     + ER  ++  F+    R +V++ V   G+D+P     V    +    
Sbjct: 111 KVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAR 170

Query: 117 THTHRIGRTGRAGNKGVA---YTLVT 139
            +  R+GR  R          Y L++
Sbjct: 171 EYIQRLGRILRPSKGKKEAVLYELIS 196

>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 = 62.1 bits (150), Expect = 2e-13
 Identities = 24/102 (23%), Positives = 42/102 (41%), Gaps = 2/102 (1%)

Query: 37  ALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAAR 96
            L+    +  AE+L + L      V  LH ++   ER  +I   +  +  +LV  ++   
Sbjct: 34  TLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLRE 93

Query: 97  GLDIPHIRTVVNYDLARD--IDTHTHRIGRTGRAGNKGVAYT 136
           GLDIP +  V   D  ++  + +    I   GRA      + 
Sbjct: 94  GLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHV 135

>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 = 62.4 bits (150), Expect = 2e-13
 Identities = 35/140 (25%), Positives = 61/140 (43%), Gaps = 4/140 (2%)

Query: 9   YTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDM 68
           Y L+          L+R ++   Q     ++    +   E+ A  L  K       H  +
Sbjct: 9   YMLMEKFKPLDQ--LMRYVQ--EQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGL 64

Query: 69  DQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRA 128
           + + R  V  KF+R + +I+VAT     G++ P++R VV++D+ R+I+++    GR GR 
Sbjct: 65  ENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRD 124

Query: 129 GNKGVAYTLVTDKDKDGELR 148
           G    A       D     R
Sbjct: 125 GLPAEAMLFYDPADMAWLRR 144

>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 = 60.5 bits (146), Expect = 4e-13
 Identities = 30/136 (22%), Positives = 48/136 (35%), Gaps = 15/136 (11%)

Query: 11  LVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQ 70
           L T  +  F G  +  LE         L+    +   +ELA  L     + +  +  +D 
Sbjct: 15  LSTTGEIPFYGKAIP-LEVIKGG--RHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDV 71

Query: 71  SERNSVITKFKRQECRILVATDVAARGLDIPH---IRTVVNYDLARDIDTHTHRIGRTGR 127
                  +        ++VATD    G        I    +    +D  + T R GRTGR
Sbjct: 72  -------SVIPTNGDVVVVATDALMTGFTGDFDSVIDCNTSDGKPQDAVSRTQRRGRTGR 124

Query: 128 AGNKGVAYTLVTDKDK 143
            G  G+ Y  V   ++
Sbjct: 125 -GKPGI-YRFVAPGER 138

>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 = 55.3 bits (132), Expect = 8e-11
 Identities = 27/127 (21%), Positives = 53/127 (41%), Gaps = 12/127 (9%)

Query: 31  NQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVA 90
           N+ +  A++       + +LA  +          H  +   +R  V   F+R   +++VA
Sbjct: 70  NEGLEKAILEENEGEMSRKLAECV---RKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVA 126

Query: 91  TDVAARGLDIPHIRTVV-------NYDLARDIDTHTHRIGRTGRAG--NKGVAYTLVTDK 141
           T   A G+++P  R +V        Y     +  +    GR GR G   +G A  +V  +
Sbjct: 127 TPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKR 186

Query: 142 DKDGELR 148
           D++  ++
Sbjct: 187 DREIAVK 193

>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 = 50.8 bits (120), Expect = 3e-09
 Identities = 42/135 (31%), Positives = 67/135 (49%), Gaps = 4/135 (2%)

Query: 9   YTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDM 68
           Y  V ++ K     L         ++  A++        E LA  +T   Y     H  M
Sbjct: 11  YAFVEERQKLHC--LNTLFS--KLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARM 66

Query: 69  DQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRA 128
            Q ERN V  +F++ + R LV +D+  RG+DI  +  V+N+D  +  +T+ HRIGR+GR 
Sbjct: 67  KQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRF 126

Query: 129 GNKGVAYTLVTDKDK 143
           G+ G+A  L+   D+
Sbjct: 127 GHLGLAINLINWNDR 141

>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 = 34.6 bits (78), Expect = 0.002
 Identities = 8/38 (21%), Positives = 16/38 (42%)

Query: 1   RAGNKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPAL 38
           R G+ G+A  L+   D+     + + L      +P  +
Sbjct: 125 RFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATI 162

>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 = 47.3 bits (112), Expect = 1e-07
 Identities = 22/108 (20%), Positives = 40/108 (37%), Gaps = 24/108 (22%)

Query: 47  AEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTV 106
           A  +A SL      V++L+    + E        K+++   ++ATD+A  G ++  +  V
Sbjct: 49  ANVMAASLRKAGKSVVVLNRKTFERE----YPTIKQKKPDFILATDIAEMGANLC-VERV 103

Query: 107 VN---------YDLARDIDTHT----------HRIGRTGRAGNKGVAY 135
           ++          D  R +               R GR GR  N+    
Sbjct: 104 LDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDS 151

>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 = 39.3 bits (90), Expect = 4e-05
 Identities = 37/84 (44%), Positives = 50/84 (59%)

Query: 65  HGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGR 124
           H  M Q ER S   +FK  + RILVAT++  RG+DI  +    NYD+  D DT+ HR+ R
Sbjct: 58  HRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVAR 117

Query: 125 TGRAGNKGVAYTLVTDKDKDGELR 148
            GR G KG+A T V+D++    L 
Sbjct: 118 AGRFGTKGLAITFVSDENDAKILN 141

>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 = 35.0 bits (79), Expect = 0.001
 Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 1/39 (2%)

Query: 1   RAGNKGVAYTLVTDK-DKEFAGHLVRNLEGANQEVPPAL 38
           R G KG+A T V+D+ D +    +    E    E+P  +
Sbjct: 120 RFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI 158

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	150
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	100.0
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	100.0
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	100.0
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.97
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.97
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.95
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.94
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.92
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.91
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.9
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.9
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.89
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.86
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.8
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.78
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.73
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	99.69
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.69
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	99.42
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	98.13
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	97.82
d2eyqa2	117	Transcription-repair coupling factor, TRCF {Escher	94.76
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	94.51
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	94.29
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	90.91
d1tq1a_	119	Thiosulfate sulfurtransferase/Senescence-associate	90.16
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	89.62
d1gmxa_	108	Sulfurtransferase GlpE {Escherichia coli [TaxId: 5	89.28
d1yt8a4	130	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	88.88
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	87.36
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	86.78
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	86.41
d1qxna_	137	Polysulfide-sulfur transferase (sulfide dehydrogen	85.04
d1urha2	120	3-mercaptopyruvate sulfurtransferase {Escherichia	84.69
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	84.55
d1yt8a1	136	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	84.35
d2b2na1	308	Transcription-repair coupling factor, TRCF {Escher	81.09
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	80.92

>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=100.00  E-value=2.1e-34  Score=191.71  Aligned_cols=137  Identities=30%  Similarity=0.482  Sum_probs=125.5

Q ss_pred             cCeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC
Q psy17637          5 KGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE   84 (150)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~   84 (150)
                      +++.+++...++..+...|.+.+...  +..++||||++++.++.++..|...++.+..+||++++++|.+++..|++|.
T Consensus         5 ~~i~q~yi~v~~~~K~~~L~~ll~~~--~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f~~~~   82 (171)
T d1s2ma2           5 KGITQYYAFVEERQKLHCLNTLFSKL--QINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGK   82 (171)
T ss_dssp             TTEEEEEEECCGGGHHHHHHHHHHHS--CCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTS
T ss_pred             cceEEEEEEcCHHHHHHHHHHHHHhC--CCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhcccCc
Confidence            46666676666666777777777665  6789999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         85 CRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        85 ~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      ..+||||+++++|+|+|++++||+||+|+++..|+||+||+||.|+.|.++.|+++.+.
T Consensus        83 ~~ilv~Td~~~~Gid~~~v~~VI~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~v~~~e~  141 (171)
T d1s2ma2          83 VRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDR  141 (171)
T ss_dssp             SSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGH
T ss_pred             cccccchhHhhhccccceeEEEEecCCcchHHHHHHHhhhcccCCCccEEEEEeCHHHH
Confidence            99999999999999999999999999999999999999999999999999999988654

>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=100.00  E-value=1.6e-34  Score=190.58  Aligned_cols=123  Identities=34%  Similarity=0.566  Sum_probs=108.9

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccC
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGL   98 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gi   98 (150)
                      ++..|.+.+...  +..++||||+++..++.+++.|...++.+..+||+|++++|..+++.|+.|+.++||||+++++|+
T Consensus        14 K~~~L~~ll~~~--~~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Tdv~~rGi   91 (162)
T d1fuka_          14 KYECLTDLYDSI--SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGI   91 (162)
T ss_dssp             HHHHHHHHHHHT--TCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGGTTTC
T ss_pred             HHHHHHHHHHhC--CCCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhcccceeeccccccccc
Confidence            445555555544  678999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         99 DIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        99 di~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      |+|++++||+||+|+++..|+||+||+||.|+.|.+++++++.|.
T Consensus        92 Di~~v~~VI~~d~P~~~~~yihR~GR~gR~g~~g~~i~~~~~~d~  136 (162)
T d1fuka_          92 DVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDV  136 (162)
T ss_dssp             CCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTH
T ss_pred             cCCCceEEEEeccchhHHHHHhhccccccCCCccEEEEEcCHHHH
Confidence            999999999999999999999999999999999999999987654

>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=100.00  E-value=4.6e-34  Score=187.27  Aligned_cols=137  Identities=35%  Similarity=0.550  Sum_probs=123.6

Q ss_pred             CcCeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcC
Q psy17637          4 NKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQ   83 (150)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g   83 (150)
                      +.++.+.+...+...+...|++.+..   ...++||||++++.++.++..|...++.+..+||++++.+|..+++.|+.|
T Consensus         1 n~nI~~~~i~v~~~~K~~~L~~ll~~---~~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~~   77 (155)
T d1hv8a2           1 NANIEQSYVEVNENERFEALCRLLKN---KEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQK   77 (155)
T ss_dssp             SSSSEEEEEECCGGGHHHHHHHHHCS---TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTT
T ss_pred             CCCeEEEEEEeChHHHHHHHHHHHcc---CCCCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhhhhcc
Confidence            35666667666666677777776643   456899999999999999999999999999999999999999999999999


Q ss_pred             CceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         84 ECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        84 ~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +..+||||+++++|+|+|++++||+|++|+++..|+||+||+||.|+.|.+++++++.|.
T Consensus        78 ~~~ilv~T~~~~~Gid~~~v~~Vi~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~d~  137 (155)
T d1hv8a2          78 KIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREY  137 (155)
T ss_dssp             SSSEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSH
T ss_pred             cceeeeehhHHhhhhhhccCcEEEEecCCCCHHHHHHHHHhcCcCCCCceEEEEEchHHH
Confidence            999999999999999999999999999999999999999999999999999999987654

>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=100.00  E-value=2.3e-34  Score=190.90  Aligned_cols=135  Identities=35%  Similarity=0.493  Sum_probs=124.2

Q ss_pred             CeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCc
Q psy17637          6 GVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQEC   85 (150)
Q Consensus         6 ~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~   85 (150)
                      |+.+++...++..+...|.+.+...  ...++||||++++.++.+++.|...++++..+||+|++++|.++++.|++|+.
T Consensus         1 ~l~q~~v~~~~~~K~~~L~~ll~~~--~~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g~~   78 (168)
T d1t5ia_           1 GLQQYYVKLKDNEKNRKLFDLLDVL--EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQR   78 (168)
T ss_dssp             CCEEEEEECCGGGHHHHHHHHHHHS--CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSC
T ss_pred             CcEEEEEEeChHHHHHHHHHHHHhC--CCCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhccccc
Confidence            4566777777777777888877665  66799999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637         86 RILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus        86 ~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      ++||+|+++++|+|+|.+++||+|++|.++..|+||+||+||.|+.+.++.|+++.+
T Consensus        79 ~iLv~T~~~~~Gid~~~~~~vi~~~~p~~~~~yiqr~GR~gR~g~~g~~i~l~~~~~  135 (168)
T d1t5ia_          79 RILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN  135 (168)
T ss_dssp             SEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHH
T ss_pred             eeeeccccccchhhcccchhhhhhhcccchhhHhhhhhhcccCCCccEEEEEECchH
Confidence            999999999999999999999999999999999999999999999999999987643

>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=100.00  E-value=6.4e-34  Score=193.30  Aligned_cols=136  Identities=24%  Similarity=0.407  Sum_probs=124.0

Q ss_pred             CCcCeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhc
Q psy17637          3 GNKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKR   82 (150)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~   82 (150)
                      +++++.|.+.+..++  +..|+..+...  ...++||||+|++.++.++..|...++.+..+||++++++|.++++.|++
T Consensus         3 ~RpNi~y~v~~~~~k--~~~L~~~l~~~--~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~   78 (200)
T d1oywa3           3 DRPNIRYMLMEKFKP--LDQLMRYVQEQ--RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQR   78 (200)
T ss_dssp             CCTTEEEEEEECSSH--HHHHHHHHHHT--TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHT
T ss_pred             CCCCcEEEEEcCCcH--HHHHHHHHHhc--CCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhc
Confidence            467888877665543  45777777664  67799999999999999999999999999999999999999999999999


Q ss_pred             CCceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637         83 QECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus        83 g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      |+.+|||||+++++|+|+|++++||+|++|.++..|+|++||+||.|..|.+++|+++.|
T Consensus        79 g~~~ilvaTd~~~~GiD~p~v~~VI~~~~P~~~~~y~qr~GR~gR~g~~g~ai~~~~~~d  138 (200)
T d1oywa3          79 DDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPAD  138 (200)
T ss_dssp             TSCSEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHH
T ss_pred             ccceEEEecchhhhccCCCCCCEEEECCCccchHHHHHHhhhhhcCCCCceEEEecCHHH
Confidence            999999999999999999999999999999999999999999999999999999998654

>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=100.00  E-value=7.4e-34  Score=188.35  Aligned_cols=137  Identities=32%  Similarity=0.557  Sum_probs=121.4

Q ss_pred             cCeeEEEeec-chhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcC
Q psy17637          5 KGVAYTLVTD-KDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQ   83 (150)
Q Consensus         5 ~~~~~~~~~~-~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g   83 (150)
                      +++.+++... ++..++..|.+.+...  +..++||||++++.++.++..|...++.+..+||++++++|..+++.|++|
T Consensus         6 ~~i~q~~v~v~~~~~K~~~L~~ll~~~--~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~fk~g   83 (168)
T d2j0sa2           6 EGIKQFFVAVEREEWKFDTLCDLYDTL--TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSG   83 (168)
T ss_dssp             TTEEEEEEEESSTTHHHHHHHHHHHHH--TSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHT
T ss_pred             CCcEEEEEEecChHHHHHHHHHHHHhC--CCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHHhcC
Confidence            4566544433 3344566776666554  667999999999999999999999999999999999999999999999999


Q ss_pred             CceEEEEcCCCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637         84 ECRILVATDVAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus        84 ~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                      +.++||||+++++|+|+|++++||+||+|+++..|+||+||+||.|+.|.+++|+++.+.
T Consensus        84 ~~~iLv~Td~~~rGiDi~~v~~VIn~d~P~~~~~yihR~GR~gR~g~~G~~i~~~~~~d~  143 (168)
T d2j0sa2          84 ASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDI  143 (168)
T ss_dssp             SSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGH
T ss_pred             CccEEeccchhcccccccCcceEEEecCCcCHHHHHhhhccccccCCCcEEEEEECHHHH
Confidence            999999999999999999999999999999999999999999999999999999987754

>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=99.97  E-value=2.8e-31  Score=175.35  Aligned_cols=121  Identities=21%  Similarity=0.303  Sum_probs=108.8

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccC
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGL   98 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gi   98 (150)
                      ....|++.+.+....+.++||||+|+++++.++..|...|+++..+||+|++.+|.+++++|++|+++|||+|+++++|+
T Consensus        16 qv~dll~~i~~~~~~g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~Gi   95 (174)
T d1c4oa2          16 QILDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGL   95 (174)
T ss_dssp             HHHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTC
T ss_pred             CHHHHHHHHHHHHhcCCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeeeeec
Confidence            34567888776656788999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccCCcEEEEecCCC-----ChhHHHHhhccccCCCCccEEEEEEec
Q psy17637         99 DIPHIRTVVNYDLAR-----DIDTHTHRIGRTGRAGNKGVAYTLVTD  140 (150)
Q Consensus        99 di~~~~~vi~~~~~~-----~~~~~~q~~GR~~R~g~~~~~~~~~~~  140 (150)
                      |+|++++||++++|+     +..+|+|++||+||.|+ +.++++...
T Consensus        96 Dip~V~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~~-g~~~~~~~~  141 (174)
T d1c4oa2          96 DIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAR-GEVWLYADR  141 (174)
T ss_dssp             CCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTT-CEEEEECSS
T ss_pred             cCCCCcEEEEeccccccccchhHHHHHHhhhhhhcCC-CeeEEeecC
Confidence            999999999999876     55889999999999875 666666544

>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=99.97  E-value=4e-31  Score=176.59  Aligned_cols=119  Identities=23%  Similarity=0.354  Sum_probs=106.4

Q ss_pred             HHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCC
Q psy17637         20 AGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLD   99 (150)
Q Consensus        20 ~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gid   99 (150)
                      ...++..+....+...++||||+++..++.++..|...|+++..+||+|++++|.++++.|++|+++|||||+++++|+|
T Consensus        17 vd~ll~~i~~~~~~~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~~rGiD   96 (181)
T d1t5la2          17 IDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLD   96 (181)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCCSSSCC
T ss_pred             HHHHHHHHHHHHhcCCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHHHccCC
Confidence            45677777765456779999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCcEEEEecCCC-----ChhHHHHhhccccCCCCccEEEEEEe
Q psy17637        100 IPHIRTVVNYDLAR-----DIDTHTHRIGRTGRAGNKGVAYTLVT  139 (150)
Q Consensus       100 i~~~~~vi~~~~~~-----~~~~~~q~~GR~~R~g~~~~~~~~~~  139 (150)
                      +|++++||+||+|.     +...|+||+||+||.|. +.++.+..
T Consensus        97 ip~v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~-~~~~~~~~  140 (181)
T d1t5la2          97 IPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAN-GHVIMYAD  140 (181)
T ss_dssp             CTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTT-CEEEEECS
T ss_pred             CCCCCEEEEecCCcccccccHHHHHHHHHhhccccC-ceeEeecc
Confidence            99999999999996     68899999999999985 44444443

>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=99.95  E-value=3.9e-28  Score=172.93  Aligned_cols=127  Identities=24%  Similarity=0.363  Sum_probs=109.4

Q ss_pred             HHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecC--------CCCHHHHHHHHHHhhcCCceEEEEcC
Q psy17637         21 GHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHG--------DMDQSERNSVITKFKRQECRILVATD   92 (150)
Q Consensus        21 ~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~--------~~~~~~r~~~~~~f~~g~~~vlv~T~   92 (150)
                      ..++..+... .+..++||||++++.++.+++.|...++++..++|        +++..+|..+++.|++|+++|||||+
T Consensus       149 ~~~l~~~~~~-~~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv~T~  227 (286)
T d1wp9a2         149 KEIIREQLQR-KQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATS  227 (286)
T ss_dssp             HHHHHHHHHH-CTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECG
T ss_pred             HHHHHHHHHh-CCCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEEEcc
Confidence            3444444333 46779999999999999999999999999888876        46677899999999999999999999


Q ss_pred             CCcccCCccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCcccccc
Q psy17637         93 VAARGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGELRS  149 (150)
Q Consensus        93 ~~~~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~~~~~~  149 (150)
                      ++++|+|+|++++||+||+|+++..|+||+||+||.+ .+.++.|+++.+.++..+|
T Consensus       228 ~~~~Gld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR~~-~~~~~~l~~~~~~ee~~~~  283 (286)
T d1wp9a2         228 VGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHM-PGRVIILMAKGTRDEAYYW  283 (286)
T ss_dssp             GGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCC-CSEEEEEEETTSHHHHHHH
T ss_pred             ceeccccCCCCCEEEEeCCCCCHHHHHHHHHhCCCCC-CCEEEEEEeCCCHHHHHHh
Confidence            9999999999999999999999999999999999975 7889999999887776655

>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=99.94  E-value=2e-27  Score=152.13  Aligned_cols=100  Identities=24%  Similarity=0.353  Sum_probs=90.5

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEec--
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYD--  110 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~--  110 (150)
                      ..+++||||+|++.++.|++.|...++.+..+|++|+.       +.|++|+..+||||+++++|+| |++++||+++  
T Consensus        34 ~~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~-------~~~~~~~~~vlvaTd~~~~GiD-~~v~~Vi~~~~~  105 (138)
T d1jr6a_          34 KGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDV-------SVIPTNGDVVVVATDALMTGFT-GDFDSVIDCNTS  105 (138)
T ss_dssp             TTSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCS-------CCCTTSSCEEEEESSSSCSSSC-CCBSEEEECSEE
T ss_pred             CCCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchh-------hhhhhhhcceeehhHHHHhccc-cccceEEEEEec
Confidence            56799999999999999999999999999999999984       4578899999999999999999 9999999854  


Q ss_pred             --CCCChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637        111 --LARDIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus       111 --~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                        +|.++.+|+||+||+|| |++| .+.|+++.|
T Consensus       106 ~~~P~~~~~y~qr~GR~gR-g~~G-~~~~i~~~e  137 (138)
T d1jr6a_         106 DGKPQDAVSRTQRRGRTGR-GKPG-IYRFVAPGE  137 (138)
T ss_dssp             TTEECCHHHHHHHHTTBCS-SSCE-EEEECCSSC
T ss_pred             CCCCCCHHHHHhHhccccC-CCCc-EEEEEcCCC
Confidence              69999999999999999 8888 477877765

>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=99.92  E-value=3.7e-26  Score=155.05  Aligned_cols=120  Identities=26%  Similarity=0.393  Sum_probs=99.3

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhhHHHHHhhcccc------------------------------CceEEEecCCCCHH
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVK------------------------------EYDVLLLHGDMDQS   71 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~------------------------------~~~~~~~~~~~~~~   71 (150)
                      .++..+..   .+.++||||+|++.++.++..|...                              ...++++||+|+++
T Consensus        31 ~l~~~~i~---~~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~~  107 (201)
T d2p6ra4          31 ELVEECVA---ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNG  107 (201)
T ss_dssp             HHHHHHHH---TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHH
T ss_pred             HHHHHHHH---cCCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhhh
Confidence            44444433   4579999999999999887776431                              01278999999999


Q ss_pred             HHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEE-------ecCCCChhHHHHhhccccCCCC--ccEEEEEEecCC
Q psy17637         72 ERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVN-------YDLARDIDTHTHRIGRTGRAGN--KGVAYTLVTDKD  142 (150)
Q Consensus        72 ~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~-------~~~~~~~~~~~q~~GR~~R~g~--~~~~~~~~~~~~  142 (150)
                      +|..+++.|++|.++|||||+.+++|+|+|..++||.       .+.|.+..+|.||+|||||.|.  .|.+++++.+.+
T Consensus       108 ~r~~ie~~f~~g~i~vlvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~q~~GRAGR~g~~~~G~~~l~~~~~~  187 (201)
T d2p6ra4         108 QRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRD  187 (201)
T ss_dssp             HHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGG
T ss_pred             hHHHHHHHHhCCCceEEEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHHHHhcccCCCCCCCeeEEEEEeCCCC
Confidence            9999999999999999999999999999999888885       6678899999999999999984  577888777665


Q ss_pred             Cc
Q psy17637        143 KD  144 (150)
Q Consensus       143 ~~  144 (150)
                      .+
T Consensus       188 ~~  189 (201)
T d2p6ra4         188 RE  189 (201)
T ss_dssp             HH
T ss_pred             hH
Confidence            44

>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=99.91  E-value=7.3e-26  Score=153.33  Aligned_cols=137  Identities=24%  Similarity=0.378  Sum_probs=105.9

Q ss_pred             CCcCeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHH--------HHHhhccc---cCceEEEecCCCCHH
Q psy17637          3 GNKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAE--------ELANSLTV---KEYDVLLLHGDMDQS   71 (150)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~--------~l~~~L~~---~~~~~~~~~~~~~~~   71 (150)
                      |+..+.-...+.+..   ..+.+.+.+....+.++.+.|+..+..+        +.++.|..   .++++..+||.|+++
T Consensus         1 GRkpI~T~vv~~~~~---~~v~~~I~~el~~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~   77 (206)
T d1gm5a4           1 GRKEVQTMLVPMDRV---NEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQE   77 (206)
T ss_dssp             SCCCCEECCCCSSTH---HHHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCS
T ss_pred             CCCCeEEEEECcccH---HHHHHHHHHHHHcCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHH
Confidence            344455444444432   3566777666677888988897655433        33444432   366788999999999


Q ss_pred             HHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCCC-ChhHHHHhhccccCCCCccEEEEEEecCC
Q psy17637         72 ERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLAR-DIDTHTHRIGRTGRAGNKGVAYTLVTDKD  142 (150)
Q Consensus        72 ~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~-~~~~~~q~~GR~~R~g~~~~~~~~~~~~~  142 (150)
                      ++++++..|++|+++|||||++++.|+|+|+++++|+++.|. ..+.+.|..||+||.|..+.|++++++.+
T Consensus        78 eke~~m~~F~~g~~~iLVaTtViE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l~~~~~~  149 (206)
T d1gm5a4          78 EKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVG  149 (206)
T ss_dssp             CSHHHHHHHTTTSSSBCCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCC
T ss_pred             HHHHHHHHHHCCCEEEEEEehhhhccccccCCcEEEEEccCCccHHHHHhhhhheeeccccceeEeeecccc
Confidence            999999999999999999999999999999999999999986 79999999999999999999999987654

>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=99.90  E-value=3e-24  Score=145.50  Aligned_cols=116  Identities=17%  Similarity=0.244  Sum_probs=99.2

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccC
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGL   98 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gi   98 (150)
                      ++..|.+.+...  +..++||||++.+.++.|++.|..     ..+||++++++|+.+++.|++|+.+|||+|+++++|+
T Consensus        80 K~~~l~~ll~~~--~~~k~lvf~~~~~~~~~l~~~l~~-----~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~~~~~Gi  152 (200)
T d2fwra1          80 KIRKLREILERH--RKDKIIIFTRHNELVYRISKVFLI-----PAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGI  152 (200)
T ss_dssp             HHHHHHHHHHHT--SSSCBCCBCSCHHHHHHHHHHTTC-----CBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSS
T ss_pred             HHHHHHHHHHhC--CCCcEEEEeCcHHHHHHHHhhcCc-----ceeeCCCCHHHHHHHHHHhhcCCeeeeeecchhhccc
Confidence            344555555543  678999999999999999998853     3479999999999999999999999999999999999


Q ss_pred             CccCCcEEEEecCCCChhHHHHhhccccCCCCcc---EEEEEEecC
Q psy17637         99 DIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKG---VAYTLVTDK  141 (150)
Q Consensus        99 di~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~---~~~~~~~~~  141 (150)
                      |+|.+++||++++|+++..|+|++||++|.|+.+   .++.|+.++
T Consensus       153 dl~~~~~vi~~~~~~s~~~~~Q~iGR~~R~~~~k~~~~i~~~v~~~  198 (200)
T d2fwra1         153 DVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRG  198 (200)
T ss_dssp             CSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEECS
T ss_pred             CCCCCCEEEEeCCCCCHHHHHHHHHhcCCCCCCCcEEEEEEEecCC
Confidence            9999999999999999999999999999998643   455566554

>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=99.90  E-value=7.5e-23  Score=137.74  Aligned_cols=135  Identities=19%  Similarity=0.232  Sum_probs=114.7

Q ss_pred             CCcCeeEEEeecchhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccc--cCceEEEecCCCCHHHHHHHHHHh
Q psy17637          3 GNKGVAYTLVTDKDKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTV--KEYDVLLLHGDMDQSERNSVITKF   80 (150)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~--~~~~~~~~~~~~~~~~r~~~~~~f   80 (150)
                      |+..+.-++...+..    .+...+.+..+.+.++.+.|+..+..+.+++.+..  .+.++..+||.|+++++++++..|
T Consensus         4 gR~pI~T~v~~~~~~----~i~~~I~~El~rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F   79 (211)
T d2eyqa5           4 RRLAVKTFVREYDSM----VVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDF   79 (211)
T ss_dssp             BCBCEEEEEEECCHH----HHHHHHHHHHTTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHH
T ss_pred             cCcCeEEEEeCCCHH----HHHHHHHHHHHcCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHH
Confidence            455566555544333    35555555556789999999999999988888865  477899999999999999999999


Q ss_pred             hcCCceEEEEcCCCcccCCccCCcEEEEecCCC-ChhHHHHhhccccCCCCccEEEEEEecC
Q psy17637         81 KRQECRILVATDVAARGLDIPHIRTVVNYDLAR-DIDTHTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus        81 ~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~~-~~~~~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                      .+|+++|||||++++.|+|+|+++++|..+... ..+++.|..||+||.+..++|++++...
T Consensus        80 ~~g~~~ILv~TtvIEvGiDvpnA~~iiI~~a~rfGLaQLhQLRGRVGR~~~~s~c~l~~~~~  141 (211)
T d2eyqa5          80 HHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  141 (211)
T ss_dssp             HTTSCCEEEESSTTGGGSCCTTEEEEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             HcCCcceEEEehhhhhccCCCCCcEEEEecchhccccccccccceeeecCccceEEEEecCC
Confidence            999999999999999999999999999998885 9999999999999999999999998654

>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=99.89  E-value=2.9e-24  Score=150.77  Aligned_cols=114  Identities=18%  Similarity=0.218  Sum_probs=96.2

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHH----------HHHHHHhhcCCceEEEEcCCCcc---cCC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSER----------NSVITKFKRQECRILVATDVAAR---GLD   99 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r----------~~~~~~f~~g~~~vlv~T~~~~~---Gid   99 (150)
                      ..+++||||+|++.+++|+..|...|+++..+|++++++.|          ...++.|..|+.+++|+|+...+   |+|
T Consensus        35 kggk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~g~~giD  114 (299)
T d1a1va2          35 KGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFS  114 (299)
T ss_dssp             HSSEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEEEEEECC
T ss_pred             cCCCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhccCCCCC
Confidence            35689999999999999999999999999999999999876          45778899999999999999888   677


Q ss_pred             ccCCcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCcccc
Q psy17637        100 IPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKDGEL  147 (150)
Q Consensus       100 i~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~~~~  147 (150)
                      ++.+.+|+++++|.|.++|+||+||+|| |.+|....+.......+.+
T Consensus       115 id~V~~VI~~d~P~SvesyIQRiGRTGR-Gr~G~~~~l~~~t~p~~~l  161 (299)
T d1a1va2         115 LDPTFTIETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVAPGERPSGMF  161 (299)
T ss_dssp             CSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEEEEESCSCCBCSCBC
T ss_pred             CCcceEEEeCCCCCCHHHHHhhccccCC-CCCceEEEEecCCCHHHHH
Confidence            7888899999999999999999999999 8788766555555444444

>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=99.86  E-value=5.5e-24  Score=148.56  Aligned_cols=106  Identities=23%  Similarity=0.192  Sum_probs=88.0

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEc----CCCccc
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVAT----DVAARG   97 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T----~~~~~G   97 (150)
                      .|...+...   +.++||||+|++.++.+++.|...      +||++++++|.++++.|++|+++|||||    +.+++|
T Consensus        16 ~l~~~l~~~---~~~~iif~~~~~~~~~l~~~l~~~------~hg~~~~~~R~~~~~~f~~g~~~vLVaT~a~~~v~~rG   86 (248)
T d1gkub2          16 TLSSILEKL---GTGGIIYARTGEEAEEIYESLKNK------FRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGTLVRG   86 (248)
T ss_dssp             TTHHHHTTS---CSCEEEEESSHHHHHHHHHTTTTS------SCEEECTTSSSHHHHHHHHTSCSEEEEECC------CC
T ss_pred             HHHHHHHHh---CCCEEEEECCHHHHHHHHHHHHHh------ccCCCCHHHHHHHHHHHHhCCCeEEEEeccccchhhhc
Confidence            444455433   468999999999999999999853      7999999999999999999999999999    678999


Q ss_pred             CCccC-CcEEEEecCCCChhHHHHhhccccCCCCccEEEEEEec
Q psy17637         98 LDIPH-IRTVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTD  140 (150)
Q Consensus        98 idi~~-~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~  140 (150)
                      +|+|+ +++||+||+|+    |.|++||+||.|..+.+++++..
T Consensus        87 lDip~~v~~VI~~d~P~----~~~r~gR~~R~g~~~~~~~~~~~  126 (248)
T d1gkub2          87 LDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLLAYLY  126 (248)
T ss_dssp             SCCTTTCCEEEEESCCE----EEEECSCGGGSCHHHHHHHHTTT
T ss_pred             cCccccccEEEEeCCCc----chhhhhhhhccCcceEeeeeccH
Confidence            99996 99999999995    78999999999987766655544

>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=99.80  E-value=3.2e-19  Score=129.39  Aligned_cols=114  Identities=14%  Similarity=0.264  Sum_probs=101.7

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCc---eEEEEcCCCcccCCccCCcEEEEe
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQEC---RILVATDVAARGLDIPHIRTVVNY  109 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~---~vlv~T~~~~~Gidi~~~~~vi~~  109 (150)
                      ++.++|||+.....++.+...|...++.+..++|+++..+|..+++.|+++..   .+|++|.+++.|+|++.+++||++
T Consensus       117 ~g~KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~vlLls~~agg~GlnL~~a~~vi~~  196 (346)
T d1z3ix1         117 TSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMF  196 (346)
T ss_dssp             CCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTTEEEEEEC
T ss_pred             cCCceeEEeehhhhhHHHHHHHhhhhccccccccchhHHHHHHHHHhhhcccccceeeeecchhhhhccccccceEEEEe
Confidence            67899999999999999999999999999999999999999999999998754   367888999999999999999999


Q ss_pred             cCCCChhHHHHhhccccCCCCcc--EEEEEEecCCCccc
Q psy17637        110 DLARDIDTHTHRIGRTGRAGNKG--VAYTLVTDKDKDGE  146 (150)
Q Consensus       110 ~~~~~~~~~~q~~GR~~R~g~~~--~~~~~~~~~~~~~~  146 (150)
                      +++|++..+.|++||+.|.|+..  .+|.|+.....++.
T Consensus       197 d~~wnp~~~~Qa~~R~~R~GQ~~~V~v~rli~~~TiEe~  235 (346)
T d1z3ix1         197 DPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIEEK  235 (346)
T ss_dssp             SCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETTSHHHH
T ss_pred             cCCCccchHhHhhhcccccCCCCceEEEEEEeCCCHHHH
Confidence            99999999999999999999865  45667776655443

>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=99.78  E-value=3.4e-19  Score=123.69  Aligned_cols=127  Identities=15%  Similarity=0.239  Sum_probs=92.0

Q ss_pred             HHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhcccc-CceEEEecCCCCHHHHHHHHHHhhcCC-ceEE-EEcCCCc
Q psy17637         19 FAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVK-EYDVLLLHGDMDQSERNSVITKFKRQE-CRIL-VATDVAA   95 (150)
Q Consensus        19 ~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~-~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~vl-v~T~~~~   95 (150)
                      ++..+.+.+......+.++||||......+.+...|... +..+..+||+++.++|..+++.|+++. ..++ +++.+.+
T Consensus        70 K~~~l~~~l~~~~~~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vll~~~~~~g  149 (244)
T d1z5za1          70 KMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGG  149 (244)
T ss_dssp             HHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCTTC
T ss_pred             HHHHHHHHHHhhcccccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccccchhccccccccc
Confidence            455666666554456889999999999999888887654 788889999999999999999998764 5556 5558999


Q ss_pred             ccCCccCCcEEEEecCCCChhHHHHhhccccCCCCcc--EEEEEEecCCCcc
Q psy17637         96 RGLDIPHIRTVVNYDLARDIDTHTHRIGRTGRAGNKG--VAYTLVTDKDKDG  145 (150)
Q Consensus        96 ~Gidi~~~~~vi~~~~~~~~~~~~q~~GR~~R~g~~~--~~~~~~~~~~~~~  145 (150)
                      .|+|++.+++||++++|+++..+.|+.||+.|.|+..  .++.|+.....++
T Consensus       150 ~Glnl~~a~~vi~~~~~wn~~~~~Qa~~R~~R~Gq~~~v~i~~l~~~~Tiee  201 (244)
T d1z5za1         150 FGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEE  201 (244)
T ss_dssp             CCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETTSHHH
T ss_pred             cccccchhhhhhhcCchhhhHHHhhhcceeeecCCCCceEEEEEeeCCCHHH
Confidence            9999999999999999999999999999999999754  4566777665444

>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=99.73  E-value=4.1e-18  Score=120.97  Aligned_cols=106  Identities=17%  Similarity=0.206  Sum_probs=86.9

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEE----
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVN----  108 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~----  108 (150)
                      ...+++|||++++.++.+++.|...++.+..+||++.+..    ...|++|...++|+|+.+++|+|++ +..||.    
T Consensus       177 ~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~l~~~~~~~~----~~~~~~~~~~~lvaT~~~~~G~~~~-~~~Vi~~~~~  251 (305)
T d2bmfa2         177 FKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSE----YIKTRTNDWDFVVTTDISEMGANFK-AERVIDPRRC  251 (305)
T ss_dssp             SCSCEEEECSCHHHHHHHHHHHHHHTCCCEECCTTCHHHH----GGGGGTSCCSEEEECGGGGTTCCCC-CSEEEECCEE
T ss_pred             hCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeCCcChHHH----HhhhhccchhhhhhhHHHHhcCCCC-ccEEEEcCCc
Confidence            4678999999999999999999999999999999986544    3478899999999999999999984 455442    


Q ss_pred             ------ec----------CCCChhHHHHhhccccCCCCccEEEEEEecCCC
Q psy17637        109 ------YD----------LARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDK  143 (150)
Q Consensus       109 ------~~----------~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~  143 (150)
                            ++          .|.|.++|+||+||+||.|+.+....++..+..
T Consensus       252 ~~~~~~~~~~~~~~~~~~~~~s~~~~~Qr~GR~GR~~~~~~~~~~~~~~~~  302 (305)
T d2bmfa2         252 MKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMGEPL  302 (305)
T ss_dssp             EEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCSSSCCCEEEEECSCCC
T ss_pred             eeeeEecCCCCceEEeccccCCHHHHhhhhcCcCcCCCCceEEEEECCCCC
Confidence                  33          356899999999999999987766666554433

>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=99.69  E-value=2.2e-16  Score=102.92  Aligned_cols=127  Identities=19%  Similarity=0.243  Sum_probs=104.2

Q ss_pred             hhhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCc
Q psy17637         16 DKEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAA   95 (150)
Q Consensus        16 ~~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~   95 (150)
                      ..++...+++.+......+.|+||+|.|.+.++.++..|...+++...+++....++-+-+  ......-.|.|+|++++
T Consensus        16 ~~eK~~AIi~eV~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea~II--~~Ag~~g~VtIATNmAG   93 (175)
T d1tf5a4          16 MEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQII--EEAGQKGAVTIATNMAG   93 (175)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHH--TTTTSTTCEEEEETTSS
T ss_pred             HHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHHHHH--HhccCCCceeehhhHHH
Confidence            3456678889998877889999999999999999999999999999999987644333322  22223347999999999


Q ss_pred             ccCCcc---CCc-----EEEEecCCCChhHHHHhhccccCCCCccEEEEEEecCCCc
Q psy17637         96 RGLDIP---HIR-----TVVNYDLARDIDTHTHRIGRTGRAGNKGVAYTLVTDKDKD  144 (150)
Q Consensus        96 ~Gidi~---~~~-----~vi~~~~~~~~~~~~q~~GR~~R~g~~~~~~~~~~~~~~~  144 (150)
                      +|.|+.   .+.     +||....|.+.....|..||+||.|++|...+|++.+|..
T Consensus        94 RGtDikl~~~v~~~GGLhVI~t~~~~s~Rid~Ql~GR~gRQGdpGs~~~~~sleD~l  150 (175)
T d1tf5a4          94 RGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDEL  150 (175)
T ss_dssp             TTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSSG
T ss_pred             cCCCccchHHHHhCCCcEEEEeccCcchhHHHHHhcchhhhCCCcccEEEEEcCHHH
Confidence            999984   222     8999999999999999999999999999999999887653

>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=99.69  E-value=5.1e-17  Score=115.17  Aligned_cols=103  Identities=22%  Similarity=0.274  Sum_probs=82.2

Q ss_pred             CCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCccCCcEEEEecCC-
Q psy17637         34 VPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDIPHIRTVVNYDLA-  112 (150)
Q Consensus        34 ~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~~~~vi~~~~~-  112 (150)
                      .+++++||++...++.+++.|...|.++..+||.+..++.+    .|.+++.+++|||+++++|+++ ++.+||+++.+ 
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~----~~~~~~~~~~~~t~~~~~~~~~-~~~~vid~g~~~  110 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYP----TIKQKKPDFILATDIAEMGANL-CVERVLDCRTAF  110 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC------------CCCSEEEESSSTTCCTTC-CCSEEEECCEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHHh----hhhcCCcCEEEEechhhhceec-CceEEEecCcee
Confidence            56899999999999999999999999999999999877765    5678999999999999999999 59999976542 


Q ss_pred             ------------------CChhHHHHhhccccCCCCccEEEEEEecC
Q psy17637        113 ------------------RDIDTHTHRIGRTGRAGNKGVAYTLVTDK  141 (150)
Q Consensus       113 ------------------~~~~~~~q~~GR~~R~g~~~~~~~~~~~~  141 (150)
                                        .+.++..||.||+||.+....++.++...
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~~~  157 (299)
T d1yksa2         111 KPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEP  157 (299)
T ss_dssp             EEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSC
T ss_pred             ceeeecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeCCC
Confidence                              37788899999999986555566666543

>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=99.42  E-value=7.6e-13  Score=87.78  Aligned_cols=125  Identities=20%  Similarity=0.209  Sum_probs=102.0

Q ss_pred             hhHHHHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCC-ceEEEEcCCCc
Q psy17637         17 KEFAGHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQE-CRILVATDVAA   95 (150)
Q Consensus        17 ~~~~~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~-~~vlv~T~~~~   95 (150)
                      ..+...+++.+......+.|+||.+.|.+..|.|...|...+++..++.+.-.  +++.-+-. +.|. -.|.|+|++++
T Consensus        17 ~~K~~Avv~ei~~~h~~GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~h--erEAeIIA-qAG~~GaVTIATNMAG   93 (219)
T d1nkta4          17 EAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYH--EQEATIIA-VAGRRGGVTVATNMAG   93 (219)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCH--HHHHHHHH-TTTSTTCEEEEETTCS
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEeeCcHHHHHHHHHHHHHhccchhccchhhH--HHHHHHHH-hcccCCcEEeeccccC
Confidence            44556888999888889999999999999999999999999999999999744  33322222 2233 36899999999


Q ss_pred             ccCCccC----------------------------------------------------CcEEEEecCCCChhHHHHhhc
Q psy17637         96 RGLDIPH----------------------------------------------------IRTVVNYDLARDIDTHTHRIG  123 (150)
Q Consensus        96 ~Gidi~~----------------------------------------------------~~~vi~~~~~~~~~~~~q~~G  123 (150)
                      +|.||.=                                                    ==+||-.....|...--|..|
T Consensus        94 RGTDI~LGgn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIGTErHeSrRIDnQLRG  173 (219)
T d1nkta4          94 RGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRG  173 (219)
T ss_dssp             TTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHH
T ss_pred             CCCceeecCchhhhhHHHhhhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcEEEeccccccccccccccc
Confidence            9999821                                                    117888888999999999999


Q ss_pred             cccCCCCccEEEEEEecCCCc
Q psy17637        124 RTGRAGNKGVAYTLVTDKDKD  144 (150)
Q Consensus       124 R~~R~g~~~~~~~~~~~~~~~  144 (150)
                      |+||+|++|.+-+|++-+|..
T Consensus       174 RsGRQGDPGsSrFflSLeDdL  194 (219)
T d1nkta4         174 RSGRQGDPGESRFYLSLGDEL  194 (219)
T ss_dssp             TSSGGGCCEEEEEEEETTSHH
T ss_pred             cccccCCCccceeEEeccHHH
Confidence            999999999999999987653

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=98.13  E-value=6.4e-06  Score=56.52  Aligned_cols=76  Identities=13%  Similarity=0.203  Sum_probs=62.1

Q ss_pred             CCCCCeeEEehhhhhHH----HHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCC-cccCCccCCcEE
Q psy17637         32 QEVPPALMNLAMQLNAE----ELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVA-ARGLDIPHIRTV  106 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~----~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~-~~Gidi~~~~~v  106 (150)
                      ..+.++++-++|.--+.    .+.+.+...+..+..+||+++..+|.+++....+|+.+|+|+|.++ ...+.+.++.+|
T Consensus       130 ~~g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~~~~f~~Lglv  209 (264)
T d1gm5a3         130 EAGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLV  209 (264)
T ss_dssp             HHTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEE
T ss_pred             hcccceeEEeehHhhhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcCCCCcccccee
Confidence            45678999999865544    5556666668899999999999999999999999999999999655 446777788876


Q ss_pred             E
Q psy17637        107 V  107 (150)
Q Consensus       107 i  107 (150)
                      |
T Consensus       210 i  210 (264)
T d1gm5a3         210 I  210 (264)
T ss_dssp             E
T ss_pred             e
Confidence            6

>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=97.82  E-value=9.8e-05  Score=49.57  Aligned_cols=76  Identities=8%  Similarity=0.125  Sum_probs=62.7

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhcc----ccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCc-ccCCccCCcEE
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLT----VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAA-RGLDIPHIRTV  106 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~----~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~-~Gidi~~~~~v  106 (150)
                      ..+.++++-+++.--+...++.++    ..+..+..+|+.++..++.+++..+.+|+..|+|+|.++- ..+.++++.+|
T Consensus       102 ~~g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~~~~~f~~LgLi  181 (233)
T d2eyqa3         102 DNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLL  181 (233)
T ss_dssp             TTTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEE
T ss_pred             HcCCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhccCCccccccce
Confidence            568899999999776666666554    4577899999999999999999999999999999997554 45777787766


Q ss_pred             E
Q psy17637        107 V  107 (150)
Q Consensus       107 i  107 (150)
                      |
T Consensus       182 I  182 (233)
T d2eyqa3         182 I  182 (233)
T ss_dssp             E
T ss_pred             e
Confidence            5

>d2eyqa2 c.37.1.19 (A:349-465) 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=94.76  E-value=0.039  Score=32.35  Aligned_cols=75  Identities=12%  Similarity=0.027  Sum_probs=54.3

Q ss_pred             HHHHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCCCcccCCc
Q psy17637         21 GHLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDVAARGLDI  100 (150)
Q Consensus        21 ~~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi  100 (150)
                      ..|...+..   ...++|+.|.+.-..+.|.+.|...++.+..+.+.          ..|.++.  +.|+...+..|.-+
T Consensus        24 ~~L~~~i~~---~~~~Vli~a~s~g~~erl~e~L~~~~i~~~~~~~~----------~~~~~~~--~~i~~~~l~~GF~~   88 (117)
T d2eyqa2          24 DALRKFLET---FDGPVVFSVESEGRREALGELLARIKIAPQRIMRL----------DEASDRG--RYLMIGAAEHGFVD   88 (117)
T ss_dssp             HHHHHHHTT---CCSCCCEEESSHHHHHHHHHHHGGGTCCCEECSSG----------GGCCTTC--CEEEECCCCSCEEE
T ss_pred             HHHHHHHHh---CCCeEEEEECCccHHHHHHHHHHHcCCCceEecCh----------hhhcCce--EEEEEecCcccccc
Confidence            344444433   35689999999999999999999999887665543          1344443  55666789999999


Q ss_pred             cCCcEEEEec
Q psy17637        101 PHIRTVVNYD  110 (150)
Q Consensus       101 ~~~~~vi~~~  110 (150)
                      |..+++|...
T Consensus        89 ~~~~l~vItE   98 (117)
T d2eyqa2          89 TVRNLALICE   98 (117)
T ss_dssp             TTTTEEEEEH
T ss_pred             CCCCEEEEEc
Confidence            9988888643

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=94.51  E-value=0.21  Score=31.93  Aligned_cols=72  Identities=14%  Similarity=0.167  Sum_probs=51.7

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-----CC-cccCCcc
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-----VA-ARGLDIP  101 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~-~~Gidi~  101 (150)
                      ..+.+++|.|+|++.+..+.+.+..    .+..+..++|+.+..+..+.+   +  ..+|+|+|+     .+ ...+++.
T Consensus        70 ~~~~~~lil~pt~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l---~--~~~IlV~TP~~l~~~l~~~~~~~~  144 (208)
T d1hv8a1          70 NNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKAL---K--NANIVVGTPGRILDHINRGTLNLK  144 (208)
T ss_dssp             SSSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHH---H--TCSEEEECHHHHHHHHHTTCSCTT
T ss_pred             ccCcceEEEeeccccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhc---C--CCCEEEEChHHHHHHHHcCCCCcc
Confidence            4567899999999988887666543    366788999998877665544   2  257999994     22 3346778


Q ss_pred             CCcEEEE
Q psy17637        102 HIRTVVN  108 (150)
Q Consensus       102 ~~~~vi~  108 (150)
                      ++.++|.
T Consensus       145 ~l~~lVi  151 (208)
T d1hv8a1         145 NVKYFIL  151 (208)
T ss_dssp             SCCEEEE
T ss_pred             cCcEEEE
Confidence            8888764

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.29  E-value=0.11  Score=33.86  Aligned_cols=73  Identities=15%  Similarity=0.125  Sum_probs=51.9

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC------CCcccCCcc
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD------VAARGLDIP  101 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~------~~~~Gidi~  101 (150)
                      ....+++|.++|++-+..+++.+..    .++.+..++|+.+..+....+   ..+ ..|+|+|.      .....+++.
T Consensus        83 ~~~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l---~~~-~~Ilv~TPgrl~~~~~~~~~~~~  158 (222)
T d2j0sa1          83 VRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKL---DYG-QHVVAGTPGRVFDMIRRRSLRTR  158 (222)
T ss_dssp             SCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHH---HHC-CSEEEECHHHHHHHHHTTSSCCT
T ss_pred             ccCceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHh---ccC-CeEEeCCCCcHHhcccccccccc
Confidence            3456799999999998888766643    467888899998876655444   233 47999994      224456777


Q ss_pred             CCcEEEE
Q psy17637        102 HIRTVVN  108 (150)
Q Consensus       102 ~~~~vi~  108 (150)
                      ++.++|.
T Consensus       159 ~l~~lVl  165 (222)
T d2j0sa1         159 AIKMLVL  165 (222)
T ss_dssp             TCCEEEE
T ss_pred             cceeeee
Confidence            8888774

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.91  E-value=0.62  Score=29.59  Aligned_cols=74  Identities=18%  Similarity=0.237  Sum_probs=49.7

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccc-----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCC-----C-cccCCc
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTV-----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDV-----A-ARGLDI  100 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~-----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~-~~Gidi  100 (150)
                      ....+++|.+++++-+..+.+.+..     .......++|+.+.......   +......|+|+|+-     + ...+++
T Consensus        67 ~~~~~~lil~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---l~~~~~~ilI~TP~rl~~~~~~~~~~l  143 (207)
T d1t6na_          67 TGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEV---LKKNCPHIVVGTPGRILALARNKSLNL  143 (207)
T ss_dssp             TTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHH---HHHSCCSEEEECHHHHHHHHHTTSSCC
T ss_pred             CCCceEEEEeccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHH---HHhcCCCEEEeCcchhhhhccCCceec
Confidence            3456799999999988777666543     23457788888776554433   33445689999962     1 234677


Q ss_pred             cCCcEEEE
Q psy17637        101 PHIRTVVN  108 (150)
Q Consensus       101 ~~~~~vi~  108 (150)
                      .++.++|.
T Consensus       144 ~~l~~lVl  151 (207)
T d1t6na_         144 KHIKHFIL  151 (207)
T ss_dssp             TTCCEEEE
T ss_pred             cccceeeh
Confidence            88888774

>d1tq1a_ c.46.1.3 (A:) Thiosulfate sulfurtransferase/Senescence-associated protein {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Thiosulfate sulfurtransferase/Senescence-associated protein
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=90.16  E-value=0.085  Score=30.72  Aligned_cols=44  Identities=7%  Similarity=0.024  Sum_probs=34.0

Q ss_pred             HHHHhccCCCCCeeEEehhhhhHHHHHhhccccCc-eEEEecCCC
Q psy17637         25 RNLEGANQEVPPALMNLAMQLNAEELANSLTVKEY-DVLLLHGDM   68 (150)
Q Consensus        25 ~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~-~~~~~~~~~   68 (150)
                      ..+.....+..++|+||.+-..+...+..|...|+ .+..+.||+
T Consensus        63 ~~~~~~~~~~~~iv~~C~~G~rs~~a~~~L~~~G~~nv~~l~GG~  107 (119)
T d1tq1a_          63 EQVSSHFGQSDNIIVGCQSGGRSIKATTDLLHAGFTGVKDIVGGY  107 (119)
T ss_dssp             HHHTTTCCTTSSEEEEESSCSHHHHHHHHHHHHHCCSEEEEECCH
T ss_pred             HHHHHhcCCCcEEEEEcCCcCcHHHHHHHHHhcccCCeEEecChH
Confidence            33333334677899999988888889999988888 488899996

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.62  E-value=1.3  Score=27.95  Aligned_cols=73  Identities=11%  Similarity=0.147  Sum_probs=49.0

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccc-----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC------CCcccCCc
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTV-----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD------VAARGLDI  100 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~-----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~------~~~~Gidi  100 (150)
                      ....+++|.+++++-+..+.+.+..     .+......+|+.........+    .....++|+|.      .....+++
T Consensus        69 ~~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l----~~~~~ivv~TPgrl~~~~~~~~~~~  144 (206)
T d1veca_          69 KDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRL----DDTVHVVIATPGRILDLIKKGVAKV  144 (206)
T ss_dssp             SCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHT----TSCCSEEEECHHHHHHHHHTTCSCC
T ss_pred             ccCcceEEEeecchhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHH----HhccCeEEeCCccccccccchhccc
Confidence            4567899999999988877766542     245677778887765554332    34568999994      12234566


Q ss_pred             cCCcEEEE
Q psy17637        101 PHIRTVVN  108 (150)
Q Consensus       101 ~~~~~vi~  108 (150)
                      .++.++|.
T Consensus       145 ~~l~~lVl  152 (206)
T d1veca_         145 DHVQMIVL  152 (206)
T ss_dssp             TTCCEEEE
T ss_pred             cccceEEE
Confidence            77887763

>d1gmxa_ c.46.1.3 (A:) Sulfurtransferase GlpE {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Sulfurtransferase GlpE
species: Escherichia coli [TaxId: 562]

Probab=89.28  E-value=0.15  Score=29.04  Aligned_cols=46  Identities=17%  Similarity=0.200  Sum_probs=35.3

Q ss_pred             HHHHHHhccCCCCCeeEEehhhhhHHHHHhhccccCce-EEEecCCCC
Q psy17637         23 LVRNLEGANQEVPPALMNLAMQLNAEELANSLTVKEYD-VLLLHGDMD   69 (150)
Q Consensus        23 ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~~   69 (150)
                      +-..+... .+..++++||.+-..+...+..|...|++ +..+.||+.
T Consensus        48 l~~~~~~~-~~~~~ivv~c~~g~rs~~~a~~L~~~G~~~v~~l~GG~~   94 (108)
T d1gmxa_          48 LGAFMRDN-DFDTPVMVMCYHGNSSKGAAQYLLQQGYDVVYSIDGGFE   94 (108)
T ss_dssp             HHHHHHHS-CTTSCEEEECSSSSHHHHHHHHHHHHTCSSEEEETTHHH
T ss_pred             HHHHhhhc-cccCcccccCCCChHHHHHHHHHHHcCCCCEEEEcChHH
Confidence            33444443 56788999999888888999999999985 778889863

>d1yt8a4 c.46.1.2 (A:243-372) Thiosulfate sulfurtransferase PA2603 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Thiosulfate sulfurtransferase PA2603
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=88.88  E-value=0.16  Score=30.07  Aligned_cols=38  Identities=16%  Similarity=0.067  Sum_probs=33.1

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCceEEEecCCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYDVLLLHGDMD   69 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~   69 (150)
                      .+..++++||.+-..+...+..|...|+.+..+.|++.
T Consensus        78 ~~~~~ivl~C~~G~rS~~aa~~L~~~G~~v~~l~GG~~  115 (130)
T d1yt8a4          78 VRGARLVLVDDDGVRANMSASWLAQMGWQVAVLDGLSE  115 (130)
T ss_dssp             SBTCEEEEECSSSSHHHHHHHHHHHTTCEEEEECSCCG
T ss_pred             CccceEEeecCCCccHHHHHHHHHHcCCCeEEEcCchH
Confidence            46678999999887888899999999999999999974

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.36  E-value=0.61  Score=29.76  Aligned_cols=80  Identities=16%  Similarity=0.233  Sum_probs=46.1

Q ss_pred             HHHHHHhccCCCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC------
Q psy17637         23 LVRNLEGANQEVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD------   92 (150)
Q Consensus        23 ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~------   92 (150)
                      +++.+... .....++|.++|++.+..+...+..    ........+++.+..++...   .  ....|+|+|.      
T Consensus        68 ~i~~l~~~-~~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~--~~~~IvI~TP~~l~~~  141 (212)
T d1qdea_          68 ALQRIDTS-VKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEG---L--RDAQIVVGTPGRVFDN  141 (212)
T ss_dssp             HHHHCCTT-CCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC-------------C--TTCSEEEECHHHHHHH
T ss_pred             hHhhhhcc-CCCcceEEEcccHHHhhhhhhhhcccccccccceeeEeeccchhHHHHH---h--cCCcEEEECCCccccc
Confidence            34444333 4567899999999988877666632    24556666666544333322   1  2357999995      


Q ss_pred             CCcccCCccCCcEEEE
Q psy17637         93 VAARGLDIPHIRTVVN  108 (150)
Q Consensus        93 ~~~~Gidi~~~~~vi~  108 (150)
                      .....+++.++.++|.
T Consensus       142 ~~~~~~~l~~l~~lVl  157 (212)
T d1qdea_         142 IQRRRFRTDKIKMFIL  157 (212)
T ss_dssp             HHTTSSCCTTCCEEEE
T ss_pred             cccCceecCcceEEee
Confidence            2244567788888774

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=86.78  E-value=1.1  Score=28.73  Aligned_cols=75  Identities=12%  Similarity=0.230  Sum_probs=49.6

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccc----c----CceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC-CCccc-CCcc
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTV----K----EYDVLLLHGDMDQSERNSVITKFKRQECRILVATD-VAARG-LDIP  101 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~----~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-~~~~G-idi~  101 (150)
                      .++.++|+.++++.-++..++.+..    .    ......+++..+...+.+.+.....  ..|+|+|. .+... .+..
T Consensus        84 ~~~~rvliv~Pt~~La~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~--~~Ilv~Tp~~l~~~~~~~~  161 (237)
T d1gkub1          84 LKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRN--FKIVITTTQFLSKHYRELG  161 (237)
T ss_dssp             TTSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG--CSEEEEEHHHHHHCSTTSC
T ss_pred             HhcCeEEEEeccHHHHHHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhhhccccc--cceeccChHHHHHhhhhcC
Confidence            3567999999999888877766643    2    2335667777777777777665543  46899984 33333 3345


Q ss_pred             CCcEEEE
Q psy17637        102 HIRTVVN  108 (150)
Q Consensus       102 ~~~~vi~  108 (150)
                      .+++||.
T Consensus       162 ~~~~vVv  168 (237)
T d1gkub1         162 HFDFIFV  168 (237)
T ss_dssp             CCSEEEE
T ss_pred             CCCEEEE
Confidence            6777663

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.41  E-value=1.8  Score=27.09  Aligned_cols=73  Identities=12%  Similarity=0.115  Sum_probs=49.9

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhcc----ccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC------CCcccCCcc
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLT----VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD------VAARGLDIP  101 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~----~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~------~~~~Gidi~  101 (150)
                      .....+++.+++...+......+.    ..++.+...+|+.........+    .....|+|+|.      .-...+++.
T Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l----~~~~~Ili~TP~~l~~~l~~~~~~l~  142 (206)
T d1s2ma1          67 LNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRL----NETVHILVGTPGRVLDLASRKVADLS  142 (206)
T ss_dssp             SCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHT----TSCCSEEEECHHHHHHHHHTTCSCCT
T ss_pred             cccccceeeccchhhhhhhhhhhhhcccccCeeEEeecCccchhhHHHHh----cccceEEEECCcccccccccceeecc
Confidence            456678888888887765554443    3478899999998876555432    34478999995      123356777


Q ss_pred             CCcEEEE
Q psy17637        102 HIRTVVN  108 (150)
Q Consensus       102 ~~~~vi~  108 (150)
                      ++.++|.
T Consensus       143 ~l~~lV~  149 (206)
T d1s2ma1         143 DCSLFIM  149 (206)
T ss_dssp             TCCEEEE
T ss_pred             cceEEEe
Confidence            8888774

>d1qxna_ c.46.1.3 (A:) Polysulfide-sulfur transferase (sulfide dehydrogenase, Sud) {Wolinella succinogenes [TaxId: 844]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Polysulfide-sulfur transferase (sulfide dehydrogenase, Sud)
species: Wolinella succinogenes [TaxId: 844]

Probab=85.04  E-value=0.2  Score=29.87  Aligned_cols=37  Identities=14%  Similarity=0.155  Sum_probs=31.7

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCc-eEEEecCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEY-DVLLLHGDM   68 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~-~~~~~~~~~   68 (150)
                      .+..++|+||.+-..+...+..|...|+ .+..+.||+
T Consensus        80 ~~~~~ivvyC~~G~rs~~aa~~L~~~G~~nV~~l~GG~  117 (137)
T d1qxna_          80 DPEKPVVVFCKTAARAALAGKTLREYGFKTIYNSEGGM  117 (137)
T ss_dssp             CTTSCEEEECCSSSCHHHHHHHHHHHTCSCEEEESSCH
T ss_pred             CcccceeeeecccchHHHHHHHHHHcCCCcEEEecCHH
Confidence            4567899999998889999999999888 477889995

>d1urha2 c.46.1.2 (A:149-268) 3-mercaptopyruvate sulfurtransferase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: 3-mercaptopyruvate sulfurtransferase
species: Escherichia coli [TaxId: 562]

Probab=84.69  E-value=0.52  Score=26.94  Aligned_cols=38  Identities=16%  Similarity=0.169  Sum_probs=30.1

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccccCce-EEEecCCCC
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTVKEYD-VLLLHGDMD   69 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~~~~~-~~~~~~~~~   69 (150)
                      ....++|+||++-..+...+..|...|++ +..|.|++.
T Consensus        80 ~~~~~ii~yC~sG~~A~~~~~~L~~lG~~~v~~y~Gs~~  118 (120)
T d1urha2          80 SYDKPIIVSCGSGVTAAVVLLALATLDVPNVKLYDGAWS  118 (120)
T ss_dssp             CSSSCEEEECCSSSTHHHHHHHHHHTTCSSCEEECCSCC
T ss_pred             CccCceEEEccchhHHHHHHHHHHHcCCCCceEcCCChh
Confidence            45678999999977777777778777874 778888875

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=84.55  E-value=2.9  Score=26.90  Aligned_cols=72  Identities=15%  Similarity=0.208  Sum_probs=49.4

Q ss_pred             CCCCeeEEehhhhhHHHHHhhcc----ccCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcC------CCcccCCccC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLT----VKEYDVLLLHGDMDQSERNSVITKFKRQECRILVATD------VAARGLDIPH  102 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~----~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~------~~~~Gidi~~  102 (150)
                      ...+++|.+++++-+..+.+.+.    ..++++..+.|+.........    ......|+|+|.      .....+++.+
T Consensus        97 ~~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~----~~~~~~ivV~TP~~l~~~~~~~~~~l~~  172 (238)
T d1wrba1          97 AYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIRE----VQMGCHLLVATPGRLVDFIEKNKISLEF  172 (238)
T ss_dssp             BCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHH----HSSCCSEEEECHHHHHHHHHTTSBCCTT
T ss_pred             CCceEEEeccchhhhcchheeeeecccCCCcEEEEEeccchhhHHHhh----cccCCceeecCHHHHHhHHccCceeccc
Confidence            45679999999999888776653    346778888888765544322    234568999995      1133566778


Q ss_pred             CcEEEE
Q psy17637        103 IRTVVN  108 (150)
Q Consensus       103 ~~~vi~  108 (150)
                      +.++|.
T Consensus       173 v~~lVi  178 (238)
T d1wrba1         173 CKYIVL  178 (238)
T ss_dssp             CCEEEE
T ss_pred             cceeee
Confidence            887774

>d1yt8a1 c.46.1.2 (A:107-242) Thiosulfate sulfurtransferase PA2603 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Thiosulfate sulfurtransferase PA2603
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=84.35  E-value=0.34  Score=28.77  Aligned_cols=36  Identities=17%  Similarity=0.013  Sum_probs=30.3

Q ss_pred             CCCCeeEEehhhhhHHHHHhhccccCc--eEEEecCCC
Q psy17637         33 EVPPALMNLAMQLNAEELANSLTVKEY--DVLLLHGDM   68 (150)
Q Consensus        33 ~~~~~ivf~~~~~~~~~l~~~L~~~~~--~~~~~~~~~   68 (150)
                      +..++++||.+.......+..|...|+  .+..+.||+
T Consensus        79 ~~~~iV~~C~~g~rs~~aa~~L~~~G~~~~V~~L~GG~  116 (136)
T d1yt8a1          79 PRTRVIVNCAGRTRSIIGTQSLLNAGIPNPVAALRNGT  116 (136)
T ss_dssp             TTSEEEEECSSSHHHHHHHHHHHHTTCSSCEEEETTHH
T ss_pred             ccceEEEEcCCCCchHHHHHHHHHcCCCceEEEeCCcH
Confidence            456799999998888899999998888  377899985

>d2b2na1 c.37.1.19 (A:26-333) 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=81.09  E-value=4.2  Score=27.43  Aligned_cols=96  Identities=15%  Similarity=0.105  Sum_probs=57.6

Q ss_pred             HHHHHHHhccCCCCCeeEEehhhhhHHHHHhhcccc-CceEEEecC-------C--C---CHHHHHHHHHHhhcCCceEE
Q psy17637         22 HLVRNLEGANQEVPPALMNLAMQLNAEELANSLTVK-EYDVLLLHG-------D--M---DQSERNSVITKFKRQECRIL   88 (150)
Q Consensus        22 ~ll~~l~~~~~~~~~~ivf~~~~~~~~~l~~~L~~~-~~~~~~~~~-------~--~---~~~~r~~~~~~f~~g~~~vl   88 (150)
                      .++..+...  ..+++||.|++...++.+++.|..- +-.+..+-+       .  .   ...+|.+++..+..++..|+
T Consensus         4 ~~~a~~~~~--~~~p~lvv~~~~~~A~~l~~~L~~~~~~~v~~fP~~e~lpyd~~s~~~~i~~~R~~~L~~l~~~~~~ii   81 (308)
T d2b2na1           4 TLVAEIAER--HAGPVVLIAPDMQNALRLHDEISQFTDQMVMNLADWETLPYDSFSPHQDIISSRLSTLYQLPTMQRGVL   81 (308)
T ss_dssp             HHHHHHHHH--CSSCEEEEESSHHHHHHHHHHHHTTCSSCEEECCCCCSCTTCSSCCCHHHHHHHHHHHHHGGGCCSSEE
T ss_pred             HHHHHHHHh--hCCCEEEEcCCHHHHHHHHHHHHhcCCCceEEcCCcccCccccCCCChHHHHHHHHHHHHHhhcCCceE
Confidence            355555554  4678999999999999999888643 222222211       1  1   12367888888888888888


Q ss_pred             EEc-CCCcccC-Ccc---CCcEEEEecCCCChhHHH
Q psy17637         89 VAT-DVAARGL-DIP---HIRTVVNYDLARDIDTHT  119 (150)
Q Consensus        89 v~T-~~~~~Gi-di~---~~~~vi~~~~~~~~~~~~  119 (150)
                      |+| .++..-+ ...   .....+..+-..+...+.
T Consensus        82 its~~al~~~~~p~~~~~~~~~~l~~g~~~~~~~l~  117 (308)
T d2b2na1          82 IVPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALR  117 (308)
T ss_dssp             EEEHHHHTBCCCCHHHHHHHCEEEETTCBCCHHHHH
T ss_pred             EeechhhhhhcccHHHHHHHHHhhhhhccccHHHHH
Confidence            888 3332222 211   122445556666665554

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.92  E-value=0.58  Score=30.06  Aligned_cols=74  Identities=16%  Similarity=0.108  Sum_probs=44.0

Q ss_pred             CCCCCeeEEehhhhhHHHHHhhccc----cCceEEEecCCCCHHHHHHHHHHhhcCCceEEEEcCC-----C-cccCCcc
Q psy17637         32 QEVPPALMNLAMQLNAEELANSLTV----KEYDVLLLHGDMDQSERNSVITKFKRQECRILVATDV-----A-ARGLDIP  101 (150)
Q Consensus        32 ~~~~~~ivf~~~~~~~~~l~~~L~~----~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~-~~Gidi~  101 (150)
                      ....++||.++|++-+..+++.+..    .+.....++++....+   .......+...|+|+|+-     + ....++.
T Consensus        78 ~~~~~alil~Pt~eL~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~~~  154 (218)
T d2g9na1          78 LKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRA---EVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPK  154 (218)
T ss_dssp             CCSCCEEEECSSHHHHHHHHHHHHHHHTTTTCCEEEECC--CCCS---TTTSSSSCCCSEEEECHHHHHHHHHTTSSCST
T ss_pred             ccCccEEEEcccchhhhhHHHHHhhhccccceeEEeeecccchhH---HHHHHhcCCCEEEEeCChhHHHHHhcCCcccc
Confidence            4567799999999988777665543    3555666666533211   111223345679999952     2 2345566


Q ss_pred             CCcEEEE
Q psy17637        102 HIRTVVN  108 (150)
Q Consensus       102 ~~~~vi~  108 (150)
                      ++.++|.
T Consensus       155 ~l~~lVl  161 (218)
T d2g9na1         155 YIKMFVL  161 (218)
T ss_dssp             TCCEEEE
T ss_pred             cceEEEe
Confidence            7777763